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Natural and Designed Molecules in Drug Discovery

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Natural Products Chemistry".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 10618

Special Issue Editors


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Guest Editor
Chemistry and Biochemistry, Baylor University, Waco, TX, USA
Interests: natural and designed molecules; small molecules; drug discovery; AI drug design and molecular docking; pharmacological activities

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Guest Editor
Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
Interests: medicinal chemical biology; molecular drug design; anti-tumor immunosuppressants; PD-1/PD-L1 small-molecule drugs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Currently, some diseases are effectively controlled and treated worldwide, but the morbidity and mortality of other diseases continue to increase, such as malignant tumors, cardiovascular and cerebrovascular diseases, and diabetes. Moreover, the understanding of the pathogenesis of some diseases is not yet clear, and the level of science and technology and medical treatment is lagging behind, making it impossible to control and cure these diseases. This urges the discovery of novel, more effective drugs. Natural and designed molecules are a source of drugs accounting for the majority of current clinical drugs. In this Special Issue, researchers are invited to contribute original research articles and reviews that focus on the use of natural and designed molecules in drug discovery. This Special Issue will cover the following topics, including, but not limited to:

  • Novel drug molecules, both natural and designed;
  • The determination of molecular structure;
  • Advances in the application of well-known molecules in drug discovery;
  • Mechanisms of the interaction between bioactive molecules and their targets;
  • Computer-aided drug design;
  • The structure–activity relationship between molecules and targets;
  • The evaluation of the druggability of molecules with theoretical and experimental studies.

Dr. Suresh Narva
Prof. Dr. Wen Zhang
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (6 papers)

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Research

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0 pages, 7540 KiB  
Article
Exploring Cinnamoyl-Substituted Mannopyranosides: Synthesis, Evaluation of Antimicrobial Properties, and Molecular Docking Studies Targeting H5N1 Influenza A Virus
by Sabina Akter, Bader Y. Alhatlani, Emad M. Abdallah, Supriyo Saha, Jannatul Ferdous, Md Emdad Hossain, Ferdausi Ali and Sarkar M. A. Kawsar
Molecules 2023, 28(24), 8001; https://doi.org/10.3390/molecules28248001 - 07 Dec 2023
Viewed by 1088
Abstract
The pursuit of innovative combinations for the development of novel antimicrobial and antiviral medications has garnered worldwide interest among scientists in recent times. Monosaccharides and their glycosides, such as methyl α-d-mannopyranoside derivatives, play a significant role in the potential treatment of [...] Read more.
The pursuit of innovative combinations for the development of novel antimicrobial and antiviral medications has garnered worldwide interest among scientists in recent times. Monosaccharides and their glycosides, such as methyl α-d-mannopyranoside derivatives, play a significant role in the potential treatment of viral respiratory pathologies. This study was undertaken to investigate and assess the synthesis and spectral characterization of methyl α-d-mannopyranoside derivatives 26, incorporating various aliphatic and aromatic groups. The investigation encompassed comprehensive in vitro antimicrobial screening, examination of physicochemical properties, molecular docking analysis, molecular dynamics simulations, and pharmacokinetic predictions. A unimolar one-step cinnamoylation reaction was employed under controlled conditions to produce methyl 6-O-cinnamoyl-α-d-mannopyranoside 2, demonstrating selectivity at the C-6 position. This represented a pivotal step in the development of potential antimicrobial derivatives based on methyl α-d-mannopyranoside. Subsequently, four additional methyl 6-O-cinnamoyl-α-d-mannopyranoside derivatives were synthesized with reasonably high yields. The chemical structures of these novel analogs were confirmed through a thorough analysis of their physicochemical properties, elemental composition, and spectroscopic data. In vitro antimicrobial assays were conducted against six bacterial strains and two fungal strains, revealing promising antifungal properties of these methyl α-d-mannopyranoside derivatives in comparison to their antibacterial activity. Moreover, cytotoxicity testing revealed that the compounds are less toxic. Further supporting these findings, molecular docking studies were performed against the H5N1 influenza A virus, indicating significant binding affinities and nonbonding interactions with the target protein 6VMZ. Notably, compounds 4 (−7.2) and 6 (−7.0) exhibited the highest binding affinities. Additionally, a 100 ns molecular dynamics simulation was conducted to assess the stability of the complex formed between the receptor 6VMZ and methyl α-d-mannopyranoside derivatives under in silico physiological conditions. The results revealed a stable conformation and binding pattern within the stimulating environment. In silico pharmacokinetic and toxicity assessments of the synthesized molecules were performed using Osiris software (version 2.9.1). Compounds 4 and 6 demonstrated favorable computational and pharmacological activities, albeit with a low drug score, possibly attributed to their higher molecular weight and irritancy. In conclusion, this study showcases the synthesis and evaluation of methyl α-d-mannopyranoside derivatives as promising candidates for antimicrobial and antifungal agents. Molecular docking and dynamics simulations, along with pharmacological predictions, contribute to our understanding of their potential therapeutic utility, although further research may be warranted to address certain pharmacological aspects. Full article
(This article belongs to the Special Issue Natural and Designed Molecules in Drug Discovery)
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21 pages, 5688 KiB  
Article
Anti-Neurodegenerating Activity: Structure–Activity Relationship Analysis of Flavonoids
by Gagan Preet, Ahlam Haj Hasan, Piteesha Ramlagan, Shameem Fawdar, Fabien Boulle and Marcel Jaspars
Molecules 2023, 28(20), 7188; https://doi.org/10.3390/molecules28207188 - 20 Oct 2023
Cited by 1 | Viewed by 1188
Abstract
An anti-neurodegeneration activity study was carried out for 80 flavonoid compounds. The structure–activity analysis of the structures was carried out by performing three different anti-neurodegeneration screening tests, showing that in these structures, the presence of a hydroxy substituent group at position C3′ as [...] Read more.
An anti-neurodegeneration activity study was carried out for 80 flavonoid compounds. The structure–activity analysis of the structures was carried out by performing three different anti-neurodegeneration screening tests, showing that in these structures, the presence of a hydroxy substituent group at position C3′ as well as C5′ of ring B and a methoxy substituent group at the C7 position of ring A play a vital role in neuroprotective and antioxidant as well as anti-inflammatory activity. Further, we found structure (5) was the top-performing active structure out of 80 structures. Subsequently, a molecular docking study was carried out for the 3 lead flavonoid compounds (4), (5), and (23) and 21 similar hypothetical proposed structures to estimate the binding strength between the tested compounds and proteins potentially involved in disease causation. Ligand-based pharmacophores were generated to guide future drug design studies. Full article
(This article belongs to the Special Issue Natural and Designed Molecules in Drug Discovery)
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18 pages, 5591 KiB  
Article
Network Pharmacology and Molecular Modeling to Elucidate the Potential Mechanism of Neem Oil against Acne vulgaris
by Adeola Tawakalitu Kola-Mustapha, Muhabat Adeola Raji, Oluwakorede Adedeji and George Oche Ambrose
Molecules 2023, 28(6), 2849; https://doi.org/10.3390/molecules28062849 - 21 Mar 2023
Cited by 1 | Viewed by 2267
Abstract
Acne vulgaris is a common skin disorder with a complicated etiology. Papules, lesions, comedones, blackheads, and other skin lesions are common physical manifestations of Acne vulgaris, but the individual who has it also regularly has psychological repercussions. Natural oils are being utilized [...] Read more.
Acne vulgaris is a common skin disorder with a complicated etiology. Papules, lesions, comedones, blackheads, and other skin lesions are common physical manifestations of Acne vulgaris, but the individual who has it also regularly has psychological repercussions. Natural oils are being utilized more and more to treat skin conditions since they have fewer negative effects and are expected to provide benefits. Using network pharmacology, this study aims to ascertain if neem oil has any anti-acne benefits and, if so, to speculate on probable mechanisms of action for such effects. The neem leaves (Azadirachta indica) were collected, verified, authenticated, and assigned a voucher number. After steam distillation was used to extract the neem oil, the phytochemical components of the oil were examined using gas chromatography–mass spectrometry (GC-MS). The components of the oil were computationally examined for drug-likeness using Lipinski’s criteria. The Pharm Mapper service was used to anticipate the targets. Prior to pathway and protein–protein interaction investigations, molecular docking was performed to predict binding affinity. Neem oil was discovered to be a potential target for STAT1, CSK, CRABP2, and SYK genes in the treatment of Acne vulgaris. In conclusion, it was discovered that the neem oil components with PubChem IDs: ID_610088 (2-(1-adamantyl)-N-methylacetamide), ID_600826 (N-benzyl-2-(2-methyl-5-phenyl-3H-1,3,4-thiadiazol-2-yl)acetamide), and ID_16451547 (N-(3-methoxyphenyl)-2-(1-phenyltetrazol-5-yl)sulfanylpropanamide) have strong affinities for these drug targets and may thus be used as therapeutic agents in the treatment of acne. Full article
(This article belongs to the Special Issue Natural and Designed Molecules in Drug Discovery)
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23 pages, 2274 KiB  
Article
Synthetic Cinnamides and Cinnamates: Antimicrobial Activity, Mechanism of Action, and In Silico Study
by Mayara Castro de Morais, Edeltrudes de Oliveira Lima, Yunierkis Perez-Castillo and Damião Pergentino de Sousa
Molecules 2023, 28(4), 1918; https://doi.org/10.3390/molecules28041918 - 17 Feb 2023
Cited by 5 | Viewed by 2119
Abstract
The severity of infectious diseases associated with the resistance of microorganisms to drugs highlights the importance of investigating bioactive compounds with antimicrobial potential. Therefore, nineteen synthetic cinnamides and cinnamates having a cinnamoyl nucleus were prepared and submitted for the evaluation of antimicrobial activity [...] Read more.
The severity of infectious diseases associated with the resistance of microorganisms to drugs highlights the importance of investigating bioactive compounds with antimicrobial potential. Therefore, nineteen synthetic cinnamides and cinnamates having a cinnamoyl nucleus were prepared and submitted for the evaluation of antimicrobial activity against pathogenic fungi and bacteria in this study. To determine the minimum inhibitory concentration (MIC) of the compounds, possible mechanisms of antifungal action, and synergistic effects, microdilution testing in broth was used. The structures of the synthesized products were characterized with FTIR spectroscopy, 1 H-NMR, 13 C-NMR, and HRMS. Derivative 6 presented the best antifungal profile, suggesting that the presence of the butyl substituent potentiates its biological response (MIC = 626.62 μM), followed by compound 4 (672.83 μM) and compound 3 (726.36 μM). All three compounds were fungicidal, with MFC/MIC ≤ 4. For mechanism of action, compounds 4 and 6 directly interacted with the ergosterol present in the fungal plasmatic membrane and with the cell wall. Compound 18 presented the best antibacterial profile (MIC = 458.15 μM), followed by compound 9 (550.96 μM) and compound 6 (626.62 μM), which suggested that the presence of an isopropyl group is important for antibacterial activity. The compounds were bactericidal, with MBC/MIC ≤ 4. Association tests were performed using the Checkerboard method to evaluate potential synergistic effects with nystatin (fungi) and amoxicillin (bacteria). Derivatives 6 and 18 presented additive effects. Molecular docking simulations suggested that the most likely targets of compound 6 in C. albicans were caHOS2 and caRPD3, while the most likely target of compound 18 in S. aureus was saFABH. Our results suggest that these compounds could be used as prototypes to obtain new antimicrobial drugs. Full article
(This article belongs to the Special Issue Natural and Designed Molecules in Drug Discovery)
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26 pages, 3181 KiB  
Article
Designing Functionally Substituted Pyridine-Carbohydrazides for Potent Antibacterial and Devouring Antifungal Effect on Multidrug Resistant (MDR) Strains
by Farooq-Ahmad Khan, Sana Yaqoob, Shujaat Ali, Nimra Tanveer, Yan Wang, Sajda Ashraf, Khwaja Ali Hasan, Shaden A. M. Khalifa, Qiyang Shou, Zaheer Ul-Haq, Zi-Hua Jiang and Hesham R. El-Seedi
Molecules 2023, 28(1), 212; https://doi.org/10.3390/molecules28010212 - 26 Dec 2022
Cited by 5 | Viewed by 2300
Abstract
The emergence of multidrug-resistant (MDR) pathogens and the gradual depletion of available antibiotics have exacerbated the need for novel antimicrobial agents with minimal toxicity. Herein, we report functionally substituted pyridine carbohydrazide with remarkable antimicrobial effect on multi-drug resistant strains. In the series, compound [...] Read more.
The emergence of multidrug-resistant (MDR) pathogens and the gradual depletion of available antibiotics have exacerbated the need for novel antimicrobial agents with minimal toxicity. Herein, we report functionally substituted pyridine carbohydrazide with remarkable antimicrobial effect on multi-drug resistant strains. In the series, compound 6 had potent activity against four MDR strains of Candida spp., with minimum inhibitory concentration (MIC) values being in the range of 16–24 µg/mL and percentage inhibition up to 92.57%, which was exceptional when compared to broad-spectrum antifungal drug fluconazole (MIC = 20 µg/mL, 81.88% inhibition). Substitution of the octyl chain in 6 with a shorter butyl chain resulted in a significant anti-bacterial effect of 4 against Pseudomonas aeruginosa (ATCC 27853), the MIC value being 2-fold superior to the standard combination of ampicillin/cloxacillin. Time-kill kinetics assays were used to discern the efficacy and pharmacodynamics of the potent compounds. Further, hemolysis tests confirmed that both compounds had better safety profiles than the standard drugs. Besides, molecular docking simulations were used to further explore their mode of interaction with target proteins. Overall results suggest that these compounds have the potential to become promising antimicrobial drugs against MDR strains. Full article
(This article belongs to the Special Issue Natural and Designed Molecules in Drug Discovery)
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Review

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17 pages, 2827 KiB  
Review
Identification of Potential Plant-Derived Pancreatic Beta-Cell-Directed Agents Using New Custom-Designed Screening Method: Gymnema sylvestre as an Example
by Altaf Al-Romaiyan, Shanta J. Persaud and Peter M. Jones
Molecules 2024, 29(1), 194; https://doi.org/10.3390/molecules29010194 - 28 Dec 2023
Viewed by 831
Abstract
Background: Folk medicines are attractive therapeutic agents for treating type 2 diabetes mellitus (T2DM). Most plant extracts that have been suggested to restore β-cells function were tested in vivo. Some only have been tested in vitro to determine whether they have a direct [...] Read more.
Background: Folk medicines are attractive therapeutic agents for treating type 2 diabetes mellitus (T2DM). Most plant extracts that have been suggested to restore β-cells function were tested in vivo. Some only have been tested in vitro to determine whether they have a direct effect on β-cells islets of Langerhans. Currently, there are no defined criteria for screening of β-cell-directed plant-based remedies as potential antidiabetic agents. Summary: In this review, we have identified certain criteria/characteristics that can be used to generate a “screening portfolio” to identify plant extracts as potential β-cell-directed agents for the treatment of T2DM. To validate our screening method, we studied the potential therapeutic efficacy of a Gymnema sylvestre (GS) extract using the screening criteria detailed in the review. Six criteria have been identified and validated using OSA®, a GS extract. By using this screening method, we show that OSA® fulfilled most of the criteria identified for an effective β-cell-directed antidiabetic therapy, being an effective insulin-releasing agent at nontoxic concentrations; maintaining β-cell insulin content by stimulating a concomitant increase in insulin gene transcription; maintaining β-cell mass by protecting against apoptosis; and being effective at maintaining normoglycemia in vivo in a mouse model and a human cohort with T2DM. Key messages: The present review has highlighted the importance of having a screening portfolio for plant extracts that have potential antidiabetic effects in the treatment of T2DM. We propose that this screening method should be adopted for future studies to identify new β-cell-directed antidiabetic plant derived agents. Full article
(This article belongs to the Special Issue Natural and Designed Molecules in Drug Discovery)
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