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Haghir Ebrahim Abadi MH, Ghasemlou A, Bayani F, Sefidbakht Y, Vosough M, Mozaffari-Jovin S, Uversky VN. AI-driven covalent drug design strategies targeting main protease (m pro) against SARS-CoV-2: structural insights and molecular mechanisms. J Biomol Struct Dyn 2024:1-29. [PMID: 38287509 DOI: 10.1080/07391102.2024.2308769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
The emergence of new SARS-CoV-2 variants has raised concerns about the effectiveness of COVID-19 vaccines. To address this challenge, small-molecule antivirals have been proposed as a crucial therapeutic option. Among potential targets for anti-COVID-19 therapy, the main protease (Mpro) of SARS-CoV-2 is important due to its essential role in the virus's life cycle and high conservation. The substrate-binding region of the core proteases of various coronaviruses, including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), could be used for the generation of new protease inhibitors. Various drug discovery methods have employed a diverse range of strategies, targeting both monomeric and dimeric forms, including drug repurposing, integrating virtual screening with high-throughput screening (HTS), and structure-based drug design, each demonstrating varying levels of efficiency. Covalent inhibitors, such as Nirmatrelvir and MG-101, showcase robust and high-affinity binding to Mpro, exhibiting stable interactions confirmed by molecular docking studies. Development of effective antiviral drugs is imperative to address potential pandemic situations. This review explores recent advances in the search for Mpro inhibitors and the application of artificial intelligence (AI) in drug design. AI leverages vast datasets and advanced algorithms to streamline the design and identification of promising Mpro inhibitors. AI-driven drug discovery methods, including molecular docking, predictive modeling, and structure-based drug repurposing, are at the forefront of identifying potential candidates for effective antiviral therapy. In a time when COVID-19 potentially threat global health, the quest for potent antiviral solutions targeting Mpro could be critical for inhibiting the virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sina Mozaffari-Jovin
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
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Mushebenge AGA, Ugbaja SC, Mbatha NA, B. Khan R, Kumalo HM. Assessing the Potential Contribution of In Silico Studies in Discovering Drug Candidates That Interact with Various SARS-CoV-2 Receptors. Int J Mol Sci 2023; 24:15518. [PMID: 37958503 PMCID: PMC10647470 DOI: 10.3390/ijms242115518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The COVID-19 pandemic has spurred intense research efforts to identify effective treatments for SARS-CoV-2. In silico studies have emerged as a powerful tool in the drug discovery process, particularly in the search for drug candidates that interact with various SARS-CoV-2 receptors. These studies involve the use of computer simulations and computational algorithms to predict the potential interaction of drug candidates with target receptors. The primary receptors targeted by drug candidates include the RNA polymerase, main protease, spike protein, ACE2 receptor, and transmembrane protease serine 2 (TMPRSS2). In silico studies have identified several promising drug candidates, including Remdesivir, Favipiravir, Ribavirin, Ivermectin, Lopinavir/Ritonavir, and Camostat Mesylate, among others. The use of in silico studies offers several advantages, including the ability to screen a large number of drug candidates in a relatively short amount of time, thereby reducing the time and cost involved in traditional drug discovery methods. Additionally, in silico studies allow for the prediction of the binding affinity of the drug candidates to target receptors, providing insight into their potential efficacy. This study is aimed at assessing the useful contributions of the application of computational instruments in the discovery of receptors targeted in SARS-CoV-2. It further highlights some identified advantages and limitations of these studies, thereby revealing some complementary experimental validation to ensure the efficacy and safety of identified drug candidates.
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Affiliation(s)
- Aganze Gloire-Aimé Mushebenge
- Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa;
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Faculty of Pharmaceutical Sciences, University of Lubumbashi, Lubumbashi 1825, Democratic Republic of the Congo
| | - Samuel Chima Ugbaja
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Africa Health Research Institute, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nonkululeko Avril Mbatha
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
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Borisevich SS, Zarubaev VV, Shcherbakov DN, Yarovaya OI, Salakhutdinov NF. Molecular Modeling of Viral Type I Fusion Proteins: Inhibitors of Influenza Virus Hemagglutinin and the Spike Protein of Coronavirus. Viruses 2023; 15:v15040902. [PMID: 37112882 PMCID: PMC10142020 DOI: 10.3390/v15040902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
The fusion of viral and cell membranes is one of the basic processes in the life cycles of viruses. A number of enveloped viruses confer fusion of the viral envelope and the cell membrane using surface viral fusion proteins. Their conformational rearrangements lead to the unification of lipid bilayers of cell membranes and viral envelopes and the formation of fusion pores through which the viral genome enters the cytoplasm of the cell. A deep understanding of all the stages of conformational transitions preceding the fusion of viral and cell membranes is necessary for the development of specific inhibitors of viral reproduction. This review systematizes knowledge about the results of molecular modeling aimed at finding and explaining the mechanisms of antiviral activity of entry inhibitors. The first section of this review describes types of viral fusion proteins and is followed by a comparison of the structural features of class I fusion proteins, namely influenza virus hemagglutinin and the S-protein of the human coronavirus.
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Affiliation(s)
- Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 450078 Ufa, Russia
- Correspondence: (S.S.B.); (O.I.Y.)
| | - Vladimir V. Zarubaev
- Laboratory of Experimental Virology, Saint-Petersburg Pasteur Institute, 197101 Saint Petersburg, Russia;
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia;
| | - Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
- Correspondence: (S.S.B.); (O.I.Y.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
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Zhou Y, Wang W, Zeng P, Feng J, Li D, Jing Y, Zhang J, Yin X, Li J, Ye H, Wang Q. Structural basis of main proteases of HCoV-229E bound to inhibitor PF-07304814 and PF-07321332. Biochem Biophys Res Commun 2023; 657:16-23. [PMID: 36965419 PMCID: PMC10020134 DOI: 10.1016/j.bbrc.2023.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
PF-07321332 and PF-07304814, inhibitors against SARS-CoV-2 developed by Pfizer, exhibit broad-spectrum inhibitory activity against the main protease (Mpro) from various coronaviruses. Structures of PF-07321332 or PF-07304814 in complex with Mpros of various coronaviruses reveal their inhibitory mechanisms against different Mpros. However, the structural information on the lower pathogenic coronavirus Mpro with PF-07321332 or PF-07304814 is currently scarce, which hinders our comprehensive understanding of the inhibitory mechanisms of these two inhibitors. Meanwhile, given that some immunocompromised individuals are still affected by low pathogenic coronaviruses, we determined the structures of lower pathogenic coronavirus HCoV-229E Mpro with PF-07321332 and PF-07304814, respectively, and analyzed and defined in detail the structural basis for the inhibition of HCoV-229E Mpro by both inhibitors. Further, we compared the crystal structures of multiple coronavirus Mpro complexes with PF-07321332 or PF-07304814 to illustrate the differences in the interaction of Mpros, and found that the inhibition mechanism of lower pathogenic coronavirus Mpro was more similar to that of moderately pathogenic coronaviruses. Our structural studies provide new insights into drug development for low pathogenic coronavirus Mpro, and provide theoretical basis for further optimization of both inhibitors to contain potential future coronaviruses.
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Affiliation(s)
- Yanru Zhou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Weiwei Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Pei Zeng
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen, 518118, China; Jiangxi Jmerry Biopharmaceutical Co, Ltd, Ganzhou, 341000, China
| | - Jingwen Feng
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Dongyang Li
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Yue Jing
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Jin Zhang
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen, 518118, China
| | - Xiushan Yin
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Heyang Ye
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
| | - Qisheng Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
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