Delving into the Inception of BODIPY Dyes: Paradigms of In Vivo Bioimaging, Chemosensing, and Photodynamic/Photothermal Therapy

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This manuscript presents a well-timed and broad review of BODIPY and Aza-BODIPY dyes, that play an important role in fluorescence imaging, sensing and phototherapeutic applications. The manuscript efficiently reviews their photophysical properties, synthetic approaches, and various applications. Because of the high fluorescent quantum yields, constrained spectral profiles, marked Stokes shifts, and outstanding resistance to photodegradation and thermal degradation of these fluorophores, the manuscript addresses a field of persistent and notable interest in the disciplines of chemical biology and materials science
To reinforce the manuscript, the authors should provide a more thorough discussion on how to rationally design BODIPY dyes and optimize them for emission in the near-infrared I and II regions rather than largely presenting descriptive analyses. Review of the challenges associated with BODIPY and Aza-BODIPY dyes including aggregation-induced phenomena, poor aqueous solubility, and synthetic hurdles would aid in delivering a more comprehensive viewpoint and point out aspects. Because sensing is a central theme of the review, a deeper analysis of BODIPY and Aza BODIPY dyes for probe specificity and functionality in diverse biological surroundings would be beneficial. Especially, investigation of the dyes’ response under exposure to reactive nitrogen, oxygen, and sulfur species would deepen the discussion and provide clearer context for the practical use of BODIPY and Aza BODIPY dyes as reported sensors.  In addition, Figure 6 contains an error in the structure of BODIPY dye 28 that requires correction.  The review manuscript would also be improved with sharper comparative analysis of BODIPY and Aza-BODIPY systems, including clarification of how structural modifications modulate spectral shifts and photostability, and potential for NIR-II imaging applications. 

Author Response

Reviewer 1:

• “should provide a more thorough discussion on how to rationally design BODIPY dyes and optimize them for emission in the near-infrared I and II regions rather than largely presenting descriptive analyses”

Yes, we have corrected this issue by adding to our work in Section 8. (Notable NIR-II Aza-BODIPY Derivatives and Design Strategies) to highlight the most significant advances to pushing the BODIPY into the NIR-II window for deeper penetration depth and longer emission wavelength. Although we did provide a descriptive analysis of the 4 design strategies in (3.5 Synthetic Modifications Favoring Bathochromic Shift), we chose to include a new section after 3.5 called “3.6 New, Novel Boron Modifications to the BODIPY Difluoride Core” where we describe the rational based approaches to how substitution of cyano and alkyne groups on the fluorophore are specific instances of how to achieve selective tuning of photophysical properties for bioimaging applications as well as creating new synthetic handles for diverse modifications.

• “a deeper analysis of BODIPY and Aza-BODIPY dyes for probe specificity and functionality in diverse biological surroundings would be beneficial”

As mentioned above, we corrected this by including section 3.6 to the manuscript describing modifications made to the boron core of the fluorophore using cyano and alkynyl units to improve the spectroscopic and photophysical properties. We also mention the use of these modifications to create new and novel derivatives that are synthetically diverse.

• “Investigation of dye’s response under exposure to reactive nitrogen, oxygen, and sulfur species”

For instance, section 5.2, we refer to the paradigm of aggregation-induced emission by conceding the molecular organization of dye monomers and how novel supramolecular strategies have emerged to formulate nano-photosensitizers. Our article is a review spanning the last 11 years of work (2014-2025); therefore, we acknowledged a quintessential example of a synthetic employment of the O’Shea’s route to structurally derivatize the Aza-BODIPY fluorophores to address this aggregation-induced limitation.

We acknowledge that our review does mention the structural modifications made to Aza-BODIPY, but we have improved the explanation to indicate the instances of notable spectral shifts and include photostability data. To accompany and bolster this addition to the manuscript, we added reference 45, which mentions the dye fluorescence response to TNP, TNT, and DNT, which accounts for the fluorophore response to reactive nitrogen and oxygen species. We address the dye response to reactive sulfur species in section 7.1 for hydrogen sulfide and nitric oxide detection.

• “Figure 6 contains an error in the structure of BODIPY dye 28 that requires correction.”

Thank you for checking. We have checked and corrected the structure to ensure there are no mistakes; however, upon review of compound 28 in Figure 6, there were no issues to correct.

Update: In your original comment, the compound was 28. Now, it has been reordered, and this is now compound 43 in Figure 8. We compared the structure, which was re-drawn from reference 43, but no errors were observed between our replicated drawn structure and the original structure found in reference 43.

• “.. Including clarification of how structural modifications modulate spectral shifts and photostability, and potential for NIR-II imaging applications.”

Thank you for this comment. We have made the changes and included a new section 8 as discussed above. Notable NIR-II Aza-BODIPY Derivatives and Design Strategies as a continuation to the advances in the NIR-II we’ve alluded to earlier in the paper in section 6.5 of the manuscript. In section 9, we describe the modifications that have successfully promoted imaging in the NIR-II window as well as their superior photostability and brightness measurements.

Reviewer 2 Report

Comments and Suggestions for Authors

In this manuscript, the authors present an overview of recent advances in the development of photoactive compounds for various applications based on BODIPY and Aza-BODIPY scaffolds.The manuscript was well organized and could be of interest to the readership of this journal, but Major Revision must be performed before further assessment is possible.

Below is a list of these issues:

1. The quality of most figures and schemes is not good with low resolution.
2. The review provides very little coverage of the use of BODIPY derivatives as sensors for nitroaromatic compounds. In particular, it cites a single review from 2023 (see reference 42). To enhance the novelty, timeliness, and comprehensiveness of the content, it is recommended to incorporate citations of some recent reviews and articles featuring innovative molecular designs of BODIPY and Aza-BODIPY-based sensors towards NAC detection, e.g., https://doi.org/10.1016/j.dyepig.2025.112848, https://doi.org/10.1002/asia.202401528
3. Similarly, for greater novelty, authors should add new reviews on biomedical imaging using BODIPY and Aza-BODIPY-based compounds.
4. The conclusion section should be expanded to include a discussion of future prospects for the development of specific advanced photoactive materials based on BODIPY and Aza-BODIPY derivatives.

Author Response

Reviewer 2:

• “The quality of most figures and schemes is not good with low resolution”

We have addressed the issue of low-quality figures and schemes. This critique has been rectified by improving the quality of all ChemDraw figures and exporting them as PNG files for inclusion into the manuscript. All images/figures/schemes have been re-added with higher visual quality. To ensure, we have exported our manuscript as a PDF to double-check the images are not blurry.

• “Provides very little coverage of the use of BODIPY derivatives as a sensor for nitroaromatic compounds… cites a single review from 2023.

Yes, we acknowledge the manuscript does not incorporate a comprehensive review of BODIPYs used as nitroaromatic sensors (NAC) but rather mentions a single study. We have improved the discussion of the application to NAC sensors by including another publication (please see reference 45) that extends the novelty of the sensing theme within the review article.

Update: In your original comment, you reference our single reference 42. This reference has been re-ordered and updated to reference 44.

• “Similar, for greater novelty, authors should add new reviews on biomedical imaging using BODIPY and Aza-BODIPY based compounds”

Yes, we agree with your critique, and we have made the changes and included a new section 8. Notable NIR-II Aza-BODIPY Derivatives and Design Strategies as a continuation to the advances in the NIR-II we’ve alluded to earlier in the paper in section 6.5 of the manuscript. In section 9, we describe the modifications that have successfully promoted imaging in the NIR-II window as well as their superior photostability and brightness measurements.

• “Conclusion section should be expanded to include a discussion on future prospects for development of specific advanced photoactive materials based on BODIPY and Aza-BODIPY derivatives”

Yes, we have expanded our conclusion section to reflect the propensity to develop specific, rationally tuned photoactive materials based on the BODIPY and Aza-BODIPY scaffold.

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript has been modified and improved according to the Reviewers' suggestions and in my opinion at this stage it is worthy of publication.

Author Response

Thank you for the suggestions.