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Dinh T, Tber Z, Rey JS, Mengshetti S, Annamalai AS, Haney R, Briganti L, Amblard F, Fuchs JR, Cherepanov P, Kim K, Schinazi RF, Perilla JR, Kim B, Kvaratskhelia M. The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir. bioRxiv 2024:2024.01.26.577387. [PMID: 38328097 PMCID: PMC10849636 DOI: 10.1101/2024.01.26.577387] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are investigational antiretroviral agents which potently impair virion maturation by inducing hyper-multimerization of IN and inhibiting its interaction with viral genomic RNA. The pyrrolopyridine-based ALLINI pirmitegravir (PIR) has recently advanced into Phase 2a clinical trials. Previous cell culture based viral breakthrough assays identified the HIV-1(Y99H/A128T IN) variant that confers substantial resistance to this inhibitor. Here, we have elucidated the unexpected mechanism of viral resistance to PIR. While both Tyr99 and Ala128 are positioned within the inhibitor binding V-shaped cavity at the IN catalytic core domain (CCD) dimer interface, the Y99H/A128T IN mutations did not substantially affect direct binding of PIR to the CCD dimer or functional oligomerization of full-length IN. Instead, the drug-resistant mutations introduced a steric hindrance at the inhibitor mediated interface between CCD and C-terminal domain (CTD) and compromised CTD binding to the CCDY99H/A128T + PIR complex. Consequently, full-length INY99H/A128T was substantially less susceptible to the PIR induced hyper-multimerization than the WT protein, and HIV-1(Y99H/A128T IN) conferred >150-fold resistance to the inhibitor compared to the WT virus. By rationally modifying PIR we have developed its analog EKC110, which readily induced hyper-multimerization of INY99H/A128T in vitro and was ~14-fold more potent against HIV-1(Y99H/A128T IN) than the parent inhibitor. These findings suggest a path for developing improved PIR chemotypes with a higher barrier to resistance for their potential clinical use.
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Affiliation(s)
- Tung Dinh
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Zahira Tber
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Juan S Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Seema Mengshetti
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Arun S Annamalai
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Reed Haney
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - James R Fuchs
- College of Pharmacy, The Ohio State University, Columbus, Ohio, United States
| | - Peter Cherepanov
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Raymond F Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Baek Kim
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke TR, Levy RM, Hughes SH, Craigie R, Lyumkis D. Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. Sci Adv 2023; 9:eadg5953. [PMID: 37478179 DOI: 10.1126/sciadv.adg5953] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/16/2023] [Indexed: 07/23/2023]
Abstract
HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.
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Affiliation(s)
- Min Li
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Zelin Shan
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Steven J Smith
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Qinfang Sun
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Avik Biswas
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Indrani Choudhuri
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | | | - Allan Haldane
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY, 10038, USA
| | - Zhaoyang Li
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xue Zhi Zhao
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Terrence R Burke
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Ronald M Levy
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Stephen H Hughes
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Robert Craigie
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
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Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. mBio 2023; 14:e0356022. [PMID: 36744954 PMCID: PMC9973045 DOI: 10.1128/mbio.03560-22] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an emerging class of small molecules that disrupt viral maturation by inducing the aberrant multimerization of IN. Here, we present cocrystal structures of HIV-1 IN with two potent ALLINIs, namely, BI-D and the drug candidate Pirmitegravir. The structures reveal atomistic details of the ALLINI-induced interface between the HIV-1 IN catalytic core and carboxyl-terminal domains (CCD and CTD). Projecting from their principal binding pocket on the IN CCD dimer, the compounds act as molecular glue by engaging a triad of invariant HIV-1 IN CTD residues, namely, Tyr226, Trp235, and Lys266, to nucleate the CTD-CCD interaction. The drug-induced interface involves the CTD SH3-like fold and extends to the beginning of the IN carboxyl-terminal tail region. We show that mutations of HIV-1 IN CTD residues that participate in the interface with the CCD greatly reduce the IN-aggregation properties of Pirmitegravir. Our results explain the mechanism of the ALLINI-induced condensation of HIV-1 IN and provide a reliable template for the rational development of this series of antiretrovirals through the optimization of their key contacts with the viral target. IMPORTANCE Despite the remarkable success of combination antiretroviral therapy, HIV-1 remains among the major causes of human suffering and loss of life in poor and developing nations. To prevail in this drawn-out battle with the pandemic, it is essential to continue developing advanced antiviral agents to fight drug resistant HIV-1 variants. Allosteric integrase inhibitors (ALLINIs) are an emerging class of HIV-1 antagonists that are orthogonal to the current antiretroviral drugs. These small molecules act as highly specific molecular glue, which triggers the aggregation of HIV-1 integrase. In this work, we present high-resolution crystal structures that reveal the crucial interactions made by two potent ALLINIs, namely, BI-D and Pirmitegravir, with HIV-1 integrase. Our results explain the mechanism of drug action and will inform the development of this promising class of small molecules for future use in antiretroviral regimens.
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Affiliation(s)
- Matthew R. Singer
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Tung Dinh
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Arun S. Annamalai
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Juan S. Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Nicola J. Cook
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Valerie E. Pye
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Baek Kim
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Peter Cherepanov
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, United Kingdom
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Kadowaki MAS, Briganti L, Evangelista DE, Echevarría-Poza A, Tryfona T, Pellegrini VOA, Nakayama DG, Dupree P, Polikarpov I. Unlocking the structural features for the xylobiohydrolase activity of an unusual GH11 member identified in a compost-derived consortium. Biotechnol Bioeng 2021; 118:4052-4064. [PMID: 34232504 DOI: 10.1002/bit.27880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/25/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/08/2022]
Abstract
The heteropolysaccharide xylan is a valuable source of sustainable chemicals and materials from renewable biomass sources. A complete hydrolysis of this major hemicellulose component requires a diverse set of enzymes including endo-β-1,4-xylanases, β-xylosidases, acetylxylan esterases, α-l-arabinofuranosidases, and α-glucuronidases. Notably, the most studied xylanases from glycoside hydrolase family 11 (GH11) have exclusively been endo-β-1,4- and β-1,3-xylanases. However, a recent analysis of a metatranscriptome library from a microbial lignocellulose community revealed GH11 enzymes capable of releasing solely xylobiose from xylan. Although initial biochemical studies clearly indicated their xylobiohydrolase mode of action, the structural features that drive this new activity still remained unclear. It was also not clear whether the enzymes acted on the reducing or nonreducing end of the substrate. Here, we solved the crystal structure of MetXyn11 in the apo and xylobiose-bound forms. The structure of MetXyn11 revealed the molecular features that explain the observed pattern on xylooligosaccharides released by this nonreducing end xylobiohydrolase.
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Affiliation(s)
- Marco A S Kadowaki
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.,PhotoBioCatalysis-Biomass transformation Lab (BTL), École Interfacultaire de Bioingénieurs (EIB), Université Libre de Bruxelles, Brussels, Belgium
| | - Lorenzo Briganti
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Danilo E Evangelista
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.,Instituto de Criminalística de Andradina, Superintendência da Polícia Técnico Científica de São Paulo, Andradina, São Paulo, Brazil
| | | | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vanessa O A Pellegrini
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Darlan G Nakayama
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Igor Polikarpov
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
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Briganti L, Capetti C, Pellegrini VO, Ghio S, Campos E, Nascimento AS, Polikarpov I. Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase. Comput Struct Biotechnol J 2021; 19:1557-1566. [PMID: 33815691 PMCID: PMC7994722 DOI: 10.1016/j.csbj.2021.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from Paenibacillus xylanivorans A57 (PxXyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The PxXyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of PxXyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.
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Affiliation(s)
- Lorenzo Briganti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Caio Capetti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Vanessa O.A. Pellegrini
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Silvina Ghio
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Los Reseros y Nicolas Repetto (s/n), Hurlingham (1686), Prov. Buenos Aires, Argentina
| | - Eleonora Campos
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Los Reseros y Nicolas Repetto (s/n), Hurlingham (1686), Prov. Buenos Aires, Argentina
| | - Alessandro S. Nascimento
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
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Sepulchro AGV, Pellegrini VO, Briganti L, de Araujo EA, de Araujo SS, Polikarpov I. Transformation of xylan into value-added biocommodities using Thermobacillus composti GH10 xylanase. Carbohydr Polym 2020; 247:116714. [DOI: 10.1016/j.carbpol.2020.116714] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/13/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
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Leite AET, Briganti L, de Araújo EA, Pellegrini VDOA, Camilo CM, Polikarpov I. Low-resolution molecular shape, biochemical characterization and emulsification properties of a halotolerant esterase from Bacillus licheniformis. Eur Biophys J 2020; 49:435-447. [PMID: 32683479 DOI: 10.1007/s00249-020-01448-7] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/28/2020] [Accepted: 07/08/2020] [Indexed: 01/16/2023]
Abstract
Bacterial esterases are highly versatile enzymes, currently widely used in detergents, biosurfactants, bioemulsifiers and as biocatalysts in paper and food industries. Present work describes heterologous expression, purification, and biophysical and biochemical characterization of a halotolerant esterase from Bacillus licheniformis (BlEstA). BlEstA preferentially cleaves pNP-octanoate and both activity and stability of the enzyme increased in the presence of 2 M NaCl, and also with several organic solvents (ethanol, methanol and DMSO). Furthermore, BlEstA has considerable emulsifying properties, particularly with olive oil as substrate. Our studies also show that the enzyme is monomeric in solution and its small-angle X-ray scattering low-resolution molecular envelope fits well its high-resolution homology model.
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Affiliation(s)
- Ana Elisa T Leite
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Lorenzo Briganti
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | | | | | - Cesar Moyses Camilo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil.
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