Rational Design of Mitochondria-Targeted Antioxidants: From Molecular Determinants to Clinical Perspectives

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Franczyk et al. reviewed the rational design of mitochondria-targeted antioxidants, focusing on SAR and redox mechanism. Manuscript composition is good and very informative for the reader. I have some minor concerns that need to be addressed.

1. Several small molecules reported as antioxidants targeting mitochondria in the literature; authors should include these with their structure to boost the drug design section.
2. Section 6 Therapeutic Potential should be broad and include more disease conditions like cancer and epilepsy, which are also associated with oxidative stress.
3. Molecular mechanisms of these discussed diseases should also be addressed, focusing on mitochondrial-associated oxidative stress.
4. The conclusion is too long; it should be short and informative.
5. Typos and grammatical errors should be removed.

Comments on the Quality of English Language

The English could be improved.

Author Response

1. Several small molecules reported as antioxidants targeting mitochondria in
the literature; authors should include these with their structure to boost the
drug design section.
We thank the Reviewer for this helpful suggestion. In response, we have added
Figure 1, which presents representative 2D chemical structures of selected small-
molecule mitochondria-targeted antioxidants (MitoQ, SkQ1, MitoTEMPO, and
MitoVitE). The figure illustrates the modular architecture of MTAs, explicitly
highlighting the lipophilic cationic carrier, linker, and antioxidant payload. This
addition provides structural context for the drug design concepts discussed in
Section 2 and facilitates interpretation of structure-activity relationships.
2. Therapeutic Potential should be broad and include more disease conditions
like cancer and epilepsy, which are also associated with oxidative stress.
The Authors thank the Reviewer for the comment. We agree that the role of
oxidative stress in these conditions is critical. Accordingly, we have expanded
Section 6 to include a discussion on the implications of our findings for cancer
and epilepsy.
3. Molecular mechanisms of these discussed diseases should also be
addressed, focusing on mitochondrial-associated oxidative stress.
We thank the Reviewer for the comment. We have revised Section 6 to include
the molecular mechanisms of the discussed diseases, with a specific focus on
mitochondrial-associated oxidative stress.
4. The conclusion is too long; it should be short and informative.
We have revised and substantially shortened the Conclusions section to adopt a
more concise and balanced tone.
5. Typos and grammatical errors should be removed.
6. Comments on the Quality of English Language - The English could be
improved.
The Authors thank the Reviewer for this comment. We have thoroughly revised the
entire manuscript to improve its clarity and accessibility. Overly complex and lengthy
sentences have been simplified or broken down, and a comprehensive grammar
check has been performed. We believe the text is now significantly more readable
and focused.

Reviewer 2 Report

Comments and Suggestions for Authors

The Manuscript “Rational Design of Mitochondria-Targeted Antioxidants: A Review of Structure-Activity Relationships and Redox Mechanisms” by B. Franczyk, K. Bojdo, J. Chłądzyńsky, K. Hossa, K. Krawiranda, N. Krupińska, N. Kustosik, K. Leszto, W. Lisińska, A. Wieczorek, J. Rysz and E. Młynarska represents a review covering the main types, mechanism of action of mitochondria-targeted antioxidants (MTA), primarily triphenylphosphonium-based molecules bearing antioxidant moieties. A particular attention has been paid to mitoquinone (MitoQ) and plastoquinone-based ions (SkQ). The potential of MTAs in treatment of pathological conditions (e.g. Alzheimer’s and Parkinson’s diseases) has been discussed. The possibilities of the use of in silico approaches to disclose a mechanism of action of existing MTAs and to discover the novel MTA has been described as well.

Overall, the review topic is actual. The review is organized well and written in a good scientific language. However there are still some questions that preclude its publishing in present form.

1. All the discussion on types of MTAs, their mechanism of action or pharmacokinetic peculiarities is not demonstrative without figures or schemes containing compounds’ structures. The total lack of illustrations of chemical structure of MTAs does spoil the impression of the review. Figures are to be added.
2. MitoQ and SkQ family seem to represent the most promising MTAs known to date. However it worth to discuss several additional examples (as luteolin, isorhamnetin) in more detail, especially given that a lot of attention is paid molecular dynamics and development of antioxidants by quantum chemical and machine learning methods.
3. Some repetitions can be detected throughout the text. For instance, paragraph in the end of section 4.2 (lines 499-518) repeats partly paragraph appeared above (lines 469-481).
4. Section 5 “In Silico and Computational Insights: Predicting and Understanding Activity” lacks of concise and concrete conclusions. What MTAs has been discovered? How have in silico methods assisted in understanding the properties and optimization of the structure of MTAs?

I can recommend publishing the manuscript by B. Franczyk and co-authors only after addition of figures with MTA structures and inclusion of the discussion on additional examples of mitochondria-targeted antioxidants. I suggest major revision.

Author Response

1. All the discussion on types of MTAs, their mechanism of action or
pharmacokinetic peculiarities is not demonstrative without figures or
schemes containing compounds’ structures. The total lack of illustrations

of the chemical structure of MTAs does spoil the impression of the review.
Figures are to be added.
We thank the Reviewer for these valuable and constructive comments. In response,
we have added Figure 1, which presents both a generalized schematic of the
modular architecture of mitochondria-targeted antioxidants and the 2D chemical
structures of representative small-molecule MTAs (MitoQ, SkQ1, MitoTEMPO, and
MitoVitE). This figure has been integrated into Section 2 to directly support the
discussion of MTA classes, mechanisms of action, and rational design principles. In
addition, subsequent sections now include dedicated schematic illustrations.
Together, these figures provide the necessary structural and mechanistic context,
substantially improving the demonstrative value and readability of the review.
Moreover, new figure has been added: Figure 2. "Therapeutic Benefits of MitoQ
Across Multiple Medical Contexts.".
2. MitoQ and SkQ family seem to represent the most promising MTAs known
to date. However it worth to discuss several additional examples (as
luteolin, isorhamnetin) in more detail, especially given that a lot of attention
is paid molecular dynamics and development of antioxidants by quantum
chemical and machine learning methods.
We thank the Reviewer for this helpful comment. In response, we have expanded
Section 5 to include additional examples of antioxidants beyond the classical
MTAs, such as MitoQ and SkQ1. In particular, we now discuss polyphenolic
compounds like luteolin and isorhamnetin, highlighting their well-defined redox
properties and potential for further functionalization toward mitochondrial
targeting.
3. Some repetitions can be detected throughout the text. For instance,
paragraph in the end of section 4.2 (lines 499-518) repeats partly paragraph
appeared above (lines 469-481).
We thank the Reviewer for this comment. The overlapping content between lines
469–481 and 499–518 has been removed in the revised version. The description
of SkQ3 is now limited to its antioxidant properties, while the paragraph on SkBQ
focuses exclusively on its distinct structural features and prooxidant behavior.
This revision eliminates redundancy and clarifies the functional differences
between the two compounds.
4. Section 5 “In Silico and Computational Insights: Predicting and
Understanding Activity” lacks concise and concrete conclusions. What
MTAs have been discovered? How have in silico methods assisted in
understanding the properties and optimization of the structure of MTAs?
We thank the Reviewer for this valuable comment. In response, we have revised
Section 5 to provide clearer conclusions and concrete examples. We now
explicitly show that in silico approaches have contributed both to understanding
and optimizing established mitochondrial-targeted antioxidants, such as MitoQ
and SkQ1, and to identifying promising antioxidant scaffolds, including
polyphenolic compounds like luteolin and isorhamnetin.

In particular, molecular dynamics simulations are discussed as tools that clarify
membrane insertion, orientation, and diffusion of MTAs, which in turn guide
rational optimization of linker length, lipophilicity, and redox-active moieties.
Quantum chemical calculations are highlighted for their role in elucidating
antioxidant mechanisms and structure-activity relationships, while emerging
machine learning approaches are shown to accelerate candidate prioritization
and structural refinement.

Reviewer 3 Report

Comments and Suggestions for Authors

The authors of this article have summarized the Rational Design of Mitochondria-Targeted Antioxidants: A Review of Structure–Activity Relationships and Redox Mechanisms. In my view, the writing in most sections of the manuscript is clear and concise, which is essential for a review article. However, the reviewer believes that a potential reader may not easily grasp the details based on the current presentation of the data. The manuscript would benefit from Major revision and improvement by addressing the following comments:

Major Suggestions

1. The title is misleading because the manuscript does not clearly outline the rational design principles for mitochondria-targeted antioxidants. When discussing SAR, the chemical structures of the identified antioxidants should be presented and followed by explanatory descriptions. The current version lacks this essential component.
2. Several closely related review articles have already been published on this topic. The present review summarizes similar findings, and the authors should clearly highlight what is novel about their approach and how it adds value to the existing literature.
3. The manuscript lacks visual illustrations in several key sections. For example, in Section 3 (3.1), the authors describe the molecular architecture and synthetic pathway of MitoQ. Such descriptions should be accompanied by corresponding figures or schemes to enhance reader comprehension. Otherwise, readers may need to consult the original referenced article (Ref. 33). Chemical structural data related to Mitoquinones cited in this section should also be included.
4. The authors should include FDA-approved MitoQ derivatives and related compounds, if any, or alternatively provide a table summarizing preclinical studies currently registered to evaluate the therapeutic effects of MitoQ in various diseases.
5. Although the authors state that their discussion encompasses structure–activity analyses of the carrier, payload (quinone derivatives), and linker components that determine optimal subcellular partitioning and scavenging efficiency, however, no structures of the quinone derivatives or linkers are provided. These should be added in the relevant section to facilitate understanding.
6. It is recommended that the authors include at least one schematic illustrating the therapeutic benefits of MitoQ in cardiovascular diseases, ocular diseases, and Alzheimer’s and Parkinson’s diseases. The schematic should describe the molecular mechanisms through which MitoQ exerts its therapeutic effects.
7. As mentioned in points 2 and 3, a similar approach should be applied when revising Section 4, particularly Section 4.1, to ensure clarity and completeness.
8. Compounds such as SkQ, SkQR1, SkQ1, SkQ3, MitoQ, SkQ2M, SkQ4, SkQ5, and all other SkQ derivatives should be presented with their full chemical names and structural representations. In the current form, their identities are ambiguous.
9. Throughout the manuscript, numerous technical terms and abbreviations (e.g., CHARMM, AMBER, GROMOS) should be defined upon first use to improve clarity.
10. The language used in the manuscript is overly complex in many places. The authors should simplify and streamline the writing to improve readability and accessibility

Author Response

1. The title is misleading because the manuscript does not clearly outline the
rational design principles for mitochondria-targeted antioxidants. When
discussing SAR, the chemical structures of the identified antioxidants should
be presented and followed by explanatory descriptions. The current version
lacks this essential component.
We thank the Reviewer for this valuable and constructive comment. To address this
point, Section 2 is now supported by Figure 1, which presents the modular molecular
architecture of MTAs together with the 2D chemical structures of representative
compounds (MitoQ, SkQ1, MitoTEMPO, and MitoVitE). In addition, quantitative
structure-activity relationship (SAR) data for representative quinone-based MTAs,
including redox window analyses and kinetic potency metrics, are summarized in
Table 1 and directly linked to the structural features shown in Figure 1. Together,
these additions provide a clear structural and mechanistic framework underlying the
rational design concepts discussed in the manuscript.
To better reflect this expanded scope and the connection between chemical design
and biological efficacy, the title has been revised to: "Rational Design of
Mitochondria-Targeted Antioxidants: From Molecular Determinants to Clinical
Perspectives."
Moreover, new figure has been added: Figure 2. "Therapeutic Benefits of MitoQ
Across Multiple Medical Contexts.".

2. Several closely related review articles have already been published on this
topic. The present review summarizes similar findings, and the authors should
clearly highlight what is novel about their approach and how it adds value to
the existing literature.
The Authors thank the Reviewer for this important point. Mitochondria-targeted
antioxidants are a rapidly evolving field, rendering some earlier reviews outdated as
they lack recent breakthroughs in both chemistry and technology. Our manuscript
adds significant value by providing a unique multidisciplinary integration that bridges
the gap between deep structural determinants (SAR) and modern computational
tools, such as Machine Learning, which are often overlooked in previous works.
Furthermore, our "molecule-to-medicine" approach connects quantum chemical
properties directly to therapeutic outcomes in advanced models (e.g., OXYS rats and
epilepsy). This updated, integrative roadmap serves as a modern resource that sets
our work apart from more generalized or dated summaries.

3. The manuscript lacks visual illustrations in several key sections. For example,
in Section 3 (3.1), the authors describe the molecular architecture and
synthetic pathway of MitoQ. Such descriptions should be accompanied by
corresponding figures or schemes to enhance reader comprehension.
Otherwise, readers may need to consult the original referenced article (Ref. 33).
Chemical structural data related to Mitoquinones cited in this section should
also be included.
We thank the reviewer for this constructive suggestion. To improve clarity and
accessibility, we have added schematic figures illustrating the molecular architecture
and synthetic pathway of MitoQ in Section 3.1, along with chemical structures of
MitoQ and related mitoquinones, thereby eliminating the need to consult the original
reference (Ref. 33).
4. The authors should include FDA-approved MitoQ derivatives and related
compounds, if any, or alternatively provide a table summarizing preclinical
studies currently registered to evaluate the therapeutic effects of MitoQ in
various diseases.
We have clarified that no FDA-approved MitoQ derivatives are currently available
and have included a new table summarizing registered and published preclinical
studies evaluating the therapeutic effects of MitoQ across various disease models
5. Although the authors state that their discussion encompasses
structure–activity analyses of the carrier, payload (quinone derivatives), and
linker components that determine optimal subcellular partitioning and
scavenging efficiency, however, no structures of the quinone derivatives or
linkers are provided. These should be added in the relevant section to facilitate
understanding.
We thank the Reviewer for this helpful comment and clarification.To address this
point, Figure 1 has been added to Section 2 to explicitly present the chemical
structures of representative mitochondria-targeted antioxidants, including quinone-
based payloads (ubiquinone in MitoQ and plastoquinone in SkQ1), together with their
associated alkyl linker chains within the full MTA architecture. These structures
directly support the discussion of carrier-, payload-, and linker-dependent structure-
activity relationships in Sections 2.1–2.3.
In addition, quantitative structure-activity relationship (SAR) data for representative
quinone-based MTAs are summarized in Table 1, linking quinone chemistry and
linker design to subcellular partitioning and scavenging efficiency.
6. It is recommended that the authors include at least one schematic illustrating
the therapeutic benefits of MitoQ in cardiovascular diseases, ocular diseases,
and Alzheimer’s and Parkinson’s diseases. The schematic should describe the
molecular mechanisms through which MitoQ exerts its therapeutic effects.
We have added an integrative schematic illustrating the therapeutic benefits of MitoQ
in cardiovascular, ocular, and neurodegenerative diseases, highlighting the key
mitochondrial and molecular mechanisms underlying its protective effects.

7. As mentioned in points 2 and 3, a similar approach should be applied when
revising Section 4, particularly Section 4.1, to ensure clarity and completeness.
In response to the reviewer’s comments, we have revised Section 4 accordingly. To
improve clarity, we added Table 3, which summarizes the key characteristics of the
discussed compounds, including their cationic carriers, quinone moieties, and
therapeutic relevance. In addition, Figure 1 presenting the structure of SkQ1 was
included earlier in the manuscript.
We believe that the tabular format provides a clear and concise overview of the
discussed molecules; however, we remain open to complementing the table with
additional structural illustrations if deemed helpful by the reviewers.
8. Compounds such as SkQ, SkQR1, SkQ1, SkQ3, MitoQ, SkQ2M, SkQ4, SkQ5,
and all other SkQ derivatives should be presented with their full chemical
names and structural representations. In the current form, their identities are
ambiguous.
The Authors thank the Reviewer for this important clarification. We agree that the
chemical identity of these analogs must be precisely defined to ensure the
manuscript's rigor. In response, we have updated the text and introduced Table 3,
which provides a comprehensive and unambiguous classification of all discussed
compounds. This table contains the full chemical name, cationic carrier, quinone
payload, key characteristics, and therapeutic focus for each derivative. By linking
these precise identities to their functional profiles, we believe the previously noted
ambiguity has been fully resolved.
9. Throughout the manuscript, numerous technical terms and abbreviations (e.g.,
CHARMM, AMBER, GROMOS) should be defined upon first use to improve
clarity.
The Authors thank the Reviewer for this suggestion. We have thoroughly revised the
manuscript to ensure that all technical terms and abbreviations are defined in full
upon their first use in the text. Furthermore, a comprehensive abbreviations table
beneath the main text has been revised to serve as a quick reference for the reader.
We believe these changes significantly improve the clarity and technical accessibility
of the manuscript.
10. The language used in the manuscript is overly complex in many places. The
authors should simplify and streamline the writing to improve readability and
accessibility.
The Authors thank the Reviewer for this comment. We have thoroughly revised the
entire manuscript to improve its clarity and accessibility. Overly complex and lengthy
sentences have been simplified or broken down, and a comprehensive grammar
check has been performed. We believe the text is now significantly more readable
and focused.

Reviewer 4 Report

Comments and Suggestions for Authors

The authors have composed an extensive review about the field of Mitochondria-Targeted Antioxidants, highlighting SAR and mechanism. Although the workload is high, there were a lot of issues that should be addressed:

1. The title highlights SAR and rational design, but: a. there was essentially no 2D chemical structures of any MTA compound; b. figure 1 was highly schematic, with a confusing "cardiolipin"; c. all SAR statements are descriptive and qualitative, with virtually no quantitative data. This is a major weakness for a review targeting SAR. Please: 1. present proper chemical structures, highlighting headgroups/linker/payload as discussed; 2. add at least one table/summary plot compiling quantitative SAR data, either from the authors or from other publications. This is a review about SAR, so this is what readers expect to read.
2. The title also highlighted "Redox mechanism", but I do not see enough detail discussed in a molecular-specific way, it was too generic. As a reader I would expect to see: a.  How the redox potentials and reaction pathways of different antioxidant cores (MitoQ vs SkQ vs others) differ; b. How these differences translate into distinct biological outcomes (e.g. true antioxidant vs redox cycling/pro-oxidant behaviour); c. Any kinetic/thermodynamic data (rate constants, E° values, BDEs) that would inform rational design. It is OK to not have a definitive answer, but at least discussion is expected. 
3. The last two sections about computational/ML studies and "therapeutic potentials" are not directly relevant to the title and dilute the main message. Either substantially shorten them or totally remove them is the better choice. 
4. Some expressions (e.g. “paradigm shift”, “transformative advance”) seem too strong given the current state of clinical evidence, which remains limited and mixed. A more neutral tone and a short dedicated “Limitations and challenges” subsection would improve the balance.

As a result, I would suggest a major revision to fix all the abovementioned issues first. 

Author Response

1. The title highlights SAR and rational design, but:

a. there was essentially no 2D chemical structures of any MTA compound;
b. figure 1 was highly schematic, with a confusing "cardiolipin";
c. all SAR statements are descriptive and qualitative, with virtually no
quantitative data. This is a major weakness for a review targeting SAR.
Please:
1. present proper chemical structures, highlighting headgroups/linker/payload
as discussed;
2. add at least one table/summary plot compiling quantitative SAR data, either
from the authors or from other publications. This is a review about SAR, so
this is what readers expect to read.
We thank the Reviewer for this detailed and valuable comment.In response, Figure 1
has been added to present proper 2D chemical structures of representative
mitochondria-targeted antioxidants (MitoQ, SkQ1, MitoTEMPO, and MitoVitE),
illustrating the carrier, linker, and antioxidant payload components discussed in the
text. These chemical structures explicitly visualize quinone-based payloads and
linker architecture and facilitate interpretation of carrier-, payload-, and linker-
dependent structure-activity relationships. To address the request for quantitative
SAR context, we have added Table 1, which compiles representative quantitative
structure-activity relationship data for quinone-based MTAs reported in the literature,
including redox window characteristics and kinetic or concentration-dependent
functional readouts. While comprehensive QSAR analyses are limited by
methodological heterogeneity across experimental systems, the included data
provide a quantitative framework consistent with the scope of a SAR-focused review.
For more readable structure Figure 2. "Therapeutic Benefits of MitoQ Across Multiple
Medical Contexts" has been added instead for Figure 2."Redox Cycling, Antioxidant
actions and context depended behavior of MitoQ within mitochondria" in paragraph
6. Therapeutic Potential: From Chemical Structure to Biological Effect.
2. The title also highlighted "Redox mechanism", but I do not see enough detail
discussed in a molecular-specific way, it was too generic.
The Authors thank the Reviewer for this comment. The title has been changed to
“Rational Design of Mitochondria-Targeted Antioxidants: From Molecular
Determinants to Clinical Perspectives”. We believe that the new title is more
reflective of the comprehensive scope of the manuscript.
3. The last two sections about computational/ML studies and "therapeutic
potentials" are not directly relevant to the title and dilute the main message.
Either substantially shorten them or totally remove them is the better choice.
The Authors appreciate the Reviewer’s feedback. We have revised the title to
“Rational Design of Mitochondria-Targeted Antioxidants: From Molecular
Determinants to Clinical Perspectives” to better reflect the full scope of the
manuscript. We have decided to retain Sections 5 and 6, as they are integral to the
article’s narrative, demonstrating how structural design principles translate into
computational models and therapeutic outcomes. These sections have been carefully
revised to ensure they complement the core message and provide a comprehensive
"molecule-to-medicine" perspective.

4. Some expressions (e.g. “paradigm shift”, “transformative advance”) seem too
strong given the current state of clinical evidence, which remains limited and
mixed. A more neutral tone and a short dedicated “Limitations and challenges”
subsection would improve the balance.
We thank the Reviewer for this important comment. In response, we have revised the
Conclusions section to adopt a more neutral and balanced tone, removing
expressions such as “paradigm shift” and “transformative advance.”

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

Authors made appropriate corrections. I suggest publishing the manuscript in its present form.

Author Response

Thank you. 

Reviewer 3 Report

Comments and Suggestions for Authors

Reviewer’s Reply to Authors.

The authors have responded to my feedback and applied the required adjustments. I suggest moving forward in line with the journal's guidelines. The updated version demonstrates improvement, and the authors have made significant efforts to incorporate changes. This work can be considered for publication as per the journal policy.

Minor observations

Previous comment: The manuscript lacks visual illustrations in several key sections. For example, in Section 3 (3.1), the authors describe the molecular architecture and
synthetic pathway of MitoQ. Such descriptions should be accompanied by
corresponding figures or schemes to enhance reader comprehension.
Otherwise, readers may need to consult the original referenced article (Ref. 33).
Chemical structural data related to Mitoquinones cited in this section should
also be included.

Author Reply: We thank the reviewer for this constructive suggestion. To improve clarity and
accessibility, we have added schematic figures illustrating the molecular architecture
and the synthetic pathway of MitoQ in Section 3.1, along with the chemical structures of
MitoQ and related mitoquinones, thereby eliminating the need to consult the original
reference (Ref. 33).

Current comment. No schematics or figures were found in Section 3.1 of the revision. Authors should take care of it.

Author Response

Author Reply: We thank the reviewer for this constructive suggestion. To improve clarity and accessibility, we have added schematic figures illustrating the molecular architecture and the synthetic pathway of MitoQ in Section 3.1, along with the chemical structures of MitoQ and related mitoquinones, thereby eliminating the need to consult the original reference (Ref. 33).

Current comment. No schematics or figures were found in Section 3.1 of the revision. Authors should take care of it.

Authors Comment (second review): We thank the Reviewer for this constructive suggestion. In response, we have revised the figures throughout the manuscript. Specifically, the figure originally included in Section 3.1 has been substituted with a new figure in Section 2.3 (Figure 1”Modular architecture and representative chemical structures of MTAs.”), and Figure 2 “Therapeutic Benefits of MTAs Across Multiple Medical Contexts.” in Section 6 has been revised. These changes were introduced to clarify the presented mechanisms and to improve the readability, coherence, and overall consistency of the manuscript. We believe that the revised figure layout better supports the structure of the article and facilitates understanding of the discussed concepts.

Reviewer 4 Report

Comments and Suggestions for Authors

The authors have clearly made a substantial effort to revise the manuscript in response to the previous round of comments. The revised version is much improved: the structural features of mitochondria-targeted antioxidants are described more clearly, the role of redox behaviour is better emphasised, and the review now provides a more coherent overview of mitocans for readers who may not have a strong chemistry background. Overall, the manuscript is scientifically sound and informative.

That said, I have a few remaining suggestions which I believe would further strengthen the paper. Most of these are optional refinements rather than mandatory changes.

1. The authors have added representative structures and some numerical data (e.g. redox windows, potency values) compared with the first version, which is appreciated. However, much of the SAR discussion still remains largely qualitative, relying on descriptive statements such as “longer chains increase accumulation but also toxicity”, “PEG linkers reduce non-specific binding”, or “SkQ compounds show a wider therapeutic window than MitoQ”.

Wherever the primary literature allows, I would encourage (but do not strictly require) the authors to push the quantitative aspect a bit further.

2. Conceptually, the manuscript introduces a very useful three-part framework (carrier – linker – payload) for mitochondria-targeted antioxidants. Later on, however, the discussion of the transition from MitoQ to SkQ-type compounds is presented almost as a separate “first-generation vs second-generation” narrative. This results in a kind of dual structure that can be confusing. On one hand, the modular carrier/linker/payload view; On the other hand, a generational MitoQ → SkQ storyline that partly overlaps with the same design elements. I would suggest (but not insist) that the authors consider modestly reorganizing Sections 2–4. 

3. other minor flaws: a. At line 540 it should be “Table 2”, not “Table 3”; b. The definition of Skulachev ions (SkQ) is currently introduced in the middle of the relevant section, after multiple SkQ compounds have already appeared in the text. For clarity, I recommend moving the definition and a brief explanation of “SkQ” to the beginning of that section, so that readers are not confronted with the abbreviation before it is defined; c. In the Abbreviations table, “TNF-γ” is listed, which clearly should be TNF-α.

Overall, the authors have responded seriously to the previous round of comments, and the manuscript is now in a much better shape. I would suggest a minor revision for this version, and after small corrections and clarifications, I will be happy to recommend this manuscript for publication.

Author Response

1. The authors have added representative structures and some numerical data (e.g. redox windows, potency values) compared with the first version, which is appreciated. However, much of the SAR discussion still remains largely qualitative, relying on descriptive statements such as “longer chains increase accumulation but also toxicity”, “PEG linkers reduce non-specific binding”, or “SkQ compounds show a wider therapeutic window than MitoQ”. Wherever the primary literature allows, I would encourage (but do not strictly require) the authors to push the quantitative aspect a bit further. We thank the Reviewer for this suggestion. While we have integrated more numerical data in the revised version, we feel that further quantitative detail might shift the focus away from the broad conceptual overview we intended. We believe the current balance between qualitative synthesis and representative quantitative data effectively serves the diverse audience of this review without becoming overly specialized.

2. Conceptually, the manuscript introduces a very useful three-part framework (carrier – linker – payload) for mitochondria-targeted antioxidants. Later on, however, the

discussion of the transition from MitoQ to SkQ-type compounds is presented almost as a separate “first-generation vs second-generation” narrative. This results in a kind of dual structure that can be confusing. On one hand, the modular carrier/linker/payload view; On the other hand, a generational MitoQ → SkQ storyline that partly overlaps with the same design elements. I would suggest (but not insist) that the authors consider modestly reorganizing Sections 2–4. The Authors thank the Reviewer for this comment. We have decided to maintain this structure to clearly distinguish between the modular design of new molecules and the historical evolution of the field. The "carrier–linker–payload" framework is essential for describing structural design, while the generational narrative highlights the functional shift from MitoQ to SkQ. This dual approach provides both a guide for medicinal chemists and a pharmacological context for biologists.

3. Other minor flaws: a. At line 540 it should be “Table 2”, not “Table 3” Thank you for your observation. The reference in the mentioned line has been corrected, and it now properly cites “Table 2” instead of “Table 3.”

b. The definition of Skulachev ions (SkQ) is currently introduced in the middle of the relevant section, after multiple SkQ compounds have already appeared in the text. For clarity, I recommend moving the definition and a brief explanation of “SkQ” to the beginning of that section, so that readers are not confronted with the abbreviation before it is defined; We thank the reviewer for this suggestion. The definition of Skulachev ions (SkQ) has been moved to the beginning of the relevant section, along with a brief explanation, so that the abbreviation is introduced before it appears in the text.

c. In the Abbreviations table, “TNF-γ” is listed, which clearly should be TNF-α.We thank the Reviewer for spotting this typographical error. We have corrected it in the Abbreviations table; "TNF-γ" has been changed to "TNF-α".