{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:07:09Z","timestamp":1772168829983,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/f1000research.123550.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T00:00:00Z","timestamp":1702252800000}},{"DOI":"10.12688\/f1000research.123550.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T00:00:00Z","timestamp":1702252800000}}],"reference-count":49,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T00:00:00Z","timestamp":1702252800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UNISINU-2022-2","award":["BS-PD\/2022-01"],"award-info":[{"award-number":["BS-PD\/2022-01"]}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    Background The severe acute respiratory syndrome coronavirus (SARS-CoV)-2 virus causes an infectious illness named coronavirus disease 2019 (COVID-19). SARS-CoV is a positive-sense single-stranded RNA virus from the\n                    <ns3:italic>Betacoronavirus<\/ns3:italic>\n                    genus. The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) has an important role in the viral life cycle and its active site is a very accessible region, thus a potential therapeutic approach may be to target this region to study the inhibition of viral replication. Various preexisting drugs have been proposed for the treatment of COVID-19 and the use of existing antiviral agents may reduce the time and cost of new drug discoveries, but the efficacy of these drugs is limited. Therefore, the aim of the present study was to evaluate a number of ligands used as SARS-CoV-2 virus inhibitors to determine the suitability of them for potential COVID-19 treatment. Methods In this study, we selected a series of ligands used as SARS-CoV-2 virus inhibitors such as: abacavir, acyclovir, amprenavir, ascorbic acid vitamin C, azithromycin, baloxavir, boceprevir, cholecalciferol vitamin D, cidofovir, edoxudine, emtricitabine, hydroxychloroquine and remdesivir. These ligands were analyzed using molecular docking, molecular quantum similarity, and chemical reactivity indices defined within a conceptual density functional theory framework. Results The analysis of molecular quantum similarity indices on inhibitors showed a high number of differences from a structural point of view. However, they are quite similar in their electronic density, obtaining the highest values in the electronic similarity index. Global and local chemical reactivity indices were analyzed. Conclusions These studies allowed for the identification of the main stabilizing interactions using the crystal structure of SARS-CoV-2 RdRp. The molecular quantum similarity and chemical reactivity descriptors provide novel insights into these ligands that can be used in the design of new COVID-19 treatments.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.123550.3","type":"journal-article","created":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T11:20:50Z","timestamp":1702293650000},"page":"914","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["New findings on ligand series used as SARS-CoV-2 virus inhibitors within the frameworks of molecular docking, molecular quantum similarity and chemical reactivity indices"],"prefix":"10.12688","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9159-5289","authenticated-orcid":false,"given":"Alejandro","family":"Morales-Bayuelo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jes\u00fas","family":"S\u00e1nchez-M\u00e1rquez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2023,12,11]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"989","DOI":"10.3201\/eid1906.121648","article-title":"Novel SARS-like Betacoronaviruses in Bats, China, 2011.","volume":"19","author":"L Yang","year":"2013","journal-title":"Emerg. 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Answer: yes  How many molecules author download or design?  Answer: 13  Why did the author only select several molecules for this study?  Answer: Taking account, the biological activity and potential use for the CoVID-19 treatment.  What is the biological role of each selected molecule here?  Answer: The main idea is to show the interaction related with these ligands with CoVID-19 protein related and in these sense can be used as potential drug related with the CoVID-19 treatment.  There is no need to explain the Quantum similarity measure so deeply here, this method is well established, and you have only used this method for your molecules.  Answer: ok  The conclusion is not clear in the manuscript, and I don\u2019t understand what the message of the author here is.  Answer: The development of new ligands or drugs for COVID-19 is crucial for several reasons:  \n<b>Variability of the Virus:<\/b> Viruses, including SARS-CoV-2 (the virus that causes COVID-19), can undergo mutations, leading to the emergence of new variants. Some variants may affect the virus's susceptibility to existing treatments. Developing new ligands or drugs allows researchers to stay ahead of these changes and ensure the effectiveness of therapeutic interventions. \n<b>Enhanced Treatment Options:<\/b> Having a diverse range of drugs or ligands allows for more treatment options. Different drugs may target the virus through various mechanisms, increasing the chances of finding effective treatments for different patient populations or stages of the disease. \n<b>Combating Drug Resistance:<\/b> As with any infectious agent, there is a risk of the virus developing resistance to existing treatments over time. By continually developing new ligands or drugs, researchers can stay ahead of potential drug resistance and provide alternative options for managing the infection. \n<b>Optimizing Therapeutic Efficacy:<\/b> Developing new ligands allows scientists to optimize the efficacy and safety profile of treatments. This can lead to drugs that are more potent, have fewer side effects, and are better suited for certain patient populations. \n<b>Addressing Unmet Needs:<\/b> The global impact of the COVID-19 pandemic has highlighted the need for effective and accessible treatments. Developing new ligands can help address unmet medical needs, especially in cases where existing treatments may not be sufficient or widely available. \n<b>Preparation for Future Pandemics:<\/b> Investing in the development of antiviral drugs and ligands not only helps in the current fight against COVID-19 but also prepares us for potential future pandemics caused by novel viruses. The knowledge gained from developing treatments for one virus can inform strategies for addressing others.   In summary, developing new ligands for COVID-19 is crucial for staying ahead of viral mutations, expanding treatment options, combating drug resistance, optimizing therapeutic efficacy, addressing unmet needs, and preparing for future pandemics.","URL":"https:\/\/f1000research.com\/articles\/11-914\/v3#referee-comment-11081","order":2,"name":"referee-comment-11081","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.159813.r437257, M. Aravinthraj Aravinthraj, Department of Physics, Sacred Heart College (Autonomous), Tirupattur, Tamil Nadu, 30 Dec 2025, version 3, indexed","URL":"https:\/\/f1000research.com\/articles\/11-914\/v3#referee-response-437257","order":3,"name":"referee-response-437257","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by UNISINU-2022-I (BS-PD\/2022-01; assigned to AMB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}