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Ou J, Lewandowski EM, Hu Y, Lipinski AA, Aljasser A, Colon-Ascanio M, Morgan RT, Jacobs LMC, Zhang X, Bikowitz MJ, Langlais PR, Tan H, Wang J, Chen Y, Choy JS. A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations. PLoS Pathog 2023; 19:e1011592. [PMID: 37651467 PMCID: PMC10499260 DOI: 10.1371/journal.ppat.1011592] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 09/13/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
The SARS-CoV-2 main protease (Mpro) is a major therapeutic target. The Mpro inhibitor, nirmatrelvir, is the antiviral component of Paxlovid, an orally available treatment for COVID-19. As Mpro inhibitor use increases, drug resistant mutations will likely emerge. We have established a non-pathogenic system, in which yeast growth serves as an approximation for Mpro activity, enabling rapid identification of mutants with altered enzymatic activity and drug sensitivity. The E166 residue is known to be a potential hot spot for drug resistance and yeast assays identified substitutions which conferred strong nirmatrelvir resistance and others that compromised activity. On the other hand, N142A and the P132H mutation, carried by the Omicron variant, caused little to no change in drug response and activity. Standard enzymatic assays confirmed the yeast results. In turn, we solved the structures of Mpro E166R, and Mpro E166N, providing insights into how arginine may drive drug resistance while asparagine leads to reduced activity. The work presented here will help characterize novel resistant variants of Mpro that may arise as Mpro antivirals become more widely used.
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Affiliation(s)
- Jin Ou
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, Washington DC, United States of America
| | - Eric M. Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Austin A. Lipinski
- Department of Medicine, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Ali Aljasser
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, Washington DC, United States of America
| | - Mariliz Colon-Ascanio
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, Washington DC, United States of America
| | - Ryan T. Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Lian M. C. Jacobs
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Drug Discovery Department, Moffit Cancer Center, Tampa, Florida, United States of America
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Melissa J. Bikowitz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Paul R. Langlais
- Department of Medicine, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - John S. Choy
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, Washington DC, United States of America
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2
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Boss L, Kędzierska B. Bacterial Toxin-Antitoxin Systems' Cross-Interactions-Implications for Practical Use in Medicine and Biotechnology. Toxins (Basel) 2023; 15:380. [PMID: 37368681 DOI: 10.3390/toxins15060380] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Toxin-antitoxin (TA) systems are widely present in bacterial genomes. They consist of stable toxins and unstable antitoxins that are classified into distinct groups based on their structure and biological activity. TA systems are mostly related to mobile genetic elements and can be easily acquired through horizontal gene transfer. The ubiquity of different homologous and non-homologous TA systems within a single bacterial genome raises questions about their potential cross-interactions. Unspecific cross-talk between toxins and antitoxins of non-cognate modules may unbalance the ratio of the interacting partners and cause an increase in the free toxin level, which can be deleterious to the cell. Moreover, TA systems can be involved in broadly understood molecular networks as transcriptional regulators of other genes' expression or modulators of cellular mRNA stability. In nature, multiple copies of highly similar or identical TA systems are rather infrequent and probably represent a transition stage during evolution to complete insulation or decay of one of them. Nevertheless, several types of cross-interactions have been described in the literature to date. This implies a question of the possibility and consequences of the TA system cross-interactions, especially in the context of the practical application of the TA-based biotechnological and medical strategies, in which such TAs will be used outside their natural context, will be artificially introduced and induced in the new hosts. Thus, in this review, we discuss the prospective challenges of system cross-talks in the safety and effectiveness of TA system usage.
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Affiliation(s)
- Lidia Boss
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, 80-309 Gdańsk, Poland
| | - Barbara Kędzierska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, 80-309 Gdańsk, Poland
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Ornelas MY, Thomas AY, Johnson Rosas LI, Scoville RO, Mehta AP. Synthetic Platforms for Characterizing and Targeting of SARS-CoV-2 Genome Capping Enzymes. ACS Synth Biol 2022; 11:3759-3771. [PMID: 36331143 PMCID: PMC9662071 DOI: 10.1021/acssynbio.2c00359] [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: 07/07/2022] [Indexed: 11/06/2022]
Abstract
Essential viral enzymes have been successfully targeted to combat the diseases caused by emerging pathogenic RNA viruses (e.g., viral RNA-dependent RNA polymerase). Because of the conserved nature of such viral enzymes, therapeutics targeting these enzymes have the potential to be repurposed to combat emerging diseases, e.g., remdesivir, which was initially developed as a potential Ebola treatment, then was repurposed for COVID-19. Our efforts described in this study target another essential and highly conserved, but relatively less explored, step in RNA virus translation and replication, i.e., capping of the viral RNA genome. The viral genome cap structure disguises the genome of most RNA viruses to resemble the mRNA cap structure of their host and is essential for viral translation, propagation, and immune evasion. Here, we developed a synthetic, phenotypic yeast-based complementation platform (YeRC0M) for molecular characterization and targeting of SARS-CoV-2 genome-encoded RNA cap-0 (guanine-N7)-methyltransferase (N7-MTase) enzyme (nsp14). In YeRC0M, the lack of yeast mRNA capping N7-MTase in yeast, which is an essential gene in yeast, is complemented by the expression of functional viral N7-MTase or its variants. Using YeRC0M, we first identified important protein domains and amino acid residues that are essential for SARS-CoV-2 nsp14 N7-MTase activity. We also expanded YeRC0M to include key nsp14 variants observed in emerging variants of SARS-CoV-2 (e.g., delta variant of SARS-CoV-2 encodes nsp14 A394V and nsp14 P46L). We also combined YeRC0M with directed evolution to identify attenuation mutations in SARS-CoV-2 nsp14. Because of the high sequence similarity of nsp14 in emerging coronaviruses, these observations could have implications on live attenuated vaccine development strategies. These data taken together reveal key domains in SARS-CoV-2 nsp14 that can be targeted for therapeutic strategies. We also anticipate that these readily tractable phenotypic platforms can also be used for the identification of inhibitors of viral RNA capping enzymes as antivirals.
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Affiliation(s)
- Marya Y. Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Angela Y. Thomas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - L. Idalee Johnson Rosas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Riley O. Scoville
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Angad P. Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign
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Ou J, Lewandowski EM, Hu Y, Lipinski AA, Morgan RT, Jacobs LM, Zhang X, Bikowitz MJ, Langlais P, Tan H, Wang J, Chen Y, Choy JS. A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations. RESEARCH SQUARE 2022:rs.3.rs-1942964. [PMID: 36052369 PMCID: PMC9435405 DOI: 10.21203/rs.3.rs-1942964/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a major therapeutic target. The Mpro inhibitor, nirmatrelvir, is the antiviral component of Paxlovid, an orally available treatment for COVID-19. As Mpro inhibitor use increases, drug resistant mutations will likely emerge. We have established a non-pathogenic system, in which yeast growth serves as a proxy for Mpro activity, enabling rapid identification of mutants with altered enzymatic activity and drug sensitivity. The E166 residue is known to be a potential hot spot for drug resistance and yeast assays showed that an E166R substitution conferred strong nirmatrelvir resistance while an E166N mutation compromised activity. On the other hand, N142A and P132H mutations caused little to no change in drug response and activity. Standard enzymatic assays confirmed the yeast results. In turn, we solved the structures of Mpro E166R, and Mpro E166N, providing insights into how arginine may drive drug resistance while asparagine leads to reduced activity. The work presented here will help characterize novel resistant variants of Mpro that may arise as Mpro antivirals become more widely used.
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Affiliation(s)
- Jin Ou
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, United States
| | - Eric M. Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Austin A. Lipinski
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85724, United States
| | - Ryan T. Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Lian M.C. Jacobs
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
- Drug Discovery Department, Moffit Cancer Center, Tampa, FL 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Melissa J. Bikowitz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Paul Langlais
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85724, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - John S. Choy
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, United States
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5
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Ou J, Lewandowski EM, Hu Y, Lipinski AA, Morgan RT, Jacobs LM, Zhang X, Bikowitz MJ, Langlais P, Tan H, Wang J, Chen Y, Choy JS. A yeast-based system to study SARS-CoV-2 M pro structure and to identify nirmatrelvir resistant mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.06.503039. [PMID: 35982672 PMCID: PMC9387140 DOI: 10.1101/2022.08.06.503039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The SARS-CoV-2 main protease (M pro ) is a major therapeutic target. The M pro inhibitor, nirmatrelvir, is the antiviral component of Paxlovid, an orally available treatment for COVID-19. As M pro inhibitor use increases, drug resistant mutations will likely emerge. We have established a non-pathogenic system, in which yeast growth serves as a proxy for M pro activity, enabling rapid identification of mutants with altered enzymatic activity and drug sensitivity. The E166 residue is known to be a potential hot spot for drug resistance and yeast assays showed that an E166R substitution conferred strong nirmatrelvir resistance while an E166N mutation compromised activity. On the other hand, N142A and P132H mutations caused little to no change in drug response and activity. Standard enzymatic assays confirmed the yeast results. In turn, we solved the structures of M pro E166R, and M pro E166N, providing insights into how arginine may drive drug resistance while asparagine leads to reduced activity. The work presented here will help characterize novel resistant variants of M pro that may arise as M pro antivirals become more widely used.
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Affiliation(s)
- Jin Ou
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, United States
| | - Eric M. Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Austin A. Lipinski
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85724, United States
| | - Ryan T. Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Lian M.C. Jacobs
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
- Drug Discovery Department, Moffit Cancer Center, Tampa, FL 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Melissa J. Bikowitz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Paul Langlais
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85724, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - John S. Choy
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, United States
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Flynn JM, Samant N, Schneider-Nachum G, Bakan DT, Yilmaz NK, Schiffer CA, Moquin SA, Dovala D, Bolon DNA. Comprehensive fitness landscape of SARS-CoV-2 M pro reveals insights into viral resistance mechanisms. eLife 2022; 11:77433. [PMID: 35723575 PMCID: PMC9323007 DOI: 10.7554/elife.77433] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
With the continual evolution of new strains of SARS-CoV-2 that are more virulent, transmissible, and able to evade current vaccines, there is an urgent need for effective anti-viral drugs SARS-CoV-2 main protease (Mpro) is a leading target for drug design due to its conserved and indispensable role in the viral life cycle. Drugs targeting Mpro appear promising but will elicit selection pressure for resistance. To understand resistance potential in Mpro, we performed a comprehensive mutational scan of the protease that analyzed the function of all possible single amino acid changes. We developed three separate high-throughput assays of Mpro function in yeast, based on either the ability of Mpro variants to cleave at a defined cut-site or on the toxicity of their expression to yeast. We used deep sequencing to quantify the functional effects of each variant in each screen. The protein fitness landscapes from all three screens were strongly correlated, indicating that they captured the biophysical properties critical to Mpro function. The fitness landscapes revealed a non-active site location on the surface that is extremely sensitive to mutation making it a favorable location to target with inhibitors. In addition, we found a network of critical amino acids that physically bridge the two active sites of the Mpro dimer. The clinical variants of Mpro were predominantly functional in our screens, indicating that Mpro is under strong selection pressure in the human population. Our results provide predictions of mutations that will be readily accessible to Mpro evolution and that are likely to contribute to drug resistance. This complete mutational guide of Mpro can be used in the design of inhibitors with reduced potential of evolving viral resistance.
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Affiliation(s)
- Julia M Flynn
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Neha Samant
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Gily Schneider-Nachum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | | | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | | | | | - Daniel N A Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? Int J Mol Sci 2021; 23:259. [PMID: 35008685 PMCID: PMC8745775 DOI: 10.3390/ijms23010259] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 01/01/2023] Open
Abstract
In this review, we collected 1765 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) M-pro inhibitors from the bibliography and other sources, such as the COVID Moonshot project and the ChEMBL database. This set of inhibitors includes only those compounds whose inhibitory capacity, mainly expressed as the half-maximal inhibitory concentration (IC50) value, against M-pro from SARS-CoV-2 has been determined. Several covalent warheads are used to treat covalent and non-covalent inhibitors separately. Chemical space, the variation of the IC50 inhibitory activity when measured by different methods or laboratories, and the influence of 1,4-dithiothreitol (DTT) are discussed. When available, we have collected the values of inhibition of viral replication measured with a cellular antiviral assay and expressed as half maximal effective concentration (EC50) values, and their possible relationship to inhibitory potency against M-pro is analyzed. Finally, the most potent covalent and non-covalent inhibitors that simultaneously inhibit the SARS-CoV-2 M-pro and the virus replication in vitro are discussed.
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Affiliation(s)
| | | | | | | | - Gerard Pujadas
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| | - Santiago Garcia-Vallvé
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
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