1
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Wang L, Ma C, Sacco MD, Xue S, Mahmoud M, Calcul L, Chen Y, Wang J, Cai J. Development of the Safe and Broad-Spectrum Aldehyde and Ketoamide Mpro inhibitors Derived from the Constrained α, γ-AA Peptide Scaffold. Chemistry 2023:e202300476. [PMID: 36920943 DOI: 10.1002/chem.202300476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/16/2023]
Abstract
SARS-CoV-2 is still wreaking havoc all over the world with surging morbidity and high mortality. The main protease (Mpro) is essential in the replication of SARS-CoV-2, enabling itself an active target for antiviral development. Herein, we reported the design and synthesis of a new class of peptidomimetics-constrained α, γ-AApeptides, based on which a series of aldehyde and ketoamide inhibitors of the Mpro of SARS-CoV-2 were prepared. The lead compounds showed excellent inhibitory activity in the FRET-based Mpro enzymatic assay not only for the Mpro of SARS-CoV-2 but also for SARS-CoV and MERS-CoV, along with HCoVs like HCoV-OC43, HCoV-229E, HCoV-NL63 and HKU1. The X-ray crystallographic results demonstrated that our compounds form a covalent bond with the catalytic Cys145. They also demonstrated effective antiviral activity against live SARS-CoV-2. Overall, the results suggest that α, γ-AApeptide could be a promising molecular scaffold in designing novel Mpro inhibitors of SARS-CoV-2 and other coronaviruses.
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Affiliation(s)
- Lei Wang
- University of South Florida College of Arts & Sciences, Department of Chemistry, UNITED STATES
| | - Chunlong Ma
- The University of Arizona College of Pharmacy, Department of Pharmacy, UNITED STATES
| | - Michael Dominic Sacco
- University of South Florida College of Medicine: University of South Florida Morsani College of Medicine, Department of Molecular Medicine, UNITED STATES
| | - Songyi Xue
- University of South Florida College of Arts & Sciences, Department of Chemistry, UNITED STATES
| | - Mentalla Mahmoud
- University of South Florida College of Arts & Sciences, Department of Chemistry, UNITED STATES
| | - Laurent Calcul
- University of South Florida College of Arts & Sciences, Department of Chemistry, UNITED STATES
| | - Yu Chen
- University of South Florida College of Medicine: University of South Florida Morsani College of Medicine, Department of Molecular Medicine, UNITED STATES
| | - Jun Wang
- Rutgers: Rutgers The State University of New Jersey, Department of Medical Chemistry, UNITED STATES
| | - Jianfeng Cai
- 4202 E. Fowler Avenue, 33620, Tampa, UNITED STATES
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2
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Sacco MD, Hu Y, Gongora MV, Meilleur F, Kemp MT, Zhang X, Wang J, Chen Y. The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition. Cell Res 2022; 32:498-500. [PMID: 35292745 PMCID: PMC8923085 DOI: 10.1038/s41422-022-00640-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/21/2022] [Indexed: 01/02/2023] Open
Affiliation(s)
- Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Maura Verenice Gongora
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Trent Kemp
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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3
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Kitamura N, Sacco MD, Ma C, Hu Y, Townsend JA, Meng X, Zhang F, Zhang X, Ba M, Szeto T, Kukuljac A, Marty MT, Schultz D, Cherry S, Xiang Y, Chen Y, Wang J. Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors. J Med Chem 2022; 65:2848-2865. [PMID: 33891389 PMCID: PMC8536799 DOI: 10.1021/acs.jmedchem.1c00509] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a validated antiviral drug target. Several Mpro inhibitors have been reported with potent enzymatic inhibition and cellular antiviral activity, including GC376, boceprevir, calpain inhibitors II, and XII, with each containing a reactive warhead that covalently modifies the catalytic Cys145. Coupling structure-based drug design with the one-pot Ugi four-component reaction, we discovered one of the most potent noncovalent inhibitors, 23R (Jun8-76-3A) that is structurally distinct from the canonical Mpro inhibitor GC376. Significantly, 23R is highly selective compared with covalent inhibitors such as GC376, especially toward host proteases. The cocrystal structure of SARS-CoV-2 Mpro with 23R revealed a previously unexplored binding site located in between the S2 and S4 pockets. Overall, this study discovered 23R, one of the most potent and selective noncovalent SARS-CoV-2 Mpro inhibitors reported to date, and a novel binding pocket in Mpro that can be explored for inhibitor design.
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Affiliation(s)
- Naoya Kitamura
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Xiangzhi Meng
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Fushun Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Mandy Ba
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Tommy Szeto
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Adis Kukuljac
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - David Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
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4
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Ma C, Xia Z, Sacco MD, Hu Y, Townsend JA, Meng X, Choza J, Tan H, Jang J, Gongora MV, Zhang X, Zhang F, Xiang Y, Marty MT, Chen Y, Wang J. Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity. J Am Chem Soc 2021; 143:20697-20709. [PMID: 34860011 PMCID: PMC8672434 DOI: 10.1021/jacs.1c08060] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 12/17/2022]
Abstract
The main protease (Mpro) is a validated antiviral drug target of SARS-CoV-2. A number of Mpro inhibitors have now advanced to animal model study and human clinical trials. However, one issue yet to be addressed is the target selectivity over host proteases such as cathepsin L. In this study we describe the rational design of covalent SARS-CoV-2 Mpro inhibitors with novel cysteine reactive warheads including dichloroacetamide, dibromoacetamide, tribromoacetamide, 2-bromo-2,2-dichloroacetamide, and 2-chloro-2,2-dibromoacetamide. The promising lead candidates Jun9-62-2R (dichloroacetamide) and Jun9-88-6R (tribromoacetamide) had not only potent enzymatic inhibition and antiviral activity but also significantly improved target specificity over caplain and cathepsins. Compared to GC-376, these new compounds did not inhibit the host cysteine proteases including calpain I, cathepsin B, cathepsin K, cathepsin L, and caspase-3. To the best of our knowledge, they are among the most selective covalent Mpro inhibitors reported thus far. The cocrystal structures of SARS-CoV-2 Mpro with Jun9-62-2R and Jun9-57-3R reaffirmed our design hypothesis, showing that both compounds form a covalent adduct with the catalytic C145. Overall, these novel compounds represent valuable chemical probes for target validation and drug candidates for further development as SARS-CoV-2 antivirals.
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Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Zilei Xia
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Xiangzhi Meng
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Juliana Choza
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Haozhou Tan
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Janice Jang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Maura V Gongora
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Fushun Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
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5
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Ma C, Sacco MD, Xia Z, Lambrinidis G, Townsend JA, Hu Y, Meng X, Szeto T, Ba M, Zhang X, Gongora M, Zhang F, Marty MT, Xiang Y, Kolocouris A, Chen Y, Wang J. Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay. ACS Cent Sci 2021; 7:1245-1260. [PMID: 34341772 PMCID: PMC8265724 DOI: 10.1021/acscentsci.1c00519] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Indexed: 05/27/2023]
Abstract
The papain-like protease (PLpro) of SARS-CoV-2 is a validated antiviral drug target. Through a fluorescence resonance energy transfer-based high-throughput screening and subsequent lead optimization, we identified several PLpro inhibitors including Jun9-72-2 and Jun9-75-4 with improved enzymatic inhibition and antiviral activity compared to GRL0617, which was reported as a SARS-CoV PLpro inhibitor. Significantly, we developed a cell-based FlipGFP assay that can be applied to predict the cellular antiviral activity of PLpro inhibitors in the BSL-2 setting. X-ray crystal structure of PLpro in complex with GRL0617 showed that binding of GRL0617 to SARS-CoV-2 induced a conformational change in the BL2 loop to a more closed conformation. Molecular dynamics simulations showed that Jun9-72-2 and Jun9-75-4 engaged in more extensive interactions than GRL0617. Overall, the PLpro inhibitors identified in this study represent promising candidates for further development as SARS-CoV-2 antivirals, and the FlipGFP-PLpro assay is a suitable surrogate for screening PLpro inhibitors in the BSL-2 setting.
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Affiliation(s)
- Chunlong Ma
- Department
of Pharmacology and Toxicology, College
of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Michael Dominic Sacco
- Department
of Molecular Medicine, Morsani College of
Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Zilei Xia
- Department
of Pharmacology and Toxicology, College
of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - George Lambrinidis
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of
Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Julia Alma Townsend
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721, United
States
| | - Yanmei Hu
- Department
of Pharmacology and Toxicology, College
of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Xiangzhi Meng
- Department
of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Tommy Szeto
- Department
of Pharmacology and Toxicology, College
of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Mandy Ba
- Department
of Pharmacology and Toxicology, College
of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Xiujun Zhang
- Department
of Molecular Medicine, Morsani College of
Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Maura Gongora
- Department
of Molecular Medicine, Morsani College of
Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Fushun Zhang
- Department
of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Michael Thomas Marty
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721, United
States
| | - Yan Xiang
- Department
of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Antonios Kolocouris
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of
Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Yu Chen
- Department
of Molecular Medicine, Morsani College of
Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Jun Wang
- Department
of Pharmacology and Toxicology, College
of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
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6
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Xia Z, Sacco MD, Ma C, Townsend JA, Kitamura N, Hu Y, Ba M, Szeto T, Zhang X, Meng X, Zhang F, Xiang Y, Marty MT, Chen Y, Wang J. Discovery of SARS-CoV-2 papain-like protease inhibitors through a combination of high-throughput screening and FlipGFP-based reporter assay. bioRxiv 2021:2021.03.15.435551. [PMID: 33758866 PMCID: PMC7987026 DOI: 10.1101/2021.03.15.435551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The papain-like protease (PL pro ) of SARS-CoV-2 is a validated antiviral drug target. PL pro is involved in the cleavage of viral polyproteins and antagonizing host innate immune response through its deubiquitinating and deISG15ylating activities, rendering it a high profile antiviral drug target. Through a FRET-based high-throughput screening, several hits were identified as PL pro inhibitors with IC 50 values at the single-digit micromolar range. Subsequent lead optimization led to potent inhibitors with IC 50 values ranging from 0.56 to 0.90 µM. To help prioritize lead compounds for the cellular antiviral assay against SARS-CoV-2, we developed the cell-based FlipGFP assay that is suitable for quantifying the intracellular enzymatic inhibition potency of PL pro inhibitors in the BSL-2 setting. Two compounds selected from the FlipGFP-PL pro assay, Jun9-53-2 and Jun9-72-2, inhibited SARS-CoV-2 replication in Caco-2 hACE2 cells with EC 50 values of 8.89 and 8.32 µM, respectively, which were 3-fold more potent than GRL0617 (EC 50 = 25.1 µM). The X-ray crystal structures of PL pro in complex with GRL0617 showed that binding of GRL0617 to SARS-CoV-2 induced a conformational change in the BL2 loop to the more closed conformation. Overall, the PL pro inhibitors identified in this study represent promising starting points for further development as SARS-CoV-2 antivirals, and FlipGFP-PL pro assay might be a suitable surrogate for screening PL pro inhibitors in the BSL-2 setting.
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Affiliation(s)
- Zilei Xia
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Naoya Kitamura
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Mandy Ba
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Tommy Szeto
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Xiangzhi Meng
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Fushun Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
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7
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Sacco MD, Ma C, Lagarias P, Gao A, Townsend JA, Meng X, Dube P, Zhang X, Hu Y, Kitamura N, Hurst B, Tarbet B, Marty MT, Kolocouris A, Xiang Y, Chen Y, Wang J. Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L. Sci Adv 2020; 6:sciadv.abe0751. [PMID: 33158912 PMCID: PMC7725459 DOI: 10.1126/sciadv.abe0751] [Citation(s) in RCA: 248] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/21/2020] [Indexed: 05/03/2023]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a key antiviral drug target. While most Mpro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently found that several Mpro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II and XII, which are also active against human cathepsin L, a host protease that is important for viral entry. In this study, we solved x-ray crystal structures of Mpro in complex with calpain inhibitors II and XII and three analogs of GC-376 The structure of Mpro with calpain inhibitor II confirmed that the S1 pocket can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. The structure of calpain inhibitor XII revealed an unexpected, inverted binding pose. Together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of dual inhibitors as SARS-CoV-2 antivirals.
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Affiliation(s)
- Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA
| | - Panagiotis Lagarias
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Ang Gao
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721, USA
| | - Xiangzhi Meng
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Peter Dube
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA
| | - Naoya Kitamura
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA
| | - Brett Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322, USA
| | - Bart Tarbet
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322, USA
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721, USA
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Yan Xiang
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA.
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8
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Ma C, Sacco MD, Hurst B, Townsend JA, Hu Y, Szeto T, Zhang X, Tarbet B, Marty MT, Chen Y, Wang J. Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Cell Res 2020; 30:678-692. [PMID: 32541865 PMCID: PMC7294525 DOI: 10.1038/s41422-020-0356-z] [Citation(s) in RCA: 557] [Impact Index Per Article: 139.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022] Open
Abstract
A new coronavirus SARS-CoV-2, also called novel coronavirus 2019 (2019-nCoV), started to circulate among humans around December 2019, and it is now widespread as a global pandemic. The disease caused by SARS-CoV-2 virus is called COVID-19, which is highly contagious and has an overall mortality rate of 6.35% as of May 26, 2020. There is no vaccine or antiviral available for SARS-CoV-2. In this study, we report our discovery of inhibitors targeting the SARS-CoV-2 main protease (Mpro). Using the FRET-based enzymatic assay, several inhibitors including boceprevir, GC-376, and calpain inhibitors II, and XII were identified to have potent activity with single-digit to submicromolar IC50 values in the enzymatic assay. The mechanism of action of the hits was further characterized using enzyme kinetic studies, thermal shift binding assays, and native mass spectrometry. Significantly, four compounds (boceprevir, GC-376, calpain inhibitors II and XII) inhibit SARS-CoV-2 viral replication in cell culture with EC50 values ranging from 0.49 to 3.37 µM. Notably, boceprevir, calpain inhibitors II and XII represent novel chemotypes that are distinct from known substrate-based peptidomimetic Mpro inhibitors. A complex crystal structure of SARS-CoV-2 Mpro with GC-376, determined at 2.15 Å resolution with three protomers per asymmetric unit, revealed two unique binding configurations, shedding light on the molecular interactions and protein conformational flexibility underlying substrate and inhibitor binding by Mpro. Overall, the compounds identified herein provide promising starting points for the further development of SARS-CoV-2 therapeutics.
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Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, USA
| | - Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Brett Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, 84322, USA
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, 84322, USA
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, USA
| | - Tommy Szeto
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Bart Tarbet
- Institute for Antiviral Research, Utah State University, Logan, UT, 84322, USA
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, 84322, USA
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, USA.
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Sacco MD, Ma C, Lagarias P, Gao A, Townsend JA, Meng X, Dube P, Zhang X, Hu Y, Kitamura N, Hurst B, Tarbet B, Marty MT, Kolocouris A, Xiang Y, Chen Y, Wang J. Structure and inhibition of the SARS-CoV-2 main protease reveals strategy for developing dual inhibitors against M pro and cathepsin L. bioRxiv 2020:2020.07.27.223727. [PMID: 32766590 PMCID: PMC7402059 DOI: 10.1101/2020.07.27.223727] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The main protease (Mpro) of SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic, is a key antiviral drug target. While most SARS-CoV-2 Mpro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently discovered several Mpro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II/XII, which are also active against human cathepsin L, a host-protease that is important for viral entry. To determine the binding mode of these calpain inhibitors and establish a structure-activity relationship, we solved X-ray crystal structures of Mpro in complex with calpain inhibitors II and XII, and three analogues of GC-376, one of the most potent Mpro inhibitors in vitro. The structure of Mpro with calpain inhibitor II confirmed the S1 pocket of Mpro can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. Interestingly, the structure of calpain inhibitor XII revealed an unexpected, inverted binding pose where the P1' pyridine inserts in the S1 pocket and the P1 norvaline is positioned in the S1' pocket. The overall conformation is semi-helical, wrapping around the catalytic core, in contrast to the extended conformation of other peptidomimetic inhibitors. Additionally, the structures of three GC-376 analogues UAWJ246, UAWJ247, and UAWJ248 provide insight to the sidechain preference of the S1', S2, S3 and S4 pockets, and the superior cell-based activity of the aldehyde warhead compared with the α-ketoamide. Taken together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of Mpro inhibitors as SARS-CoV-2 antivirals.
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Affiliation(s)
- Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Panagiotis Lagarias
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Ang Gao
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Xiangzhi Meng
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Peter Dube
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Naoya Kitamura
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Brett Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, 84322, United States
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, 84322, United States
| | - Bart Tarbet
- Institute for Antiviral Research, Utah State University, Logan, UT, 84322, United States
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, 84322, United States
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
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