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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

Morales-Bayuelo et al., F1000Research, doi:10.12688/f1000research.123550.3

Dec 2023

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Vitamin C for COVID-19

6th treatment shown to reduce risk in September 2020, now with p = 0.00000002 from 73 studies, recognized in 12 countries.

Lower risk for mortality, ICU, hospitalization, and recovery.

No treatment is 100% effective. Protocols combine treatments.

5,100+ studies for 112 treatments. c19early.org

In Silico analysis showing that vitamin C can stably bind within the SARS-CoV-2 RNA-dependent RNA polymerase binding pocket. Notable stabilizing interactions were seen between vitamin C and residue lysine 621, similar to the antiviral remdesivir.

14 preclinical studies support the efficacy of vitamin C for COVID-19:

6 In Silico studies1-6

7 In Vitro studies5,7-12

1 In Vivo animal study10

Vitamin C has been identified by the European Food Safety Authority (EFSA) as having sufficient evidence for a causal relationship between intake and optimal immune system function13-15. Vitamin C plays a key role in the immune system, supporting the production and function of leukocytes, or white blood cells, which defend against infection and disease, including the production of lymphocytes, which make antibodies, and enhancing phagocytosis, the process by which immune system cells ingest and destroy viruses and infected cells. Vitamin C is an antioxidant, protecting cells from damage caused by free radicals. Vitamin C inhibits SARS-CoV-2 3CL^pro5,9, inhibits SARS-CoV-2 infection by reducing ACE2 levels in a dose-dependent manner10, and may limit COVID-19 induced cardiac damage by acting as an antioxidant and potentially reducing the reactive oxygen species (ROS) production induced by the spike protein that contributes to the activation of profibrotic pathways16. Vitamin C reduces inflammation, oxidative stress, and NETosis, supporting immune function and vascular protection17. Intracellular levels of vitamin C decline during COVID-19 hospitalization suggesting ongoing utilization and depletion of vitamin C18. Threonic acid, a metabolite of vitamin C, is lower in mild and severe cases, consistent with increased need for and metabolization of vitamin C with moderate infection, but more limited ability to produce threonic acid in severe infection due to depletion or existing lower levels of vitamin C19. Symptomatic COVID-19 is associated with a lower frequency of natural killer (NK) cells, and vitamin C has been shown to improve NK cell numbers and functioning20,21.

Important missing comments or errors? Let us know.

Study covers vitamin D and vitamin C.

1. Agamah et al., Network-based multi-omics-disease-drug associations reveal drug repurposing candidates for COVID-19 disease phases, ScienceOpen, doi:10.58647/DRUGARXIV.PR000010.v1.scienceopen.com, doi.org.

2. Morales-Bayuelo et al., 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, F1000Research, doi:10.12688/f1000research.123550.3.f1000research.com, doi.org.

3. Alkafaas et al., A study on the effect of natural products against the transmission of B.1.1.529 Omicron, Virology Journal, doi:10.1186/s12985-023-02160-6.biomedcentral.com, doi.org.

4. Pandya et al., Unravelling Vitamin B12 as a potential inhibitor against SARS-CoV-2: A computational approach, Informatics in Medicine Unlocked, doi:10.1016/j.imu.2022.100951.sciencedirect.com, doi.org.

5. Malla et al., Vitamin C inhibits SARS coronavirus-2 main protease essential for viral replication, bioRxiv, doi:10.1101/2021.05.02.442358.biorxiv.org, doi.org.

6. Kumar et al., In silico virtual screening-based study of nutraceuticals predicts the therapeutic potentials of folic acid and its derivatives against COVID-19, VirusDisease, doi:10.1007/s13337-020-00643-6.springer.com, doi.org.

7. Van Tin et al., Spike Protein of SARS-CoV-2 Activates Cardiac Fibrogenesis through NLRP3 Inflammasomes and NF-κB Signaling, Cells, doi:10.3390/cells13161331.mdpi.com, doi.org.

8. Moatasim et al., Potent Antiviral Activity of Vitamin B12 against Severe Acute Respiratory Syndrome Coronavirus 2, Middle East Respiratory Syndrome Coronavirus, and Human Coronavirus 229E, Microorganisms, doi:10.3390/microorganisms11112777.mdpi.com, doi.org.

9. Đukić et al., Inhibition of SARS-CoV-2 Mpro with Vitamin C, L-Arginine and a Vitamin C/L-Arginine Combination, Frontiers in Bioscience-Landmark, doi:10.31083/j.fbl2801008.imrpress.com, doi.org.

10. Zuo et al., Vitamin C promotes ACE2 degradation and protects against SARS‐CoV‐2 infection, EMBO reports, doi:10.15252/embr.202256374.wiley.com, doi.org.

11. Hajdrik et al., In Vitro Determination of Inhibitory Effects of Humic Substances Complexing Zn and Se on SARS-CoV-2 Virus Replication, Foods, doi:10.3390/foods11050694.mdpi.com, doi.org.

12. Goc et al., Inhibitory effects of specific combination of natural compounds against SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants, European Journal of Microbiology and Immunology, doi:10.1556/1886.2021.00022.akjournals.com, doi.org.

13. Galmés et al., Suboptimal Consumption of Relevant Immune System Micronutrients Is Associated with a Worse Impact of COVID-19 in Spanish Populations, Nutrients, doi:10.3390/nu14112254.mdpi.com, doi.org.

14. Galmés (B) et al., Current State of Evidence: Influence of Nutritional and Nutrigenetic Factors on Immunity in the COVID-19 Pandemic Framework, Nutrients, doi:10.3390/nu12092738.mdpi.com, doi.org.

15. EFSA, Scientific Opinion on the substantiation of health claims related to vitamin C and protection of DNA, proteins and lipids from oxidative damage (ID 129, 138, 143, 148), antioxidant function of lutein (ID 146), maintenance of vision (ID 141, 142), collagen formation (ID 130, 131, 136, 137, 149), function of the nervous system (ID 133), function of the immune system (ID 134), function of the immune system during and after extreme physical exercise (ID 144), non-haem iron absorption (ID 132, 147), energy-yielding metabolism (ID 135), and relief in case of irritation in the upper respiratory tract (ID 1714, 1715) pursuant to Article 13(1) of Regulation (EC) No 1924/2006, EFSA Journal, doi:10.2903/j.efsa.2009.1226.europa.eu, doi.org.

16. Van Tin (B) et al., Spike Protein of SARS-CoV-2 Activates Cardiac Fibrogenesis through NLRP3 Inflammasomes and NF-κB Signaling, Cells, doi:10.3390/cells13161331.mdpi.com, doi.org.

17. Xie et al., The role of reactive oxygen species in severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) infection-induced cell death, Cellular & Molecular Biology Letters, doi:10.1186/s11658-024-00659-6.biomedcentral.com, doi.org.

18. Boerenkamp et al., Low Levels of Serum and Intracellular Vitamin C in Hospitalized COVID-19 Patients, Nutrients, doi:10.3390/nu15163653.mdpi.com, doi.org.

19. Albóniga et al., Differential abundance of lipids and metabolites related to SARS-CoV-2 infection and susceptibility, Scientific Reports, doi:10.1038/s41598-023-40999-5.nature.com, doi.org.

20. Graydon et al., High baseline frequencies of natural killer cells are associated with asymptomatic SARS-CoV-2 infection, Current Research in Immunology, doi:10.1016/j.crimmu.2023.100064.sciencedirect.com, doi.org.

21. Vojdani et al., In vivo effect of ascorbic acid on enhancement of human natural killer cell activity, Nutrition Research, doi:10.1016/S0271-5317(05)80799-7.sciencedirect.com, doi.org.

Morales-Bayuelo et al., 11 Dec 2023, peer-reviewed, 2 authors. Contact: amorales@unisinucartagena.edu.co.

In Silico studies are an important part of preclinical research, however results may be very different in vivo.

This Paper Vitamin C All

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

Alejandro Morales-Bayuelo, Jesús Sánchez-Márquez

F1000Research, doi:10.12688/f1000research.123550.1

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 Betacoronavirus 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

Open Peer Review Is the study design appropriate and is the work technically sound? Yes Are sufficient details of methods and provided to allow replication by others? Yes If applicable, is the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required. Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Partly Competing Interests: No competing interests were disclosed. Reviewer Expertise: Computational chemistry; DFT; Nanotechnology; Docking simulation I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Author Response 17 Jul 2023 Alejandro Morales-Bayuelo 1. What are the novelties of the manuscript? What's new in this manuscript compared to similar papers? Answer: There is currently no effective treatment for Covid-19. Therefore, there are a series of drugs such as those listed in this article that have been used for the treatment of this disease, however they have not been associated as solutions for covid-19. That is why carrying out studies that show that the drugs used are directly related to the Covid-19 proteins is pertinent. 2. The introduction section should be written in a higher quality way, i.e. more up-to-date references. The..

References

Abdrabbo, Birch, Brandt, Vitamin D and COVID-19: A review on the role of vitamin D in preventing and reducing the severity of COVID-19 infection, Protein Sci, doi:10.1002/pro.4190

Adamsick, Gandhi, Bidell, Remdesivir in patients with acute or chronic kidney disease and COVID-19, J. Am. Soc

Amat, Carbó-Dorca, Quantum similarity measures under atomic shell approximation: First order density fitting using elementary Jacobi rotations, J. Comput. Chem, doi:10.1002/(SICI)1096-987X(199712)18:162023::AID-JCC73.0.CO;2-N

Bultinck, Gironés, Carbó-Dorca, Molecular quantum similarity using conceptual DFT descriptors, Rev. Comput. Chem, doi:10.1002/0471720895.ch2

Burley, Berman, Bhikadiya, RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy, Nucleic Acids Res, doi:10.1093/nar/gky1004

Carbó-Dorca, Amat, Besalú, Quantum Similarity. Advanced Molecular Similarity

Carbó-Dorca, Amat, Besalú, Quantum mechanical origin of QSAR: theory and applications, J. Mol. Struct. THEOCHEM, doi:10.1016/S0166-1280(00)00363-8

Carbó-Dorca, Gironés, Foundation of quantum similarity measures and their relationship to QSPR: density function structure, approximations, and application examples, Int. J. Quantum Chem, doi:10.1002/qua.20191

Carbó-Dorca, Leyda, Arnau, How Similar is a Molecule to Another? An Electron Density Measure of Similarity Between Two Molecular Structures, Int. J. Quantum Chem, doi:10.1002/qua.560170612

Chattaraj, Sarkar, Roy, Electrophilicity index, Chem. Rev, doi:10.1021/cr040109f

Constans, Amat, Carbó-Dorca, Tagged sets, convex sets and quantum similarity measures, J. Comput. Chem, doi:10.1002/(SICI)1096-987X(19970430)18:6826::AID-JCC83.0.CO;2-U

Constans, Carbo, Atomic shell approximation: electron density fitting algorithm restricting coefficients to positive values, J. Chem. Inf. Comput. Sci

Elfiky, SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective, J. Biomol. Struct. Dyn, doi:10.1080/07391102.2020.1761882

Emili, Xavier, Amat, Molecular Quantum Similarity and the Fundamentals of QSAR, Acc. Chem. Res, doi:10.1021/ar010048x

Friesner, Banks, Murphy, Glide: A New Approach for Rapid, Accurate Docking and Scor-ing. 1. Method and Assessment of Docking Accuracy, J. Med. Chem, doi:10.1021/jm0306430

Frisch, Trucks, Schlegel, Gaussian Inc

Fuentealba, Pérez, Contreras, On the Condensed Fukui Function, J. Chem. Phys, doi:10.1063/1.1305879

Galván, Pérez, Contreras, A direct evaluation of regional Fukui functions in molecules, Chem. Phys. Lett

Geerlings, Proft, Langenaeker, Conceptual density functional theory, Chem. Rev, doi:10.1021/cr990029p

Hagar, Ahmed, Aljohani, Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations, Int. J. Mol. Sci, doi:10.3390/ijms21113922

Halgren, Mainz, Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy, J. Med. Chem, doi:10.1021/jm0306430

Jorgensen, Maxwell, Tirado-Rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, J. Am. Chem. Soc, doi:10.1021/ja9621760

Morales-Bayuelo, Baldiris, Vivas-Reyes, Scale Alpha and Beta of Quantitative Convergence and Chemical Reactivity Analysis in Dual Cholinesterase/Monoamine Oxidase Inhibitors for the Alzheimer Disease Treatment using Density Functional Theory (DFT), J. Theor. Chem

Morales-Bayuelo, Matute, Caballero, New Insights from the CoMSIA Analysis within the Framework of Density Functional Theory, J. Mol. Model, doi:10.1007/s00894-015-2690-5

Morales-Bayuelo, New insights in series of ligands used as SARS-CoV-2 virus inhibitors within molecular docking, molecular quantum similarity, and chemical reactivity indices frameworks, Harvard Dataverse, doi:10.7910/DVN/MSIGUS

Morales-Bayuelo, Torres, Baldiris, Theoretical Study of the Chemical Reactivity and Molecular Quantum Similarity in a Series of Derivatives of 2-Adamantyl-thiazolidine-4-one. Using Density Functional Theory and the Topo-Geometrical Superposition Approach, Int. J. Quantum Chem, doi:10.1002/qua.23288

Morales-Bayuelo, Torres, Vivas-Reyes, Hückel treatment of pyrrole and pentalene as a function of cyclopentadienyl using Local Quantum Similarity Index (LQSI) and the Topo-Geometrical Superposition Approach (TGSA), J. Theor. Comput. Chem

Morales-Bayuelo, Valdiris, Vivas-Reyes, Mathematic analysis on a series of 4-Acetylamino-2-(3,5dimethylpyrazol-1-yl)-6-pyridylpyrimidines: a simple way to relate quantum similarity with local chemical reactivity using the Gaussian orbitals localized theory, J. Theor. Chem

Morales-Bayuelo, Vivas-Reyes, Theoretical Calculations and Modeling for the Molecular Polarization of Furan and Thiophene under the Action of an Electric Field Using Quantum Similarity, J. Quantum Chem, doi:10.1155/2014/585394

Morales-Bayuelo, Vivas-Reyes, Theoretical model for the polarization molecular and Hückel treatment of Phospho-Cyclopentadiene in an external electric field: Hirschfeld study, J. Math. Chem, doi:10.1007/s10910-013-0182-3

Morales-Bayuelo, Vivas-Reyes, Topological model on the inductive effect in alkyl halides. Using local quantum similarity and reactivity descriptors in the Density Functional Theory (DFT), J. Quantum Chem, doi:10.1155/2014/850163

Morales-Bayuelo, Vivas-Reyes, Topological model to quantify the global reactivity indexes as local in Diels-Alder reactions, using Density Function Theory (DFT) and Local Quantum Similarity (LQS), J. Math. Chem, doi:10.1007/s10910-012-0069-8

Morales-Bayuelo, Vivas-Reyes, Understanding the Polar Character Trend in a Series of Diels-Alder Reactions Using Molecular Quantum Similarity and Chemical Reactivity Descriptors, J. Quantum Chem, doi:10.1155/2014/239845

Mortier, Yang, The use of global and local molecular parameters for the analysis of the gas-phase basicity of amines, J. Am. Chem. Soc, doi:10.1021/ja00279a008

Parr, Pearson, Absolute hardness: companion parameter to absolute electronegativity, J. Am. Chem. Soc, doi:10.1021/ja00364a005

Parr, Szentpaly, Liu, Electrophilicity Index, J. Am. Chem. Soc, doi:10.1021/ja983494x

Parr, Weitao, Density-Functional Theory of Atoms and Molecules, doi:10.1093/oso/9780195092769.001.0001

Perdew, Wang, Accurate and simple analytic representation of the electron-gas correlation energy, Phys. Rev. B, doi:10.1103/PhysRevB.45.13244

Pye, Ziegler, Van Lenthe, An implementation of the conductor-like screening model of solvation within the Amsterdam density functional package -Part II. COSMO for real solventes, Can. J. Chem, doi:10.1139/V09-008

Qayyum, Mohammad, Slominski, Vitamin D and lumisterol novel metabolites can inhibit SARS-CoV-2 replication machinery enzymes, American Journal of Physiology-Endocrinology and Metabolism, doi:10.1152/ajpendo.00174.2021

Sastry, Adzhigirey, Day, Protein and ligand preparation: parameters, protocols, and influence on virtual screen-ing enrichments, J. Comput. Aided Mol. Des, doi:10.1007/s10822-013-9644-8

Schipper, Gritsenko, Van Gisbergen, Molecular calculations of excitation energies and (hyper) polarizabilities with a statistical average of orbital model exchange-correlation potentials, J. Chem. Phys, doi:10.1063/1.480688

Valdes, Brown, Morales-Bayuelo, Adenosine Derivates as Antioxidant Agents: Synthesis, Characterization, in vitro Activity, and Theoretical Insights, Antioxidants, doi:10.3390/antiox8100468

Van Lenthe, Baerends, Snijders, Relativistic total energy using regular approximations, J. Chem. Phys, doi:10.1063/1.467943

Velde, Bickelhaupt, Baerends, Interaction of Atoms with Grain Surfaces in Steel: Periodic Dependence of Binding Energy on Atomic Number and Influence on Wear Resistance, J. Comput. Chem

Vivas-Reyes, Morales-Bayuelo, Gueto, Study of interaction energies between residues of the active site of Hsp90 and geldanamycin analogues using quantum mechanics/molecular mechanics methods [version 2; peer review: 2 approved, Res, doi:10.12688/f1000research.20844.2

Xu, Liu, Weiss, Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design, Nucleic Acids Res, doi:10.1093/nar/gkg916

Yang, Lin, Na, Homointerface covalent organic framework membranes for efficient desalination, J. Chem. Inf. Model, doi:10.1021/acs.jcim.1c00355

Yang, Wu, Ren, Novel SARS-like Betacoronaviruses in Bats, China, Emerg. Infect. Dis

Young, Ong, Kalimuddin, Epidemiologic Features and Clinical Course of Patients Infected With SARS-CoV-2 in Singapore, JAMA, doi:10.1001/jama.2020.3204

Zhao, Truhlar, The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals, Theoretical Chemical Account, doi:10.1007/s00214-007-0310-x

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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. 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Chem.'}, { 'key': 'ref8', 'doi-asserted-by': 'publisher', 'first-page': '1739-1749', 'DOI': '10.1021/jm0306430', 'article-title': 'Glide: A New Approach for Rapid, Accurate Docking and Scor- ing. 1. ' 'Method and Assessment of Docking Accuracy.', 'volume': '47', 'author': 'R Friesner', 'year': '2004', 'journal-title': 'J. Med. Chem.'}, { 'key': 'ref9', 'doi-asserted-by': 'publisher', 'first-page': '221-234', 'DOI': '10.1007/s10822-013-9644-8', 'article-title': 'Protein and ligand preparation: parameters, protocols, and influence on ' 'virtual screen- ing enrichments.', 'volume': '27', 'author': 'G Madhavi Sastry', 'year': '2013', 'journal-title': 'J. Comput. Aided Mol. Des.'}, { 'key': 'ref10', 'doi-asserted-by': 'publisher', 'first-page': '11225-11236', 'DOI': '10.1021/ja9621760', 'article-title': 'Development and Testing of the OPLS All-Atom Force Field on ' 'Conformational Energetics and Properties of Organic Liquids.', 'volume': '118', 'author': 'W Jorgensen', 'year': '1996', 'journal-title': 'J. Am. Chem. Soc.'}, { 'key': 'ref12', 'doi-asserted-by': 'publisher', 'first-page': '156', 'DOI': '10.1007/s00894-015-2690-5', 'article-title': 'New Insights from the CoMSIA Analysis within the Framework of Density ' 'Functional Theory.', 'volume': '21', 'author': 'A Morales-Bayuelo', 'year': '2015', 'journal-title': 'J. Mol. Model.'}, { 'key': 'ref13', 'first-page': '931', 'article-title': 'Interaction of Atoms with Grain Surfaces in Steel: Periodic Dependence ' 'of Binding Energy on Atomic Number and Influence on Wear Resistance.', 'volume': '22', 'author': 'G Te Velde', 'year': '2001', 'journal-title': 'J. Comput. Chem.'}, { 'key': 'ref14', 'doi-asserted-by': 'publisher', 'first-page': '9783-9792', 'DOI': '10.1063/1.467943', 'article-title': 'Relativistic total energy using regular approximations.', 'volume': '101', 'author': 'E Lenthe', 'year': '1994', 'journal-title': 'J. Chem. Phys.'}, { 'key': 'ref15', 'doi-asserted-by': 'publisher', 'first-page': '13244-13249', 'DOI': '10.1103/PhysRevB.45.13244', 'article-title': 'Accurate and simple analytic representation of the electron-gas ' 'correlation energy.', 'volume': '45', 'author': 'J Perdew', 'year': '1992', 'journal-title': 'Phys. Rev. B.'}, { 'key': 'ref16', 'doi-asserted-by': 'publisher', 'first-page': '790-797', 'DOI': '10.1139/V09-008', 'article-title': 'An implementation of the conductor-like screening model of solvation ' 'within the Amsterdam density functional package — Part II. COSMO for ' 'real solventes.', 'volume': '87', 'author': 'C Pye', 'year': '2009', 'journal-title': 'Can. J. Chem.'}, { 'key': 'ref17', 'doi-asserted-by': 'publisher', 'first-page': '1344-1352', 'DOI': '10.1063/1.480688', 'article-title': 'Molecular calculations of excitation energies and (hyper) ' 'polarizabilities with a statistical average of orbital model ' 'exchange-correlation potentials.', 'volume': '112', 'author': 'P Schipper', 'year': '2000', 'journal-title': 'J. Chem. Phys.'}, { 'key': 'ref18', 'doi-asserted-by': 'publisher', 'first-page': '1185-1189', 'DOI': '10.1002/qua.560170612', 'article-title': 'How Similar is a Molecule to Another? An Electron Density Measure of ' 'Similarity Between Two Molecular Structures.', 'volume': '17', 'author': 'R Carbó-Dorca', 'year': '1980', 'journal-title': 'Int. J. Quantum Chem.'}, { 'key': 'ref19', 'doi-asserted-by': 'publisher', 'first-page': '8-20', 'DOI': '10.1002/qua.20191', 'article-title': 'Foundation of quantum similarity measures and their relationship to ' 'QSPR: density function structure, approximations, and application ' 'examples.', 'volume': '101', 'author': 'R Carbó-Dorca', 'year': '2005', 'journal-title': 'Int. J. Quantum Chem.'}, { 'key': 'ref20', 'doi-asserted-by': 'publisher', 'first-page': '127', 'DOI': '10.1002/0471720895.ch2', 'article-title': 'Molecular quantum similarity using conceptual DFT descriptors.', 'volume': '21', 'author': 'P Bultinck', 'year': '2005', 'journal-title': 'Rev. Comput. Chem.'}, { 'key': 'ref21', 'doi-asserted-by': 'publisher', 'first-page': '826-846', 'DOI': '10.1002/(SICI)1096-987X(19970430)18:6<826::AID-JCC8>3.0.CO;2-U', 'article-title': 'Tagged sets, convex sets and quantum similarity measures.', 'volume': '18', 'author': 'P Constans', 'year': '1997', 'journal-title': 'J. Comput. Chem.'}, { 'key': 'ref22', 'doi-asserted-by': 'publisher', 'first-page': '2023-2039', 'DOI': '10.1002/(SICI)1096-987X(199712)18:16<2023::AID-JCC7>3.0.CO;2-N', 'article-title': 'Quantum similarity measures under atomic shell approximation: First ' 'order density fitting using elementary Jacobi rotations.', 'volume': '18', 'author': 'L Amat', 'journal-title': 'J. Comput. Chem.'}, { 'key': 'ref23', 'first-page': '1046-1053', 'article-title': 'Atomic shell approximation: electron density fitting algorithm ' 'restricting coefficients to positive values.', 'volume': '35', 'author': 'P Constans', 'journal-title': 'J. Chem. Inf. Comput. Sci.'}, { 'key': 'ref24', 'doi-asserted-by': 'publisher', 'first-page': '181-228', 'DOI': '10.1016/S0166-1280(00)00363-8', 'article-title': 'Quantum mechanical origin of QSAR: theory and applications.', 'volume': '504', 'author': 'R Carbó-Dorca', 'journal-title': 'J. Mol. Struct. THEOCHEM.'}, { 'key': 'ref25', 'doi-asserted-by': 'publisher', 'first-page': '468', 'DOI': '10.3390/antiox8100468', 'article-title': 'Adenosine Derivates as Antioxidant Agents: Synthesis, Characterization, ' 'in vitro Activity, and Theoretical Insights.', 'volume': '8', 'author': 'F Valdes', 'year': '2019', 'journal-title': 'Antioxidants (Basel).'}, { 'key': 'ref26', 'doi-asserted-by': 'publisher', 'DOI': '10.12688/f1000research.20844.2', 'article-title': 'Study of interaction energies between residues of the active site of ' 'Hsp90 and geldanamycin analogues using quantum mechanics/molecular ' 'mechanics methods [version 2; peer review: 2 approved].', 'volume': '8', 'author': 'R Vivas-Reyes', 'year': '2020', 'journal-title': 'F1000Res.'}, { 'key': 'ref27', 'doi-asserted-by': 'publisher', 'first-page': '2681-2687', 'DOI': '10.1002/qua.23288', 'article-title': 'Theoretical Study of the Chemical Reactivity and Molecular Quantum ' 'Similarity in a Series of Derivatives of ' '2-Adamantyl-thiazolidine-4-one. Using Density Functional Theory and the ' 'Topo-Geometrical Superposition Approach.', 'volume': '112', 'author': 'A Morales-Bayuelo', 'year': '2012', 'journal-title': 'Int. J. Quantum Chem.'}, { 'key': 'ref28', 'doi-asserted-by': 'crossref', 'first-page': '223-239', 'DOI': '10.1142/S0219633612500150', 'article-title': 'Hückel treatment of pyrrole and pentalene as a function of ' 'cyclopentadienyl using Local Quantum Similarity Index (LQSI) and the ' 'Topo-Geometrical Superposition Approach (TGSA).', 'volume': '11', 'author': 'A Morales-Bayuelo', 'year': '2012', 'journal-title': 'J. Theor. Comput. Chem.'}, { 'key': 'ref29', 'doi-asserted-by': 'publisher', 'first-page': '125-143', 'DOI': '10.1007/s10910-012-0069-8', 'article-title': 'Topological model to quantify the global reactivity indexes as local in ' 'Diels–Alder reactions, using Density Function Theory (DFT) and Local ' 'Quantum Similarity (LQS).', 'volume': '51', 'author': 'A Morales-Bayuelo', 'year': '2013', 'journal-title': 'J. Math. Chem.'}, { 'key': 'ref30', 'doi-asserted-by': 'publisher', 'first-page': '1835-1852', 'DOI': '10.1007/s10910-013-0182-3', 'article-title': 'Theoretical model for the polarization molecular and Hückel treatment ' 'of Phospho-Cyclopentadiene in an external electric field: Hirschfeld ' 'study.', 'volume': '51', 'author': 'A Morales-Bayuelo', 'year': '2013', 'journal-title': 'J. Math. Chem.'}, { 'key': 'ref31', 'first-page': '1-13', 'article-title': 'Scale Alpha and Beta of Quantitative Convergence and Chemical ' 'Reactivity Analysis in Dual Cholinesterase/Monoamine Oxidase Inhibitors ' 'for the Alzheimer Disease Treatment using Density Functional Theory ' '(DFT).', 'volume': '13', 'author': 'A Morales-Bayuelo', 'year': '2013', 'journal-title': 'J. Theor. Chem.'}, { 'key': 'ref32', 'doi-asserted-by': 'publisher', 'first-page': '1-10', 'DOI': '10.1155/2014/585394', 'article-title': 'Theoretical Calculations and Modeling for the Molecular Polarization of ' 'Furan and Thiophene under the Action of an Electric Field Using Quantum ' 'Similarity.', 'volume': '2014', 'author': 'A Morales-Bayuelo', 'year': '2014', 'journal-title': 'J. Quantum Chem.'}, { 'key': 'ref33', 'doi-asserted-by': 'publisher', 'first-page': '1-12', 'DOI': '10.1155/2014/850163', 'article-title': 'Topological model on the inductive effect in alkyl halides. Using local ' 'quantum similarity and reactivity descriptors in the Density Functional ' 'Theory (DFT).', 'volume': '2014', 'author': 'A Morales-Bayuelo', 'year': '2014', 'journal-title': 'J. Quantum Chem.'}, { 'key': 'ref34', 'first-page': '1-13', 'article-title': 'Mathematic analysis on a series of ' '4-Acetylamino-2-(3,5-dimethylpyrazol-1-yl)-6-pyridylpyrimidines: a ' 'simple way to relate quantum similarity with local chemical reactivity ' 'using the Gaussian orbitals localized theory.', 'volume': '14', 'author': 'A Morales-Bayuelo', 'year': '2014', 'journal-title': 'J. Theor. Chem.'}, { 'key': 'ref35', 'doi-asserted-by': 'publisher', 'first-page': '1-19', 'DOI': '10.1155/2014/239845', 'article-title': 'Understanding the Polar Character Trend in a Series of Diels-Alder ' 'Reactions Using Molecular Quantum Similarity and Chemical Reactivity ' 'Descriptors.', 'volume': '2014', 'author': 'A Morales-Bayuelo', 'year': '2014', 'journal-title': 'J. Quantum Chem.'}, { 'key': 'ref36', 'doi-asserted-by': 'publisher', 'first-page': '7512-7516', 'DOI': '10.1021/ja00364a005', 'article-title': 'Absolute hardness: companion parameter to absolute electronegativity.', 'volume': '105', 'author': 'R Parr', 'year': '1983', 'journal-title': 'J. Am. Chem. Soc.'}, { 'key': 'ref37', 'doi-asserted-by': 'publisher', 'first-page': '1793-1874', 'DOI': '10.1021/cr990029p', 'article-title': 'Conceptual density functional theory.', 'volume': '103', 'author': 'P Geerlings', 'year': '2003', 'journal-title': 'Chem. Rev.'}, { 'key': 'ref38', 'doi-asserted-by': 'publisher', 'first-page': '2065-2091', 'DOI': '10.1021/cr040109f', 'article-title': 'Electrophilicity index.', 'volume': '106', 'author': 'P Chattaraj', 'year': '2006', 'journal-title': 'Chem. Rev.'}, { 'key': 'ref39', 'doi-asserted-by': 'publisher', 'first-page': '1922-1924', 'DOI': '10.1021/ja983494x', 'article-title': 'Electrophilicity Index.', 'volume': '121', 'author': 'R Parr', 'year': '1999', 'journal-title': 'J. Am. Chem. Soc.'}, { 'key': 'ref40', 'first-page': '405', 'article-title': 'A direct evaluation of regional Fukui functions in molecules.', 'volume': '30', 'author': 'M Galván', 'year': '1999', 'journal-title': 'Chem. Phys. Lett.'}, { 'key': 'ref41', 'doi-asserted-by': 'publisher', 'first-page': '5708-5711', 'DOI': '10.1021/ja00279a008', 'article-title': 'The use of global and local molecular parameters for the analysis of ' 'the gas-phase basicity of amines.', 'volume': '108', 'author': 'W Mortier', 'year': '1986', 'journal-title': 'J. Am. Chem. Soc.'}, { 'key': 'ref42', 'doi-asserted-by': 'publisher', 'first-page': '2544-2551', 'DOI': '10.1063/1.1305879', 'article-title': 'On the Condensed Fukui Function.', 'volume': '113', 'author': 'P Fuentealba', 'year': '2000', 'journal-title': 'J. Chem. Phys.'}, { 'key': 'ref43', 'doi-asserted-by': 'publisher', 'first-page': '215-241', 'DOI': '10.1007/s00214-007-0310-x', 'article-title': 'The M06 suite of density functionals for main group thermochemistry, ' 'thermochemical kinetics, non-covalent interactions, excited states, and ' 'transition elements: two new functionals and systematic testing of four ' 'M06-class functionals and 12 other functionals.', 'volume': '120', 'author': 'Y Zhao', 'year': '2008', 'journal-title': 'Theoretical Chemical Account.'}, { 'key': 'ref45', 'doi-asserted-by': 'publisher', 'first-page': '3917-3926', 'DOI': '10.1021/acs.jcim.1c00355', 'article-title': 'Homointerface covalent organic framework membranes for efficient ' 'desalination.', 'volume': '61', 'author': 'J Yang', 'year': '2021, 23', 'journal-title': 'J. Chem. Inf. Model.'}, { 'key': 'ref46', 'doi-asserted-by': 'publisher', 'first-page': 'E246-E251', 'DOI': '10.1152/ajpendo.00174.2021', 'article-title': 'Vitamin D and lumisterol novel metabolites can inhibit SARS-CoV-2 ' 'replication machinery enzymes.', 'volume': '321', 'author': 'S Qayyum', 'year': '2021', 'journal-title': 'American Journal of Physiology-Endocrinology and Metabolism.'}, { 'key': 'ref47', 'doi-asserted-by': 'publisher', 'first-page': '3204-3212', 'DOI': '10.1080/07391102.2020.1761882', 'article-title': 'SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico ' 'perspective.', 'volume': '39', 'author': 'A Elfiky', 'year': '2021', 'journal-title': 'J. Biomol. Struct. Dyn.'}, { 'key': 'ref48', 'doi-asserted-by': 'publisher', 'first-page': '3922', 'DOI': '10.3390/ijms21113922', 'article-title': 'Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: ' 'Molecular Docking and DFT Calculations.', 'volume': '21', 'author': 'M Hagar', 'year': '2020', 'journal-title': 'Int. J. Mol. Sci.'}, { 'key': 'ref49', 'doi-asserted-by': 'publisher', 'first-page': '2206-2220', 'DOI': '10.1002/pro.4190', 'article-title': 'Vitamin D and COVID-19: A review on the role of vitamin D in preventing ' 'and reducing the severity of COVID-19 infection.', 'volume': '30', 'author': 'M Abdrabbo', 'year': '2021', 'journal-title': 'Protein Sci.'}, { 'key': 'ref50', 'doi-asserted-by': 'publisher', 'first-page': '1488-1494', 'DOI': '10.1001/jama.2020.3204', 'article-title': 'Epidemiologic Features and Clinical Course of Patients Infected With ' 'SARS-CoV-2 in Singapore.', 'volume': '323', 'author': 'B Young', 'year': '2020', 'journal-title': 'JAMA.'}, { 'key': 'ref51', 'doi-asserted-by': 'publisher', 'article-title': 'New insights in series of ligands used as SARS-CoV-2 virus inhibitors ' 'within molecular docking, molecular quantum similarity, and chemical ' 'reactivity indices frameworks. [Dataset].', 'author': 'A Morales-Bayuelo', 'year': '2022', 'DOI': '10.7910/DVN/MSIGUS'}], 'container-title': 'F1000Research', 'original-title': [], 'language': 'en', 'link': [ { 'URL': 'https://f1000research.com/articles/11-914/v3/xml', 'content-type': 'application/xml', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://f1000research.com/articles/11-914/v3/pdf', 'content-type': 'application/pdf', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://f1000research.com/articles/11-914/v3/iparadigms', 'content-type': 'unspecified', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': { 'date-parts': [[2023, 12, 11]], 'date-time': '2023-12-11T16:21:05Z', 'timestamp': 1702311665000}, 'score': 1, 'resource': {'primary': {'URL': 'https://f1000research.com/articles/11-914/v3'}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2023, 12, 11]]}, 'references-count': 49, 'URL': 'http://dx.doi.org/10.12688/f1000research.123550.3', 'relation': {}, 'ISSN': ['2046-1402'], 'subject': [ 'General Pharmacology, Toxicology and Pharmaceutics', 'General Immunology and Microbiology', 'General Biochemistry, Genetics and Molecular Biology', 'General Medicine'], 'container-title-short': 'F1000Res', 'published': {'date-parts': [[2023, 12, 11]]}, 'assertion': [ { 'value': 'Approved', 'URL': 'https://f1000research.com/articles/11-914/v3#article-reports', 'order': 0, 'name': 'referee-status', 'label': 'Referee status', 'group': {'name': 'current-referee-status', 'label': 'Current Referee Status'}}, { 'value': '10.5256/f1000research.153172.r195605, Truong Tan Trung, Dong Nai Technology ' 'University, Vietnam, 22 Aug 2023, version 2, 1 approved', 'URL': 'https://f1000research.com/articles/11-914/v2#referee-response-195605', 'order': 0, 'name': 'referee-response-195605', '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': 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'}]}

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