Black Gold in Medicine: Rediscovering the Pharmacological Potential

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This manuscript presents a conceptual and literature-based perspective on the pharmacological potential of crude oil and its molecular constituents. It discusses petroleum-derived structures—such as steranes, hopanes, adamantanes, porphyrins, naphthenic acids, and organosulfur compounds—as potential drug scaffolds. The article links petroleum chemistry with medicinal chemistry, advocating for a multidisciplinary approach integrating petroleomics, cheminformatics, and pharmacology to explore crude oil as a novel feedstock for drug discovery.

How ever need Revisions as follows

Lack of Empirical Validation:

The article remains entirely conceptual, without experimental or computational results to substantiate claims about pharmacological potential. Even a brief in silico screening summary or dataset illustration would strengthen the argument.

Safety and Toxicity Considerations:

While the manuscript acknowledges toxicity risks of polyaromatic hydrocarbons and naphthenic acids, it could better emphasize the biohazard and environmental implications of using petroleum derivatives in biomedical contexts.

Scope and Focus:

The discussion occasionally becomes too broad, extending into geochemical detail that may not directly advance the pharmacological thesis. A tighter focus on translational and mechanistic aspects would improve impact.

Terminology and Definition:

The proposed term “petroleum-based pharmacology” needs clearer operational definition and distinction from petrochemical applications or environmental toxicology.

Reference Integration:

While references are current and relevant, some statements (e.g., regarding computational prediction of toxicity and multi-target potential) would benefit from specific data presentation or citation to peer-reviewed modeling studies.

 

Comments on the Quality of English Language

Formatting: Ensure consistent citation numbering and alignment with MDPI format.

Figures / Schemes: The manuscript would greatly benefit from schematic representations of key molecular scaffolds (adamantane, sterane, porphyrin) and their pharmacophoric relevance.

Language: A few sentences could be simplified for readability without loss of precision.

Abbreviations: Define “QSAR,” “PASS,” and “petroleomics” at first mention for a multidisciplinary readership.

Author Response

We thank the reviewer for the thoughtful evaluation of our Perspective. The manuscript is intentionally framed as a conceptual, literature-based piece, aiming to outline a translational framework rather than present new primary data. Please find file attached below.

Reviewer:

Lack of Empirical Validation: The article remains entirely conceptual, without experimental or computational results to substantiate claims about pharmacological potential. Even a brief in silico screening summary or dataset illustration would strengthen the argument.

Authors: This work is submitted as a Perspective, not as an original research article, and therefore does not seek to provide new experimental datasets. Nonetheless, the manuscript already refers to (i) clinical and experimental data on Naftalan therapy [22–27];  (ii) published in silico analyses of Naftalan biomarkers (reactivity descriptors, PASS, QSAR, LD₅₀ estimates) by Kolchina et al. [47], and (iii) the clinically validated adamantane scaffolds, originally identified in petroleum and now forming the core of approved drugs such as amantadine, rimantadine and memantine [35–38]. These examples serve to illustrate feasibility and existing empirical/computational work, while the main goal remains to articulate a conceptual framework for future studies.

Reviewer:

Safety and Toxicity Considerations: While the manuscript acknowledges toxicity risks of polyaromatic hydrocarbons and naphthenic acids, it could better emphasize the biohazard and environmental implications of using petroleum derivatives in biomedical contexts.

Authors: We fully agree that toxicity and environmental risks are critical. The manuscript already emphasizes that PAHs and certain naphthenic acid fractions are toxic and ecotoxicologically problematic (Sections 3–4), and explicitly states that early toxicity prediction and rigorous filtering are prerequisites before any pharmacological exploration.

Reviewer: Scope and Focus: The discussion occasionally becomes too broad, extending into geochemical detail that may not directly advance the pharmacological thesis. A tighter focus on translational and mechanistic aspects would improve impact.

Authors: The geochemical background is included deliberately and in a targeted way, as it explains what the molecular components of crude oil are and why their structural features make them potentially relevant for pharmacology. We also highlight, where possible, mechanistic aspects of how these scaffold classes may interact with biological systems and pharmacological targets.

Reviewer: Terminology and Definition: The proposed term “petroleum-based pharmacology” needs clearer operational definition and distinction from petrochemical applications or environmental toxicology.

Authors: We do not present “petroleum-derived pharmacology” as an established field; in the Conclusion we explicitly state that it is “in its infancy and not [a] clearly defined field”. Rather, the term is used to denote a proposed research direction — the systematic study of structurally defined motifs originating from crude oil using conventional tools of medicinal chemistry, chemoinformatics and pharmacology (safety assessment, biological profiling, in silico design). In this sense, it is clearly distinguished from petrochemical applications (fuels, materials) and from environmental toxicology.

Reviewer: Reference Integration: While references are current and relevant, some statements (e.g., regarding computational prediction of toxicity and multi-target potential) would benefit from specific data presentation or citation to peer-reviewed modeling studies.

Authors: Statements on predicted bioactivity and toxicity are grounded in peer-reviewed sources. For Naftalan biomarkers, we explicitly refer to Kolchina et al. [47], who report calculated descriptors, PASS predictions and QSAR-based LD₅₀ estimates; broader claims about multi-target design and in silico workflows are supported by dedicated reviews [63-71]

Reviewer: Formatting: Ensure consistent citation numbering and alignment with MDPI format.

Authors: We revised the reference list and in-text citations to ensure consistent numbering and alignment with MDPI formatting requirements.

Reviewer: Figures / Schemes: The manuscript would greatly benefit from schematic representations of key molecular scaffolds (adamantane, sterane, porphyrin) and their pharmacophoric relevance.

Authors: We agree with the reviewer that schematic representations of key scaffolds would enhance the manuscript. Due to time constraints and the absence of ready-to-publish graphical material, we were not able to include such figures in the current revision.

Reviewer: Abbreviations: Define “QSAR,” “PASS,” and “petroleomics” at first mention for a multidisciplinary readership.

Authors: We have now defined QSAR (quantitative structure–activity relationship), PASS (Prediction of Activity Spectra for Substances), and petroleomics (ultrahigh-resolution molecular analysis of crude oil) at their first mention to support a multidisciplinary readership.

Reviewer 2 Report

Comments and Suggestions for Authors

 

1. Considering the word "Rediscovering" in your title, including a historical section (A few sentences are insufficient to give a comprehensive idea of ​​the historical roots of this subject) is so important (e.g. Historical Perspectives on Crude Oil in Medicine). It provides the necessary context and supports the idea that crude oil's pharmacological potential has been known or suspected in the past but is now being revisited with new scientific insights. A historical overview will also enrich readers' understanding of the evolution of crude oil use in medicine and justify the renewed interest today.

 

2. The manuscript currently lacks any figures or tables. Including such visual materials is essential to enhance the readers’ understanding and to summarize key information effectively. I recommend adding relevant tables and figures to support the text and improve the overall clarity and readability of the review. For example,

Figures:

1. Under subtitle "Pharma matrix of crude oil: structure insights": Chemical structures and classification of major bioactive compounds in crude oil
2. Under subtitle "Historical Perspectives on Crude Oil in Medicine": "Timeline of the historical use of crude oil and petroleum products in medicine highlighting key milestones and discoveries."

Tables:

1. Under subtitle "Petroleum in medicine: practical insights": "Summary of crude oil-derived substances historically and currently used in medicinal formulations, including their sources, traditional uses, and pharmacological effects."
2. Under subtitle "Translational perspectives of crude oil–derived drug discovery": "Overview of recent advances and candidate drug molecules derived from crude oil components with pharmacological potential, highlighting mechanisms of action, target diseases, and stages of research."

 

3. Adding a methodology section showing literature search strategy

 

4. Addressing limitations, challenges, or regulatory issues in crude oil-derived drug research

 

5. Page 3 (line 104): The references written twice, correct it please.

Author Response

We sincerely thank the reviewer for the careful reading of our manuscript and for the constructive comments, which have helped us refine the scope, clarify the conceptual framework, and improve the overall presentation of the Perspective. Below we address each point raised.

Reviewer: Considering the word "Rediscovering" in your title, including a historical section (A few sentences are insufficient to give a comprehensive idea of ​​the historical roots of this subject) is so important (e.g. Historical Perspectives on Crude Oil in Medicine). It provides the necessary context and supports the idea that crude oil's pharmacological potential has been known or suspected in the past but is now being revisited with new scientific insights. A historical overview will also enrich readers' understanding of the evolution of crude oil use in medicine and justify the renewed interest today.

Authors: We agree that the historical dimension is important to justify the term “rediscovering”. In the current version, we already provide a concise historical context in Section 2, referencing ancient medical sources (Mesopotamia, Rome, medieval Middle East and Europe) and the long-standing therapeutic use of Naftalan oil [17–19, 20–27]. This material is intended to show that crude oil’s medicinal use has deep historical roots and that modern analytical tools now allow these empirical observations to be revisited mechanistically. The available literature in this area is also highly fragmented and predominantly framed in industrial or environmental terms rather than as a continuous medical narrative, which makes it challenging to construct a comprehensive historical account within the space of a single Perspective. So, we have opted to keep this historical overview integrated into the existing section rather than expand it into a full, standalone chapter. 

Reviewer: The manuscript currently lacks any figures or tables. Including such visual materials is essential to enhance the readers’ understanding and to summarize key information effectively. I recommend adding relevant tables and figures to support the text and improve the overall clarity and readability of the review. For example,

Figures:

1. Under subtitle "Pharma matrix of crude oil: structure insights": Chemical structures and classification of major bioactive compounds in crude oil
2. Under subtitle "Historical Perspectives on Crude Oil in Medicine": "Timeline of the historical use of crude oil and petroleum products in medicine highlighting key milestones and discoveries."

Tables:

1. Under subtitle "Petroleum in medicine: practical insights": "Summary of crude oil-derived substances historically and currently used in medicinal formulations, including their sources, traditional uses, and pharmacological effects."
2. Under subtitle "Translational perspectives of crude oil–derived drug discovery": "Overview of recent advances and candidate drug molecules derived from crude oil components with pharmacological potential, highlighting mechanisms of action, target diseases, and stages of research."

Authors: We fully agree that figures and tables (e.g., scaffold schemes, timelines, and summary tables) would further enhance readability and synthesis. However, due to time constraints and the absence of ready-to-publish graphical material and tables for this revision cycle, we were not able to implement the full set of visual elements suggested by the reviewer.

Reviewer:  Adding a methodology section showing literature search strategy

Authors: We appreciate the suggestion to add a methodology section. However, this manuscript is intentionally conceived as a narrative Perspective rather than a systematic review or meta-analysis, and thus does not follow a formal PRISMA-type search and selection protocol. The cited literature reflects a targeted, expert-driven selection of key publications, rather than an exhaustive or systematic survey. For this reason, we have not introduced a separate “Methods” section.

Reviewer: Addressing limitations, challenges, or regulatory issues in crude oil-derived drug research

Authors: We agree that limitations and challenges are essential to highlight. The manuscript already discusses several intrinsic obstacles in Section 4, including the extreme chemical complexity of crude oil, the presence of toxic and ecotoxicologically relevant fractions (PAHs, certain naphthenic acid mixtures), unresolved isomeric ensembles, technical barriers to separation/scale-up, and the need for early toxicity prediction and rigorous filtering before any pharmacological exploration. At the same time, most of these challenges fall within the familiar interface between pharmaceutical development and petrochemistry: they are conceptually similar to those encountered with complex plant or microbial extracts and petrochemical intermediates and are addressed within existing toxicological, environmental and regulatory fram

Reviewer: Page 3 (line 104): The references written twice, correct it please.

Authors: We thank the reviewer for noticing this. The duplicated reference has been removed and the citation list and in-text numbering have been corrected accordingly.

 

Reviewer 3 Report

Comments and Suggestions for Authors

Abstract:

- ‘Crude oil may hold promise for drug discovery’

Although this is a conceptual hypothesis, the text gives the impression of immediate practical applicability, which is unproven. The statement may lead readers to believe that petroleum components are bioactive or easily transformable into drugs, which is not supported by experimental data.

 

- ‘Rigid sp³-rich frameworks, together with sterane/hopane biomarkers, porphyrins, and functional aromatics, overlap structurally and pharmacologically with established therapeutic classes’

Problematic: structural overlap does not imply pharmacological overlap. Extrapolating chemical structure to direct therapeutic effect is scientifically incorrect.

 

- ‘Naturally present in crude oil in suitable abundance, offering opportunities to reduce synthetic effort’

Although some hydrocarbons exist in large quantities, almost none are immediately usable as drugs. The statement exaggerates the practical relevance for drug discovery.

 

- ‘Characterized in terms of drug-likeness, bioactivity, and toxicity’

Petroleomics and in silico methods allow chemical profiling, but they do not provide experimental evidence of bioactivity or safety. Stating that these molecules can be characterized as ‘drug-like’ is an exaggeration and gives a false impression of pharmacological validation.

 

- ‘Scientifically tractable resource for pharmaceutical innovation’

This suggests that crude oil is a viable source of drugs, which is currently not supported by experimental data.

 

 

Keywords:

 

- petroleum-based medicine – suggests that petroleum is a validated source of drugs, which is not proven. Suggested alternatives: “petroleum chemistry” or “petroleum-derived scaffolds” are more neutral and scientifically accurate.

- petroleum biomarkers – although “biomarkers” usually refers to biological indicators, here it is geological, but acceptable.

- carbon nanostructures – only if fullerenes, buckybowls, etc., are actually discussed; if only briefly mentioned, may be less relevant.

- drug discovery – suggests real pharmacological applicability, which is not validated. Alternative: “medicinal chemistry concepts” or “chemical scaffold exploration.”

- multi-target therapeutics – also problematic, as it suggests proven biological effect. Alternative: “potential bioactive scaffolds” or omit.

- Naftalan crude, sp³ scaffolds, naphthenic acids – accurate and appropriate.

 

 

Introduction:

- Statement about the ‘severe constraint’ imposed on medicinal chemistry by drug-likeness filters (Lipinski, lead-like, fragment-like)

While it is true that these filters reduce chemical space, it is not correct to claim that they ‘severely restrict’ or that they ‘exclude many promising molecules’ in a general way. These filters are not rigid rules, and modern industry already widely uses beyond-Rule-of-5 (bRo5) compounds, macrocycles, PROTACs, degraders, and peptidomimetics. The statement is outdated

 

- Statement that the synthetic toolbox ‘has changed little for decades’. This claim is partially false. Over the past 15–20 years there have been highly significant advances in synthetic chemistry applied to drug discovery, including: photoredox catalysis, electrochemistry, C–H activation, borylation, Ni/Fe catalysis; scalable biocatalysis; click chemistry (awarded the 2022 Nobel Prize); continuous-flow reactions. Therefore, it is not correct to say that the toolbox has changed little.

 

- Conclusion that the reliance on couplings such as Suzuki and amide formation ‘keeps compounds confined to planar sp² space’. Although these methods do produce flatter structures, this does not causally imply low metabolic stability or toxicity. Moreover, the industry has already developed robust strategies to increase sp³/3D character (e.g., saturated bioisosteres, bridged bicyclics, oxetanes). The association ‘planar = toxicity’ is simplistic and not universally supported.

 

- Direct attribution of the 90% failure rate to the use of drug-likeness filters and sp² chemistry

The high attrition rate has multiple, far more dominant contributors: efficacy failures, unexpected toxicity, poor animal→human translation, clinical issues, biological complexity.

There is no evidence that physicochemical filters or sp² coupling chemistry are responsible for the majority of the 90% rate. This is an incorrect implied correlation.

 

- The expression ‘metabolite-likeness’ and ‘endogenite-orientation’ as mainstream trends

These concepts do exist, but they are not dominant trends in the pharmaceutical industry. They are academic niches and exploratory strategies, not central paradigms.

 

- The claim that natural sources are ‘drivers of modern therapeutic modalities associated with safety, sustainability, and efficacy’. Sustainability: this depends strongly on the source (petroleum, for example, is not sustainable). Safety and efficacy: natural products are not inherently superior — many are toxic. The statement is overly generalized and scientifically weak.

 

- The central idea that petroleum is a promising source of ‘rigid and sp³-rich scaffolds for drug design’

This is the most scientifically problematic point: Crude petroleum is a complex mixture of simple hydrocarbons (alkanes, cycloalkanes, aromatics), many of which have low functionality.

For medicinal chemistry, it lacks functionalization, diversity, and anchoring points for bioactive interactions. Simple saturated and aromatic hydrocarbons have extremely low biological activity and are metabolically problematic.

The idea of ‘biogenic derivatives’ in petroleum is misleading; petroleum does not contain intact biological molecules, only highly transformed remnants over millions of years.

Thus, the claim that petroleum is a ‘vast reservoir of sp³-rich scaffolds’ is scientifically incorrect, or at the very least requires very strong justification

 

 

Petroleum in medicine: practical insights

- Statement that ‘labile functional groups and side chains are progressively eliminated’ but some backbones (steroids, hopanoids, porphyrins) are retained

It is true that biomarkers such as steroids, hopanoids, and porphyrins can indeed be detected in petroleum.

The problem is that these structures are residual, present in minute amounts, and highly derivatized. Therefore, it is not correct to imply that they are bioactive or readily useful for drug discovery.

 

- Statement that petroleum accounts for ‘99% of pharmaceutical feedstock’

Exaggeration: petroleum provides aromatics and olefins for fine chemistry, but 99% seems inflated. Polymers such as PEG, PVC, and excipients can be petroleum-derived, but this does not mean that all pharmaceutical raw materials rely exclusively on petroleum. Alternative sources exist (biomass, synthetics)

 

- Historical medicinal use of petroleum as evidence of pharmaceutical potential

It is historical/ethnographic, but not scientific: references to petroleum in Mesopotamia or Rome do not constitute modern evidence of therapeutic efficacy. The extrapolation to modern drug discovery is very weak.

 

- Statements about Naftalan and ‘empirical clinical validation’

There are reports of therapeutic use, but: Modern clinical evidence is scarce, non-randomized, and often anecdotal. Claims of efficacy in conditions such as psoriasis, arthritis, neuropathies, or vascular complications lack robust scientific validation.

 

- Statement that Naftalan ‘targets multiple pathophysiological pathways’

There is no modern biochemical evidence that petroleum components act selectively on nociceptive signaling, inflammation, neurodegeneration, or endothelium.

The phrase implies a plausible molecular mechanism, which is scientifically incorrect without robust experimental data.

 

- Mamedaliyev’s precursor theory (1940s)

Historically interesting, but: The claim that steranes could be metabolized into bioactive compounds has no modern experimental support. Implying direct pharmacological potential is misleading.

 

- Statement that ‘modern techniques allow the identification of molecules with significant pharmaceutical potential’. Although analytical characterization is possible, the translation of petroleum hydrocarbons into relevant bioactive molecules has not yet been demonstrated.

Therefore, the statement is speculative, not scientific.

 

- Implication that petroleum could be a source of ‘drug-like candidates’. In practical terms, simple saturated or aromatic hydrocarbons are chemically inert for most biological interactions. Without extensive chemical functionalization, petroleum is not a realistic source of bioactive scaffolds.

 

 

Pharma matrix of crude oil: structure insights

- Generalization that Naftalan crude is a ‘sp³-rich, non-flat, ready-to-use scaffold’. While it is true that it contains many saturated hydrocarbons (decahydronaphthalenes, naphthenes), this does not automatically imply pharmacological relevance.

The phrase ‘ready-made bioisosteric replacements’ is not experimentally supported; converting naphthenes or diamondoids into drugs requires extensive chemical modification.

 

- Claim that decahydronaphthalenes, steranes, and hopanes directly contribute to the ‘reported therapeutic effects’ of Naftalan. There are no robust modern clinical data demonstrating bioactivity of these compounds.

This statement extrapolates chemical occurrence to pharmacological effect, which is scientifically incorrect.

 

- Statements about diamondoids (adamantanes)

Diamondoids have limited applications in medicinal chemistry as lipophilic groups or pharmacokinetic modifiers, but claiming: ‘effectiveness in pharmacology and medicine’ or ‘intrinsic activity linked to modulation of NMDA receptors and viral proton channels’ is highly speculative and lacks solid experimental support.

Only amantadine, rimantadine, and memantine are approved drugs; extrapolation to other diamondoids is misleading.

 

- Drimanes, decalins, and other terpenoids in petroleum

They are found in small amounts and are often chemically altered during diagenesis. Claims of broad anticancer, anti-inflammatory, or antiviral activity in petroleum are not validated; such activities come from intact natural compounds, not from petrochemical residues.

 

- Attribution of pharmacological activity to steranes and hopanes

These are geological biomarkers, and there is no evidence that the human body can reliably metabolize them into pharmacologically active molecules. Extrapolation to ‘membrane-associated signaling’ is speculative.

 

- Fullerenes in asphaltenes as potential drugs

Although fullerenes may have interesting chemical properties, there is no evidence of direct bioactivity from fullerenes extracted from crude oil. Claims regarding biomedical applications are hypothetical.

 

- Naphthenic acids as prostaglandin bioisosteres

Structural analogy does not guarantee biological activity. Pharmacological data are limited and contradictory; suggesting therapeutic function is an exaggeration.

 

- Aromatic hydrocarbons and PAHs

It is true that aromatics are fundamental in medicinal chemistry. However, extrapolating from PAHs found in petroleum to safe bioactivity ignores the high risk of genotoxicity and carcinogenicity.

 

- Petroporphyrins as pharmaceutical scaffolds

Despite structural stability, no studies demonstrate that petroleum-derived petroporphyrins are bioactive or safe for pharmacological use. Extrapolation from natural porphyrins (heme, chlorophyll) to petroleum petroporphyrins is misleading.

 

- Organosulfur compounds

It is correct that Ichthyol has dermatological use, but this does not mean that all sulfur compounds from petroleum are bioactive or safe.

 

 

Translational perspectives of crude oil – derived drug discovery

- Statement that crude oil can serve as ‘direct templates for medicinal chemistry’

Although petroleum contains a diversity of hydrocarbons, there is no evidence that crude oil components are directly useful as pharmacological scaffolds. The extrapolation from structural complexity → biological activity is highly speculative.

 

- ‘Identified biological activities of petroleum-derived scaffolds’

The phrase suggests that bioactivity has been demonstrated. In reality, reported activities are predictive, in silico, or based on small molecules isolated from plants or chemical derivatives, not from pure petroleum compounds. Therefore, it is scientifically incorrect to claim that biological activities have been identified in petroleum.

 

- Prediction of low toxicity and multi-target potential of Naftalan biomarkers

Toxicity assessment is computational (QSAR/PASS), not experimental. Extrapolating this to clinical safety or therapeutic potential is misleading, especially considering the known risks of PAHs and naphthenic acids.

 

- Direct comparison with natural products from plants or microorganisms

The extrapolation suggests that petroleum could provide pharmacologically equivalent scaffolds to natural products, which is not supported by evidence. Natural products are bioactive through evolution, whereas petroleum hydrocarbons are geological residues.

 

- Petroleomics and integration into the drug discovery pipeline

Although petroleomics identifies thousands of molecules, most lack chemical functionality useful for biological interactions. Transforming a chemical fingerprint into pharmacologically meaningful data is not trivial and does not guarantee active scaffolds.

 

- Use of virtual screening, docking, QSAR, and in vitro/in vivo validation

This is a theoretical extrapolation. There are no published studies showing that molecules isolated from crude petroleum have verifiable pharmacological activity in vitro or in vivo

 

- Comparison with natural products: toxicity and complexity

It is true that natural products have similar challenges, but the toxicity of petroleum and PAHs is much more severe. The statement downplays real risks and may give a misleading impression of safety.

 

- Phrases suggesting ‘translational potential’

The entire passage conveys the idea that petroleum could be directly used as a source of innovative drugs. Scientifically, this is not supported; most compounds are chemically inert, toxic, or present at minute concentrations.

 

 

Conclusion

- Statement that ‘crude oil harbors a broad spectrum of biologically relevant scaffolds’

Problematic: although petroleum contains molecules such as adamantanes, steranes, hopanes, porphyrins, and aromatics, there is no robust evidence that they are bioactive in humans or animals without chemical modification. The phrase implies direct biological activity, which is scientifically incorrect.

 

- Comparison with ‘established therapeutic classes’

The conclusion suggests that petroleum structures could replace or overlap with existing drugs. This is an unsupported extrapolation; structural presence does not imply pharmacological effect.

 

- Statement of ‘industrial scale’ as an advantage for drug discovery

Although it is true that petroleum exists in large quantities, this does not mean its molecules are readily usable as drugs. Many compounds are inert, toxic, or present in minute amounts, making the statement misleading.

 

- ‘Petroleum-based pharmacology’ as a potential field

Creating a field based on petroleum pharmacology is premature. Currently, there is insufficient experimental evidence to justify a separate scientific field.

 

- Integration of petroleomics in drug discovery

Although petroleomics provides detailed chemical data, there are no proven examples of transforming petroleum fingerprints into bioactive scaffolds ready for pharmacological assays. The statement may create exaggerated expectations about practical applicability.

 

 

References

- The references are not in the same format. Then there are others in bold.

It’s advisable to standardize this entire section.

Author Response

We are grateful to the reviewer for the time and effort invested in evaluating our manuscript, and we appreciate the opportunity to refine our arguments and provide additional clarification. Below, we address each comment point-by-point.

 

Abstract

• Reviewer: “Crude oil may hold promise for drug discovery.”
  Although this statement is presented as a conceptual hypothesis, the text gives the impression of immediate practical applicability, which is unproven. The wording may lead readers to believe that petroleum components are bioactive or easily transformable into drugs, which is not supported by experimental data.

Authors: We thank the Reviewer for this comment. Our intention was not to suggest immediate practical applicability, but rather to indicate a long-term conceptual potential. The expression “may hold promise” was deliberately was chosen as a cautious, non-committal formulation that does not imply current practical utility. After discussing this expression with linguists specializing in scientific English, it was confirmed that it is commonly used in this cautious, hypothesis-generating sense; therefore, we decided to leave this sentence unchanged

• Reviewer: “Rigid sp³-rich frameworks, together with sterane/hopane biomarkers, porphyrins, and functional aromatics, overlap structurally and pharmacologically with established therapeutic classes.”
  Structural overlap does not imply pharmacological overlap. Extrapolating chemical structure to therapeutic activity is incorrect.

Authors: We thank the Reviewer for this comment. We have revised the text to restrict this comparison to structural similarity only.

• Reviewer: “Naturally present in crude oil in suitable abundance, offering opportunities to reduce synthetic effort.”
  Although some hydrocarbons exist in large quantities, almost none are immediately usable as drugs. The sentence overstates the practical relevance.

Authors: We thank the Reviewer for this clarification. We do not regard crude oil as a source of immediately usable pharmaceuticals, but as a reservoir of pre-formed, rigid sp³-rich molecular frameworks. Should some of these structures later prove promising, their natural occurrence could reduce the synthetic effort required to access such frameworks compared with fully de novo synthesis. Moreover, several molecules of particular interest to materials science and biotechnology—such as higher diamondoids and selected polycyclic frameworks—are found exclusively in crude oil and are notoriously challenging to obtain synthetically.

• Reviewer: “Characterized in terms of drug-likeness, bioactivity, and toxicity.”
  Petroleomics and in silico methods permit profiling but not experimental evidence of bioactivity or safety. The wording suggests validated pharmacological claims.

Authors: We thank the reviewer for this important comment.

Petroleomics and in silico methods cannot and should not be regarded as experimental evidence of bioactivity or safety and are not intended to replace wet-lab validation. In this manuscript, we explicitly discuss only the generally accepted early-stage workflow used for other natural product resources, where compounds are first evaluated in silico for predicted drug-likeness, bioactivity and toxicity in order to filter and prioritise candidates for subsequent experimental testing, rather than to claim pharmacological validation.

• Reviewer: “Scientifically tractable resource for pharmaceutical innovation.”
  This implies crude oil is already a viable drug source, which is unsupported.

Authors: The term “scientifically tractable” is used strictly to indicate that crude oil can be interrogated using modern analytical techniques and computational tools that are relevant for pharmaceutical research. It does not infer current validation or clinical applicability.

• Reviewer: The statement on the “severe constraint” imposed by drug-likeness filters is outdated; industry explores beyond-Rule-of-5 space.

Authors: We agree the original wording was too categorical. Our point was not that filters are rigidly enforced, but that they still bias chemical space and virtual libraries toward flat, sp²-rich scaffolds. This is supported by recent literature, which we now cite. We have softened the phrasing accordingly.

 

Keywords:

• Reviewer:

- petroleum-based medicine – suggests that petroleum is a validated source of drugs, which is not proven. Suggested alternatives: “petroleum chemistry” or “petroleum-derived scaffolds” are more neutral and scientifically accurate.

- petroleum biomarkers – although “biomarkers” usually refers to biological indicators, here it is geological, but acceptable.

- carbon nanostructures – only if fullerenes, buckybowls, etc., are actually discussed; if only briefly mentioned, may be less relevant.

- drug discovery – suggests real pharmacological applicability, which is not validated. Alternative: “medicinal chemistry concepts” or “chemical scaffold exploration.”

- multi-target therapeutics – also problematic, as it suggests proven biological effect. Alternative: “potential bioactive scaffolds” or omit.

- Naftalan crude, sp³ scaffolds, naphthenic acids – accurate and appropriate.

Authors: We thank the reviewer for these helpful suggestions regarding the keywords and agree that they should remain strictly neutral and non-validated in tone. We have therefore revised the keyword list.

 

Introduction:

• Reviwer: Statement about the ‘severe constraint’ imposed on medicinal chemistry by drug-likeness filters (Lipinski, lead-like, fragment-like). While it is true that these filters reduce chemical space, it is not correct to claim that they ‘severely restrict’ or that they ‘exclude many promising molecules’ in a general way. These filters are not rigid rules, and modern industry already widely uses beyond-Rule-of-5 (bRo5) compounds, macrocycles, PROTACs, degraders, and peptidomimetics. The statement is outdated

Authors: We thank the reviewer for this comment. We agree that the original phrasing may have sounded too categorical. Our argument is not speculative but is supported by recent methodological and perspective studies demonstrating that Ro5-, lead-like-, and fragment-like filters still influence the chemical space prioritized in contemporary small-molecule drug discovery. These filters continue to bias widely used virtual screening tools and generative models toward a relatively narrow region of physicochemical space, while more three-dimensional scaffolds remain comparatively underrepresented.

• Reviewer: Statement that the synthetic toolbox ‘has changed little for decades’. This claim is partially false. Over the past 15–20 years there have been highly significant advances in synthetic chemistry applied to drug discovery, including: photoredox catalysis, electrochemistry, C–H activation, borylation, Ni/Fe catalysis; scalable biocatalysis; click chemistry (awarded the 2022 Nobel Prize); continuous-flow reactions. Therefore, it is not correct to say that the toolbox has changed little.

Authors: We thank the reviewer for this important comment and agree that synthetic organic chemistry has undergone substantial methodological advances over the past 15–20 years. However, multiple analyses indicate that the routinely used reaction toolbox in medicinal and process chemistry has remained comparatively conservative. This point is clearly articulated in the widely cited study by Brown and Boström (J. Med. Chem. 2016, 59, 4443–4458. https://doi.org/10.1021/acs.jmedchem.5b01409) and in the recent industrial perspective by Federsel (Cell Rep. Phys. Sci. 2023, 4, 101493. https://doi.org/10.1016/j.xcrp.2023.101493 ). Both highlight that a small number of robust “workhorse” transformations still dominates large-scale and medicinal chemistry practice, while newer methods are adopted more slowly, more selectively, and predominantly within academic environments.

• Reviewer: Conclusion that the reliance on couplings such as Suzuki and amide formation ‘keeps compounds confined to planar sp² space’. Although these methods do produce flatter structures, this does not causally imply low metabolic stability or toxicity. Moreover, the industry has already developed robust strategies to increase sp³/3D character (e.g., saturated bioisosteres, bridged bicyclics, oxetanes). The association ‘planar = toxicity’ is simplistic and not universally supported.

Authors: The manuscript does not claim that planar sp²-rich structures are intrinsically toxic or of low pharmacological value. Our point is simply that the predominant reliance on cross-coupling reactions such as Suzuki–Miyaura and amide formation has historically biased drug libraries toward flat, aromatic scaffolds. This trend is well documented in peer-reviewed analyses and has led to industry-wide efforts to enhance molecular three-dimensionality through increased sp³ character and conformational complexity. Accordingly, our argument reflects an established trajectory in medicinal chemistry rather than opinion or speculation.

• Reviewer: Direct attribution of the 90% failure rate to the use of drug-likeness filters and sp² chemistry.The high attrition rate has multiple, far more dominant contributors: efficacy failures, unexpected toxicity, poor animal→human translation, clinical issues, biological complexity. There is no evidence that physicochemical filters or sp² coupling chemistry are responsible for the majority of the 90% rate. This is an incorrect implied correlation.

Authors: The manuscript does not attribute attrition primarily to physicochemical rules. Our citation of Waring et al. (2015) serves only to contextualize the broader challenges in drug discovery and to illustrate that conventional design paradigms—while influential in shaping the chemical space explored—represent just one of several contributing factors ( Waring, M. J.; Arrowsmith, J.; Leach, A. R.; Leeson, P. D.; Mandrell, S.; Owen, R. M.; Pairaudeau, G.; Pennie, W. D.; Pickett, S. D.; Wang, J.; Wallace, O.; Weir, A. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nat. Rev. Drug Discov. 2015, 14(7), 475–486. https://doi.org/10.1038/nrd4609 )

• Reviewer: The expression ‘metabolite-likeness’ and ‘endogenite-orientation’ as mainstream trends. These concepts do exist, but they are not dominant trends in the pharmaceutical industry. They are academic niches and exploratory strategies, not central paradigms.

Authors: We thank the reviewer for this comment. We do not present “metabolite-likeness” or “endogenite-orientation” as dominant industrial paradigms. Their mention in the manuscript serves only to illustrate analytically documented academic efforts to explore alternative regions of chemical space beyond traditional Rule-of-5 frameworks. These concepts are supported by published analyses rather than by conjecture, and are included solely to contextualize the diversification of design strategies currently under discussion, not to imply their mainstream adoption in pharmaceutical development.

• Reviewer: The claim that natural sources are ‘drivers of modern therapeutic modalities associated with safety, sustainability, and efficacy’. Sustainability: this depends strongly on the source (petroleum, for example, is not sustainable). Safety and efficacy: natural products are not inherently superior — many are toxic. The statement is overly generalized and scientifically weak.

Authors: We thank the reviewer for this comment. The manuscript does not claim intrinsic superiority, safety, or sustainability of natural products. Rather, it refers to a well-documented, policy-driven trend in global health and pharmaceutical development: the renewed interest in natural sources, which have historically contributed to the emergence of new therapeutic modalities and are now being incorporated into innovation frameworks prioritizing reduced environmental burden, lower energy inputs, and diversification of design principles beyond exclusively synthetic pipelines. The manuscript neither idealizes natural products nor attributes therapeutic advantage to their origin; it merely acknowledges their growing relevance within sustainability-oriented innovation agendas.

• Reviewer: The central idea that petroleum is a promising source of ‘rigid and sp³-rich scaffolds for drug design’. This is the most scientifically problematic point: Crude petroleum is a complex mixture of simple hydrocarbons (alkanes, cycloalkanes, aromatics), many of which have low functionality. For medicinal chemistry, it lacks functionalization, diversity, and anchoring points for bioactive interactions. Simple saturated and aromatic hydrocarbons have extremely low biological activity and are metabolically problematic. The idea of ‘biogenic derivatives’ in petroleum is misleading; petroleum does not contain intact biological molecules, only highly transformed remnants over millions of years. Thus, the claim that petroleum is a ‘vast reservoir of sp³-rich scaffolds’ is scientifically incorrect, or at the very least requires very strong justification

Authors: We thank the reviewer for this comment. The reviewer’s description of crude petroleum as “a complex mixture of simple hydrocarbons (alkanes, cycloalkanes, aromatics) with low functionality” does not reflect the current state of petroleum chemistry and geochemistry. While light fractions indeed contain simple hydrocarbons, they represent only a limited subset of petroleum’s molecular space.

Crude oil—particularly heavy crudes such as Naftalan—contains thousands of distinct molecular species, and its structural diversity increases markedly toward the heavy fractions. With the advent of modern analytical platforms (FT-ICR MS, Orbitrap MS, AFM/STM, advanced NMR), many of these components are only now being structurally resolved, consistently revealing previously uncharacterized, complex polycyclic, heteroatom-containing, and metal-chelating molecules. These also include rigid, sp³-rich frameworks such as hopanes, steranes, diamantanes/adamantanes, pentacyclic triterpanes, as well as structurally complex aromatic systems such as metalloporphyrins and various sulfur- and nitrogen-containing heterocycles — compounds that are neither simple nor functionally impoverished. Their ability to withstand geological diagenesis and catagenesis while retaining recognizable structural signatures derived from ancient biolipids, pigments, and membrane components is precisely what makes them robust geobiomarkers. Moreover, crude oil and its fractions are demonstrably not biologically inert: extensive occupational, environmental, and ecotoxicological literature documents effects on human and animal organisms. These data do not imply therapeutic usefulness or safety, but they are fundamentally incompatible with an assumption that petroleum is merely a metabolically irrelevant mixture of “simple” hydrocarbons. They show that multiple petroleum-derived structures can and do interact with biological systems.

In our manuscript we do not claim that petroleum contains ready-to-use drugs or intact biological molecules. Our point is strictly structural and translational: petroleum represents a natural repository of evolutionarily derived, structurally differentiated, rigid, sp³-rich polycyclic architectures that are difficult and costly to construct de novo, and that can be considered as scaffolds—not as finished pharmacophores—for future derivatization and testing.

 

Petroleum in Medicine: Practical Insights

• Reviewer: Statement that ‘labile functional groups and side chains are progressively eliminated’ but some backbones (steroids, hopanoids, porphyrins) are retained.It is true that biomarkers such as steroids, hopanoids, and porphyrins can indeed be detected in petroleum.The problem is that these structures are residual, present in minute amounts, and highly derivatized. Therefore, it is not correct to imply that they are bioactive or readily useful for drug discovery.

Authors: This point has partially been addressed in our response to the previous comment and is based on a misinterpretation of what we state in the manuscript. We do not claim that sterane, hopane, or petroporphyrin backbones in petroleum are “readily useful” as drugs. The fact that such motifs occur at low abundance is not a limitation per se; in natural product chemistry, the relevance of a scaffold has historically been determined by its structural properties rather than by its initial concentration. Importantly, in petroleum geochemistry, “low abundance” does not refer to nanomolar or picomolar levels, but to concentrations sufficient for routine detection, quantification, and structural elucidation—precisely why these molecules function reliably as geobiomarkers.

• Reviewer: Statement that petroleum accounts for ‘99% of pharmaceutical feedstock’. Exaggeration: petroleum provides aromatics and olefins for fine chemistry, but 99% seems inflated. Polymers such as PEG, PVC, and excipients can be petroleum-derived, but this does not mean that all pharmaceutical raw materials rely exclusively on petroleum. Alternative sources exist (biomass, synthetics)

Authors: The statement that petrochemicals account for nearly 99% of pharmaceutical feedstocks and reagents is not an exaggeration but a documented quantitative assessment. Hess et al. (2011) explicitly state that “approximately 3% of petroleum production is used for pharmaceutical manufacture, but nearly 99% of pharmaceutical feedstocks and reagents are derived from petrochemicals” (Am. J. Public Health 101, 1568–1579; https://doi.org/10.2105/AJPH.2011.300233). Comparable figures are reported in sectoral analyses examining the dependency of fine and specialty chemical supply chains on fossil-derived hydrocarbons. Our manuscript does not argue that biomass- or synthetically derived alternatives are absent, only that—on a global basis—they currently constitute a minor share of the chemical inputs supporting pharmaceutical manufacturing.

• Reviewer: Historical medicinal use of petroleum as evidence of pharmaceutical potential It is historical/ethnographic, but not scientific: references to petroleum in Mesopotamia or Rome do not constitute modern evidence of therapeutic efficacy. The extrapolation to modern drug discovery is very weak.

Authors: You are correct that historical references alone cannot be regarded as modern clinical evidence. However, our manuscript does not present Mesopotamian or Roman uses of petroleum as “proof of efficacy”, but rather as part of a long-standing therapeutic tradition that has motivated contemporary interest. This reasoning is fully aligned with current global policy frameworks: in May 2024, the World Health Assembly adopted the third WHO global strategy on traditional, complementary and integrative medicine for 2025–2034, which explicitly calls for “universal access to safe, effective and people-centred TCIM” and emphasizes the need to develop an evidence base and appropriate regulatory mechanisms. In this framework, traditional and ethnomedicinal practices are recognized at the highest policy level not as substitutes for evidence-based medicine, but as legitimate starting points for systematic preclinical and clinical evaluation.

In this sense, Naftalan and related petroleum-based interventions are not presented as validated therapies, but as historically utilized “remedy”, that now warrant rigorous investigation of their composition, mechanisms of action, and safety using modern analytical, pharmacological, and regulatory tools. Our argument follows precisely this logic: historical and ethnographic data justify a focused contemporary examination of petroleum-derived formulations, but they are not offered as definitive evidence of therapeutic efficacy.

• Reviewer: Statements about Naftalan and “empirical clinical validation”. There are reports of therapeutic use, but: Modern clinical evidence is scarce, non-randomized, and often anecdotal. Claims of efficacy in conditions such as psoriasis, arthritis, neuropathies, or vascular complications lack robust scientific validation.

Authors: We thank the reviewer for this comment. However, we respectfully disagree with the characterization of the existing data as merely “anecdotal”. Over several decades of use in the former USSR and neighbouring countries (and its continued application today in Azerbaijan and Croatia), Naftalan therapy was integrated into official sanatorium and rehabilitation medicine and generated a substantial body of hospital records, experimental studies, doctoral theses and peer-reviewed publications in dermatology, rheumatology and rehabilitation medicine. In our manuscript we cite only the most illustrative examples, as the purpose of this perspective is not to provide a systematic review of Naftalan’s clinical efficacy, but to contextualize its historically documented use as a rationale for exploring its pharmacological potential and identifying active components. Existing clinical data are indeed heterogeneous in design and frequently lack randomization or blinding, but they clearly go beyond isolated case reports and represent a systematically documented clinical practice of their time. We fully agree that the currently available clinical evidence on Naftalan oil needs to be reassessed according to contemporary “gold standards” of evidence-based medicine, i.e., large, randomized, double-blind, placebo-controlled trials. Yet the aim of the present perspective is not to claim guideline-level efficacy, but to argue that this historically accumulated clinical and experimental experience justifies a modern re-evaluation of Naftalan with up-to-date analytical, pharmacological and clinical tools.

• Reviewer: Statement that Naftalan ‘targets multiple pathophysiological pathways’There is no modern biochemical evidence that petroleum components act selectively on nociceptive signaling, inflammation, neurodegeneration, or endothelium.The phrase implies a plausible molecular mechanism, which is scientifically incorrect without robust experimental data.

Authors: We thank the reviewer for raising this point, but we respectfully disagree with the characterization of our statement as “scientifically incorrect”. The passage does not claim that specific molecular targets of Naftalan oil are known. Rather, it summarizes a convergent pattern of clinical and experimental observations—namely, analgesic, anti-inflammatory and vasoregulatory effects across diverse patient groups and experimental models—which reasonably suggests the involvement of more than one pathophysiological pathway, even though the precise molecular targets remain to be identified. Historically, many widely used drugs were introduced on the basis of robust clinical benefit long before their receptors or enzymes were characterized—for example, acetylsalicylic acid, lithium, or metformin. Therefore, this wording refers to an empirically observed pattern of action, and we explicitly state that the underlying molecular mechanisms of Naftalan oil still require systematic investigation using modern biochemical and pharmacological approaches.

• Reviewer: Mamedaliyev’s precursor theory (1940s) Historically interesting, but: The claim that steranes could be metabolized into bioactive compounds has no modern experimental support. Implying direct pharmacological potential is misleading.

Authors: We were somewhat puzzled by this comment, as we believe that our current wording already reflects the points raised here. In the manuscript, we explicitly state that Mamedaliev’s hypothesis “lacked experimental validation, primarily because technologies capable of tracing such biochemical transformations at the molecular level did not yet exist”, and we do not present it as a validated or currently accepted mechanism of action.

• Reviewer: Statement that ‘modern techniques allow the identification of molecules with significant pharmaceutical potential’. Although analytical characterization is possible, the translation of petroleum hydrocarbons into relevant bioactive molecules has not yet been demonstrated. Therefore, the statement is speculative, not scientific.

Authors: We would like to emphasize that this manuscript is submitted as a Perspective, whose purpose is not to report completed translational outcomes, but to outline emerging conceptual and methodological directions with potential relevance to pharmaceutical research. In this context, our statement does not assert that petroleum-derived compounds have already been translated into bioactive drugs; rather, it highlights that modern analytical, computational and screening technologies now make such exploration technically feasible. –

• Reviewer: Implication that petroleum could be a source of ‘drug-like candidates’. In practical terms, simple saturated or aromatic hydrocarbons are chemically inert for most biological interactions. Without extensive chemical functionalization, petroleum is not a realistic source of bioactive scaffolds.

Authors: This comment appears to result from a misunderstanding of the terminology used in our manuscript. We do not discuss petroleum in the sense of refined fuel fractions composed predominantly of simple saturated or monocyclic aromatic hydrocarbons. Our manuscript explicitly refers to crude oil, which is a geochemically complex mixture comprising structurally diverse aliphatic, alicyclic, polycyclic, heterocyclic and NSO-containing organic molecules, including sterane-, hopane- and naphthenic-acid–type frameworks. Equating crude oil with simple, chemically inert hydrocarbons is scientifically inaccurate and does not reflect established petrochemical classification. Moreover, the reviewer’s assertion that petroleum-derived structures are biologically “inert” is difficult to reconcile with the extensive toxicological and ecotoxicological literature demonstrating endocrine, inflammatory, neuroactive and mutagenic responses to specific crude-oil constituents. The existence of these documented biological interactions directly contradicts the claim of inertness. A molecule cannot simultaneously be biologically inert and produce measurable biological effects. Our manuscript does not claim that crude oil contains ready-to-use pharmaceuticals, nor that unmodified hydrocarbons represent clinically viable drug candidates. Rather, as stated, we argue that the structural diversity present in crude oil provides a chemically rich starting space that modern analytical, computational and screening techniques can interrogate for drug-like scaffolds, just as they have done for plant, microbial and marine natural products. Identifying candidates with pharmaceutical potential is an accepted early-stage objective in drug discovery and aligns with the remit of a Perspective article, which is intended to delineate emerging conceptual opportunities rather than report completed translational outcomes.

 

 Pharma matrix of crude oil: structure insights 

• Reviewer:

Generalization that Naftalan crude is a ‘sp³-rich, non-flat, ready-to-use scaffold’. While it is true that it contains many saturated hydrocarbons (decahydronaphthalenes, naphthenes), this does not automatically imply pharmacological relevance. The phrase ‘ready-made bioisosteric replacements’ is not experimentally supported; converting naphthenes or diamondoids into drugs requires extensive chemical modification.

Claim that decahydronaphthalenes, steranes, and hopanes directly contribute to the ‘reported therapeutic effects’ of Naftalan. There are no robust modern clinical data demonstrating bioactivity of these compounds. This statement extrapolates chemical occurrence to pharmacological effect, which is scientifically incorrect.

Authors: We do not claim that Naftalan crude, or any individual petroleum-derived component, is a “ready-to-use drug” or that decahydronaphthalenes, steranes or hopanes have proven therapeutic efficacy. Terms such as “sp³-rich, non-flat scaffolds” and “bioisosteric replacements” are used strictly in this structural sense and are not intended to suggest native pharmacological activity or clinical validation. Moreover, no small molecule—whether isolated from a natural source or designed de novo—is ever “ready-made” as a drug. In all cases, medicinal chemistry proceeds through cycles of functionalization, optimization and derivatization to convert a chemically attractive scaffold into a viable therapeutic candidate. Our discussion of Naftalan and other petroleum-derived frameworks is fully aligned with this logic: we do not present any component as an ideal or finished medicine, but as part of an underexplored, sp³-rich, three-dimensional chemical space that warrants systematic exploration and refinement rather than being dismissed a priori.

• Reviewer: Statements about diamondoids (adamantanes) Diamondoids have limited applications in medicinal chemistry as lipophilic groups or pharmacokinetic modifiers, but claiming: ‘effectiveness in pharmacology and medicine’ or ‘intrinsic activity linked to modulation of NMDA receptors and viral proton channels’ is highly speculative and lacks solid experimental support. Only amantadine, rimantadine, and memantine are approved drugs; extrapolation to other diamondoids is misleading.

Authors: The mechanisms we mention are not speculative; they reflect established textbook pharmacology. Specifically, memantine is a well-characterized uncompetitive NMDA receptor channel blocker approved for the treatment of moderate-to-severe Alzheimer’s disease and has been investigated as a therapeutic candidate for several other neurodegenerative and neuropsychiatric disorders (e.g., Parkinson’s disease, Huntington’s disease, neuropathic pain, depression). A simple PubMed search for “memantine NMDA” yields well over one hundred indexed articles, illustrating the extent of published evidence. Likewise, amantadine and rimantadine inhibit the M2 proton channel of influenza A virus, a mechanism that underpins their clinical use as antiviral agents; an analogous PubMed search for “amantadine M2 influenza” and “rimantadine M2 influenza” returns several hundred entries. Moreover, amantadine “has additional and less well-defined pharmacological effects, including anticholinergic and serotonergic actions, and evidence from randomized controlled trials in recent years has confirmed its efficacy in treating levodopa-induced dyskinesias and reducing motor fluctuations in patients with Parkinson’s disease” (Rascol O, Fabbri M, Poewe W. Amantadine in the treatment of Parkinson's disease and other movement disorders. Lancet Neurol. 2021;20(12):1048–1056. doi:10.1016/S1474-4422(21)00249-0).

These examples are not hypothetical: they represent clinically deployed aminoadamantane drugs whose biological activity depends directly on the adamantane cage, which is the precise context of our statement. With regard to higher diamondoids, our manuscript does not claim any established pharmacological role; we explicitly discuss them only as structurally attractive candidates for future biomedical applications. Higher diamondoids (tetramantanes, pentamantanes, hexamantanes and beyond) are exceptionally rigid, three-dimensional sp³-carbon frameworks that are extremely difficult to synthesize in the laboratory. Crude oil remains the only proven natural source of these structures: they have been isolated from heavy, high-boiling petroleum fractions (vacuum distillates) and structurally characterized in pure form using chromatographic separation and single-crystal X-ray diffraction (Dahl JE, Liu SG, Carlson RM. Isolation and structure of higher diamondoids, nanometer-sized diamond molecules. Science. 2003 Jan 3;299(5603):96-9. doi: 10.1126/science.1078239. Epub 2002 Nov 29. PMID: 12459548.). Although no clinically approved pharmaceuticals based on higher diamondoids currently exist, their unique three-dimensional architecture, exceptional rigidity and chemical stability position them—as repeatedly emphasized in the literature rather than as our personal conjecture—as promising scaffolds for future applications in drug discovery, biotechnology and advanced materials science ( Bai X, Feng Z, Zhang X, Huo Q, Jin W, Sun J, Zeng H. Discovery and genesis mechanism of high content diamondoids in the Gulong shale oil. Sci Rep. 2025 Aug 9;15(1):29186. doi: 10.1038/s41598-025-14009-9. PMID: 40783446; PMCID: PMC12335552; Schwertfeger H, Fokin AA, Schreiner PR. Diamonds are a chemist's best friend: diamondoid chemistry beyond adamantane. Angew Chem Int Ed Engl. 2008;47(6):1022-36. doi: 10.1002/anie.200701684. PMID: 18081112. Etc) 

• Reviewer: Drimanes, decalins, and other terpenoids in petroleum They are found in small amounts and are often chemically altered during diagenesis. Claims of broad anticancer, anti-inflammatory, or antiviral activity in petroleum are not validated; such activities come from intact natural compounds, not from petrochemical residues.

Authors: The reviewer’s characterization of these structures as present only in “minor amounts” or “chemically altered” during diagenesis contradicts established geochemical evidence. Bicyclic sesquiterpanes—including drimane-type frameworks—are well-recognized, persistent constituents of crude oils and refined petroleum products. Their high resistance to biodegradation and environmental weathering has led to their use as forensic biomarkers for oil-source correlation, product differentiation, and spill identification, particularly in lighter petroleum fractions (Wang, Z., Yang, C., Fingas, M., Hellebust, B., Peng, X., Hansen, A. B., & Christensen, J. H. (2005). Characterization, weathering, and application of sesquiterpanes to source identification of spilled lighter petroleum products. Environmental Science & Technology, 39(22), 8700–8707. doi:10.1021/es051371o; Yang, C., Wang, Z., Hollebone, B. P., Brown, C. E., & Landriault, M. (2009). Characteristics of bicyclic sesquiterpanes in crude oils and petroleum products. Journal of Chromatography A, 1216(20), 4475–4484. doi:10.1016/j.chroma.2009.03.024 etc)

A compound class cannot simultaneously be “chemically altered” and serve as a diagnostic marker in environmental forensics; the reviewer’s premise is therefore internally inconsistent. Moreover, naphthenic crudes such as Naftalan oil contain abundant decalin-type hydrocarbons, with decahydronaphthalenes constituting up to ~60% of the saturate fraction—values far exceeding any reasonable definition of a “minor” presence.

Our manuscript does not equate geochemical persistence with pharmacological activity. Rather, we note that certain petroleum-derived motifs overlap structurally with scaffolds known in medicinal chemistry, which rationalizes interest in their translational potential.

• Reviewer: Attribution of pharmacological activity to steranes and hopanes These are geological biomarkers, and there is no evidence that the human body can reliably metabolize them into pharmacologically active molecules. Extrapolation to ‘membrane-associated signaling’ is speculative.

Authors: Our manuscript explicitly focuses on the perspectives of identifying and using crude-oil–derived motifs in drug discovery, not on established drugs. Steranes and hopanes are indeed geological biomarkers, but in the strict geochemical sense: they are geological marker compounds of biological origin, formed from steroids and hopanoids and preserved through diagenesis and catagenesis as structurally recognizable polycyclic hydrocarbon frameworks. For sterane and hopane derivatives from Naftalan oil, we report only first in-silico predictions (Kolchina et al., 2022); we do not claim that these compounds are already pharmacologically active in humans or are reliably metabolized to active species. The phrase “may provide a basis for biomedical applications targeting membrane-associated signaling” is intended purely as a hypothesis-generating statement. Indeed, the article as a whole follows a standard translational pipeline—from chemical characterization, through in-silico profiling, to prospective in vitro and in vivo validation—rather than presenting crude-oil components as ready-made drugs.

• Reviewer: Fullerenes in asphaltenes as potential drugs Although fullerenes may have interesting chemical properties, there is no evidence of direct bioactivity from fullerenes extracted from crude oil. Claims regarding biomedical applications are hypothetical.

Authors: We do not claim that fullerenes extracted from crude oil exhibit any demonstrated biological activity. We state only that heavy crude oils “may host nanostructures of pharmaceutical relevance” and cite Farmani et al. (2020) as evidence that a broad spectrum of fullerenes and buckybowls can be identified in the asphaltene fraction using advanced analytical methods. The biomedical aspect is explicitly framed at the level of structural potential: it reflects the well-documented interest in functionalized C₆₀ and related fullerene derivatives as antioxidant, photodynamic, or nanocarrier systems in experimental studies, not claims about direct bioactivity of crude-oil extracts. Importantly, the very fact that fullerenes occur naturally in petroleum and asphaltenes has revolutionized the understanding of their formation, demonstrating that they are not merely artifacts of high-temperature synthetic methods (e.g., arc discharge), but can arise under geological conditions (Dreschmann J., Schrader W. Studying the Formation of Fullerenes During Catagenesis. Molecules. 2025;30(12):2516. doi:10.3390/molecules30122516

• Reviewer: Naphthenic acids as prostaglandin bioisosteres Structural analogy does not guarantee biological activity. Pharmacological data are limited and contradictory; suggesting therapeutic function is an exaggeration.

Authors: The reviewer is quoting a passage in which we explicitly state that “biomedical data remain limited and at times contradictory” precisely in order to avoid overinterpretation and to acknowledge the current uncertainty.  We fully agree that structural analogy alone does not guarantee biological activity. At the same time, it would be incorrect to dismiss naphthenic acids as biologically inert: their biological activity has been documented repeatedly in ecotoxicological studies using mechanistic in vitro and in vivo assays (Wang J. et al. Developmental toxicity and endocrine disruption of naphthenic acids on the early life stage of zebrafish (Danio rerio). Journal of Applied Toxicology. 2015;35(8):945–955. doi:10.1002/jat.3166; Sotoudeh, Y., Niksokhan, M.H., Karbassi, A.R., Sarafrazi, M.R. (2023). Review on Naphthenic Acids: An Important Environmental Pollutants Caused by Oil Extraction and Industries. Pollution, 9(1): 254-270. http//doi.org/10.22059/poll.2022.344876.1532^ etc) and selected naphthenic acid derivatives are included in fungicide and pesticide formulations. These findings clearly show that at least some naphthenic acid structures are capable of interacting with biological systems.

• Reviewer: Aromatic hydrocarbons and PAHs It is true that aromatics are fundamental in medicinal chemistry. However, extrapolating from PAHs found in petroleum to safe bioactivity ignores the high risk of genotoxicity and carcinogenicity.

Authors: In this section we explicitly do not extrapolate from crude-oil PAHs to “safe bioactivity”. We state that “polycyclic fractions within asphaltenes are generally regarded as waste and a source of environmental concern” and that “extended PAHs can intercalate into DNA, a mechanism underlying the activity of anthracyclines and related agents, but also their genotoxic liabilities… increasing aromatic ring count correlates negatively with oral bioavailability and aqueous solubility and raises safety risks through high plasma-protein binding and CYP/hERG liabilities (Ritchie et al., 2011).” The discussion in this section addresses the inherent toxicological liabilities of extended polycyclic aromatic systems as chemical entities—irrespective of their source—rather than attributing these risks specifically to crude oil. In other words, the risks are a consequence of molecular architecture, not petroleum origin.

• Reviewer: Petroporphyrins as pharmaceutical scaffolds Despite structural stability, no studies demonstrate that petroleum-derived petroporphyrins are bioactive or safe for pharmacological use. Extrapolation from natural porphyrins (heme, chlorophyll) to petroleum petroporphyrins is misleading.

Authors: The statement that “no studies demonstrate that petroleum-derived petroporphyrins are bioactive” is not entirely accurate. Petroleum-derived porphyrins have only very recently begun to be explored in biological settings. In particular, Pavlov R.V. et al. (Pavlov, R.V., Mironov, N.A., Gaynanova, G.A. et al. Preparation and cytotoxic properties of porphysomes based on petroleum porphyrins. Russ Chem Bull 71, 1992–1997 (2022). https://doi.org/10.1007/s11172-022-3619-7) reported the preparation and in vitro cytotoxic properties of porphysomes based on petroleum porphyrins, showing that such constructs can modulate mammalian cell viability under controlled conditions. These data do not establish safety or therapeutic efficacy and we do not present them as such, but they do indicate that petroleum-derived porphyrins cannot be regarded as completely untested or biologically inert. The analogy we draw is not a functional extrapolation from biological porphyrins to petroleum petroporphyrins, but a structural one. Petroporphyrins are well-defined geochemical markers of biological origin, derived from chlorophyll-type tetrapyrroles and related light- and oxygen-capturing biomolecules. During diagenesis and catagenesis, the chlorophyll core undergoes phytol loss, demetallation, aromatization, peripheral ring attachment, sulfur insertion and Ni/V derivatization, yet the tetrapyrrolic porphyrin macrocycle and its substitution pattern remain recognizable, which is precisely why these molecules function as robust petroleum biomarkers (McKenna A.M. et al., Advances and Challenges in the Molecular Characterization of Petroporphyrins, Energy & Fuels, 2021, 35(11), 18056–18077, doi:10.1021/acs.energyfuels.1c02002). This preserved architecture motivates our discussion of petroporphyrins as structurally tractable porphyrin scaffolds. We do not infer pharmacological properties from heme or chlorophyll; we highlight that petroleum contains porphyrin frameworks of biological origin whose macrocyclic integrity makes them suitable starting points for future derivatization and testing.

• Reviewer: Organosulfur compounds It is correct that Ichthyol has dermatological use, but this does not mean that all sulfur compounds from petroleum are bioactive or safe.

Authors: The reviewer’s statement does not correspond to what we wrote. We do not generalize the biological activity of Ichthyol to all petroleum-derived organosulfur compounds. The manuscript explicitly presents Ichthyol as an isolated, historically validated example, and makes no class-level pharmacological claims.

 

Translational perspectives of crude oil – derived drug discovery

• Reviewer: Statement that crude oil can serve as ‘direct templates for medicinal chemistry’ Although petroleum contains a diversity of hydrocarbons, there is no evidence that crude oil components are directly useful as pharmacological scaffolds. The extrapolation from structural complexity → biological activity is highly speculative.

Authors: Modern drug discovery routinely begins with structural space exploration, not with pre-existing biological data: fragment-based design, sp³-enriched scaffold discovery, and natural-product–inspired medicinal chemistry all rely on structural motifs long before experimental targets or activities are known. In this context, referring to crude-oil–derived architectures as “templates” reflects the standard logic of scaffold-centric discovery, not an assertion of inherent bioactivity.

• Reviewer: ‘Identified biological activities of petroleum-derived scaffolds’ The phrase suggests that bioactivity has been demonstrated. In reality, reported activities are predictive, in silico, or based on small molecules isolated from plants or chemical derivatives, not from pure petroleum compounds. Therefore, it is scientifically incorrect to claim that biological activities have been identified in petroleum.

Authors: We do not claim that crude oil components are directly useful as drugs, nor that structural complexity guarantees biological effect. Nevertheless, the foundational premise of modern petroleum ecotoxicology—that specific crude-oil constituents perturb endocrine, developmental, inflammatory, and neural pathways in exposed organisms—rests precisely on their capacity to engage biological targets. If these molecules were biologically irrelevant, the extensive ecotoxicological literature documenting their measurable effects would not exist.

• Reviewer: Prediction of low toxicity and multi-target potential of Naftalan biomarkers Toxicity assessment is computational (QSAR/PASS), not experimental. Extrapolating this to clinical safety or therapeutic potential is misleading, especially considering the known risks of PAHs and naphthenic acids.

Authors: The reviewer’s comment conflates distinct chemical classes and therefore misinterprets the purpose of the computational analysis. The QSAR/PASS predictions in the manuscript pertain specifically to sterane- and hopane-derived frameworks—rigid, sp³-rich biomarkers—rather than to polycyclic aromatic hydrocarbons (PAHs) or naphthenic acids. These scaffold classes differ fundamentally in physicochemical properties, reactivity, and toxicological profiles; accordingly, extrapolating risks associated with PAHs or naphthenic acids to steranes and hopanes is not scientifically justified.

• Reviewer: Direct comparison with natural products from plants or microorganisms The extrapolation suggests that petroleum could provide pharmacologically equivalent scaffolds to natural products, which is not supported by evidence. Natural products are bioactive through evolution, whereas petroleum hydrocarbons are geological residues.

Authors: We appreciate the Reviewer’s comment but respectfully disagree with the assumption that evolutionary provenance determines pharmacological potential. If bioactivity depended on evolutionary origin, the entire domain of de novo drug design, synthetic scaffolds, combinatorial libraries, and fragment-based discovery would have no rationale. Modern medicinal chemistry operates precisely on the opposite principle: architectural novelty can be functionally valuable irrespective of evolutionary history. Furthermore, the argument that natural products are “bioactive through evolution” does not align with biological reality. Plants, fungi, and microorganisms did not evolve their secondary metabolites to modulate human targets. Their chemical repertoires serve ecological and defensive purposes in organisms whose metabolic and signal-transduction networks, receptor architectures etc are phylogenetically and functionally distant from those of humans. If evolutionary alignment were required for pharmacological relevance, then the vast majority of natural-product-derived drugs would lack justification, as their original biological roles do not correspond to human physiology. Their therapeutic use results from pharmacological repurposing, not evolutionary design. Our comparison to natural products concerns methodological parallels—specifically, the need to navigate heterogeneous molecular matrices through fractionation, annotation, and prioritization—not any claim of shared evolutionary intent.

• Reviewer: Petroleomics and integration into the drug discovery pipeline Although petroleomics identifies thousands of molecules, most lack chemical functionality useful for biological interactions. Transforming a chemical fingerprint into pharmacologically meaningful data is not trivial and does not guarantee active scaffolds.

Authors: We agree that transforming petroleomic fingerprints into pharmacologically meaningful information is non-trivial and does not in itself guarantee the identification of active scaffolds. As with natural products, combinatorial libraries or fragment collections, no platform can guarantee that a given molecule will become a drug. This is precisely the challenge our Perspective aims to articulate. However, the statement that most petroleum components “lack chemical functionality useful for biological interactions” is, at this stage, an a priori assumption rather than a demonstrated fact. Petroleomics currently provides a compositional map of a very broad and heterogeneous structural space that has scarcely been interrogated using medicinal-chemistry criteria. At the same time, modern medicinal chemistry already depends on petroleum-derived structures; our proposal is simply to explore those parts of this space that have never been examined for biological relevance.

• Reviewer: Use of virtual screening, docking, QSAR, and in vitro/in vivo validation This is a theoretical extrapolation. There are no published studies showing that molecules isolated from crude petroleum have verifiable pharmacological activity in vitro or in vivo

Authors: The absence of an established pipeline for crude-oil constituents is not a weakness of our argument—it is the gap our Perspective identifies. Existing studies are scattered and lack integration, but it is incorrect to suggest that crude petroleum has not yielded pharmacologically relevant scaffolds or that no research exists. As cited in the manuscript, petroleum-derived frameworks have already entered medicinal chemistry, and the most substantive body of experimental work to date concerns the toxicity and biological activity of Naftalan-derived fractions, particularly in Croatia and Azerbaijan.

• Reviewer: Comparison with natural products: toxicity and complexity It is true that natural products have similar challenges, but the toxicity of petroleum and PAHs is much more severe. The statement downplays real risks and may give a misleading impression of safety.

Authors: We fully acknowledge the documented ecotoxicity of petroleum-derived fractions, including PAHs and certain naphthenic acids. However, toxicity per se does not preclude scientific investigation. A considerable number of successful therapeutic agents originate from molecules that were initially recognized as hazardous or lethal. Botulinum neurotoxin, curare alkaloids, cardiac glycosides, and anthracyclines entered medicine not because they were inherently safe, but because their structural features proved amenable to controlled administration, carefully managed dosing, and targeted use.

• Reviewer: Phrases suggesting ‘translational potential’ The entire passage conveys the idea that petroleum could be directly used as a source of innovative drugs. Scientifically, this is not supported; most compounds are chemically inert, toxic, or present at minute concentrations.

Authors: We respectfully disagree with this interpretation, which does not reflect the wording or intent of the manuscript. Our position concerns the translational relevance of specific petroleum-derived structural motifs within an underexplored chemical space, assuming prior fractionation, selection, functionalization, and toxicological filtering. Moreover, the Reviewer’s assertion that petroleum components are both chemically inert and toxic is logically incompatible. Toxicity is not a property of inert molecules; it necessarily implies biologically meaningful interactions with receptors, membranes, enzymes, or signal-transduction pathways. The extensive toxicological and ecotoxicological literature on PAHs, naphthenic acids, and petroleum-derived porphyrins exists precisely because these molecules are not inert and demonstrably engage biological systems. The Reviewer’s objection that “most compounds are chemically inert, toxic, or present at minute concentrations” is also not specific to petroleum. It applies—often more severely—to every major reservoir used in drug discovery. The majority of entries in combinatorial libraries and fragment collections are inactive against any given target. Natural-product matrices frequently contain molecules that are highly toxic, unstable, or occur at trace levels. Hit rates in early-stage discovery are sparse by design; this is not an argument against investigation but the operational premise of the field. Accordingly, the fact that only a minority of petroleum-derived components may prove chemically or pharmacologically useful does not invalidate exploration. It simply defines the starting conditions of any realistic discovery pipeline—one that proceeds by aggressive filtering, prioritization, and refinement rather than by assuming intrinsic suitability of all constituents.

 

Conclusion

• Reviewer: a)Statement that ‘crude oil harbors a broad spectrum of biologically relevant scaffolds’ Problematic: although petroleum contains molecules such as adamantanes, steranes, hopanes, porphyrins, and aromatics, there is no robust evidence that they are bioactive in humans or animals without chemical modification. The phrase implies direct biological activity, which is scientifically incorrect. –

1. b) Comparison with ‘established therapeutic classes’ The conclusion suggests that petroleum structures could replace or overlap with existing drugs. This is an unsupported extrapolation; structural presence does not imply pharmacological effect.

c)Statement of ‘industrial scale’ as an advantage for drug discovery Although it is true that petroleum exists in large quantities, this does not mean its molecules are readily usable as drugs. Many compounds are inert, toxic, or present in minute amounts, making the statement misleading. –

 d)‘Petroleum-based pharmacology’ as a potential field Creating a field based on petroleum pharmacology is premature. Currently, there is insufficient experimental evidence to justify a separate scientific field. –

1. e) Integration of petroleomics in drug discovery Although petroleomics provides detailed chemical data, there are no proven examples of transforming petroleum fingerprints into bioactive scaffolds ready for pharmacological assays. The statement may create exaggerated expectations about practical applicability.

Authors: To avoid repeating points already addressed in detail above, we would like here to clarify the overarching logic of this part of the manuscript.

Our Perspective does not claim that crude oil in its bulk form contains ready-to-use drugs, that petroleum-derived chemotypes can substitute established therapeutic classes, or that a fully developed “petroleum-based pharmacology” already exists. Rather, our central thesis is that crude oil represents a chemically rich, globally abundant and largely unexplored structural space which, in some cases, mirrors medicinal chemistry in its molecular frameworks and contains components that may be difficult to isolate but are even harder to synthesize de novo. In this sense, our use of terms such as “biologically relevant scaffolds”, “translational potential” or “integration of petroleomics into drug discovery” is explicitly conceptual and conditional: it presupposes rigorous fractionation, selection, functionalization and toxicological filtering, and does not assert intrinsic bioactivity or immediate pharmacological utility of unmodified crude-oil constituents. The Reviewer’s observation that there is currently no established field, no validated workflow and no published examples of petroleomic fingerprints being transformed into drug candidates describes, in fact, the very knowledge gap that this Perspective aims to deliver. If such pipelines and empirically validated scaffolds already existed, a Perspective article would be redundant and the topic would no longer require conceptual framing. Our contribution is therefore to define why this neglected chemical space is worth systematic and tightly controlled exploration, to delineate its constraints, and to outline how existing petroleomic tools could be repurposed into a testable, stepwise translational agenda.

 

References

• Reviewer: The references are not in the same format. Then there are others in bold. It’s advisable to standardize this entire section.

Authors: We thank the reviewer for pointing this out. The reference list has now been fully standardized according to the journal’s formatting guidelines, and all inconsistencies (including bolded entries) have been corrected.

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

Dear Authors,
Thank you for your revisions and for addressing some aspects of my previous feedback. However, I note that key suggestions from my review remain unaddressed, which significantly impacts the manuscript's quality and alignment with the journal's expectations for a comprehensive "Perspective" article.
Specifically:
A few sentences are insufficient about historical issues; a dedicated overview with key milestones would enrich the narrative and justify the renewed interest.

The manuscript still lacks any figures or tables, which are essential for clarity, summarization, and reader engagement.

Without these essential elements, the manuscript does not fully meet the standards for publication.

Author Response

REVIEWER:

Thank you for your revisions and for addressing some aspects of my previous feedback. However, I note that key suggestions from my review remain unaddressed, which significantly impacts the manuscript's quality and alignment with the journal's expectations for a comprehensive "Perspective" article.
Specifically:
A few sentences are insufficient about historical issues; a dedicated overview with key milestones would enrich the narrative and justify the renewed interest.

The manuscript still lacks any figures or tables, which are essential for clarity, summarization, and reader engagement.

Without these essential elements, the manuscript does not fully meet the standards for publication.

 

AUTHORS:

Dear Reviwer,

Thank you for your constructive comments. We have made the following revisions to the manuscript.

(1) Historical timeline.
We introduced a dedicated historical timeline summarizing the medical use of petroleum across key periods. Due to its length (approximately two manuscript pages), this material has been placed in the Appendix to maintain the balance and readability of the main text.

(2) Schematic figures.
We also added six new schematic figures illustrating representative chemical structures discussed in the text.

Thank you for your consideration.

Reviewer 3 Report

Comments and Suggestions for Authors

- Although the term “scientifically tractable resource for pharmaceutical innovation” is technically defensible and its explanation is correct, it could be interpreted as a claim that crude oil is already a viable source of drugs, which is not proven. To reduce the risk of overinterpretation and facilitate acceptance by reviewers, it would be prudent to consider a more conservative rephrasing.

For example:

“Scientifically tractable chemical space relevant to pharmaceutical research”

“Analytically and computationally tractable resource for exploratory pharmaceutical research”

These options retain the scientific value of the phrase but make it clear that it refers to exploration and analysis, not immediate practical applicability.

 

- Although the current wording is correct and scientifically defensible, there remains a small risk that it could be misinterpreted as suggesting that flat, sp²-rich structures might be considered toxic or of low pharmacological value. To avoid any misunderstanding, we recommend a slight rephrasing that makes it clear that this refers only to a historical bias in drug libraries, without implying negative pharmacological effects.

For example:

“The predominant use of cross-coupling reactions such as Suzuki–Miyaura and amide formation has historically biased drug libraries toward flat, aromatic scaffolds, without implying intrinsic toxicity or reduced pharmacological potential.”

This version retains the scientific point about the influence of synthetic practices, but eliminates any possibility of misinterpretation.

 

- Although the current wording is technically correct, there remains some risk that it could be interpreted as suggesting that physicochemical filters or sp² chemistry are responsible for most of the high (~90%) failure rate in drug development. To avoid any misunderstanding, we recommend a slight rephrasing that makes it clear that these factors represent only one of several contributing elements, without implying that they are the main cause.

For example:

“Our citation of Waring et al. (2015) serves only to contextualize the broader challenges in drug discovery and to illustrate that conventional design paradigms—while influential in shaping the chemical space explored—represent just one of several contributing factors, without implying they are the primary cause of the 90% attrition rate.”

This version retains the scientific point but eliminates any possibility of misinterpretation.

 

- Although the current wording is correct and well-founded, there remains a risk that some readers might interpret “metabolite-likeness” and “endogenite-orientation” as mainstream trends in the pharmaceutical industry, which is not the case. To avoid any misunderstanding, we recommend a slight rephrasing that makes it clear that these are academic and exploratory strategies.

For example:

“These concepts are explored academically and are not considered mainstream industrial paradigms. Their mention in the manuscript serves to illustrate analytically documented efforts to explore alternative regions of chemical space beyond traditional Rule-of-5 frameworks.”

This version retains the scientific point but eliminates any possibility of misinterpretation.

 

- Although the current wording is detailed and scientifically sound, there remains some risk that it could be interpreted as suggesting that petroleum contains ready-to-use drugs or intact biological molecules, which is not the case. To eliminate any possibility of misunderstanding, we recommend adding a qualifying sentence emphasizing that petroleum provides only structural scaffolds for future derivatization, not finished pharmacophores.

For example:

“These scaffolds are not pharmacophores or bioactive compounds per se, but provide a structural starting point for future medicinal chemistry exploration.”

This addition retains the scientific point about structural diversity and rigid sp³-rich frameworks, but makes it explicit that petroleum is not an immediate source of drugs.

 

- The current answer is technically correct, but there is still some risk of it being interpreted as implying that steroid, hopanoid, or petro-porphyrin backbones are bioactive or readily usable in drug discovery, especially by readers less familiar with geoscience. To avoid misunderstandings, we suggest explicitly emphasizing that these molecules are relevant for their structural properties and detectability, not for immediate bioactivity.

For example, one could add a sentence such as:

“These motifs are not inherently bioactive nor immediately useful as drugs; their relevance lies in their structural features and detectability, which allow them to function as geobiomarkers.”

This addition makes it clear that the point of the manuscript is structural and geobiomarker-related, without implying any direct pharmacological potential.

Author Response

Dear Reviewer,

Thank you for your comments regarding language and clarity. The manuscript was carefully revised accordingly, and suggested changes were incorporated.  

Reviewer

Although the term “scientifically tractable resource for pharmaceutical innovation” is technically defensible and its explanation is correct, it could be interpreted as a claim that crude oil is already a viable source of drugs, which is not proven. To reduce the risk of overinterpretation and facilitate acceptance by reviewers, it would be prudent to consider a more conservative rephrasing.

For example:

“Scientifically tractable chemical space relevant to pharmaceutical research”

“Analytically and computationally tractable resource for exploratory pharmaceutical research”

These options retain the scientific value of the phrase but make it clear that it refers to exploration and analysis, not immediate practical applicability.

Authors:

Thank you for this comment. We have adopted the suggested rephrasing and implemented it in lines 27–28.

 Reviewer

- Although the current wording is correct and scientifically defensible, there remains a small risk that it could be misinterpreted as suggesting that flat, sp²-rich structures might be considered toxic or of low pharmacological value. To avoid any misunderstanding, we recommend a slight rephrasing that makes it clear that this refers only to a historical bias in drug libraries, without implying negative pharmacological effects.

For example:

“The predominant use of cross-coupling reactions such as Suzuki–Miyaura and amide formation has historically biased drug libraries toward flat, aromatic scaffolds, without implying intrinsic toxicity or reduced pharmacological potential.”

This version retains the scientific point about the influence of synthetic practices, but eliminates any possibility of misinterpretation.

Authors:

Thank you for this comment. We have adopted the suggested rephrasing and implemented it in lines 45–47 to avoid any potential misinterpretation.

Reviewer

- Although the current wording is technically correct, there remains some risk that it could be interpreted as suggesting that physicochemical filters or sp² chemistry are responsible for most of the high (~90%) failure rate in drug development. To avoid any misunderstanding, we recommend a slight rephrasing that makes it clear that these factors represent only one of several contributing elements, without implying that they are the main cause.

For example:

“Our citation of Waring et al. (2015) serves only to contextualize the broader challenges in drug discovery and to illustrate that conventional design paradigms—while influential in shaping the chemical space explored—represent just one of several contributing factors, without implying they are the primary cause of the 90% attrition rate.”

This version retains the scientific point but eliminates any possibility of misinterpretation.

Authors:

Thank you for this comment. The text has been revised accordingly to avoid any potential overinterpretation (lines 47–50).

 Reviewer

- Although the current wording is correct and well-founded, there remains a risk that some readers might interpret “metabolite-likeness” and “endogenite-orientation” as mainstream trends in the pharmaceutical industry, which is not the case. To avoid any misunderstanding, we recommend a slight rephrasing that makes it clear that these are academic and exploratory strategies.

For example:

“These concepts are explored academically and are not considered mainstream industrial paradigms. Their mention in the manuscript serves to illustrate analytically documented efforts to explore alternative regions of chemical space beyond traditional Rule-of-5 frameworks.”

This version retains the scientific point but eliminates any possibility of misinterpretation.

Authors:

Thank you for this comment. We have revised the text to reflect this point, clarifying that “metabolite-likeness” and “endogenite-orientation” are academic and exploratory concepts rather than mainstream industrial paradigms (lines 56–60).

Reviewer

- Although the current wording is detailed and scientifically sound, there remains some risk that it could be interpreted as suggesting that petroleum contains ready-to-use drugs or intact biological molecules, which is not the case. To eliminate any possibility of misunderstanding, we recommend adding a qualifying sentence emphasizing that petroleum provides only structural scaffolds for future derivatization, not finished pharmacophores.

For example:

“These scaffolds are not pharmacophores or bioactive compounds per se, but provide a structural starting point for future medicinal chemistry exploration.”

This addition retains the scientific point about structural diversity and rigid sp³-rich frameworks, but makes it explicit that petroleum is not an immediate source of drugs.

Authors:

Thank you for this comment. We have revised the text accordingly and added a clarifying statement emphasizing that petroleum provides structural scaffolds for future derivatization rather than ready-to-use pharmacophores (lines 57-58)

 Reviewer

- The current answer is technically correct, but there is still some risk of it being interpreted as implying that steroid, hopanoid, or petro-porphyrin backbones are bioactive or readily usable in drug discovery, especially by readers less familiar with geoscience. To avoid misunderstandings, we suggest explicitly emphasizing that these molecules are relevant for their structural properties and detectability, not for immediate bioactivity.

For example, one could add a sentence such as:

“These motifs are not inherently bioactive nor immediately useful as drugs; their relevance lies in their structural features and detectability, which allow them to function as geobiomarkers.”

This addition makes it clear that the point of the manuscript is structural and geobiomarker-related, without implying any direct pharmacological potential.

Authors:

Thank you for this comment. We have clarified this point in the revised text to explicitly state that structural overlap does not imply direct pharmacophoricity (line 355).