1. bookVolume 72 (2022): Issue 1 (March 2022)
Journal Details
License
Format
Journal
First Published
28 Feb 2007
Publication timeframe
4 times per year
Languages
English
access type Open Access

Evaluation of COVID-19 protease and HIV inhibitors interactions

Published Online: 30 Aug 2021
Page range: 1 - 8
Accepted: 27 Feb 2021
Journal Details
License
Format
Journal
First Published
28 Feb 2007
Publication timeframe
4 times per year
Languages
English
Abstract

The epidemic of the novel coronavirus disease (COVID-19) that started in 2019 has evoked an urgent demand for finding new potential therapeutic agents. In this study, we performed a molecular docking of anti-HIV drugs to refine HIV protease inhibitors and nucleotide analogues to target COVID-19. The evaluation was based on docking scores calculated by AutoDock Vina and top binding poses were analyzed. Our results suggested that lopinavir, darunavir, atazanavir, remdesivir, and tipranavir have the best binding affinity for the 3-chymotrypsin-like protease of COVID-19. The comparison of the binding sites of three drugs, namely, darunavir, atazanavir and remdesivir, showed an overlap region of the protein pocket. Our study showed a strong affinity between lopinavir, darunavir, atazanavir, tipranavir and COVID-19 protease. However, their efficacy should be confirmed by in vitro studies since there are concerns related to interference with their active sites.

Keywords

1. F. Wu, S. Zhao, B. Yu, Y.-M. Chen, W. Wang, Z.-G. Song, Y. Hu, Z.-W. Tao, J.-H. Tian, Y.-Y. Pei, M.-L. Yuan, Y.-L. Zhang, F.-H. Dai, Y. Liu, Q.-M. Wang, J.-J. Zheng, L. Xu, E. C. Holmes and Y.-Z. Zhang, A new coronavirus associated with human respiratory disease in China, Nature 579 (2020) 265–269; https://doi.org/10.1038/s41586-020-2008-3 Search in Google Scholar

2. J. Xu, S. Zhao, T. Teng, A. E. Abdalla, W. Zhu, L. Xie, Y. Wang and X. Guo, Systematic comparison of two animal-to-human transmitted human coronaviruses: SARS-CoV-2 and SARS-CoV, Viruses 12 (2020) Article ID 244; https://doi.org/10.3390/v12020244 Search in Google Scholar

3. Z. Wang, X. Chen, Y. Lu, F. Chen and W. Zhang, Clinical characteristics and therapeutic procedure for four cases with 2019 novel coronavirus pneumonia receiving combined Chinese and Western medicine treatment, Biosci. Trends 14 (2020) 64–68; https://doi.org/10.5582/bst.2020.01030 Search in Google Scholar

4. J. Lim, S. Jeon, H. Y. Shin, M. J. Kim, Y. M. Seong, W. J. Lee, K. W. Choe, Y. M. Kang, B. Lee and S. J. Park, Case of the index patient who caused tertiary transmission of COVID-19 infection in Korea: the application of lopinavir/ritonavir for the treatment of COVID-19 infected pneumonia monitored by quantitative RT-PCR, J. Korean Med. Sci. 35 (2020) e79; https://doi.org/10.3346/jkms.2020.35.e79 Search in Google Scholar

5. C. M. Chu, V. C. Cheng, I. F. Hung, M. M. Wong, K. H. Chan, K. S. Chan, R. Y. Kao, L. L. Poon, C. L. Wong, Y. Guan, J. S. Peiris and K. Y. Yuen, Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings, Thorax 59 (2004) 252–256; https://doi.org/10.1136/thorax.2003.012658 Search in Google Scholar

6. S. J. Hurwitz and R. F. Schinazi, Practical considerations for developing nucleoside reverse transcriptase inhibitors, Drug Discov. Today Technol. 9 (2012) e183–e193; https://doi.org/10.1016/j.ddtec.2012.09.003 Search in Google Scholar

7. N. Atatreh, S. Hasan, B. R. Ali and M. A. Ghattas, Computer-aided approaches reveal trihydroxychroman and pyrazolone derivatives as potential inhibitors of SARS-CoV-2 virus main protease, Acta Pharm. 71 (2021) 325–333; https://doi.org/10.2478/acph-2021-0040 Search in Google Scholar

8. Z. Lv, Y. Chu and Y. Wang, HIV protease inhibitors: a review of molecular selectivity and toxicity, HIV/AIDS (Auckland) 7 (2015) 95–104; https://doi.org/10.2147/HIV.S79956 Search in Google Scholar

9. Y. Wang, J. Xiao, T. O. Suzek, J. Zhang, J. Wang, Z. Zhou, L. Han, K. Karapetyan, S. Dracheva, B. A. Shoemaker, E. Bolton, A. Gindulyte and S. H. Bryant, PubChem’s BioAssay Database, Nucleic Acids Res. 40 (2012) D400-D412; https://doi.org/10.1093/nar/gkr1132 Search in Google Scholar

10. N. M. O’Boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch and G. R. Hutchison, Open Babel: An open chemical toolbox, J. Cheminform. 3 (2011) Article ID 33; https://doi.org/10.1186/1758-2946-3-33 Search in Google Scholar

11. O. Trott and A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem. 31 (2010) 455–461; https://doi.org/10.1002/jcc.21334 Search in Google Scholar

12. R. A. Laskowski and M. B. Swindells, LigPlot+: multiple ligand-protein interaction diagrams for drug discovery, J. Chem. Inf. Model. 51 (2011) 2778–2786; https://doi.org/10.1021/ci200227u Search in Google Scholar

13. M. Wang, R. Cao, L. Zhang, X. Yang, J. Liu, M. Xu, Z. Shi, Z. Hu, W. Zhong and G. Xiao, Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro, Cell Res. 30 (2020) 269–271; https://doi.org/10.1038/s41422-020-0282-0 Search in Google Scholar

14. S. Daoud, S. J. Alabed, L. A. Dahabiyeh, Identification of potential COVID-19 main protease inhibitors using structure-based pharmacophore approach, molecular docking and repurposing studies, Acta Pharm. 71 (2021) 163–174; https://doi.org/10.2478/acph-2021-0016 Search in Google Scholar

15. T. P. Sheahan, A. C. Sims, S. R. Leist, A. Schäfer, J. Won, A. J. Brown, S. A. Montgomery, A. Hogg, D. Babusis, M. O. Clarke, J. E. Spahn, L. Bauer, S. Sellers, D. Porter, J. Y. Feng, T. Cihlar, R. Jordan, M. R. Denison and R. S. Baric, Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV, Nat. Commun. 11 (2020) Article ID 222; https://doi.org/10.1038/s41467-019-13940-6 Search in Google Scholar

16. A. H. de Wilde, D. Jochmans, C. C. Posthuma, J. C. Zevenhoven-Dobbe, S. van Nieuwkoop, T. M. Bestebroer, B. G. van den Hoogen, J. Neyts and E. J. Snijder, Screening of an FDA-approved compound library identifies four small-molecule inhibitors of Middle East respiratory syndrome coronavirus replication in cell culture, Antimicrob. Agents Chemother. 58 (2014) 4875–4884; https://doi.org/10.1128/AAC.03011-14 Search in Google Scholar

17. E. C. Vatansever, K. S. Yang, K. Kratch, A. Drelich, C.-C. Cho, D. M. Mellot, S. Xu, C.-T. K. Tseng and W. R. Liu, Targeting the SARS-CoV-2 main protease to repurpose drugs for COVID-19, bioRxiv preprint [Internet], posted May 23, 2020; https://doi.org/10.1101/2020.05.23.112235 Search in Google Scholar

18. B. R. Beck, B. Shin, Y. Choi, S. Park and K. Kang, Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model, Comput. Struct. Biotechnol. J. 18 (2020) 784–790; https://doi.org/10.1016/j.csbj.2020.03.025 Search in Google Scholar

19. M. A. M. Subbaiah, S. Mandlekar, S. Desikan, T. Ramar, L. Subramani, M. Annadurai, S. D. Desai, S. Sinha, S. M. Jenkins and M. R. Krystal, Design, synthesis, and pharmacokinetic evaluation of phosphate and amino acid ester prodrugs for improving the oral bioavailability of the HIV-1 protease inhibitor atazanavir, J. Med. Chem. 62 (2019) 3553–3574; https://doi.org/10.1021/acs.jmedchem.9b00002 Search in Google Scholar

20. M. Rittweger and K. Arastéh, Clinical pharmacokinetics of darunavir, Clin. Pharmacokin. 46 (2007) 739–756; https://doi.org/10.2165/00003088-200746090-00002 Search in Google Scholar

21. M. Mahdi, J. A. Mótyán, Z. I. Szojka, M. Golda, M. Miczi and J. Tőzsér, Analysis of the efficacy of HIV protease inhibitors against SARS-CoV-2’s main protease, Virol. J. 17 (2020) Article ID 190; https://doi.org/10.1186/s12985-020-01457-0 Search in Google Scholar

22. S. Jo, S. Kim and D. H. Shin, Inhibition of SARS-CoV 3CL protease by flavonoids, J. Enzyme Inhib. Med. Chem. 35 (2020) 145–151; https://doi.org/10.1080/14756366.2019.1690480 Search in Google Scholar

23. L. Zhang, D. Lin, Y. Kusov, Y. Nian, Q. Ma, J. Wang, A. von Brunn, P. Leyssen, K. Lanko, J. Neyts, A. de Wilde, E. J. Snijder and H. Liu, α-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication: structure-based design, synthesis, and activity assessment, J. Med. Chem. 63 (2020) 4562–4578; https://doi.org/10.1021/acs.jmedchem.9b01828 Search in Google Scholar

24. M. M. Ghahremanpour, J. Tirado-Rives, M. Deshmukh, J. A. Ippolito, C.-H. Zhang, I. Cabeza de Vaca, M.-E. Liosi, K. S. Anderson and W. L. Jorgensen, Identification of 14 known drugs as inhibitors of the main protease of SARS-CoV-2, ACS Med. Chem. Lett. 11 (2020) 2526–2533; https://doi.org/10.1021/acsmedchemlett.0c00521 Search in Google Scholar

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