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Tamura TJ, Choudhary MC, Deo R, Yousuf F, Gomez AN, Edelstein GE, Boucau J, Glover OT, Barry M, Gilbert RF, Reynolds Z, Li Y, Tien D, Vyas TD, Passell E, Su K, Drapkin S, Abar EG, Kawano Y, Sparks JA, Wallace ZS, Vyas JM, Shafer RW, Siedner MJ, Barczak AK, Lemieux JE, Li JZ. Emerging SARS-CoV-2 Resistance After Antiviral Treatment. JAMA Netw Open 2024; 7:e2435431. [PMID: 39320890 PMCID: PMC11425144 DOI: 10.1001/jamanetworkopen.2024.35431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/26/2024] Open
Abstract
Importance Previous studies have identified mutations in SARS-CoV-2 strains that confer resistance to nirmatrelvir, yet how often this resistance arises and its association with posttreatment virologic rebound is not well understood. Objective To examine the prevalence of emergent antiviral resistance after nirmatrelvir treatment and its association with virologic rebound. Design, Setting, and Participants This cohort study enrolled outpatient adults with acute COVID-19 infection from May 2021 to October 2023. Participants were divided into those who received antiviral therapy and those who did not. The study was conducted at a multicenter health care system in Boston, Massachusetts. Exposure Treatment regimen, including none, nirmatrelvir, and remdesivir. Main Outcomes and Measures The primary outcome was emergent SARS-CoV-2 antiviral resistance, defined as the detection of antiviral resistance mutations, which were not present at baseline, were previously associated with decreased antiviral efficacy, and emerged during or after completion of a participant's treatment. Next-generation sequencing was used to detect low frequency mutations down to 1% of the total viral population. Results Overall, 156 participants (114 female [73.1%]; median [IQR] age, 56 [38-69] years) were included. Compared with 63 untreated individuals, the 79 who received nirmatrelvir were older and more commonly immunosuppressed. After sequencing viral RNA from participants' anterior nasal swabs, nirmatrelvir resistance mutations were detected in 9 individuals who received nirmatrelvir (11.4%) compared with 2 of those who did not (3.2%) (P = .09). Among the individuals treated with nirmatrelvir, those who were immunosuppressed had the highest frequency of resistance emergence (5 of 22 [22.7%]), significantly greater than untreated individuals (2 of 63 [3.1%]) (P = .01). Similar rates of nirmatrelvir resistance were found in those who had virologic rebound (3 of 23 [13.0%]) vs those who did not (6 of 56 [10.7%]) (P = .86). Most of these mutations (10 of 11 [90.9%]) were detected at low frequencies (<20% of viral population) and reverted to the wild type at subsequent time points. Emerging remdesivir resistance mutations were only detected in immunosuppressed individuals (2 of 14 [14.3%]) but were similarly low frequency and transient. Global Initiative on Sharing All Influenza Data analysis showed no evidence of increased nirmatrelvir resistance in the United States after the authorization of nirmatrelvir. Conclusions and Relevance In this cohort study of 156 participants, treatment-emergent nirmatrelvir resistance mutations were commonly detected, especially in individuals who were immunosuppressed. However, these mutations were generally present at low frequencies and were transient in nature, suggesting a low risk for the spread of nirmatrelvir resistance in the community with the current variants and drug usage patterns.
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Affiliation(s)
| | - Manish C Choudhary
- Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Rinki Deo
- Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Fizah Yousuf
- Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Gregory E Edelstein
- Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Julie Boucau
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge
| | - Owen T Glover
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge
| | | | | | | | - Yijia Li
- Brigham and Women's Hospital, Boston, Massachusetts
- Massachusetts General Hospital, Boston
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | | | - Karry Su
- Massachusetts General Hospital, Boston
| | | | | | - Yumeko Kawano
- Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Jeffrey A Sparks
- Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Zachary S Wallace
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Boston
| | - Jatin M Vyas
- Brigham and Women's Hospital, Boston, Massachusetts
- Massachusetts General Hospital, Boston
- Broad Institute, Cambridge, Massachusetts
| | - Robert W Shafer
- Stanford University School of Medicine, Palo Alto, California
| | - Mark J Siedner
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Boston
| | - Amy K Barczak
- Harvard Medical School, Boston, Massachusetts
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge
- Massachusetts General Hospital, Boston
| | - Jacob E Lemieux
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Boston
- Broad Institute, Cambridge, Massachusetts
| | - Jonathan Z Li
- Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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2
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Jiang H, Li W, Zhou X, Zhang J, Li J. Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77. Int J Biol Macromol 2024; 276:133706. [PMID: 38981557 DOI: 10.1016/j.ijbiomac.2024.133706] [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: 05/17/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/11/2024]
Abstract
Main proteases (Mpros) are a class of conserved cysteine hydrolases among coronaviruses and play a crucial role in viral replication. Therefore, Mpros are ideal targets for the development of pan-coronavirus drugs. X77, previously developed against SARS-CoV Mpro, was repurposed as a non-covalent tight binder inhibitor against SARS-CoV-2 Mpro during COVID-19 pandemic. Many novel inhibitors with favorable efficacy have been discovered using X77 as a reference, suggesting that X77 could be a valuable scaffold for drug design. However, the broad-spectrum performance of X77 and underlying mechanism remain less understood. Here, we reported the crystal structures of Mpros from SARS-CoV-2, SARS-CoV, and MERS-CoV, and several Mpro mutants from SARS-CoV-2 variants bound to X77. A detailed analysis of these structures revealed key structural determinants essential for interaction and elucidated the binding modes of X77 with different coronaviral Mpros. The potencies of X77 against these investigated Mpros were further evaluated through molecular dynamic simulation and binding free energy calculation. These data provide molecular insights into broad-spectrum inhibition against coronaviral Mpros by X77 and the similarities and differences of X77 when bound to various Mpros, which will promote X77-based design of novel antivirals with broad-spectrum efficacy against different coronaviruses and SARS-CoV-2 variants.
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Affiliation(s)
- Haihai Jiang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Wenwen Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Xuelan Zhou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.
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3
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Zhou X, Lu X, Lin C, Zou X, Li W, Zeng X, Wang J, Zeng P, Wang W, Zhang J, Jiang H, Li J. Structural basis for the inhibition of coronaviral main proteases by PF-00835231. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39076076 DOI: 10.3724/abbs.2024122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024] Open
Abstract
The main protease (M pro) of coronaviruses plays a key role in viral replication, thus serving as a hot target for drug design. PF-00835231 is a promising inhibitor of SARS-CoV-2 M pro. Here, we report the inhibitory potency of PF-00835231 against SARS-CoV-2 M pro and seven M pro mutants (G15S, M49I, Y54C, K90R, P132H, S46F, and V186F) from SARS-CoV-2 variants. The results confirm that PF-00835231 has broad-spectrum inhibition against various coronaviral M pros. In addition, the crystal structures of SARS-CoV-2 M pro, SARS-CoV M pro, MERS-CoV M pro, and seven SARS-CoV-2 M pro mutants (G15S, M49I, Y54C, K90R, P132H, S46F, and V186F) in complex with PF-00835231 are solved. A detailed analysis of these structures reveals key determinants essential for inhibition and elucidates the binding modes of different coronaviral M pros. Given the importance of the main protease for the treatment of coronaviral infection, structural insights into M pro inhibition by PF-00835231 can accelerate the design of novel antivirals with broad-spectrum efficacy against different human coronaviruses.
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Affiliation(s)
- Xuelan Zhou
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Xiaolu Lu
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Cheng Lin
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen 518118, China
| | - Xiaofang Zou
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Wenwen Li
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Xiangyi Zeng
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Jie Wang
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Pei Zeng
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Weiwei Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Jin Zhang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Haihai Jiang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Jian Li
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China
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4
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Xia YL, Du WW, Li YP, Tao Y, Zhang ZB, Liu SM, Fu YX, Zhang KQ, Liu SQ. Computational Insights into SARS-CoV-2 Main Protease Mutations and Nirmatrelvir Efficacy: The Effects of P132H and P132H-A173V. J Chem Inf Model 2024; 64:5207-5218. [PMID: 38913174 PMCID: PMC11235099 DOI: 10.1021/acs.jcim.4c00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Nirmatrelvir, a pivotal component of the oral antiviral Paxlovid for COVID-19, targets the SARS-CoV-2 main protease (Mpro) as a covalent inhibitor. Here, we employed combined computational methods to explore how the prevalent Omicron variant mutation P132H, alone and in combination with A173V (P132H-A173V), affects nirmatrelvir's efficacy. Our findings suggest that P132H enhances the noncovalent binding affinity of Mpro for nirmatrelvir, whereas P132H-A173V diminishes it. Although both mutants catalyze the rate-limiting step more efficiently than the wild-type (WT) Mpro, P132H slows the overall rate of covalent bond formation, whereas P132H-A173V accelerates it. Comprehensive analysis of noncovalent and covalent contributions to the overall binding free energy of the covalent complex suggests that P132H likely enhances Mpro sensitivity to nirmatrelvir, while P132H-A173V may confer resistance. Per-residue decompositions of the binding and activation free energies pinpoint key residues that significantly affect the binding affinity and reaction rates, revealing how the mutations modulate these effects. The mutation-induced conformational perturbations alter drug-protein local contact intensities and the electrostatic preorganization of the protein, affecting noncovalent binding affinity and the stability of key reaction states, respectively. Our findings inform the mechanisms of nirmatrelvir resistance and sensitivity, facilitating improved drug design and the detection of resistant strains.
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Affiliation(s)
- Yuan-Ling Xia
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
- Editorial
Office of Journal of Yunnan University (Natural Sciences Edition), Yunnan University, Kunming, Yunnan 650091, China
| | - Wen-Wen Du
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
| | - Yong-Ping Li
- School
of Agriculture, Yunnan University, Kunming, Yunnan 650091, China
| | - Yan Tao
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
- Yunnan
University Library, Yunnan University, Kunming, Yunnan 650091, China
| | - Zhi-Bi Zhang
- Yunnan
Key Laboratory of Stem Cell and Regenerative Medicine & Biomedical
Engineering Research Center, Kunming Medical
University, Kunming, Yunnan 650500, China
| | - Song-Ming Liu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
| | - Yun-Xin Fu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
- Human Genetics
Center and Department of Biostatistics and Data Science, School of
Public Health, The University of Texas Health
Science Center, Houston, Texas 77030, United States
| | - Ke-Qin Zhang
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
| | - Shu-Qun Liu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
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5
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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6
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Jiang H, Zou X, Zhou X, Zhang J, Li J. Crystal structure of SARS-CoV-2 main protease (M pro) mutants in complex with the non-covalent inhibitor CCF0058981. Biochem Biophys Res Commun 2024; 692:149352. [PMID: 38056159 DOI: 10.1016/j.bbrc.2023.149352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
SARS-CoV-2 constantly circulates and evolves worldwide, generating many variants and posing a menace to global health. It is urgently needed to discover effective medicines to treat the disease caused by SARS-CoV-2 and its variants. An established target for anti-SARS-CoV-2 drug discovery is the main protease (Mpro), since it exerts an irreplaceable action in viral life cycle. CCF0058981, derived from ML300, is a non-covalent inhibitor that exhibits low nanomolar potency against SARS-CoV-2 Mpro and submicromolar anti-SARS-CoV-2 activity, thereby providing a valuable starting point for drug design. However, structural basis underlying inhibition of SARS-CoV-2 Mpro by CCF0058981 remains undetermined. In this study, the crystal structures of CCF0058981 in complex with two SARS-CoV-2 Mpro mutants (M49I and V186F), which have been identified in the recently emerged Omicron subvariants, were solved. Structural analysis defined the pivotal molecular factors responsible for the interactions between CCF0058981 and these two Mpro mutants, and revealed the binding modes of CCF0058981 to Mpro M49I and V186F mutants. These data not only provide structural insights for SARS-CoV-2 Mpro inhibition by CCF0058981, but also add to develop effective broad-spectrum drugs against SARS-CoV-2 as well as its variants.
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Affiliation(s)
- Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Xiaofang Zou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Xuelan Zhou
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, 341000, China; Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, 518118, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
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7
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Zhao Z, Zhu Q, Zhou X, Li W, Yin X, Li J. Structural Basis for the Inhibition of SARS-CoV-2 M pro D48N Mutant by Shikonin and PF-07321332. Viruses 2023; 16:65. [PMID: 38257765 PMCID: PMC10818409 DOI: 10.3390/v16010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Preventing the spread of SARS-CoV-2 and its variants is crucial in the fight against COVID-19. Inhibition of the main protease (Mpro) of SARS-CoV-2 is the key to disrupting viral replication, making Mpro a promising target for therapy. PF-07321332 and shikonin have been identified as effective broad-spectrum inhibitors of SARS-CoV-2 Mpro. The crystal structures of SARS-CoV-2 Mpro bound to PF-07321332 and shikonin have been resolved in previous studies. However, the exact mechanism regarding how SARS-CoV-2 Mpro mutants impact their binding modes largely remains to be investigated. In this study, we expressed a SARS-CoV-2 Mpro mutant, carrying the D48N substitution, representing a class of mutations located near the active sites of Mpro. The crystal structures of Mpro D48N in complex with PF-07321332 and shikonin were solved. A detailed analysis of the interactions between Mpro D48N and two inhibitors provides key insights into the binding pattern and its structural determinants. Further, the binding patterns of the two inhibitors to Mpro D48N mutant and wild-type Mpro were compared in detail. This study illustrates the possible conformational changes when the Mpro D48N mutant is bound to inhibitors. Structural insights derived from this study will inform the development of new drugs against novel coronaviruses.
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Affiliation(s)
- Zhenyu Zhao
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Qinyao Zhu
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China;
| | - Xuelan Zhou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Wenwen Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Xiushan Yin
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China;
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
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