7,082
Views
56
CrossRef citations to date
0
Altmetric
Research Articles

Chemical-informatics approach to COVID-19 drug discovery: Monte Carlo based QSAR, virtual screening and molecular docking study of some in-house molecules as papain-like protease (PLpro) inhibitors

ORCID Icon, , ORCID Icon & ORCID Icon
Pages 4764-4773 | Received 30 May 2020, Accepted 04 Jun 2020, Published online: 22 Jun 2020

References

  • Aanouz, I., Belhassan, A., El Khatabi, K., Lakhlifi, T., El Idrissi, M., & Bouachrine, M. (2020). Moroccan Medicinal plants as inhibitors of COVID-19: Computational investigations. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1758790
  • Adeoye, A. O., Oso, B. J., Olaoye, I. F., Tijjani, H., & Adebayo, A. I. (2020). Repurposing of chloroquine and some clinically approved antiviral drugs as effective therapeutics to prevent cellular entry and replication of coronavirus. Journal of Biomolecular Structure and Dynamics, 1–4. https://doi.org/10.1080/07391102.2020.1765876
  • Adhikari, N., Baidya, S. K., Saha, A., & Jha, T. (2017). Structural insight into the viral 3C-like protease inhibitors: Comparative SAR/QSAR approaches. In Satya P. Gupta (Ed.), Viral proteases and their inhibitors (pp. 317–409). Academic Press.
  • Adhikari, N., Halder, A. K., Mallick, S., Saha, A., Saha, K. D., & Jha, T. (2016). Robust design of some selective matrix metalloproteinase-2 inhibitors over matrix metalloproteinase-9 through in silico/fragment-based lead identification and de novo lead modification: Syntheses and biological assays . Bioorganic & Medicinal Chemistry, 24(18), 4291–4309. https://doi.org/10.1016/j.bmc.2016.07.023
  • Ahmad, S., Abbasi, H. W., Shahid, S., Gul, S., & Abbasi, S. W. (2020). Molecular docking, simulation and MM-PBSA studies of Nigella Sativa compounds: A computational quest to identify potential natural antiviral for COVID-19 treatment. Journal of Biomolecular Structure and Dynamics, 1–6. https://doi.org/10.1080/07391102.2020.1775129
  • Al-Khafaji, K., Al-DuhaidahawiL, D., & Tok, T. T. (2020). Using integrated computational approaches to identify safe and rapid treatment for SARS -CoV-2. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1764392
  • Amin, M., & Abbas, G. (2020). Docking study of Chloroquine and Hydroxychloroquine interaction with SARS-CoV-2 spike glycoprotein-An in silico insight into the comparative efficacy of repurposing antiviral drugs. Journal of Biomolecular Structure and Dynamics, 1, 1–11. https://doi.org/10.1080/07391102.2020.1775703
  • Amin, S. A., Adhikari, N., & Jha, T. (2018). Design of aminopeptidase N inhibitors as anti-cancer agents. Journal of Medicinal Chemistry, 61(15), 6468–6490. https://doi.org/10.1021/acs.jmedchem.7b00782
  • Anwar, F., Altayb, H. N., Al-Abbasi, F. A., Al-Malki, A. L., Kamal, M. A., & Kumar, V. (2020). Antiviral effects of probiotic metabolites on COVID-19. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1775123
  • Ap, K., & Vs, A. (2020). Design of multi-epitope vaccine candidate against SARS-CoV-2: A in-silico study. Journal of Biomolecular Structure & Dynamics. https://doi.org/10.1080/07391102.2020.1770127
  • Arya, A., & Dwivedi, V. D. (2020). Synergistic effect of Vitamin D and Remdesivir can fight COVID-19. Journal of Biomolecular Structure and Dynamics, 1–2. https://doi.org/10.1080/07391102.2020.1773929
  • Báez-Santos, Y. M., Barraza, S. J., Wilson, M. W., Agius, M. P., Mielech, A. M., Davis, N. M., Baker, S. C., Larsen, S. D., & Mesecar, A. D. (2014). X-ray structural and biological evaluation of a series of potent and highly selective inhibitors of human coronavirus papain-like proteases. Journal of Medicinal Chemistry, 57(6), 2393–2412. https://doi.org/10.1021/jm401712t
  • Báez-Santos, Y. M., John, S. E., & Mesecar, A. D. (2015). The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds. Antiviral Research, 115, 21–38. https://doi.org/10.1016/j.antiviral.2014.12.015
  • Bandyopadhyay, D., Kreatsoulas, C., Brady, P. G., Boyer, J., He, Z., Scavello, G., Peryea, T., Jadhav, A., Nguyen, D.-T., & Guha, R. (2019). Scaffold-based analytics: Enabling hit-to-lead decisions by visualizing chemical series linked across large datasets. Journal of Chemical Information and Modeling, 59(11), 4880–4892. https://doi.org/10.1021/acs.jcim.9b00243
  • Banerjee, S., Amin, S. A., Baidya, S. K., Adhikari, N., & Jha, T. (2020). Exploring the structural aspects of ureido-amino acid-based APN inhibitors: A validated comparative multi-QSAR modelling study. SAR and QSAR in Environment Research, 31(5), 325–345. https://doi.org/10.1080/1062936X.2020.1734080
  • Basit, A., Ali, T., & Rehman, S. U. (2020). Truncated human Angiotensin Converting Enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent. Journal of Biomolecular Structure and Dynamics, 1–7. https://doi.org/10.1080/07391102.2020.1768150
  • Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2020). Identification of bioactive molecules from Tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1766572
  • Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1758788
  • Borkotoky, S., & Banerjee, M. (2020). A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem). Journal of Biomolecular Structure and Dynamics, 1–7. https://doi.org/10.1080/07391102.2020.1774419
  • Chandra, A., Gurjar, V., Qamar, I., & Singh, N. (2020). Identification of potential inhibitors of SARS-COV-2 endoribonuclease (EndoU) from FDA approved drugs: A drug repurposing approach to find therapeutics for COID19. Journal of Biomolecular Structure and Dynamics, 1–6. https://doi.org/10.1080/07391102.2020.1775127
  • Cheng, K. W., Cheng, S. C., Chen, W. Y., Lin, M. H., Chuang, S. J., Cheng, I. H., Sun, C. Y., & Chou, C. Y. (2015). Thiopurine analogs and mycophenolic acid synergistically inhibit the papain-like protease of Middle East respiratory syndrome coronavirus . Antiviral Research, 115, 9–16. https://doi.org/10.1016/j.antiviral.2014.12.011
  • Chou, C.-Y., Chien, C.-H., Han, Y.-S., Prebanda, M. T., Hsieh, H.-P., Turk, B., Chang, G.-G., & Chen, X. (2008). Thiopurine analogues inhibit papain-like protease of severe acute respiratory syndrome coronavirus. Biochemical Pharmacology, 75(8), 1601–1609. https://doi.org/10.1016/j.bcp.2008.01.005
  • Choudhury, C. (2020). Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease. Journal of Biomolecular Structure and Dynamics, 1–5. https://doi.org/10.1080/07391102.2020.1771424
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
  • Das, S., Sarmah, S., Lyndem, S., & Roy, A. S. (2020). An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1763201
  • de Oliveira, O. V., Rocha, G. B., Paluch, A. S., & Costa, L. T. (2020). Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening. Journal of Biomolecular Structure and Dynamics, 1–4. https://doi.org/10.1080/07391102.2020.1772885
  • DS Visualizer 3.5, Accelrys Software Inc.
  • Dutta, S., Halder, A. K., Adhikari, N., Amin, S. A., Das, S., Saha, A., & Jha, T. (2019). Synthesis, anticancer activity, structure-activity relationship and binding mode of interaction studies of substituted pentanoic acids. Future Medicinal Chemistry, 11(14), 1679–1702. https://doi.org/10.4155/fmc-2018-0361
  • Elasnaoui, K., & Chawki, Y. (2020). Using X-ray images and deep learning for automated detection of coronavirus disease. Journal of Biomolecular Structure and Dynamics, 1–22. https://doi.org/10.1080/07391102.2020.1767212
  • Elfiky, A. A. (2020a). SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An insilico perspective. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1761882
  • Elfiky, A. A. (2020b). Natural products may interfere with SARS-CoV-2 attachment to the host cell. Journal of Biomolecular Structure and Dynamics, 1–6. https://doi.org/10.1080/07391102.2020.1761881
  • Elfiky, A. A., & Azzam, E. B. (2020). Novel Guanosine Derivatives against MERS CoV polymerase: An in silico perspective. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1758789
  • Elmezayen, A. D., Al-Obaidi, A., Şahin, A. T., & Yelekçi, K. (2020). Drug repurposing for coronavirus (COVID-19): In silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1758791
  • Enayatkhani, M., Hasaniazad, M., Faezi, S., Guklani, H., Davoodian, P., Ahmadi, N., Einakian, M. A., Karmostaji, A., & Ahmadi, K. (2020). Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: An in silico study. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1756411
  • Enmozhi, S. K., Raja, K., Sebastine, I., & Joseph, J. (2020). Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: An in silico approach. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1760136
  • Frieman, M., Basu, D., Matthews, K., Taylor, J., Jones, G., Pickles, R., Baric, R., & Engel, D. A. (2011). Yeast based small molecule screen for inhibitors of SARS-CoV. PLoS One, 6, e28479.
  • Ghosh, A. K., Brindisi, M., Shahabi, D., Chapman, M. E., & Mesecar, A. D. (2020). Drug development and medicinal chemistry efforts toward SARS-coronavirus and Covid-19 therapeutics. ChemMedChem, 15(11), 907–932.
  • Ghosh, A. K., Takayama, J., Aubin, Y., Ratia, K., Chaudhuri, R., Baez, Y., Sleeman, K., Coughlin, M., Nichols, D. B., Mulhearn, D. C., Prabhakar, B. S., Baker, S. C., Johnson, M. E., & Mesecar, A. D. (2009). Structure-based design, synthesis, and biological evaluation of a series of novel and reversible inhibitors for the severe acute respiratory syndrome-coronavirus papain-like protease. Journal of Medicinal Chemistry, 52(16), 5228–5240. https://doi.org/10.1021/jm900611t
  • Ghosh, A. K., Takayama, J., Rao, K. V., Ratia, K., Chaudhuri, R., Mulhearn, D. C., Lee, H., Nichols, D. B., Baliji, S., Baker, S. C., Johnson, M. E., & Mesecar, A. D. (2010). Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: Design, synthesis, protein-ligand X-ray structure and biological evaluation . Journal of Medicinal Chemistry, 53(13), 4968–4979. https://doi.org/10.1021/jm1004489
  • Gupta, M. K., Vemula, S., Donde, R., Gouda, G., Behera, L., & Vadde, R. (2020). In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1751300
  • Gyebi, G. A., Ogunro, O. B., Adegunloye, A. P., Ogunyemi, O. M., & Afolabi, S. O. (2020). Potential Inhibitors of Coronavirus 3-Chymotrypsin-Like Protease (3CLpro): An in-silico screening of Alkaloids and Terpenoids from African medicinal plants. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1764868
  • Hajjo, R., Setola, V., Roth, B. L., & Tropsha, A. (2012). Chemocentric informatics approach to drug discovery: Identification and experimental validation of selective estrogen receptor modulators as ligands of 5-hydroxytryptamine-6 receptors and as potential cognition enhancers. Journal of Medicinal Chemistry, 55(12), 5704–5719. https://doi.org/10.1021/jm2011657
  • Halder, A. K., Mallick, S., Shikha, D., Saha, A., Saha, K. D., & Jha, T. (2015). Design of dual MMP-2/HDAC-8 inhibitors by pharmacophore mapping, molecular docking, synthesis and biological activity. RSC Advances, 5(88), 72373–72386. https://doi.org/10.1039/C5RA12606A
  • Halder, A. K., Saha, A., & Jha, T. (2013). Exploration of structural and physicochemical requirements andsearch of virtual hits for aminopeptidase N inhibitors. Molecular Diversity, 17(1), 123–137. https://doi.org/10.1007/s11030-013-9422-5
  • Hasan, A., Paray, B. A., Hussain, A., Qadir, F. A., Attar, F., Aziz, F. M., Sharifi, M., Derakhshankhah, H., Rasti, B., Mehrabi, M., & Shahpasand, K. (2020). A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1754293
  • Hendaus, M. A. (2020). Remdesivir in the treatment of Coronavirus Disease 2019 (COVID-19): A simplified summary. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1767691
  • Hendaus, M. A., & Jomha, F. A. (2020). Covid-19 induced superimposed bacterial infection. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1772110
  • http://www.swissadme.ch/ (as accessed on 24th May 2020)
  • http://www.who.int/csr/sars/archive/2003_05_07a/en (as accessed on 10th May 2020)
  • https://prosa.services.came.sbg.ac.at/prosa.php (as accessed on 10th May 2020)
  • https://pymol.org/2/ (as accessed on 10th May 2020)
  • https://servicesn.mbi.ucla.edu/SAVES/ (as accessed on 10th May 2020)
  • https://servicesn.mbi.ucla.edu/Verify3D/ (as accessed on 10th May 2020)
  • https://spdbv.vital-it.ch/ (as accessed on 10th May 2020)
  • https://swissmodel.expasy.org/ (as accessed on 10th May 2020)
  • https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19—11-march-2020 (as accessed on 17th May 2020)
  • https://www.who.int/emergencies/diseases/novel-coronavirus-2019 (as accessed on 3rd June 2020)
  • Islam, R., Parves, R., Paul, A. S., Uddin, N., Rahman, M. S., Mamun, A. A., Hossain, M. N., Ali, M. A., & Halim, M. A. (2020). A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–20. https://doi.org/10.1080/07391102.2020.1761883
  • Jain, S., Amin, S. A., Adhikari, N., Jha, T., & Gayen, S. (2020). Good and bad molecular fingerprints for human rhinovirus 3C protease inhibition: Identification, validation, and application in designing of new inhibitors through Monte Carlo-based QSAR study. Journal of Biomolecular Structure & Dynamics, 38(1), 66–77. https://doi.org/10.1080/07391102.2019.1566093
  • Joshi, R. S., Jagdale, S. S., Bansode, S. B., Shankar, S. S., Tellis, M. B., Pandya, V. K., Chugh, A., Giri, A. P., & Kulkarni, M. J. (2020). Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1760137
  • Khan, M. T., Ali, A., Wang, Q., Irfan, M., Khan, A., Zeb, M. T., Zhang, Y. J., Chinnasamy, S., & Wei, D. Q. (2020). Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2. A molecular dynamic study. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1769733
  • Khan, R. J., Jha, R. K., Amera, G. M., Jain, M., Singh, E., Pathak, A., Singh, R. P., Muthukumaran, J., & Singh, A. K. (2020). Targeting SARS-CoV-2: A systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2′-O-ribose methyltransferase. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1753577
  • Khan, S. A., Zia, K., Ashraf, S., Uddin, R., & Ul-Haq, Z. (2020). Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1751298
  • Kumar, D., Kumari, K., Jayaraj, A., Kumar, V., Kumar, R. V., Dass, S. K., Chandra, R. & Singh, P. (2020). Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1752310
  • Lin, M. H., Moses, D. C., Hsieh, C. H., Cheng, S. C., Chen, Y. H., Sun, C. Y., & Chou, C. Y. (2018). Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes. Antiviral Research, 150, 155–163. https://doi.org/10.1016/j.antiviral.2017.12.015
  • Lobo-Galo, N., Terrazas-López, M., Martínez-Martínez, A., & Díaz-Sánchez, Á. G. (2020). FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication. Journal of Biomolecular Structure and Dynamics, 1–2. https://doi.org/10.1080/07391102.2020.1764393
  • Mahanta, S., Chowdhury, P., Gogoi, N., Goswami, N., Borah, D., Kumar, R., Chetia, D., Borah, P., Buragohain, A. K., & Gogoi, B. (2020). Potential anti-viral activity of approved repurposed drug against main protease of SARS-CoV-2: An in silico based approach. Journal of Biomolecular Structure and Dynamics, 1–5. https://doi.org/10.1080/07391102.2020.1768902
  • Mittal, L., Kumari, A., Srivastava, M., Singh, M., & Asthana, S. (2020). Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1768151
  • Mukherjee, A., Adhikari, N., & Jha, T. (2017). A pentanoic acid derivative targeting matrix metalloproteinase-2 (MMP-2) induces apoptosis in a chronic myeloid leukemia cell line. European Journal of Medicinal Chemistry, 141, 37–50. https://doi.org/10.1016/j.ejmech.2017.09.052
  • Muralidharan, N., Sakthivel, R., Velmurugan, D., & Gromiha, M. M. (2020). Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 Protease against COVID-19. Journal of Biomolecular Structure and Dynamics, 1–6. https://doi.org/10.1080/07391102.2020.1752802
  • N., Babadaei, M. M., Hasan, A., Vahdani, Y., Haj Bloukh, S., Sharifi, M., Kachooei, E., Haghighat, S., & Falahati, M. (2020b). Development of Remdesivir repositioning as a nucleotide analog against COVID-19 RNA dependent RNA polymerase. Journal of Biomolecular Structure and Dynamics, 1–2. https://doi.org/10.1080/07391102.2020.1767210
  • Nejadi Babadaei, M. M., Hasan, A., Haj Bloukh, S., Edis, Z., Sharifi, M., Kachooei, E., & Falahati, M. (2020a). The expression level of angiotensin-converting enzyme 2 determine the severity of COVID-19: Lung and heart tissue as targets. Journal of Biomolecular Structure and Dynamic, 1–3. https://doi.org/10.1080/07391102.2020.1767211
  • Paniri, A., Hosseini, M. M., & Akhavan-Niaki, H. (2020). First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations. Journal of Biomolecular Structure and Dynamics, 1–8. https://doi.org/10.1080/07391102.2020.1767690
  • Pant, S., Singh, M., Ravichandiran, V., Murty, U. S. N., & Srivastava, H. K. (2020). Peptide-like and small-molecule inhibitors against Covid-19. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1757510Z
  • Park, J.-Y., Kim, J. H., Kim, Y. M., Jeong, H. J., Kim, D. W., Park, K. H., Kwon, H.-J., Park, S.-J., Lee, W. S., & Ryu, Y. B. (2012). Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases. Bioorganic & Medicinal Chemistry, 20(19), 5928–5935. https://doi.org/10.1016/j.bmc.2012.07.038
  • Patil, V. M., Singhal, S., & Masand, N. (2020). A systematic review on use of aminoquinolines for the therapeutic management of COVID-19: Efficacy, safety and clinical trials. Life Sciences, 254, 117775. https://doi.org/10.1016/j.lfs.2020.117775
  • Pillaiyar, T., Meenakshisundaram, S., & Manickam, M. (2020). Recent discovery and development of inhibitors targeting coronaviruses. Drug Discovery Today.
  • Polishchuk, P. (2017). Interpretation of quantitative structure-activity relationship models: Past, present, and future. Journal of Chemical Information and Modeling, 57(11), 2618–2639. https://doi.org/10.1021/acs.jcim.7b00274
  • Ratia, K., Pegan, S., Takayama, J., Sleeman, K., Coughlin, M., Baliji, S., Chaudhuri, R., Fu, W., Prabhakar, B. S., Johnson, M. E., Baker, S. C., Ghosh, A. K., & Mesecar, A. D. (2008). A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication. Proceedings of the National Academy of Sciences of the United States of America, 105(42), 16119–16124. https://doi.org/10.1073/pnas.0805240105
  • Ratia, K., Saikatendu, K. S., Santarsiero, B. D., Barretto, N., Baker, S. C., Stevens, R. C., & Mesecar, A. D. (2006). Severe acute respiratory syndrome coronavirus papain-like protease: Structure of a viral deubiquitinating enzyme. Proceedings of the National Academy of Sciences, 103(15), 5717–5722. https://doi.org/10.1073/pnas.0510851103
  • Sarma, P., Sekhar, N., Prajapat, M., Avti, P., Kaur, H., Kumar, S., Singh, S., Kumar, H., Prakash, A., Dhibar, D. P., & Medhi, B. (2020). In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1753580
  • Sinha, S. K., Shakya, A., Prasad, S. K., Singh, S., Gurav, N. S., Prasad, R. S., & Gurav, S. S. (2020). An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets. Journal of Biomolecular Structure and Dynamics, 1–3. https://doi.org/10.1080/07391102.2020.1762741
  • Sk, M. F., Roy, R., Jonniya, N. A., Poddar, S., & Kar, P. (2020). Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations. Journal of Biomolecular Structure and Dynamics, 1–21. https://doi.org/10.1080/07391102.2020.1768149
  • Toropova, A. P., Toropov, A. A., & Benfenati, E. (2015). A quasi-QSPR modelling for the photocatalytic decolourization rate constants and cellular viability (CV%) of nanoparticles by CORAL. SAR and QSAR in Environmental Research, 26(1), 29–40. https://doi.org/10.1080/1062936X.2014.984327
  • Toropov, A. A., Toropova, A. P., Puzyn, T., Benfenati, E., Gini, G., Leszczynska, D., & Leszczynski, J. (2013). QSAR as a random event: Modeling of nanoparticles uptake in PaCa2 cancer cells. Chemosphere, 92(1), 31–37. https://doi.org/10.1016/j.chemosphere.2013.03.012
  • Toropov, A. A., Toropova, A. P., Raitano, G., & Benfenati, E. (2018). CORAL: Building up QSAR models for the chromosome aberration test. Saudi Journal of Biological Sciences, 26(6), 1101–1106. https://doi.org/10.1016/j.sjbs.2018.05.013
  • Trott, O., & Olson, A. J. (2009). AutoDockVina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461. https://doi.org/10.1002/jcc.21334
  • Van Hilten, H. N., Chevillard, F., & Kolb, P. (2019). Virtual compound libraries in computer-assisted drug discovery. Journal of Chemical Information and Modeling, 59, 644–651.
  • Wahedi, H. M., Ahmad, S., & Abbasi, S. W. (2020). Stilbene-based natural compounds as promising drug candidates against COVID-19. Journal of Biomolecular Structure and Dynamics, 1–6. https://doi.org/10.1080/07391102.2020.1762743
  • Worachartcheewan, A., Mandi, P., Prachayasittikul, V., Toropova, A. P., Toropov, A. A., & Nantasenamat, C. (2014). Large-scale QSAR study of aromatase inhibitors using SMILES-based descriptors. Chemometrics and Intelligent Laboratory Systems, 138, 120–126. https://doi.org/10.1016/j.chemolab.2014.07.017

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.