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

{ 'indexed': { 'date-parts': [[2023, 12, 12]], 'date-time': '2023-12-12T00:47:42Z', 'timestamp': 1702342062283}, 'update-to': [ { 'updated': { 'date-parts': [[2023, 12, 11]], 'date-time': '2023-12-11T00:00:00Z', 'timestamp': 1702252800000}, 'DOI': '10.12688/f1000research.123550.1', 'type': 'new_version', 'label': 'New version'}, { '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'}], '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': 'http://creativecommons.org/licenses/by/4.0/'}], 'funder': [{'name': 'UNISINU-2022-2', 'award': ['BS-PD/2022-01']}], 'content-domain': {'domain': ['f1000research.com'], 'crossmark-restriction': False}, 'abstract': '<ns3:p>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 <ns3:italic>Betacoronavirus</ns3:italic> 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.</ns3:p>', 'DOI': '10.12688/f1000research.123550.3', 'type': 'journal-article', 'created': { 'date-parts': [[2023, 12, 11]], 'date-time': '2023-12-11T16:20:50Z', 'timestamp': 1702311650000}, 'page': '914', 'update-policy': 'http://dx.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': 'http://orcid.org/0000-0001-9159-5289', 'authenticated-orcid': False, 'given': 'Alejandro', 'family': 'Morales-Bayuelo', 'sequence': 'first', 'affiliation': []}, {'given': 'Jesús', 'family': 'Sánchez-Márquez', 'sequence': 'additional', 'affiliation': []}], '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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The ' 'funders had no role in study design, data collection and analysis, decision to ' 'publish, or preparation of the manuscript.', 'order': 1, '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'}]}