1
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Xiao YQ, Long J, Zhang SS, Zhu YY, Gu SX. Non-peptidic inhibitors targeting SARS-CoV-2 main protease: A review. Bioorg Chem 2024; 147:107380. [PMID: 38636432 DOI: 10.1016/j.bioorg.2024.107380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
The COVID-19 pandemic continues to pose a threat to global health, and sounds the alarm for research & development of effective anti-coronavirus drugs, which are crucial for the patients and urgently needed for the current epidemic and future crisis. The main protease (Mpro) stands as an essential enzyme in the maturation process of SARS-CoV-2, playing an irreplaceable role in regulating viral RNA replication and transcription. It has emerged as an ideal target for developing antiviral agents against SARS-CoV-2 due to its high conservation and the absence of homologous proteases in the human body. Among the SARS-CoV-2 Mpro inhibitors, non-peptidic compounds hold promising prospects owing to their excellent antiviral activity and improved metabolic stability. In this review, we offer an overview of research progress concerning non-peptidic SARS-CoV-2 Mpro inhibitors since 2020. The efforts delved into molecular structures, structure-activity relationships (SARs), biological activity, and binding modes of these inhibitors with Mpro. This review aims to provide valuable clues and insights for the development of anti-SARS-CoV-2 agents as well as broad-spectrum coronavirus Mpro inhibitors.
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Affiliation(s)
- Ya-Qi Xiao
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Jiao Long
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang-Shuang Zhang
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Shuang-Xi Gu
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
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2
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Liu X, Sun S, Liu J, Dang Q, Gao Y, Fang L, Min W. Isolation, Virtual Screening, and Evaluation of Hazelnut-Derived Immunoactive Peptides for the Inhibition of SARS-CoV-2 Main Protease. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11561-11576. [PMID: 38739709 DOI: 10.1021/acs.jafc.4c01942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The aim of this study is to validate the activity of hazelnut (Corylus avellana L.)-derived immunoactive peptides inhibiting the main protease (Mpro) of SARS-CoV-2 and further unveil their interaction mechanism using in vitro assays, molecular dynamics (MD) simulations, and binding free energy calculations. In general, the enzymatic hydrolysis components, especially molecular weight < 3 kDa, possess good immune activity as measured by the proliferation ability of mouse splenic lymphocytes and phagocytic activity of mouse peritoneal macrophages. Over 866 unique peptide sequences were isolated, purified, and then identified by nanohigh-performance liquid chromatography/tandem mass spectrometry (NANO-HPLC-MS/MS) from hazelnut protein hydrolysates, but Trp-Trp-Asn-Leu-Asn (WWNLN) and Trp-Ala-Val-Leu-Lys (WAVLK) in particular are found to increase the cell viability and phagocytic capacity of RAW264.7 macrophages as well as promote the secretion of the cytokines nitric oxide (NO), tumor necrosis factor-α (TNF-α), and interleukin-1β (IL-1β). Fluorescence resonance energy transfer assay elucidated that WWNLN and WAVLK exhibit excellent inhibitory potency against Mpro, with IC50 values of 6.695 and 16.750 μM, respectively. Classical all-atom MD simulations show that hydrogen bonds play a pivotal role in stabilizing the complex conformation and protein-peptide interaction. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculation indicates that WWNLN has a lower binding free energy with Mpro than WAVLK. Furthermore, adsorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions illustrate favorable drug-likeness and pharmacokinetic properties of WWNLN compared to WAVLK. This study provides a new understanding of the immunomodulatory activity of hazelnut hydrolysates and sheds light on peptide inhibitors targeting Mpro.
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Affiliation(s)
- Xiaoting Liu
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, Jilin, P. R. China
| | - Shuo Sun
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, Jilin, P. R. China
| | - Jiale Liu
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, Jilin, P. R. China
| | - Qiao Dang
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, Jilin, P. R. China
| | - Yawen Gao
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, Jilin, P. R. China
| | - Li Fang
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, Jilin, P. R. China
| | - Weihong Min
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University, Changchun 130118, Jilin, P. R. China
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, P. R. China
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3
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Lis K, Plewka J, Menezes F, Bielecka E, Chykunova Y, Pustelny K, Niebling S, Garcia AS, Garcia-Alai M, Popowicz GM, Czarna A, Kantyka T, Pyrc K. SARS-CoV-2 M pro oligomerization as a potential target for therapy. Int J Biol Macromol 2024; 267:131392. [PMID: 38582483 DOI: 10.1016/j.ijbiomac.2024.131392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The main protease (Mpro) of SARS-CoV-2 is critical in the virus's replication cycle, facilitating the maturation of polyproteins into functional units. Due to its conservation across taxa, Mpro is a promising target for broad-spectrum antiviral drugs. Targeting Mpro with small molecule inhibitors, such as nirmatrelvir combined with ritonavir (Paxlovid™), which the FDA has approved for post-exposure treatment and prophylaxis, can effectively interrupt the replication process of the virus. A key aspect of Mpro's function is its ability to form a functional dimer. However, the mechanics of dimerization and its influence on proteolytic activity remain less understood. In this study, we utilized biochemical, structural, and molecular modelling approaches to explore Mpro dimerization. We evaluated critical residues, specifically Arg4 and Arg298, that are essential for dimerization. Our results show that changes in the oligomerization state of Mpro directly affect its enzymatic activity and dimerization propensity. We discovered a synergistic relationship influencing dimer formation, involving both intra- and intermolecular interactions. These findings highlight the potential for developing allosteric inhibitors targeting Mpro, offering promising new directions for therapeutic strategies.
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Affiliation(s)
- Kinga Lis
- Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland; Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24,31-155 Cracow, Poland
| | - Jacek Plewka
- Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Filipe Menezes
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Ewa Bielecka
- Jagiellonian University, Malopolska Centre of Biotechnology, Laboratory of Proteolysis and Post-translational Modification of Proteins, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Yuliya Chykunova
- Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland; Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Microbiology Department, Gronostajowa 7, 30-387, Cracow, Poland
| | - Katarzyna Pustelny
- Jagiellonian University, Malopolska Centre of Biotechnology, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Stephan Niebling
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, Hamburg, Germany; Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, Hamburg, Germany; Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, Hamburg, Germany; Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Grzegorz M Popowicz
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Anna Czarna
- Jagiellonian University, Malopolska Centre of Biotechnology, Gronostajowa 7a, 30-387 Cracow, Poland.
| | - Tomasz Kantyka
- Jagiellonian University, Malopolska Centre of Biotechnology, Laboratory of Proteolysis and Post-translational Modification of Proteins, Gronostajowa 7a, 30-387 Cracow, Poland.
| | - Krzysztof Pyrc
- Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland.
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4
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Shellenberger BM, Basile ON, Cassel J, Olsen MR, Salvino JM, Montaner LJ, Tietjen I, Henry GE. Synthesis, SARS-CoV-2 main protease inhibition, molecular docking and in silico ADME studies of furanochromene-quinoline hydrazone derivatives. Bioorg Med Chem Lett 2024; 102:129679. [PMID: 38423371 DOI: 10.1016/j.bmcl.2024.129679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Seven furanochromene-quinoline derivatives containing a hydrazone linker were synthesized by condensing a furanochromene hydrazide with quinoline 2-, 3-, 4-, 5-, 6-, and 8-carbaldehydes, including 8-hydroxyquinoline-2-carbaldehye. Structure-activity correlations were investigated to determine the influence of the location of the hydrazone linker on the quinoline unit on SARS-CoV-2 Mpro enzyme inhibition. The 3-, 5-, 6- and 8-substituted derivatives showed moderate inhibition of SARS-CoV-2 Mpro with IC50 values ranging from 16 to 44 μM. Additionally, all of the derivatives showed strong interaction with the SARS-CoV-2 Mpro substrate binding pocket, with docking energy scores ranging from -8.0 to -8.5 kcal/mol. These values are comparable to that of N3 peptide (-8.1 kcal/mol) and more favorable than GC-373 (-7.6 kcal/mol) and ML-188 (-7.5 kcal/mol), all of which are known SARS-CoV-2 Mpro inhibitors. Furthermore, in silico absorption, distribution, metabolism, and excretion (ADME) profiles indicate that the derivatives have good drug-likeness properties. Overall, this study highlights the potential of the furanochromene-quinoline hydrazone scaffold as a SARS-CoV-2 Mpro inhibitor.
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Affiliation(s)
- Blake M Shellenberger
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Olivia N Basile
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Joel Cassel
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Morgan R Olsen
- Department of Chemistry, Bucknell University, One Dent Drive, Lewisburg, PA 17837, USA
| | | | | | - Ian Tietjen
- The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Geneive E Henry
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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5
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Carney DW, Leffler AE, Bell JA, Chandrasinghe AS, Cheng C, Chang E, Dornford A, Dougan DR, Frye LL, Grimes ME, Knehans T, Knight JL, Komandla M, Lane W, Li H, Newman SR, Phimister K, Saikatendu KS, Silverstein H, Vafaei S. Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity. Bioorg Med Chem 2024; 103:117577. [PMID: 38518735 DOI: 10.1016/j.bmc.2023.117577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 03/24/2024]
Abstract
Small-molecule antivirals that prevent the replication of the SARS-CoV-2 virus by blocking the enzymatic activity of its main protease (Mpro) are and will be a tenet of pandemic preparedness. However, the peptidic nature of such compounds often precludes the design of compounds within favorable physical property ranges, limiting cellular activity. Here we describe the discovery of peptide aldehyde Mpro inhibitors with potent enzymatic and cellular antiviral activity. This structure-activity relationship (SAR) exploration was guided by the use of calculated hydration site thermodynamic maps (WaterMap) to drive potency via displacement of waters from high-energy sites. Thousands of diverse compounds were designed to target these high-energy hydration sites and then prioritized for synthesis by physics- and structure-based Free-Energy Perturbation (FEP+) simulations, which accurately predicted biochemical potencies. This approach ultimately led to the rapid discovery of lead compounds with unique SAR that exhibited potent enzymatic and cellular activity with excellent pan-coronavirus coverage.
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Affiliation(s)
- Daniel W Carney
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States.
| | - Abba E Leffler
- Schrödinger, Inc, 1540 Broadway, New York, NY 10036, United States.
| | - Jeffrey A Bell
- Schrödinger, Inc, 1540 Broadway, New York, NY 10036, United States
| | | | - Cecilia Cheng
- Schrödinger, Inc, 9868 Scranton Road, Suite 3200, San Diego, CA 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Adam Dornford
- Schrödinger, Inc, 1 Main St, 11th Floor, Cambridge, MA 02142, United States
| | - Douglas R Dougan
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Leah L Frye
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Mary E Grimes
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Tim Knehans
- Schrödinger GmbH, Glücksteinallee 25, 68163 Mannheim, Germany
| | | | - Mallareddy Komandla
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Weston Lane
- Treeline Biosciences, 500 Arsenal Way, Watertown, MA 02472, United States
| | - Hubert Li
- Schrödinger, Inc, 9868 Scranton Road, Suite 3200, San Diego, CA 92121, United States
| | - Sophia R Newman
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Katalin Phimister
- Schrödinger Technologies Limited, 1st Floor West, Davidson House, Forbury Square, Reading RG1 3EU, United Kingdom
| | - Kumar S Saikatendu
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Hercules Silverstein
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
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6
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Desantis J, Bazzacco A, Eleuteri M, Tuci S, Bianconi E, Macchiarulo A, Mercorelli B, Loregian A, Goracci L. Design, synthesis, and biological evaluation of first-in-class indomethacin-based PROTACs degrading SARS-CoV-2 main protease and with broad-spectrum antiviral activity. Eur J Med Chem 2024; 268:116202. [PMID: 38394929 DOI: 10.1016/j.ejmech.2024.116202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
To date, Proteolysis Targeting Chimera (PROTAC) technology has been successfully applied to mediate proteasomal-induced degradation of several pharmaceutical targets mainly related to oncology, immune disorders, and neurodegenerative diseases. On the other hand, its exploitation in the field of antiviral drug discovery is still in its infancy. Recently, we described two indomethacin (INM)-based PROTACs displaying broad-spectrum antiviral activity against coronaviruses. Here, we report the design, synthesis, and characterization of a novel series of INM-based PROTACs that recruit either Von-Hippel Lindau (VHL) or cereblon (CRBN) E3 ligases. The panel of INM-based PROTACs was also enlarged by varying the linker moiety. The antiviral activity resulted very susceptible to this modification, particularly for PROTACs hijacking VHL as E3 ligase, with one piperazine-based compound (PROTAC 6) showing potent anti-SARS-CoV-2 activity in infected human lung cells. Interestingly, degradation assays in both uninfected and virus-infected cells with the most promising PROTACs emerged so far (PROTACs 5 and 6) demonstrated that INM-PROTACs do not degrade human PGES-2 protein, as initially hypothesized, but induce the concentration-dependent degradation of SARS-CoV-2 main protease (Mpro) both in Mpro-transfected and in SARS-CoV-2-infected cells. Importantly, thanks to the target degradation, INM-PROTACs exhibited a considerable enhancement in antiviral activity with respect to indomethacin, with EC50 values in the low-micromolar/nanomolar range. Finally, kinetic solubility as well as metabolic and chemical stability were measured for PROTACs 5 and 6. Altogether, the identification of INM-based PROTACs as the first class of SARS-CoV-2 Mpro degraders demonstrating activity also in SARS-CoV-2-infected cells represents a significant advance in the development of effective, broad-spectrum anti-coronavirus strategies.
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Affiliation(s)
- Jenny Desantis
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy
| | | | - Michela Eleuteri
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy
| | - Sara Tuci
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Elisa Bianconi
- Department of Pharmaceutical Science, University of Perugia, Italy
| | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Laura Goracci
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy.
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7
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Gentile D, Chiummiento L, Santarsiere A, Funicello M, Lupattelli P, Rescifina A, Venuti A, Piperno A, Sciortino MT, Pennisi R. Targeting Viral and Cellular Cysteine Proteases for Treatment of New Variants of SARS-CoV-2. Viruses 2024; 16:338. [PMID: 38543704 PMCID: PMC10976049 DOI: 10.3390/v16030338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 04/21/2024] Open
Abstract
The continuous emergence of SARS-CoV-2 variants caused the persistence of the COVID-19 epidemic and challenged the effectiveness of the existing vaccines. The viral proteases are the most attractive targets for developing antiviral drugs. In this scenario, our study explores the use of HIV-1 protease inhibitors against SARS-CoV-2. An in silico screening of a library of HIV-1 proteases identified four anti-HIV compounds able to interact with the 3CLpro of SARS-CoV-2. Thus, in vitro studies were designed to evaluate their potential antiviral effectiveness against SARS-CoV-2. We employed pseudovirus technology to simulate, in a highly safe manner, the adsorption of the alpha (α-SARS-CoV-2) and omicron (ο-SARS-CoV-2) variants of SARS-CoV-2 and study the inhibitory mechanism of the selected compounds for cell-virus interaction. The results reported a mild activity against the viral proteases 3CLpro and PLpro, but efficient inhibitory effects on the internalization of both variants mediated by cathepsin B/L. Our findings provide insights into the feasibility of using drugs exhibiting antiviral effects for other viruses against the viral and host SARS-CoV-2 proteases required for entry.
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Affiliation(s)
- Davide Gentile
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - Lucia Chiummiento
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Alessandro Santarsiere
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Maria Funicello
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Paolo Lupattelli
- Department of Chimica, Sapienza University of Roma, p. le Aldo Moro 5, 00185 Roma, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, V. le A. Doria, 95125 Catania, Italy
| | - Assunta Venuti
- International Agency for Research on Cancer (IARC), World Health Organization, 69366 LYON CEDEX 07, France
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
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8
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Huang Q, Quan B, Chen Y, Zhao X, Zhou Y, Huang C, Qiao J, Wang Y, Li Y, Yang S, Lei J, Li L. Discovery of α-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups. Bioorg Chem 2024; 143:107001. [PMID: 38101266 DOI: 10.1016/j.bioorg.2023.107001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023]
Abstract
Although the SARS-CoV-2 pandemic has ended, multiple sporadic cases still exist, posing a request for more antivirals. The main protease (Mpro) of SARS-CoV-2, a key enzyme for viral replication, is an attractive target for drug development. Here, we report the discovery of a new potent α-ketoamide-containing Mpro inhibitor, N-((R)-1-cyclohexyl-2-(((R)-3-methoxy-1-oxo-1-((1-(2-oxo-2-((thiazol-2-ylmethyl)amino)acetyl)cyclobutyl)amino)propan-2-yl)amino)-2-oxoethyl)-4,4-difluorocyclohexane-1-carboxamide (20j). This compound presented promising enzymatic inhibitory activity against SARS-CoV-2 Mpro with an IC50 value of 19.0 nM, and an excellent antiviral activity in cell-based assay with an EC50 value of 138.1 nM. This novel covalent inhibitor may be used as a lead compound for subsequent drug discovery against SARS-CoV-2.
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Affiliation(s)
- Qiao Huang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Baoxue Quan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yan Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiu Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanmei Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chong Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jingxin Qiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yifei Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yueyue Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengyong Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan 610212, China
| | - Jian Lei
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China.
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9
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Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
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Affiliation(s)
- A V Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - I S Ilin
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - A S Tashchilova
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - O A Kondakova
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - D C Kutov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - V B Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
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10
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Gao S, Song L, Sylvester K, Mercorelli B, Loregian A, Toth K, Weiße RH, Useini A, Sträter N, Yang M, Ye B, Tollefson AE, Müller CE, Liu X, Zhan P. Design, Synthesis, and Biological Evaluation of Trisubstituted Piperazine Derivatives as Noncovalent Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors with Improved Antiviral Activity and Favorable Druggability. J Med Chem 2023; 66:16426-16440. [PMID: 37992202 DOI: 10.1021/acs.jmedchem.3c01876] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
The ongoing transmission of SARS-CoV-2 necessitates the development of additional potent antiviral agents capable of combating the current highly infectious variants and future coronaviruses. Here, we present the discovery of potent nonpeptide main protease (Mpro) inhibitors with prominent antiviral activity and improved pharmacokinetic properties. Three series of 1,2,4-trisubstituted piperazine derivatives were designed and synthesized, and the optimal GC-78-HCl demonstrated high enzyme-inhibitory potency (IC50 = 0.19 μM) and exhibited excellent antiviral activity (EC50 = 0.40 μM), reaching the same level as Nirmatrelvir (EC50 = 0.38 μM). Additionally, GC-78-HCl displayed potent antiviral activities against various SARS-CoV-2 variants as well as HCoV-OC43 and HCoV-229E, indicating its potential broad-spectrum anticoronaviral activity. Notably, the pharmacokinetic properties of GC-78-HCl were somewhat enhanced compared to those of the lead compound. Furthermore, the cocrystal and molecular docking elucidated the mechanism of action. In conclusion, we discovered a novel nonpeptidic Mpro inhibitor with promising antiviral activity and a favorable pharmacokinetic profile.
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Affiliation(s)
- Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Shenzhen Research Institute of Shandong University, A301 Virtual University Park in South District of Shenzhen, Shenzhen, Guangdong 518057, PR China
| | - Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Katharina Sylvester
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113 Bonn, Germany
| | - Beatrice Mercorelli
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Karoly Toth
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63103, United States
| | - Renato H Weiße
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany
| | - Abibe Useini
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Ann E Tollefson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63103, United States
| | - Christa E Müller
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113 Bonn, Germany
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
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