1
|
Lockbaum GJ, Rusere LN, Henes M, Kosovrasti K, Rao DN, Spielvogel E, Lee SK, Nalivaika EA, Swanstrom R, Yilmaz NK, Schiffer CA, Ali A. HIV-1 protease inhibitors with a P1 phosphonate modification maintain potency against drug-resistant variants by increased interactions with flap residues. Eur J Med Chem 2023; 257:115501. [PMID: 37244161 DOI: 10.1016/j.ejmech.2023.115501] [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: 02/27/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
Protease inhibitors are the most potent antivirals against HIV-1, but they still lose efficacy against resistant variants. Improving the resistance profile is key to developing more robust inhibitors, which may be promising candidates for simplified next-generation antiretroviral therapies. In this study, we explored analogs of darunavir with a P1 phosphonate modification in combination with increasing size of the P1' hydrophobic group and various P2' moieties to improve potency against resistant variants. The phosphonate moiety substantially improved potency against highly mutated and resistant HIV-1 protease variants, but only when combined with more hydrophobic moieties at the P1' and P2' positions. Phosphonate analogs with a larger hydrophobic P1' moiety maintained excellent antiviral potency against a panel of highly resistant HIV-1 variants, with significantly improved resistance profiles. The cocrystal structures indicate that the phosphonate moiety makes extensive hydrophobic interactions with the protease, especially with the flap residues. Many residues involved in these protease-inhibitor interactions are conserved, enabling the inhibitors to maintain potency against highly resistant variants. These results highlight the need to balance inhibitor physicochemical properties by simultaneous modification of chemical groups to further improve resistance profiles.
Collapse
Affiliation(s)
- Gordon J Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States
| | - Linah N Rusere
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States
| | - Desaboini Nageswara Rao
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States
| | - Ean Spielvogel
- Department of Biochemistry and Biophysics, And the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Sook-Kyung Lee
- Department of Biochemistry and Biophysics, And the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, And the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States.
| | - Akbar Ali
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, United States.
| |
Collapse
|
2
|
Spielvogel E, Lee SK, Zhou S, Lockbaum GJ, Henes M, Sondgeroth A, Kosovrasti K, Nalivaika EA, Ali A, Yilmaz NK, Schiffer CA, Swanstrom R. Selection of HIV-1 for resistance to fifth generation protease inhibitors reveals two independent pathways to high-level resistance. eLife 2023; 12:80328. [PMID: 36920025 PMCID: PMC10065791 DOI: 10.7554/elife.80328] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 05/16/2022] [Accepted: 03/14/2023] [Indexed: 03/16/2023] Open
Abstract
Darunavir (DRV) is exceptional among potent HIV-1 protease inhibitors (PIs) in high drug concentrations that are achived in vivo. Little is known about the de novo resistance pathway for DRV. We selected for resistance to high drug concentrations against ten PIs and their structural precursor DRV. Mutations accumulated through two pathways (anchored by protease mutations I50V or I84V). Small changes in the inhibitor P1'-equivalent position led to preferential use of one pathway over the other. Changes in the inhbitor P2'-equivalent position determined differences in potency that were retained in the resistant viruses and that impacted the selected mutations. Viral variants from the two pathways showed differential selection of compensatory mutations in Gag cleavage sites. These results reveal the high level of selective pressure that is attainable with fifth generation PIs, and how features of the inhibitor affect both the resistance pathway and the residual potency in the face of resistance.
Collapse
Affiliation(s)
- Ean Spielvogel
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Sook-Kyung Lee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
| | - Amy Sondgeroth
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Biotechnology, 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
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| |
Collapse
|
3
|
Mondal S, Chen Y, Lockbaum GJ, Sen S, Chaudhuri S, Reyes AC, Lee JM, Kaur AN, Sultana N, Cameron MD, Shaffer SA, Schiffer CA, Fitzgerald KA, Thompson PR. Dual Inhibitors of Main Protease (M Pro) and Cathepsin L as Potent Antivirals against SARS-CoV2. J Am Chem Soc 2022; 144:21035-21045. [PMID: 36356199 PMCID: PMC9662648 DOI: 10.1021/jacs.2c04626] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Indexed: 11/12/2022]
Abstract
Given the current impact of SARS-CoV2 and COVID-19 on human health and the global economy, the development of direct acting antivirals is of paramount importance. Main protease (MPro), a cysteine protease that cleaves the viral polyprotein, is essential for viral replication. Therefore, MPro is a novel therapeutic target. We identified two novel MPro inhibitors, D-FFRCMKyne and D-FFCitCMKyne, that covalently modify the active site cysteine (C145) and determined cocrystal structures. Medicinal chemistry efforts led to SM141 and SM142, which adopt a unique binding mode within the MPro active site. Notably, these inhibitors do not inhibit the other cysteine protease, papain-like protease (PLPro), involved in the life cycle of SARS-CoV2. SM141 and SM142 block SARS-CoV2 replication in hACE2 expressing A549 cells with IC50 values of 8.2 and 14.7 nM. Detailed studies indicate that these compounds also inhibit cathepsin L (CatL), which cleaves the viral S protein to promote viral entry into host cells. Detailed biochemical, proteomic, and knockdown studies indicate that the antiviral activity of SM141 and SM142 results from the dual inhibition of MPro and CatL. Notably, intranasal and intraperitoneal administration of SM141 and SM142 lead to reduced viral replication, viral loads in the lung, and enhanced survival in SARS-CoV2 infected K18-ACE2 transgenic mice. In total, these data indicate that SM141 and SM142 represent promising scaffolds on which to develop antiviral drugs against SARS-CoV2.
Collapse
Affiliation(s)
- Santanu Mondal
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Yongzhi Chen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Sudeshna Sen
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Sauradip Chaudhuri
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Archie C. Reyes
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jeong Min Lee
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Arshia N. Kaur
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Nadia Sultana
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Michael D. Cameron
- Department of Molecular Medicine, The Scripps Research Institute,130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott A. Shaffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Paul R. Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| |
Collapse
|
4
|
Shaqra AM, Zvornicanin SN, Huang QYJ, Lockbaum GJ, Knapp M, Tandeske L, Bakan DT, Flynn J, Bolon DNA, Moquin S, Dovala D, Kurt Yilmaz N, Schiffer CA. Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance. Nat Commun 2022; 13:3556. [PMID: 35729165 PMCID: PMC9211792 DOI: 10.1038/s41467-022-31210-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 01/01/2023] Open
Abstract
Coronaviruses can evolve and spread rapidly to cause severe disease morbidity and mortality, as exemplified by SARS-CoV-2 variants of the COVID-19 pandemic. Although currently available vaccines remain mostly effective against SARS-CoV-2 variants, additional treatment strategies are needed. Inhibitors that target essential viral enzymes, such as proteases and polymerases, represent key classes of antivirals. However, clinical use of antiviral therapies inevitably leads to emergence of drug resistance. In this study we implemented a strategy to pre-emptively address drug resistance to protease inhibitors targeting the main protease (Mpro) of SARS-CoV-2, an essential enzyme that promotes viral maturation. We solved nine high-resolution cocrystal structures of SARS-CoV-2 Mpro bound to substrate peptides and six structures with cleavage products. These structures enabled us to define the substrate envelope of Mpro, map the critical recognition elements, and identify evolutionarily vulnerable sites that may be susceptible to resistance mutations that would compromise binding of the newly developed Mpro inhibitors. Our results suggest strategies for developing robust inhibitors against SARS-CoV-2 that will retain longer-lasting efficacy against this evolving viral pathogen.
Collapse
Affiliation(s)
- Ala M Shaqra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Sarah N Zvornicanin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Qiu Yu J Huang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Mark Knapp
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Laura Tandeske
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - David T Bakan
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Julia Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Stephanie Moquin
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Dustin Dovala
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US.
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US.
| |
Collapse
|
5
|
Lockbaum GJ, Henes M, Lee JM, Timm J, Nalivaika EA, Thompson PR, Kurt Yilmaz N, Schiffer CA. Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode. Biochemistry 2021; 60:2925-2931. [PMID: 34506130 PMCID: PMC8457326 DOI: 10.1021/acs.biochem.1c00414] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 11/28/2022]
Abstract
Rupintrivir targets the 3C cysteine proteases of the picornaviridae family, which includes rhinoviruses and enteroviruses that cause a range of human diseases. Despite being a pan-3C protease inhibitor, rupintrivir activity is extremely weak against the homologous 3C-like protease of SARS-CoV-2. In this study, the crystal structures of rupintrivir were determined bound to enterovirus 68 (EV68) 3C protease and the 3C-like main protease (Mpro) from SARS-CoV-2. While the EV68 3C protease-rupintrivir structure was similar to previously determined complexes with other picornavirus 3C proteases, rupintrivir bound in a unique conformation to the active site of SARS-CoV-2 Mpro splitting the catalytic cysteine and histidine residues. This bifurcation of the catalytic dyad may provide a novel approach for inhibiting cysteine proteases.
Collapse
Affiliation(s)
- Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, Worcester,
Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, Worcester,
Massachusetts 01605, United States
| | - Jeong Min Lee
- Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, Worcester,
Massachusetts 01605, United States
| | - Jennifer Timm
- Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, Worcester,
Massachusetts 01605, United States
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, Worcester,
Massachusetts 01605, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, Worcester,
Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, Worcester,
Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, Worcester,
Massachusetts 01605, United States
| |
Collapse
|
6
|
Matthew AN, Leidner F, Lockbaum GJ, Henes M, Zephyr J, Hou S, Desaboini NR, Timm J, Rusere LN, Ragland DA, Paulsen JL, Prachanronarong K, Soumana DI, Nalivaika EA, Yilmaz NK, Ali A, Schiffer CA. Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond. Chem Rev 2021; 121:3238-3270. [PMID: 33410674 PMCID: PMC8126998 DOI: 10.1021/acs.chemrev.0c00648] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Drug resistance is prevalent across many diseases, rendering therapies ineffective with severe financial and health consequences. Rather than accepting resistance after the fact, proactive strategies need to be incorporated into the drug design and development process to minimize the impact of drug resistance. These strategies can be derived from our experience with viral disease targets where multiple generations of drugs had to be developed to combat resistance and avoid antiviral failure. Significant efforts including experimental and computational structural biology, medicinal chemistry, and machine learning have focused on understanding the mechanisms and structural basis of resistance against direct-acting antiviral (DAA) drugs. Integrated methods show promise for being predictive of resistance and potency. In this review, we give an overview of this research for human immunodeficiency virus type 1, hepatitis C virus, and influenza virus and the lessons learned from resistance mechanisms of DAAs. These lessons translate into rational strategies to avoid resistance in drug design, which can be generalized and applied beyond viral targets. While resistance may not be completely avoidable, rational drug design can and should incorporate strategies at the outset of drug development to decrease the prevalence of drug resistance.
Collapse
Affiliation(s)
- Ashley N. Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Virginia Commonwealth University
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nages Rao Desaboini
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jennifer Timm
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Rutgers University
| | - Linah N. Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Raybow Pharmaceutical
| | - Debra A. Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- University of North Carolina, Chapel Hill
| | - Janet L. Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Schrodinger, Inc
| | - Kristina Prachanronarong
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Icahn School of Medicine at Mount Sinai
| | - Djade I. Soumana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Cytiva
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| |
Collapse
|
7
|
Lockbaum GJ, Henes M, Talledge N, Rusere LN, Kosovrasti K, Nalivaika EA, Somasundaran M, Ali A, Mansky LM, Yilmaz NK, Schiffer CA. Inhibiting HTLV-1 Protease: A Viable Antiviral Target. ACS Chem Biol 2021; 16:529-538. [PMID: 33619959 PMCID: PMC8126997 DOI: 10.1021/acschembio.0c00975] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human T-cell lymphotropic virus type 1 (HTLV-1) is a retrovirus that can cause severe paralytic neurologic disease and immune disorders as well as cancer. An estimated 20 million people worldwide are infected with HTLV-1, with prevalence reaching 30% in some parts of the world. In stark contrast to HIV-1, no direct acting antivirals (DAAs) exist against HTLV-1. The aspartyl protease of HTLV-1 is a dimer similar to that of HIV-1 and processes the viral polyprotein to permit viral maturation. We report that the FDA-approved HIV-1 protease inhibitor darunavir (DRV) inhibits the enzyme with 0.8 μM potency and provides a scaffold for drug design against HTLV-1. Analogs of DRV that we designed and synthesized achieved submicromolar inhibition against HTLV-1 protease and inhibited Gag processing in viral maturation assays and in a chronically HTLV-1 infected cell line. Cocrystal structures of these inhibitors with HTLV-1 protease highlight opportunities for future inhibitor design. Our results show promise toward developing highly potent HTLV-1 protease inhibitors as therapeutic agents against HTLV-1 infections.
Collapse
Affiliation(s)
- Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nathaniel Talledge
- Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Linah N. Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Louis M. Mansky
- Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| |
Collapse
|
8
|
Lockbaum GJ, Reyes AC, Lee JM, Tilvawala R, Nalivaika EA, Ali A, Kurt Yilmaz N, Thompson PR, Schiffer CA. Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188. Viruses 2021; 13:174. [PMID: 33503819 PMCID: PMC7911568 DOI: 10.3390/v13020174] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [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: 12/24/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 01/08/2023] Open
Abstract
Viral proteases are critical enzymes for the maturation of many human pathogenic viruses and thus are key targets for direct acting antivirals (DAAs). The current viral pandemic caused by SARS-CoV-2 is in dire need of DAAs. The Main protease (Mpro) is the focus of extensive structure-based drug design efforts which are mostly covalent inhibitors targeting the catalytic cysteine. ML188 is a non-covalent inhibitor designed to target SARS-CoV-1 Mpro, and provides an initial scaffold for the creation of effective pan-coronavirus inhibitors. In the current study, we found that ML188 inhibits SARS-CoV-2 Mpro at 2.5 µM, which is more potent than against SAR-CoV-1 Mpro. We determined the crystal structure of ML188 in complex with SARS-CoV-2 Mpro to 2.39 Å resolution. Sharing 96% sequence identity, structural comparison of the two complexes only shows subtle differences. Non-covalent protease inhibitors complement the design of covalent inhibitors against SARS-CoV-2 main protease and are critical initial steps in the design of DAAs to treat CoVID 19.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; (G.J.L.); (A.C.R.); (J.M.L.); (R.T.); (E.A.N.); (A.A.); (N.K.Y.); (P.R.T.)
| |
Collapse
|
9
|
Harshbarger WD, Deming D, Lockbaum GJ, Attatippaholkun N, Kamkaew M, Hou S, Somasundaran M, Wang JP, Finberg RW, Zhu QK, Schiffer CA, Marasco WA. Unique structural solution from a V H3-30 antibody targeting the hemagglutinin stem of influenza A viruses. Nat Commun 2021; 12:559. [PMID: 33495478 PMCID: PMC7835374 DOI: 10.1038/s41467-020-20879-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/19/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
Broadly neutralizing antibodies (bnAbs) targeting conserved influenza A virus (IAV) hemagglutinin (HA) epitopes can provide valuable information for accelerating universal vaccine designs. Here, we report structural details for heterosubtypic recognition of HA from circulating and emerging IAVs by the human antibody 3I14. Somatic hypermutations play a critical role in shaping the HCDR3, which alone and uniquely among VH3-30 derived antibodies, forms contacts with five sub-pockets within the HA-stem hydrophobic groove. 3I14 light-chain interactions are also key for binding HA and contribute a large buried surface area spanning two HA protomers. Comparison of 3I14 to bnAbs from several defined classes provide insights to the bias selection of VH3-30 antibodies and reveals that 3I14 represents a novel structural solution within the VH3-30 repertoire. The structures reported here improve our understanding of cross-group heterosubtypic binding activity, providing the basis for advancing immunogen designs aimed at eliciting a broadly protective response to IAV.
Collapse
Affiliation(s)
- Wayne D Harshbarger
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derrick Deming
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Maliwan Kamkaew
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennifer P Wang
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Robert W Finberg
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Quan Karen Zhu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Wayne A Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
10
|
Rusere LN, Lockbaum GJ, Henes M, Lee SK, Spielvogel E, Rao DN, Kosovrasti K, Nalivaika EA, Swanstrom R, Kurt Yilmaz N, Schiffer CA, Ali A. Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-tetrahydrofuran in a Pseudosymmetric Dipeptide Isostere. J Med Chem 2020; 63:8296-8313. [PMID: 32672965 DOI: 10.1021/acs.jmedchem.0c00529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design, synthesis, and X-ray structural analysis of hybrid HIV-1 protease inhibitors (PIs) containing bis-tetrahydrofuran (bis-THF) in a pseudo-C2-symmetric dipeptide isostere are described. A series of PIs were synthesized by incorporating bis-THF of darunavir on either side of the Phe-Phe isostere of lopinavir in combination with hydrophobic amino acids on the opposite P2/P2' position. Structure-activity relationship studies indicated that the bis-THF moiety can be attached at either the P2 or P2' position without significantly affecting potency. However, the group on the opposite P2/P2' position had a dramatic effect on potency depending on the size and shape of the side chain. Cocrystal structures of inhibitors with wild-type HIV-1 protease revealed that the bis-THF moiety retained similar interactions as observed in the darunavir-protease complex regardless of the position on the Phe-Phe isostere. Analyses of cocrystal structures and molecular dynamics simulations provide insights into optimizing HIV-1 PIs containing bis-THF in non-sulfonamide dipeptide isosteres.
Collapse
Affiliation(s)
- Linah N Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Sook-Kyung Lee
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ean Spielvogel
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Desaboini Nageswara Rao
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| |
Collapse
|
11
|
Zephyr J, Matthew AN, Rao DN, Henes M, Kamran W, Hedger AK, Lockbaum GJ, Timm J, Akbar A, Yilmaz NK, Schiffer CA. Avoiding Drug Resistance by Substrate Envelope Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.08779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Mina Henes
- University of Massachusetts Medical School
| | | | | | | | | | - Ali Akbar
- University of Massachusetts Medical School
| | | | | |
Collapse
|
12
|
Matthew AN, Zephyr J, Nageswara Rao D, Henes M, Kamran W, Kosovrasti K, Hedger AK, Lockbaum GJ, Timm J, Ali A, Kurt Yilmaz N, Schiffer CA. Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors. mBio 2020; 11:e00172-20. [PMID: 32234812 PMCID: PMC7157764 DOI: 10.1128/mbio.00172-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 01/31/2020] [Accepted: 02/11/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatitis C virus (HCV) infects millions of people worldwide, causing chronic liver disease that can lead to cirrhosis, hepatocellular carcinoma, and liver transplant. In the last several years, the advent of direct-acting antivirals, including NS3/4A protease inhibitors (PIs), has remarkably improved treatment outcomes of HCV-infected patients. However, selection of resistance-associated substitutions and polymorphisms among genotypes can lead to drug resistance and in some cases treatment failure. A proactive strategy to combat resistance is to constrain PIs within evolutionarily conserved regions in the protease active site. Designing PIs using the substrate envelope is a rational strategy to decrease the susceptibility to resistance by using the constraints of substrate recognition. We successfully designed two series of HCV NS3/4A PIs to leverage unexploited areas in the substrate envelope to improve potency, specifically against resistance-associated substitutions at D168. Our design strategy achieved better resistance profiles over both the FDA-approved NS3/4A PI grazoprevir and the parent compound against the clinically relevant D168A substitution. Crystallographic structural analysis and inhibition assays confirmed that optimally filling the substrate envelope is critical to improve inhibitor potency while avoiding resistance. Specifically, inhibitors that enhanced hydrophobic packing in the S4 pocket and avoided an energetically frustrated pocket performed the best. Thus, the HCV substrate envelope proved to be a powerful tool to design robust PIs, offering a strategy that can be translated to other targets for rational design of inhibitors with improved potency and resistance profiles.IMPORTANCE Despite significant progress, hepatitis C virus (HCV) continues to be a major health problem with millions of people infected worldwide and thousands dying annually due to resulting complications. Recent antiviral combinations can achieve >95% cure, but late diagnosis, low access to treatment, and treatment failure due to drug resistance continue to be roadblocks against eradication of the virus. We report the rational design of two series of HCV NS3/4A protease inhibitors with improved resistance profiles by exploiting evolutionarily constrained regions of the active site using the substrate envelope model. Optimally filling the S4 pocket is critical to avoid resistance and improve potency. Our results provide drug design strategies to avoid resistance that are applicable to other quickly evolving viral drug targets.
Collapse
Affiliation(s)
- Ashley N Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Desaboini Nageswara Rao
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Wasih Kamran
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Adam K Hedger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jennifer Timm
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| |
Collapse
|
13
|
Lockbaum GJ, Leidner F, Royer WE, Kurt Yilmaz N, Schiffer CA. Optimizing the refinement of merohedrally twinned P6 1 HIV-1 protease-inhibitor cocrystal structures. Acta Crystallogr D Struct Biol 2020; 76:302-310. [PMID: 32133994 PMCID: PMC7057220 DOI: 10.1107/s2059798320001989] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/11/2020] [Indexed: 11/10/2022] Open
Abstract
Twinning is a crystal-growth anomaly in which protein monomers exist in different orientations but are related in a specific way, causing diffraction reflections to overlap. Twinning imposes additional symmetry on the data, often leading to the assignment of a higher symmetry space group. Specifically, in merohedral twinning, reflections from each monomer overlap and require a twin law to model unique structural data from overlapping reflections. Neglecting twinning in the crystallographic analysis of quasi-rotationally symmetric homo-oligomeric protein structures can mask the degree of structural non-identity between monomers. In particular, any deviations from perfect symmetry will be lost if higher than appropriate symmetry is applied during crystallographic analysis. Such cases warrant choosing between the highest symmetry space group possible or determining whether the monomers have distinguishable structural asymmetries and thus require a lower symmetry space group and a twin law. Using hexagonal cocrystals of HIV-1 protease, a C2-symmetric homodimer whose symmetry is broken by bound ligand, it is shown that both assigning a lower symmetry space group and applying a twin law during refinement are critical to achieving a structural model that more accurately fits the electron density. By re-analyzing three recently published HIV-1 protease structures, improvements in nearly every crystallographic metric are demonstrated. Most importantly, a procedure is demonstrated where the inhibitor can be reliably modeled in a single orientation. This protocol may be applicable to many other homo-oligomers in the PDB.
Collapse
Affiliation(s)
- Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - William E. Royer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
14
|
Henes M, Lockbaum GJ, Kosovrasti K, Leidner F, Nachum GS, Nalivaika EA, Lee SK, Spielvogel E, Zhou S, Swanstrom R, Bolon DN, Yilmaz NK, Schiffer CA. Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance. ACS Chem Biol 2019; 14:2441-2452. [PMID: 31361460 PMCID: PMC6941144 DOI: 10.1021/acschembio.9b00370] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Drug resistance continues to be a growing global problem. The efficacy of small molecule inhibitors is threatened by pools of genetic diversity in all systems, including antibacterials, antifungals, cancer therapeutics, and antivirals. Resistant variants often include combinations of active site mutations and distal "secondary" mutations, which are thought to compensate for losses in enzymatic activity. HIV-1 protease is the ideal model system to investigate these combinations and underlying molecular mechanisms of resistance. Darunavir (DRV) binds wild-type (WT) HIV-1 protease with a potency of <5 pM, but we have identified a protease variant that loses potency to DRV 150 000-fold, with 11 mutations in and outside the active site. To elucidate the roles of these mutations in DRV resistance, we used a multidisciplinary approach, combining enzymatic assays, crystallography, and molecular dynamics simulations. Analysis of protease variants with 1, 2, 4, 8, 9, 10, and 11 mutations showed that the primary active site mutations caused ∼50-fold loss in potency (2 mutations), while distal mutations outside the active site further decreased DRV potency from 13 nM (8 mutations) to 0.76 μM (11 mutations). Crystal structures and simulations revealed that distal mutations induce subtle changes that are dynamically propagated through the protease. Our results reveal that changes remote from the active site directly and dramatically impact the potency of the inhibitor. Moreover, we find interdependent effects of mutations in conferring high levels of resistance. These mechanisms of resistance are likely applicable to many other quickly evolving drug targets, and the insights may have implications for the design of more robust inhibitors.
Collapse
Affiliation(s)
- Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gily S. Nachum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Sook-Kyung Lee
- Department of Biochemistry and Biophysics and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ean Spielvogel
- Department of Biochemistry and Biophysics and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shuntai Zhou
- Department of Biochemistry and Biophysics and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel N.A. Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States,Corresponding authors Celia A. Schiffer: Phone: +1 508 856 8008; , Nese Kurt Yilmaz: Phone: +1 508 856 1867;
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States,Corresponding authors Celia A. Schiffer: Phone: +1 508 856 8008; , Nese Kurt Yilmaz: Phone: +1 508 856 1867;
| |
Collapse
|
15
|
Henes M, Kosovrasti K, Lockbaum GJ, Leidner F, Nachum GS, Nalivaika EA, Bolon DN, Yilmaz NK, Schiffer CA, Whitfield TW. Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance. Biochemistry 2019; 58:3711-3726. [PMID: 31386353 PMCID: PMC6941756 DOI: 10.1021/acs.biochem.9b00446] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protease inhibitors have the highest potency among antiviral therapies against HIV-1 infections, yet the virus can evolve resistance. Darunavir (DRV), currently the most potent Food and Drug Administration-approved protease inhibitor, retains potency against single-site mutations. However, complex combinations of mutations can confer resistance to DRV. While the interdependence between mutations within HIV-1 protease is key for inhibitor potency, the molecular mechanisms that underlie this control remain largely unknown. In this study, we investigated the interdependence between the L89V and L90M mutations and their effects on DRV binding. These two mutations have been reported to be positively correlated with one another in HIV-1 patient-derived protease isolates, with the presence of one mutation making the probability of the occurrence of the second mutation more likely. The focus of our investigation is a patient-derived isolate, with 24 mutations that we call "KY"; this variant includes the L89V and L90M mutations. Three additional KY variants with back-mutations, KY(V89L), KY(M90L), and the KY(V89L/M90L) double mutation, were used to experimentally assess the individual and combined effects of these mutations on DRV inhibition and substrate processing. The enzymatic assays revealed that the KY(V89L) variant, with methionine at residue 90, is highly resistant, but its catalytic function is compromised. When a leucine to valine mutation at residue 89 is present simultaneously with the L90M mutation, a rescue of catalytic efficiency is observed. Molecular dynamics simulations of these DRV-bound protease variants reveal how the L90M mutation induces structural changes throughout the enzyme that undermine the binding interactions.
Collapse
Affiliation(s)
- Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Gily S. Nachum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Daniel N.A. Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA,Corresponding Author Celia A. Schiffer: Phone: +1 508 856 8008; , Troy W. Whitfield: Phone: +1 508 856 4401;
| | - Troy W. Whitfield
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA,Corresponding Author Celia A. Schiffer: Phone: +1 508 856 8008; , Troy W. Whitfield: Phone: +1 508 856 4401;
| |
Collapse
|
16
|
Rusere LN, Lockbaum GJ, Lee SK, Henes M, Kosovrasti K, Spielvogel E, Nalivaika EA, Swanstrom R, Yilmaz NK, Schiffer CA, Ali A. HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands To Optimize Hydrogen Bonding in the Substrate Envelope. J Med Chem 2019; 62:8062-8079. [PMID: 31386368 DOI: 10.1021/acs.jmedchem.9b00838] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A structure-guided design strategy was used to improve the resistance profile of HIV-1 protease inhibitors by optimizing hydrogen bonding and van der Waals interactions with the protease while staying within the substrate envelope. Stereoisomers of 4-(1-hydroxyethyl)benzene and 4-(1,2-dihydroxyethyl)benzene moieties were explored as P2' ligands providing pairs of diastereoisomers epimeric at P2', which exhibited distinct potency profiles depending on the configuration of the hydroxyl group and size of the P1' group. While compounds with the 4-(1-hydroxyethyl)benzene P2' moiety maintained excellent antiviral potency against a panel of multidrug-resistant HIV-1 strains, analogues with the polar 4-(1,2-dihydroxyethyl)benzene moiety were less potent, and only the (R)-epimer incorporating a larger 2-ethylbutyl P1' group showed improved potency. Crystal structures of protease-inhibitor complexes revealed strong hydrogen bonding interactions of both (R)- and (S)-stereoisomers of the hydroxyethyl group with Asp30'. Notably, the (R)-dihydroxyethyl group was involved in a unique pattern of direct hydrogen bonding interactions with the backbone amides of Asp29' and Asp30'. The SAR data and analysis of crystal structures provide insights for optimizing these promising HIV-1 protease inhibitors.
Collapse
Affiliation(s)
- Linah N Rusere
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Sook-Kyung Lee
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Ean Spielvogel
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| |
Collapse
|
17
|
Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Bolon DNA, Ali A, Kurt Yilmaz N, Schiffer CA. Correction to Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. ACS Infect Dis 2019; 5:1044. [PMID: 30990653 DOI: 10.1021/acsinfecdis.9b00098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
18
|
Lockbaum GJ, Henes M, Leidner F, Kosovrasti K, Nalivaika E, Kurt‐Yilmaz N, Schiffer CA. pM to μM: Elucidating the Interdependence of Highly Resistant HIV‐1 Proteases. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.784.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
19
|
Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Bolon DN, Ali A, Yilmaz NK, Schiffer CA. Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. ACS Infect Dis 2019; 5:316-325. [PMID: 30543749 PMCID: PMC6941150 DOI: 10.1021/acsinfecdis.8b00336] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
HIV-1 protease is one of the prime targets of agents used in antiretroviral therapy against HIV. However, under selective pressure of protease inhibitors, primary mutations at the active site weaken inhibitor binding to confer resistance. Darunavir (DRV) is the most potent HIV-1 protease inhibitor in clinic; resistance is limited, as DRV fits well within the substrate envelope. Nevertheless, resistance is observed due to hydrophobic changes at residues including I50, V82, and I84 that line the S1/S1' pocket within the active site. Through enzyme inhibition assays and a series of 12 crystal structures, we interrogated susceptibility of DRV and two potent analogues to primary S1' mutations. The analogues had modifications at the hydrophobic P1' moiety compared to DRV to better occupy the unexploited space in the S1' pocket where the primary mutations were located. Considerable losses of potency were observed against protease variants with I84V and I50V mutations for all three inhibitors. The crystal structures revealed an unexpected conformational change in the flap region of I50V protease bound to the analogue with the largest P1' moiety, indicating interdependency between the S1' subsite and the flap region. Collective analysis of protease-inhibitor interactions in the crystal structures using principle component analysis was able to distinguish inhibitor identity and relative potency solely based on van der Waals contacts. Our results reveal the complexity of the interplay between inhibitor P1' moiety and S1' mutations and validate principle component analyses as a useful tool for distinguishing resistance and inhibitor potency.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Nese Kurt Yilmaz
- Corresponding Author Celia A. Schiffer: Phone: +1 508 856 8008; , Nese Kurt Yilmaz: Phone: +1 508 856-1867;
| | - Celia A. Schiffer
- Corresponding Author Celia A. Schiffer: Phone: +1 508 856 8008; , Nese Kurt Yilmaz: Phone: +1 508 856-1867;
| |
Collapse
|
20
|
Rusere LN, Matthew AN, Lockbaum GJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A. Quinoxaline-Based Linear HCV NS3/4A Protease Inhibitors Exhibit Potent Activity against Drug Resistant Variants. ACS Med Chem Lett 2018; 9:691-696. [PMID: 30034602 DOI: 10.1021/acsmedchemlett.8b00150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/17/2018] [Indexed: 02/07/2023] Open
Abstract
A series of linear HCV NS3/4A protease inhibitors was designed by eliminating the P2-P4 macrocyclic linker in grazoprevir, which, in addition to conferring conformational flexibility, allowed structure-activity relationship (SAR) exploration of diverse quinoxalines at the P2 position. Biochemical and replicon data indicated preference for small hydrophobic groups at the 3-position of P2 quinoxaline for maintaining potency against resistant variants R155K, A156T, and D168A/V. The linear inhibitors, though generally less potent than the corresponding macrocyclic analogues, were relatively easier to synthesize and less susceptible to drug resistance. Three inhibitor cocrystal structures bound to wild-type NS3/4A protease revealed a conformation with subtle changes in the binding of P2 quinoxaline, depending on the 3-position substituent, likely impacting both inhibitor potency and resistance profile. The SAR and structural analysis highlight inhibitor features that strengthen interactions of the P2 moiety with the catalytic triad residues, providing valuable insights to improve potency against resistant variants.
Collapse
Affiliation(s)
- Linah N. Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ashley N. Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Muhammad Jahangir
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Alicia Newton
- Monogram Biosciences, South San Francisco, California 94080, United States
| | | | - Wei Huang
- Monogram Biosciences, South San Francisco, California 94080, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| |
Collapse
|