1
|
Biswas A, Choudhuri I, Arnold E, Lyumkis D, Haldane A, Levy RM. Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proc Natl Acad Sci U S A 2024; 121:e2316662121. [PMID: 38557187 PMCID: PMC11009627 DOI: 10.1073/pnas.2316662121] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/23/2024] [Indexed: 04/04/2024] Open
Abstract
Drug resistance in HIV type 1 (HIV-1) is a pervasive problem that affects the lives of millions of people worldwide. Although records of drug-resistant mutations (DRMs) have been extensively tabulated within public repositories, our understanding of the evolutionary kinetics of DRMs and how they evolve together remains limited. Epistasis, the interaction between a DRM and other residues in HIV-1 protein sequences, is key to the temporal evolution of drug resistance. We use a Potts sequence-covariation statistical-energy model of HIV-1 protein fitness under drug selection pressure, which captures epistatic interactions between all positions, combined with kinetic Monte-Carlo simulations of sequence evolutionary trajectories, to explore the acquisition of DRMs as they arise in an ensemble of drug-naive patient protein sequences. We follow the time course of 52 DRMs in the enzymes protease, RT, and integrase, the primary targets of antiretroviral therapy. The rates at which DRMs emerge are highly correlated with their observed acquisition rates reported in the literature when drug pressure is applied. This result highlights the central role of epistasis in determining the kinetics governing DRM emergence. Whereas rapidly acquired DRMs begin to accumulate as soon as drug pressure is applied, slowly acquired DRMs are contingent on accessory mutations that appear only after prolonged drug pressure. We provide a foundation for using computational methods to determine the temporal evolution of drug resistance using Potts statistical potentials, which can be used to gain mechanistic insights into drug resistance pathways in HIV-1 and other infectious agents.
Collapse
Affiliation(s)
- Avik Biswas
- Center for Biophysics and Computational Biology, College of Science and Technology, Temple University, Philadelphia, PA19122
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA92037
- Department of Physics, University of California San Diego, La Jolla, CA92093
| | - Indrani Choudhuri
- Center for Biophysics and Computational Biology, College of Science and Technology, Temple University, Philadelphia, PA19122
- Department of Chemistry, Temple University, Philadelphia, PA19122
| | - Eddy Arnold
- Department of Chemistry and Chemical Biology, Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ08854
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA92037
- Graduate School of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Allan Haldane
- Center for Biophysics and Computational Biology, College of Science and Technology, Temple University, Philadelphia, PA19122
- Department of Physics, Temple University, Philadelphia, PA19122
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, College of Science and Technology, Temple University, Philadelphia, PA19122
- Department of Chemistry, Temple University, Philadelphia, PA19122
| |
Collapse
|
2
|
Tan B, Zhang X, Ansari A, Jadhav P, Tan H, Li K, Chopra A, Ford A, Chi X, Ruiz FX, Arnold E, Deng X, Wang J. Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. Science 2024; 383:1434-1440. [PMID: 38547259 DOI: 10.1126/science.adm9724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. We designed and synthesized 85 noncovalent PLpro inhibitors that bind to a recently discovered ubiquitin binding site and the known BL2 groove pocket near the S4 subsite. Leads inhibited PLpro with the inhibitory constant Ki values from 13.2 to 88.2 nanomolar. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 micromolar. Oral treatment with Jun12682 improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting that PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.
Collapse
Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ahmadullah Ansari
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alexandra Ford
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Xiang Chi
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| |
Collapse
|
3
|
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. Structures, functions and adaptations of the human LINE-1 ORF2 protein. Nature 2024; 626:194-206. [PMID: 38096902 PMCID: PMC10830420 DOI: 10.1038/s41586-023-06947-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one-third of the human genome through a 'copy and paste' mechanism catalysed by its multifunctional enzyme, open reading frame 2 protein (ORF2p)1. ORF2p reverse transcriptase (RT) and endonuclease activities have been implicated in the pathophysiology of cancer2,3, autoimmunity4,5 and ageing6,7, making ORF2p a potential therapeutic target. However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it. We report structures of the human ORF2p 'core' (residues 238-1061, including the RT domain) by X-ray crystallography and cryo-electron microscopy in several conformational states. Our analyses identified two previously undescribed folded domains, extensive contacts to RNA templates and associated adaptations that contribute to unique aspects of the L1 replication cycle. Computed integrative structural models of full-length ORF2p show a dynamic closed-ring conformation that appears to open during retrotransposition. We characterize ORF2p RT inhibition and reveal its underlying structural basis. Imaging and biochemistry show that non-canonical cytosolic ORF2p RT activity can produce RNA:DNA hybrids, activating innate immune signalling through cGAS/STING and resulting in interferon production6-8. In contrast to retroviral RTs, L1 RT is efficiently primed by short RNAs and hairpins, which probably explains cytosolic priming. Other biochemical activities including processivity, DNA-directed polymerization, non-templated base addition and template switching together allow us to propose a revised L1 insertion model. Finally, our evolutionary analysis demonstrates structural conservation between ORF2p and other RNA- and DNA-dependent polymerases. We therefore provide key mechanistic insights into L1 polymerization and insertion, shed light on the evolutionary history of L1 and enable rational drug development targeting L1.
Collapse
Affiliation(s)
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Bryant D Miller
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Luciano H Di Stefano
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Matthew Hancock
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Esin Işik
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Carlos Mendez-Dorantes
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Thomas Walpole
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Charles Nichols
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Paul Wan
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Kirsi Riento
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Rowan Halls-Kass
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | | | - Alfred Lammens
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Anja Jestel
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Paula Upla
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Kera Xibinaku
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | | | - Kacper B Rogala
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna M Schneider
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | | | | | | | | | | | | | | | | | | | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Oliver Weichenrieder
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Kathleen H Burns
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA.
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
| | | | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands.
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
4
|
Tan B, Zhang X, Ansari A, Jadhav P, Tan H, Li K, Chopra A, Ford A, Chi X, Ruiz FX, Arnold E, Deng X, Wang J. Design of SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. bioRxiv 2023:2023.12.01.569653. [PMID: 38076941 PMCID: PMC10705561 DOI: 10.1101/2023.12.01.569653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. In this study, we designed and synthesized 85 noncovalent PLpro inhibitors that bind to the newly discovered Val70Ub site and the known BL2 groove pocket. Potent compounds inhibited PLpro with inhibitory constant Ki values from 13.2 to 88.2 nM. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 μM. Oral treatment with Jun12682 significantly improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.
Collapse
Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Ahmadullah Ansari
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Alexandra Ford
- Deprtment of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiang Chi
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| |
Collapse
|
5
|
Jiang X, Huang B, Rumrill S, Pople D, Zalloum WA, Kang D, Zhao F, Ji X, Gao Z, Hu L, Wang Z, Xie M, De Clercq E, Ruiz FX, Arnold E, Pannecouque C, Liu X, Zhan P. Discovery of diarylpyrimidine derivatives bearing piperazine sulfonyl as potent HIV-1 nonnucleoside reverse transcriptase inhibitors. Commun Chem 2023; 6:83. [PMID: 37120482 PMCID: PMC10148624 DOI: 10.1038/s42004-023-00888-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
HIV-1 reverse transcriptase is one of the most attractive targets for the treatment of AIDS. However, the rapid emergence of drug-resistant strains and unsatisfactory drug-like properties seriously limit the clinical application of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Here we show that a series of piperazine sulfonyl-bearing diarylpyrimidine-based NNRTIs were designed to improve the potency against wild-type and NNRTI-resistant strains by enhancing backbone-binding interactions. Among them, compound 18b1 demonstrates single-digit nanomolar potency against the wild-type and five mutant HIV-1 strains, which is significantly better than the approved drug etravirine. The co-crystal structure analysis and molecular dynamics simulation studies were conducted to explain the broad-spectrum inhibitory activity of 18b1 against reverse transcriptase variants. Besides, compound 18b1 demonstrates improved water solubility, cytochrome P450 liability, and other pharmacokinetic properties compared to the currently approved diarylpyrimidine (DAPY) NNRTIs. Therefore, we consider compound 18b1 a potential lead compound worthy of further study.
Collapse
Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Shawn Rumrill
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - David Pople
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882, Amman, 11821, Jordan
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Fabao Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Xiangkai Ji
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Zhen Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Lide Hu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U.Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium
| | - Francesc X Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA.
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA.
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U.Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China.
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan, 250012, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, Shandong, PR China.
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan, 250012, Shandong, PR China.
| |
Collapse
|
6
|
Chopra A, Bauman JD, Ruiz FX, Arnold E. Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening. J Med Chem 2023; 66:6013-6024. [PMID: 37115705 PMCID: PMC10184123 DOI: 10.1021/acs.jmedchem.2c01681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
X-ray crystallographic fragment screening (XCFS) uses fragment-sized molecules (∼60 to 300 Da) to access binding sites on proteins that may be inaccessible to larger drug-like molecules (>300 Da). Previous studies have shown that fragments containing halogen atoms bind more often to proteins than non-halogenated fragments. Here, we designed the Halo Library containing 46 halogenated fragments (including the "universal fragment" 4-bromopyrazole), a majority of which have been reported to bind to or inhibit one or more targets. The library was screened against the crystals of HIV-1 reverse transcriptase with the drug rilpivirine, yielding an overall hit rate of 26%. Two new binding sites were discovered, and several hot spots were identified. This small library may thus provide a convenient tool for rapidly assessing the feasibility of a target for XCFS, mapping hot spots and cryptic sites, as well as finding fragment binders that can be useful for developing drug leads.
Collapse
Affiliation(s)
- Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Joseph D Bauman
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Francesc X Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| |
Collapse
|
7
|
Mansouri M, Rumrill S, Dawson S, Johnson A, Pinson JA, Gunzburg MJ, Latham CF, Barlow N, Mbogo GW, Ellenberg P, Headey SJ, Sluis-Cremer N, Tyssen D, Bauman JD, Ruiz FX, Arnold E, Chalmers DK, Tachedjian G. Targeting HIV-1 Reverse Transcriptase Using a Fragment-Based Approach. Molecules 2023; 28:3103. [PMID: 37049868 PMCID: PMC10095864 DOI: 10.3390/molecules28073103] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Human immunodeficiency virus type I (HIV-1) is a retrovirus that infects cells of the host's immune system leading to acquired immunodeficiency syndrome and potentially death. Although treatments are available to prevent its progression, HIV-1 remains a major burden on health resources worldwide. Continued emergence of drug-resistance mutations drives the need for novel drugs that can inhibit HIV-1 replication through new pathways. The viral protein reverse transcriptase (RT) plays a fundamental role in the HIV-1 replication cycle, and multiple approved medications target this enzyme. In this study, fragment-based drug discovery was used to optimize a previously identified hit fragment (compound B-1), which bound RT at a novel site. Three series of compounds were synthesized and evaluated for their HIV-1 RT binding and inhibition. These series were designed to investigate different vectors around the initial hit in an attempt to improve inhibitory activity against RT. Our results show that the 4-position of the core scaffold is important for binding of the fragment to RT, and a lead compound with a cyclopropyl substitution was selected and further investigated. Requirements for binding to the NNRTI-binding pocket (NNIBP) and a novel adjacent site were investigated, with lead compound 27-a minimal but efficient NNRTI-offering a starting site for the development of novel dual NNIBP-Adjacent site inhibitors.
Collapse
Affiliation(s)
- Mahta Mansouri
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Shawn Rumrill
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shane Dawson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Adam Johnson
- Retroviral Biology and Antivirals Laboratory, Disease Elimination Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia
| | - Jo-Anne Pinson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Menachem J. Gunzburg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Catherine F. Latham
- Retroviral Biology and Antivirals Laboratory, Disease Elimination Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - George W. Mbogo
- Retroviral Biology and Antivirals Laboratory, Disease Elimination Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia
| | - Paula Ellenberg
- Retroviral Biology and Antivirals Laboratory, Disease Elimination Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia
| | - Stephen J. Headey
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - David Tyssen
- Retroviral Biology and Antivirals Laboratory, Disease Elimination Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David K. Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Gilda Tachedjian
- Retroviral Biology and Antivirals Laboratory, Disease Elimination Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia
- Department of Microbiology, Monash University, Clayton, VIC 3168, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| |
Collapse
|
8
|
Musa A, Arnold E, Carpenter-Thompson R, Anavim A, Ter-Oganesyan R, Harvill M, Kakos R, Salamo R, Carle T, Harb A. Abstract No. 185 Superior Hypogastric Nerve Blockade to Reduce Pain after Uterine Fibroid Artery Embolization: A Systematic Review of the Literature. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
|
9
|
Yadav R, Courouble VV, Dey SK, Harrison JJE, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E. Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 2022; 8:eadd2191. [PMID: 36490335 PMCID: PMC9733933 DOI: 10.1126/sciadv.add2191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.
Collapse
Affiliation(s)
- Ruchi Yadav
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Valentine V. Courouble
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
| | - Sanjay K. Dey
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | | | - Jennifer Timm
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
| | - Jesse B. Hopkins
- BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Ryan L. Slack
- Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G. Sarafianos
- Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
- Department of Molecular Medicine, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| |
Collapse
|
10
|
Harrison JJEK, Passos DO, Bruhn JF, Bauman JD, Tuberty L, DeStefano JJ, Ruiz FX, Lyumkis D, Arnold E. Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation. Sci Adv 2022; 8:eabn9874. [PMID: 35857464 PMCID: PMC9258950 DOI: 10.1126/sciadv.abn9874] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields the HIV structural proteins and enzymes. Structures of the mature enzymes PR, reverse transcriptase (RT), and integrase (IN) aided understanding of catalysis and design of antiretrovirals, but knowledge of the Pol precursor architecture and function before PR cleavage is limited. We developed a system to produce stable HIV-1 Pol and determined its cryo-electron microscopy structure. RT in Pol has a similar arrangement to the mature RT heterodimer, and its dimerization may draw together two PR monomers to activate proteolytic processing. HIV-1 thus may leverage the dimerization interfaces in Pol to regulate assembly and maturation of polyprotein precursors.
Collapse
Affiliation(s)
- Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
- Department of Chemistry, University of Ghana, Legon, Ghana
| | | | - Jessica F. Bruhn
- The Salk Institute for Biological Studies, La Jolla, CA, USA
- NanoImaging Services, San Diego, CA, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Lynda Tuberty
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| |
Collapse
|
11
|
Musa A, Afify O, Al-Hihi M, Anavim A, Holton J, Azar S, Kumar V, Cassella K, Ledbetter K, Trivedi P, Arnold E, Ter-Oganesyan R. Abstract No. 526 How do interventional radiology residency program directors prefer to increase female and under-represented minority (URM) representation? J Vasc Interv Radiol 2022. [DOI: 10.1016/j.jvir.2022.03.508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
12
|
Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alfaro Alvarado LH, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie‐Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, Ortiz‐Alvarez de la Campa M, Paredes I, Wheeler B, Rupert A, Sam A, See K, Soto Zapata S, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. Proteins 2022; 90:1054-1080. [PMID: 34580920 PMCID: PMC8661935 DOI: 10.1002/prot.26250] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 12/21/2020] [Revised: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 01/18/2023]
Abstract
Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
Collapse
Affiliation(s)
- Joseph H. Lubin
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Christine Zardecki
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Elliott M. Dolan
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Changpeng Lu
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Zhuofan Shen
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Shuchismita Dutta
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - John D. Westbrook
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Brian P. Hudson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - David S. Goodsell
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- The Scripps Research InstituteLa JollaCaliforniaUSA
| | - Jonathan K. Williams
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Maria Voigt
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Vidur Sarma
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Lingjun Xie
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Thejasvi Venkatachalam
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Steven Arnold
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | - Aaliyah Khan
- University of Maryland Baltimore CountyBaltimoreMarylandUSA
| | | | | | | | | | | | | | - Helen Zheng
- Watchung Hills Regional High SchoolWarrenNew JerseyUSA
| | | | | | - Mark Dresel
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | | | | | | | | | - Evan Lenkeit
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | | | | | - Andrew Sam
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Katherine See
- Rochester Institute of TechnologyRochesterNew YorkUSA
| | | | - Paul A. Craig
- Rochester Institute of TechnologyRochesterNew YorkUSA
| | | | - Jennifer Jiang
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | - Yana Bromberg
- Department of Biochemistry and MicrobiologyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Jay Tischfield
- Department of GeneticsRutgers, The State University of New Jersey, and Human Genetics Institute of New JerseyPiscatawayNew JerseyUSA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Eddy Arnold
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jean Baum
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jesse Sandberg
- Center for Computational and Integrative BiologyRutgers, The State University of New JerseyCamdenNew JerseyUSA
| | - Grace Brannigan
- Center for Computational and Integrative BiologyRutgers, The State University of New JerseyCamdenNew JerseyUSA
- Department of PhysicsRutgers, The State University of New JerseyCamdenNew JerseyUSA
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Stephen K. Burley
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaSan Diego, La JollaCaliforniaUSA
| |
Collapse
|
13
|
Ruiz FX, Hoang A, Dilmore CR, DeStefano JJ, Arnold E. Structural basis of HIV inhibition by L-nucleosides: opportunities for drug development and repurposing. Drug Discov Today 2022; 27:1832-1846. [PMID: 35218925 DOI: 10.1016/j.drudis.2022.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/15/2021] [Revised: 01/15/2022] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
Infection with HIV can cripple the immune system and lead to AIDS. Hepatitis B virus (HBV) is a hepadnavirus that causes human liver diseases. Both pathogens are major public health problems affecting millions of people worldwide. The polymerases from both viruses are the most common drug target for viral inhibition, sharing common architecture at their active sites. The L-nucleoside drugs emtricitabine and lamivudine are widely used HIV reverse transcriptase (RT) and HBV polymerase (Pol) inhibitors. Nevertheless, structural details of their binding to RT(Pol)/nucleic acid remained unknown until recently. Here, we discuss the implications of these structures, alongside related complexes with L-dNTPs, for the development of novel L-nucleos(t)ide drugs, and prospects for repurposing them.
Collapse
Affiliation(s)
- Francesc X Ruiz
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Anthony Hoang
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher R Dilmore
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA
| | - Jeffrey J DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
14
|
Losada N, Ruiz FX, Curreli F, Gruber K, Pilch A, Altieri A, Kurkin AV, Das K, Debnath AK, Arnold E. Correction to "HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites". J Med Chem 2021; 65:885. [PMID: 34915707 DOI: 10.1021/acs.jmedchem.1c02061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Losada N, Ruiz FX, Curreli F, Gruber K, Pilch A, Das K, Debnath AK, Arnold E. HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites. J Med Chem 2021; 64:16530-16540. [PMID: 34735153 PMCID: PMC10655131 DOI: 10.1021/acs.jmedchem.1c01104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/28/2022]
Abstract
HIV-1 infection is typically treated using ≥2 drugs, including at least one HIV-1 reverse transcriptase (RT) inhibitor. Drugs targeting RT comprise nucleos(t)ide RT inhibitors (NRTIs) and non-nucleoside RT inhibitors (NNRTIs). NRTI-triphosphates bind at the polymerase active site and, following incorporation, inhibit DNA elongation. NNRTIs bind at an allosteric pocket ∼10 Å away from the polymerase active site. This study focuses on compounds ("NBD derivatives") originally developed to bind to HIV-1 gp120, some of which inhibit RT. We have determined crystal structures of three NBD compounds in complex with HIV-1 RT, correlating with RT enzyme inhibition and antiviral activity, to develop structure-activity relationships. Intriguingly, these compounds bridge the dNTP and NNRTI-binding sites and inhibit the polymerase activity of RT in the enzymatic assays (IC50 < 5 μM). Two of the lead compounds, NBD-14189 and NBD-14270, show potent antiviral activity (EC50 < 200 nM), and NBD-14270 shows low cytotoxicity (CC50 > 100 μM).
Collapse
Affiliation(s)
- Natalie Losada
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065, USA
| | - Kevin Gruber
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Alyssa Pilch
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Asim K. Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| |
Collapse
|
16
|
Loza-Gomez A, NokLam C, Arnold E, Menchine M. 293 Barriers in Telephone CPR Instruction by 911 Dispatchers for Out-of-Hospital Cardiac Arrest Before and During the COVID-19 Pandemic. Ann Emerg Med 2021. [DOI: 10.1016/j.annemergmed.2021.09.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
17
|
Harrison JJEK, Tuske S, Das K, Ruiz FX, Bauman JD, Boyer PL, DeStefano JJ, Hughes SH, Arnold E. Crystal Structure of a Retroviral Polyprotein: Prototype Foamy Virus Protease-Reverse Transcriptase (PR-RT). Viruses 2021; 13:v13081495. [PMID: 34452360 PMCID: PMC8402755 DOI: 10.3390/v13081495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022] Open
Abstract
In most cases, proteolytic processing of the retroviral Pol portion of the Gag-Pol polyprotein precursor produces protease (PR), reverse transcriptase (RT), and integrase (IN). However, foamy viruses (FVs) express Pol separately from Gag and, when Pol is processed, only the IN domain is released. Here, we report a 2.9 Å resolution crystal structure of the mature PR-RT from prototype FV (PFV) that can carry out both proteolytic processing and reverse transcription but is in a configuration not competent for proteolytic or polymerase activity. PFV PR-RT is monomeric and the architecture of PFV PR is similar to one of the subunits of HIV-1 PR, which is a dimer. There is a C-terminal extension of PFV PR (101-145) that consists of two helices which are adjacent to the base of the RT palm subdomain, and anchors PR to RT. The polymerase domain of PFV RT consists of fingers, palm, thumb, and connection subdomains whose spatial arrangements are similar to the p51 subunit of HIV-1 RT. The RNase H and polymerase domains of PFV RT are connected by flexible linkers. Significant spatial and conformational (sub)domain rearrangements are therefore required for nucleic acid binding. The structure of PFV PR-RT provides insights into the conformational maturation of retroviral Pol polyproteins.
Collapse
Affiliation(s)
- Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry, University of Ghana, Legon P.O. Box LG 56, Ghana
| | - Steve Tuske
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Paul L. Boyer
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA; (P.L.B.); (S.H.H.)
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA;
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA; (P.L.B.); (S.H.H.)
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- Correspondence:
| |
Collapse
|
18
|
Courouble VV, Dey SK, Yadav R, Timm J, Harrison JJEK, Ruiz FX, Arnold E, Griffin PR. Revealing the Structural Plasticity of SARS-CoV-2 nsp7 and nsp8 Using Structural Proteomics. J Am Soc Mass Spectrom 2021; 32:1618-1630. [PMID: 34121407 PMCID: PMC8231661 DOI: 10.1021/jasms.1c00086] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 06/12/2023]
Abstract
Coronavirus (CoV) nonstructural proteins (nsps) assemble to form the replication-transcription complex (RTC) responsible for viral RNA synthesis. nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase and other nsps. To date, no structure of the full-length SARS-CoV-2 nsp7:nsp8 complex has been published. The current understanding of this complex is based on structures from truncated constructs, with missing electron densities, or from related CoV species where SARS-CoV-2 nsp7 and nsp8 share upward of 90% sequence identity. Despite available structures solved using crystallography and cryo-EM representing detailed static snapshots of the nsp7:nsp8 complex, it is evident that the complex has a high degree of structural plasticity. However, relatively little is known about the conformational dynamics of the individual proteins and how they complex to interact with other nsps. Here, the solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and cross-linking mass spectrometry (XL-MS), illuminate the dynamics of SARS-CoV-2 full-length nsp7 and nsp8 proteins and the nsp7:nsp8 protein complex. Results presented from the two techniques are complementary and validate the interaction surfaces identified from the published three-dimensional heterotetrameric crystal structure of the SARS-CoV-2 truncated nsp7:nsp8 complex. Furthermore, mapping of XL-MS data onto higher-order complexes suggests that SARS-CoV-2 nsp7 and nsp8 do not assemble into a hexadecameric structure as implied by the SARS-CoV full-length nsp7:nsp8 crystal structure. Instead, our results suggest that the nsp7:nsp8 heterotetramer can dissociate into a stable dimeric unit that might bind to nsp12 in the RTC without significantly altering nsp7-nsp8 interactions.
Collapse
Affiliation(s)
- Valentine V. Courouble
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Sanjay Kumar Dey
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ruchi Yadav
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jennifer Timm
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry, School of Physical and Mathematical Sciences, University of Ghana, Legon, Box LG 56, Legon-Accra, Ghana
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| |
Collapse
|
19
|
Chesterman C, Arnold E. Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry. Structure 2021; 29:598-605.e3. [PMID: 33636101 PMCID: PMC8178225 DOI: 10.1016/j.str.2021.02.001] [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: 03/16/2020] [Revised: 10/05/2020] [Accepted: 02/08/2021] [Indexed: 01/09/2023]
Abstract
This work presents a method for introducing synthetic symmetry into protein crystallization samples using an antibody fragment termed a diabody (Dab). These Dabs contain two target binding sites, and engineered disulfide bonds have been included to modulate Dab flexibility. The impacts of Dab engineering have been observed through assessment of thermal stability, small-angle X-ray scattering, and high-resolution crystal structures. Complexes between the engineered Dabs and HIV-1 reverse transcriptase (RT) bound to a high-affinity DNA aptamer were also generated to explore the capacity of engineered Dabs to enable the crystallization of bound target proteins. This strategy increased the crystallization hit frequency obtained for RT-aptamer, and the structure of a Dab-RT-aptamer complex was determined to 3.0-Å resolution. Introduction of synthetic symmetry using a Dab could be a broadly applicable strategy, especially when monoclonal antibodies for a target have previously been identified.
Collapse
Affiliation(s)
- Chelsy Chesterman
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA; GSK, Rockville, MD 20850, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
20
|
Kang D, Ruiz FX, Sun Y, Feng D, Jing L, Wang Z, Zhang T, Gao S, Sun L, De Clercq E, Pannecouque C, Arnold E, Zhan P, Liu X. 2,4,5-Trisubstituted Pyrimidines as Potent HIV-1 NNRTIs: Rational Design, Synthesis, Activity Evaluation, and Crystallographic Studies. J Med Chem 2021; 64:4239-4256. [PMID: 33734714 PMCID: PMC8594587 DOI: 10.1021/acs.jmedchem.1c00268] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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
There is an urgent unmet medical need for novel human immunodeficiency virus type 1 (HIV-1) inhibitors that are effective against a variety of NNRTI-resistance mutations. We report our research efforts aimed at discovering a novel chemotype of anti-HIV-1 agents with improved potency against a variety of NNRTI-resistance mutations in this paper. Structural modifications of the lead K-5a2 led to the identification of a potent inhibitor 16c. 16c yielded highly potent anti-HIV-1 activities and improved resistance profiles compared with the approved drug etravirine. The co-crystal structure revealed the key role of the water networks surrounding the NNIBP for binding and for resilience against resistance mutations, while suggesting further extension of 16c toward the NNRTI-adjacent site as a lead development strategy. Furthermore, 16c demonstrated favorable pharmacokinetic and safety properties, suggesting the potential of 16c as a promising anti-HIV-1 drug candidate.
Collapse
Affiliation(s)
- Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, United States
| | - Yanying Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Da Feng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Tao Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| |
Collapse
|
21
|
Courouble VV, Dey SK, Yadav R, Timm J, Harrison JJEK, Ruiz FX, Arnold E, Griffin PR. Resolving the Dynamic Motions of SARS-CoV-2 nsp7 and nsp8 Proteins Using Structural Proteomics. bioRxiv 2021:2021.03.06.434214. [PMID: 33688660 PMCID: PMC7941636 DOI: 10.1101/2021.03.06.434214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Coronavirus (CoV) non-structural proteins (nsps) assemble to form the replication-transcription complex (RTC) responsible for viral RNA synthesis. nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase (RdRp) and other nsps. To date, no structure of full-length SARS-CoV-2 nsp7:nsp8 complex has been published. Current understanding of this complex is based on structures from truncated constructs or with missing electron densities and complexes from related CoV species with which SARS-CoV-2 nsp7 and nsp8 share upwards of 90% sequence identity. Despite available structures being solved using crystallography and cryo-EM representing detailed snapshots of the nsp7:nsp8 complex, it is evident that the complex has a high degree of structural plasticity. However, relatively little is known about the conformational dynamics of the complex and how it assembles to interact with other nsps. Here, the solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS), illuminate the structural dynamics of the SARS-CoV-2 full-length nsp7:nsp8 complex. The results presented from the two techniques are complementary and validate the interaction surfaces identified from the published three-dimensional heterotetrameric crystal structure of SARS-CoV-2 truncated nsp7:nsp8 complex. Furthermore, mapping of XL-MS data onto higher order complexes suggests that SARS-CoV-2 nsp7 and nsp8 do not assemble into a hexadecameric structure as implied by the SARS-CoV full-length nsp7:nsp8 crystal structure. Instead our results suggest that the nsp7:nsp8 heterotetramer can dissociate into a stable dimeric unit that might bind to nsp12 in the RTC without altering nsp7-nsp8 interactions.
Collapse
Affiliation(s)
- Valentine V. Courouble
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Sanjay Kumar Dey
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ruchi Yadav
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jennifer Timm
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry, School of Physical and Mathematical Sciences, University of Ghana, Legon, Box LG 56, Legon-Accra, Ghana
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| |
Collapse
|
22
|
Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alvarado LHA, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie-Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, de la Campa MOA, Paredes I, Wheeler B, Rupert A, Sam A, See K, Zapata SS, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic. bioRxiv 2020. [PMID: 33299989 DOI: 10.1101/2020.12.01.406637] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
Collapse
|
23
|
Tuske S, Zheng J, Olson ED, Ruiz FX, Pascal BD, Hoang A, Bauman JD, Das K, DeStefano JJ, Musier-Forsyth K, Griffin PR, Arnold E. Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer. Curr Res Struct Biol 2020; 2:116-129. [PMID: 33870216 PMCID: PMC8052095 DOI: 10.1016/j.crstbi.2020.06.002] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/03/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
The high-resolution crystal structure of HIV-1 reverse transcriptase (RT) bound to a 38-mer DNA hairpin aptamer with low pM affinity was previously described. The high-affinity binding aptamer contained 2'-O-methyl modifications and a seven base-pair GC-rich tract and the structure of the RT-aptamer complex revealed specific contacts between RT and the template strand of the aptamer. Similar to all crystal structures of RT bound to nucleic acid template-primers, the aptamer bound RT with a bend in the duplex DNA. To understand the structural basis for the ultra-high-affinity aptamer binding, an integrative structural biology approach was used. Hydrogen-deuterium exchange coupled to liquid chromatography-mass spectrometry (HDX-MS) was used to examine the structural dynamics of RT alone and in the presence of the DNA aptamer. RT was selectively labeled with 15N to unambiguously identify peptides from each subunit. HDX of unliganded RT shows a mostly stable core. The p66 fingers and thumb subdomains, and the RNase H domain are relatively dynamic. HDX indicates that both the aptamer and a scrambled version significantly stabilize regions of RT that are dynamic in the absence of DNA. No substantial differences in RT dynamics are observed between aptamer and scrambled aptamer binding, despite a large difference in binding affinity. Small-angle X-ray scattering and circular dichroism spectroscopy were used to investigate the aptamer conformation in solution and revealed a pre-bent DNA that possesses both A- and B-form helical character. Both the 2'-O-methyl modifications and the GC tract appear to contribute to an energetically favorable conformation for binding to RT that contributes to the aptamer's ultra-high affinity for RT. The X-ray structure of RT with an RNA/DNA version of the aptamer at 2.8 Å resolution revealed a potential role of the hairpin positioning in affinity. Together, the data suggest that both the 2'-O-methyl modifications and the GC tract contribute to an energetically favorable conformation for high-affinity binding to RT.
Collapse
Affiliation(s)
- Steve Tuske
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Erik D. Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, And Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Bruce D. Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Anthony Hoang
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20740, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, And Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| |
Collapse
|
24
|
Himmel DM, Arnold E. Non-Nucleoside Reverse Transcriptase Inhibitors Join Forces with Integrase Inhibitors to Combat HIV. Pharmaceuticals (Basel) 2020; 13:ph13060122. [PMID: 32545407 PMCID: PMC7345359 DOI: 10.3390/ph13060122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
In the treatment of acquired immune deficiency syndrome (AIDS), the diarylpyrimidine (DAPY) analogs etravirine (ETR) and rilpivirine (RPV) have been widely effective against human immunodeficiency virus (HIV) variants that are resistant to other non-nucleoside reverse transcriptase inhibitors (NNRTIs). With non-inferior or improved efficacy, better safety profiles, and lower doses or pill burdens than other NNRTIs in the clinic, combination therapies including either of these two drugs have led to higher adherence than other NNRTI-containing treatments. In a separate development, HIV integrase strand transfer inhibitors (INSTIs) have shown efficacy in treating AIDS, including raltegravir (RAL), elvitegravir (EVG), cabotegravir (CAB), bictegravir (BIC), and dolutegravir (DTG). Of these, DTG and BIC perform better against a wide range of resistance mutations than other INSTIs. Nevertheless, drug-resistant combinations of mutations have begun to emerge against all DAPYs and INSTIs, attributable in part to non-adherence. New dual therapies that may promote better adherence combine ETR or RPV with an INSTI and have been safer and non-inferior to more traditional triple-drug treatments. Long-acting dual- and triple-therapies combining ETR or RPV with INSTIs are under study and may further improve adherence. Here, highly resistant emergent mutations and efficacy data on these novel treatments are reviewed. Overall, ETR or RPV, in combination with INSTIs, may be treatments of choice as long-term maintenance therapies that optimize efficacy, adherence, and safety.
Collapse
Affiliation(s)
- Daniel M. Himmel
- Himmel Sci Med Com, L.L.C., Bala Cynwyd, PA 19004, USA
- Correspondence: ; Tel.: +1-848-391-5973
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA;
| |
Collapse
|
25
|
Nguyen PDM, Zheng J, Gremminger TJ, Qiu L, Zhang D, Tuske S, Lange MJ, Griffin PR, Arnold E, Chen SJ, Zou X, Heng X, Burke DH. Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase. Nucleic Acids Res 2020; 48:2709-2722. [PMID: 31943114 PMCID: PMC7049723 DOI: 10.1093/nar/gkz1224] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022] Open
Abstract
RNA aptamers that bind HIV-1 reverse transcriptase (RT) inhibit RT in enzymatic and viral replication assays. Some aptamers inhibit RT from only a few viral clades, while others show broad-spectrum inhibition. Biophysical determinants of recognition specificity are poorly understood. We investigated the interface between HIV-1 RT and a broad–spectrum UCAA-family aptamer. SAR and hydroxyl radical probing identified aptamer structural elements critical for inhibition and established the role of signature UCAA bulge motif in RT-aptamer interaction. HDX footprinting on RT ± aptamer shows strong contacts with both subunits, especially near the C-terminus of p51. Alanine scanning revealed decreased inhibition by the aptamer for mutants P420A, L422A and K424A. 2D proton nuclear magnetic resonance and SAXS data provided constraints on the solution structure of the aptamer and enable computational modeling of the docked complex with RT. Surprisingly, the aptamer enhanced proteolytic cleavage of precursor p66/p66 by HIV-1 protease, suggesting that it stabilizes the productive conformation to allow maturation. These results illuminate features at the RT-aptamer interface that govern recognition specificity by a broad-spectrum antiviral aptamer, and they open new possibilities for accelerating RT maturation and interfering with viral replication.
Collapse
Affiliation(s)
- Phuong D M Nguyen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University Missouri, Columbia, MO 65211, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Liming Qiu
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Dong Zhang
- Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA
| | - Steve Tuske
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Margaret J Lange
- Department of Molecular Microbiology & Immunology, University Missouri, Columbia, MO 65211, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA.,Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University Missouri, Columbia, MO 65211, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University Missouri, Columbia, MO 65211, USA.,Department of Molecular Microbiology & Immunology, University Missouri, Columbia, MO 65211, USA
| |
Collapse
|
26
|
Ginn RE, Packard VS, Fox TL, Arnold E, Barnett J, Bulthaus M, Bushman P, Case R, Crevey N, Fenelon M, Fuqua R, Gilman C, Hawkinson J, Heady J, Hendrickson H, Koenig E, Messer J, Mullen R, Phillips M, Santorello J, Slamp R, Wehr M, Zimmerman A. Enumeration of Total Bacteria and Coliforms in Milk by Dry Rehydratable Film Methods: Collaborative Study. J AOAC Int 2020. [DOI: 10.1093/jaoac/69.3.527] [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: 11/13/2022]
Abstract
Abstract
Eleven laboratories participated in a collaborative study to compare the dry rehydratable film (Petrifilm® SM and Petrifilm® VRB) methods, respectively, to the standard plate count (SPC) and violet red bile agar (VRBA) standard methods for estimation of total bacteria and coliform counts in raw and homogenized pasteurized milk. Each laboratory analyzed 16 samples (8 different samples in blind duplicate) for total count by both the SPC and Petrifilm SM methods. A second set of 16 samples was analyzed by the VRBA and Petrifilm VRB methods. The repeatability standard deviations (the square root of the between-replicates variance) of the SPC, Petrifilm SM, VRBA, and Petrifilm VRB methods were 0.0S104, 0.0444, 0.14606, and 0.13806, respectively; the reproducibility standard deviations were 0.7197, C.06380, 0.15326, and 0.13806, respectively. The difference between the mean Iog10 SPC and the mean logio Petrifilm SM results was 0.027. For the VRBA and Petrifilm VRB methods, the mean log10 difference was 0.013. These results generally indicate the suitability of the dry rehydratable film methods as alternatives to the SPC and VRBA methods for milk samples. The methods have been adopted official first action.
Collapse
Affiliation(s)
- Roy E Ginn
- Dairy Quality Control Institute, Inc., 2353 Rice St, St. Paul, MN 55113
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Kang D, Ruiz FX, Feng D, Pilch A, Zhao T, Wei F, Wang Z, Sun Y, Fang Z, De Clercq E, Pannecouque C, Arnold E, Zhan P, Liu X. Discovery and Characterization of Fluorine-Substituted Diarylpyrimidine Derivatives as Novel HIV-1 NNRTIs with Highly Improved Resistance Profiles and Low Activity for the hERG Ion Channel. J Med Chem 2020; 63:1298-1312. [PMID: 31935327 PMCID: PMC9677951 DOI: 10.1021/acs.jmedchem.9b01769] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 12/13/2022]
Abstract
Our previous efforts have led to the development of two potent NNRTIs, K-5a2 and 25a, exhibiting effective anti-HIV-1 potency and resistance profiles compared with etravirine. However, both inhibitors suffered from potent hERG inhibition and short half-life. In this article, with K-5a2 and etravirine as leads, series of novel fluorine-substituted diarylpyrimidine derivatives were designed via molecular hybridization and bioisosterism strategies. The results indicated 24b was the most active inhibitor, exhibiting broad-spectrum activity (EC50 = 3.60-21.5 nM) against resistant strains, significantly lower cytotoxicity (CC50= 155 μM), and reduced hERG inhibition (IC50 > 30 μM). Crystallographic studies confirmed the binding of 24b and the role of the fluorine atom, as well as optimal contacts of a nitrile group with the main-chain carbonyl group of H235. Furthermore, 24b showed longer half-life and favorable safety properties. All the results demonstrated that 24b has significant promise in circumventing drug resistance as an anti-HIV-1 candidate.
Collapse
Affiliation(s)
- Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- Suzhou Research Institute, Shandong University, Room522, Building H of NUSP, NO.388 Ruoshui Road, SIP, Suzhou, 215123 Jiangsu, P.R. China
| | - F. Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, United States
| | - Da Feng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Alyssa Pilch
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, United States
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Fenju Wei
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Yanying Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zengjun Fang
- The Second Hospital, Shandong University, No. 247 Beiyuan Avenue, Jinan 250033, China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| |
Collapse
|
28
|
Xavier Ruiz F, Arnold E. Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance. Curr Opin Struct Biol 2020; 61:113-123. [PMID: 31935541 DOI: 10.1016/j.sbi.2019.11.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
Abstract
The essential role of reverse transcription in the HIV life cycle is illustrated by the fact that half of the ∼30 FDA-approved drugs for HIV treatment target HIV-1 reverse transcriptase (RT). Even though more than 160 structures of RT deposited in the Protein Data Bank (PDB) have revealed the molecular architecture of RT in great detail, some key states of RT function and inhibition remain still unknown. Recent structures of RT initiation complexes, RT poised for RNA hydrolysis, and RT with approved drugs and investigational compounds have provided a deeper understanding of RT function and inhibition, suggesting novel avenues for targeting this central enzyme of HIV.
Collapse
Affiliation(s)
- Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, 08854, NJ, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, 08854, NJ, USA.
| |
Collapse
|
29
|
Abstract
HIV-1 reverse transcriptase (RT) is an essential enzyme, targeting half of approved anti-AIDS drugs. While nucleoside RT inhibitors (NRTIs) are DNA chain terminators, the nucleotide-competing RT inhibitor (NcRTI) INDOPY-1 blocks dNTP binding to RT. Lack of structural information hindered INDOPY-1 improvement. Here we report the HIV-1 RT/DNA/INDOPY-1 crystal structure, revealing a unique mode of inhibitor binding at the polymerase active site without involving catalytic metal ions. The structure may enable new strategies for developing NcRTIs.
Collapse
Affiliation(s)
| | | | - Kalyan Das
- Rega Institute for Medical Research , 3000 Leuven , Belgium.,Department of Microbiology, Immunology and Transplantation , KU Leuven , 3000 Leuven , Belgium
| | | |
Collapse
|
30
|
Abstract
The development of drug resistance in HIV is the result of primary mutations whose effects on viral fitness depend on the entire genetic background, a phenomenon called 'epistasis'. Based on protein sequences derived from drug-experienced patients in the Stanford HIV database, we use a co-evolutionary (Potts) Hamiltonian model to provide direct confirmation of epistasis involving many simultaneous mutations. Building on earlier work, we show that primary mutations leading to drug resistance can become highly favored (or entrenched) by the complex mutation patterns arising in response to drug therapy despite being disfavored in the wild-type background, and provide the first confirmation of entrenchment for all three drug-target proteins: protease, reverse transcriptase, and integrase; a comparative analysis reveals that NNRTI-induced mutations behave differently from the others. We further show that the likelihood of resistance mutations can vary widely in patient populations, and from the population average compared to specific molecular clones.
Collapse
Affiliation(s)
- Avik Biswas
- Center for Biophysics and Computational BiologyTemple UniversityPhiladelphiaUnited States
- Department of PhysicsTemple UniversityPhiladelphiaUnited States
| | - Allan Haldane
- Center for Biophysics and Computational BiologyTemple UniversityPhiladelphiaUnited States
- Department of PhysicsTemple UniversityPhiladelphiaUnited States
| | - Eddy Arnold
- Center for Advanced Biotechnology and MedicineRutgers UniversityPiscatawayUnited States
- Department of Chemistry and Chemical BiologyRutgers UniversityPiscatawayUnited States
| | - Ronald M Levy
- Center for Biophysics and Computational BiologyTemple UniversityPhiladelphiaUnited States
- Department of PhysicsTemple UniversityPhiladelphiaUnited States
- Department of ChemistryTemple UniversityPhiladelphiaUnited States
| |
Collapse
|
31
|
Arnold E, Hasan SS, Johnson JE, Wu H, Zhao R. Michael G. Rossmann (1930–2019): pioneer in crystallography of macromolecules and viruses. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319095618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
32
|
Chesterman C, Arnold E. Co-crystallization with Dab antibody fragments: a universal method for the introduction of synthetic symmetry. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319097800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
33
|
Sagong HY, Bauman JD, Nogales A, Martínez-Sobrido L, Arnold E, LaVoie EJ. Aryl and Arylalkyl Substituted 3-Hydroxypyridin-2(1H)-ones: Synthesis and Evaluation as Inhibitors of Influenza A Endonuclease. ChemMedChem 2019; 14:1204-1223. [PMID: 30983160 PMCID: PMC6581572 DOI: 10.1002/cmdc.201900084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/09/2019] [Revised: 04/07/2019] [Indexed: 02/06/2023]
Abstract
Seasonal influenza infections are associated with an estimated 250-500 000 deaths annually. Resistance to the antiviral M2 ion-channel inhibitors has largely invalidated their clinical utility. Resistance to neuraminidase inhibitors has also been observed in several influenza A virus (IAV) strains. These data have prompted research on inhibitors that target the cap-snatching endonuclease activity of the polymerase acidic protein (PA). Baloxavir marboxil (Xofluza®), recently approved for clinical use, inhibits cap-snatching endonuclease. Resistance to Xofluza® has been reported in both in vitro systems and in the clinic. An X-ray crystallographic screening campaign of a fragment library targeting IAV endonuclease identified 5-chloro-3-hydroxypyridin-2(1H)-one as a bimetal chelating agent at the active site. We have reported the structure-activity relationships for 3-hydroxypyridin-2(1H)-ones and 3-hydroxyquinolin-2(1H)-ones as endonuclease inhibitors. These studies identified two distinct binding modes associated with inhibition of this enzyme that are influenced by the presence of substituents at the 5- and 6-positions of 3-hydroxypyridin-2(1H)-ones. Herein we report the structure-activity relationships associated with various para-substituted 5-phenyl derivatives of 6-(p-fluorophenyl)-3-hydroxypyridin-2(1H)-ones and the effect of using naphthyl, benzyl, and naphthylmethyl groups as alternatives to the p-fluorophenyl substituent on their activity as endonuclease inhibitors.
Collapse
Affiliation(s)
- Hye Yeon Sagong
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA
| | - Joseph D Bauman
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Hoes Lane, Piscataway, NJ, 08854-5627, USA
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 672, Rochester, NY, 14642, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 672, Rochester, NY, 14642, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Hoes Lane, Piscataway, NJ, 08854-5627, USA
| | - Edmond J LaVoie
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA
| |
Collapse
|
34
|
Arnold E, Wu H, Johnson JE. Michael G. Rossmann (1930-2019), pioneer in macromolecular and virus crystallography: scientist, mentor and friend. Acta Crystallogr D Struct Biol 2019; 75:523-527. [PMID: 31205014 DOI: 10.1107/s2059798319008398] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Michael George Rossmann, who made monumental contributions to science, passed away peacefully in West Lafayette, Indiana on 14 May 2019 at the age of 88, following a courageous five-year battle with cancer. Michael was born in Frankfurt, Germany on 30 July 1930. As a young boy, he emigrated to England with his mother just as World War II ignited. Michael was a highly innovative and energetic person, well known for his intensity, persistence and focus in pursuing his research goals. Michael was a towering figure in crystallography as a highly distinguished faculty member at Purdue University for 55 years. Michael made many seminal contributions to crystallography in a career that spanned the entirety of structural biology, beginning in the 1950s at Cambridge where the first protein structures were determined in the laboratories of Max Perutz (hemoglobin, 1960) and John Kendrew (myoglobin, 1958). Michael's work was central in establishing and defining the field of structural biology, which amazingly has described the structures of a vast array of complex biological molecules and assemblies in atomic detail. Knowledge of three-dimensional biological structure has important biomedical significance including understanding the basis of health and disease at the molecular level, and facilitating the discovery of many drugs.
Collapse
Affiliation(s)
- Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
35
|
Martinez SE, Bauman JD, Das K, Arnold E. Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes. Protein Sci 2018; 28:587-597. [PMID: 30499174 DOI: 10.1002/pro.3559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 09/24/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/22/2022]
Abstract
Stavudine (d4T, 2',3'-didehydro-2',3'-dideoxythymidine) was one of the first chain-terminating nucleoside analogs used to treat HIV infection. We present the first structure of the active, triphosphate form of d4T (d4TTP) bound to a catalytic complex of HIV-1 RT/dsDNA template-primer. We also present a new strategy for disulfide (S-S) chemical cross-linking between N6 of a modified adenine at the second overhang base to I63C in the fingers subdomain of RT. The cross-link site is upstream of the duplex-binding region of RT, however, the structure is very similar to published RT structures with cross-linking to Q258C in the thumb, which suggests that cross-linking at either site does not appreciably perturb the RT/DNA structures. RT has a catalytic maximum at pH 7.5. We determined the X-ray structures of the I63C-RT/dsDNA/d4TTP cross-linked complexes at pH 7, 7.5, 8, 8.5, 9, and 9.5. We found small (~0.5 Å), pH-dependent motions of the fingers subdomain that folds in to form the dNTP-binding pocket. We propose that the pH-activity profile of RT relates to this motion of the fingers. Due to side effects of neuropathy and lipodystrophy, use of d4T has been stopped in most countries, however, chemical modification of d4T might lead to the development of a new class of nucleoside analogs targeting RNA and DNA polymerases.
Collapse
Affiliation(s)
- Sergio E Martinez
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854.,Rega Institute for Medical Research and Department of Microbiology and Immunology, KU Leuven, Leuven, 3000, Belgium
| | - Joseph D Bauman
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| | - Kalyan Das
- Rega Institute for Medical Research and Department of Microbiology and Immunology, KU Leuven, Leuven, 3000, Belgium
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| |
Collapse
|
36
|
Vedithi SC, Malhotra S, Das M, Daniel S, Kishore N, George A, Arumugam S, Rajan L, Ebenezer M, Ascher DB, Arnold E, Blundell TL. Publisher Correction: Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae. Sci Rep 2018; 8:8250. [PMID: 29789675 PMCID: PMC5964081 DOI: 10.1038/s41598-018-26451-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Collapse
Affiliation(s)
- Sundeep Chaitanya Vedithi
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK.
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India.
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK
| | - Madhusmita Das
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Sheela Daniel
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Nanda Kishore
- Department of Dermatology, Father Muller Medical College & Hospital, Mangalore, Karnataka, 575 002, India
| | - Anuja George
- Department of Dermatology, Trivandrum Medical College, Trivandrum, Kerala, 695011, India
| | - Shantha Arumugam
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Lakshmi Rajan
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Mannam Ebenezer
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), and Rutgers University Department of Chemistry and Chemical Biology, 679 Hoes Lane, Piscataway, NJ, 08854, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK.
| |
Collapse
|
37
|
Vedithi SC, Malhotra S, Das M, Daniel S, Kishore N, George A, Arumugam S, Rajan L, Ebenezer M, Ascher DB, Arnold E, Blundell TL. Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae. Sci Rep 2018; 8:5016. [PMID: 29567948 PMCID: PMC5864748 DOI: 10.1038/s41598-018-23423-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 12/08/2017] [Accepted: 03/09/2018] [Indexed: 11/09/2022] Open
Abstract
The rpoB gene encodes the β subunit of RNA polymerase holoenzyme in Mycobacterium leprae (M. leprae). Missense mutations in the rpoB gene were identified as etiological factors for rifampin resistance in leprosy. In the present study, we identified mutations corresponding to rifampin resistance in relapsed leprosy cases from three hospitals in southern India which treat leprosy patients. DNA was extracted from skin biopsies of 35 relapse/multidrug therapy non-respondent leprosy cases, and PCR was performed to amplify the 276 bp rifampin resistance-determining region of the rpoB gene. PCR products were sequenced, and mutations were identified in four out of the 35 cases at codon positions D441Y, D441V, S437L and H476R. The structural and functional effects of these mutations were assessed in the context of three-dimensional comparative models of wild-type and mutant M. leprae RNA polymerase holoenzyme (RNAP), based on the recently solved crystal structures of RNAP of Mycobacterium tuberculosis, containing a synthetic nucleic acid scaffold and rifampin. The resistance mutations were observed to alter the hydrogen-bonding and hydrophobic interactions of rifampin and the 5' ribonucleotide of the growing RNA transcript. This study demonstrates that rifampin-resistant strains of M. leprae among leprosy patients in southern India are likely to arise from mutations that affect the drug-binding site and stability of RNAP.
Collapse
Affiliation(s)
- Sundeep Chaitanya Vedithi
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK. .,Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India.
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK
| | - Madhusmita Das
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Sheela Daniel
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Nanda Kishore
- Department of Dermatology, Father Muller Medical College & Hospital, Mangalore, Karnataka, 575 002, India
| | - Anuja George
- Department of Dermatology, Trivandrum Medical College, Trivandrum, Kerala, 695011, India
| | - Shantha Arumugam
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Lakshmi Rajan
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Mannam Ebenezer
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), and Rutgers University Department of Chemistry and Chemical Biology, 679 Hoes Lane, Piscataway, NJ, 08854, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK.
| |
Collapse
|
38
|
Chesterman C, Tuske S, Zheng J, Jeon Y, Zhang C, Cantara W, Musier-Forsyth K, Griffin PR, Lyumkis D, Arnold E. Structural investigation of the HIV-1 reverse transcriptase initiation complex by HDX, SAXS, CryoEM and X-ray crystallography. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317097185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
39
|
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH. Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition. Mol Cell 2017; 66:169-179.e8. [PMID: 28392175 DOI: 10.1016/j.molcel.2017.03.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [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: 02/02/2017] [Revised: 02/15/2017] [Accepted: 02/28/2017] [Indexed: 01/22/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone and in complex with Rif, at 3.8-4.4 Å resolution. The results identify an Mtb-specific structural module of Mtb RNAP and establish that Rif functions by a steric-occlusion mechanism that prevents extension of RNA. We also report non-Rif-related compounds-Nα-aroyl-N-aryl-phenylalaninamides (AAPs)-that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. AAPs bind to a different site on Mtb RNAP than Rif, exhibit no cross-resistance with Rif, function additively when co-administered with Rif, and suppress resistance emergence when co-administered with Rif.
Collapse
Affiliation(s)
- Wei Lin
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Soma Mandal
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shengjian Li
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Sukhendu Mandal
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yi Jiang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shuang Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Meliza Talaue
- Center for Biodefense and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Nancy Connell
- Center for Biodefense and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
40
|
Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E. Correction to Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet. ACS Chem Biol 2016; 11:3226. [PMID: 27696816 DOI: 10.1021/acschembio.6b00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
41
|
Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy RM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M, Arnold E. A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain. J Biol Chem 2016; 291:23569-23577. [PMID: 27645997 DOI: 10.1074/jbc.m116.753384] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 08/15/2016] [Indexed: 12/29/2022] Open
Abstract
HIV-1 integrase (IN) is essential for virus replication and represents an important multifunctional therapeutic target. Recently discovered quinoline-based allosteric IN inhibitors (ALLINIs) potently impair HIV-1 replication and are currently in clinical trials. ALLINIs exhibit a multimodal mechanism of action by inducing aberrant IN multimerization during virion morphogenesis and by competing with IN for binding to its cognate cellular cofactor LEDGF/p75 during early steps of HIV-1 infection. However, quinoline-based ALLINIs impose a low genetic barrier for the evolution of resistant phenotypes, which highlights a need for discovery of second-generation inhibitors. Using crystallographic screening of a library of 971 fragments against the HIV-1 IN catalytic core domain (CCD) followed by a fragment expansion approach, we have identified thiophenecarboxylic acid derivatives that bind at the CCD-CCD dimer interface at the principal lens epithelium-derived growth factor (LEDGF)/p75 binding pocket. The most active derivative (5) inhibited LEDGF/p75-dependent HIV-1 IN activity in vitro with an IC50 of 72 μm and impaired HIV-1 infection of T cells at an EC50 of 36 μm The identified lead compound, with a relatively small molecular weight (221 Da), provides an optimal building block for developing a new class of inhibitors. Furthermore, although structurally distinct thiophenecarboxylic acid derivatives target a similar pocket at the IN dimer interface as the quinoline-based ALLINIs, the lead compound, 5, inhibited IN mutants that confer resistance to quinoline-based compounds. Collectively, our findings provide a plausible path for structure-based development of second-generation ALLINIs.
Collapse
Affiliation(s)
- Disha Patel
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854
| | - Janet Antwi
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy and
| | - Pratibha C Koneru
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210
| | - Erik Serrao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Stefano Forli
- Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, MB-112, The Scripps Research Institute, La Jolla, California 92037
| | - Jacques J Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, and
| | - Lei Feng
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210
| | - Nanjie Deng
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy and
| | - Arthur J Olson
- Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, MB-112, The Scripps Research Institute, La Jolla, California 92037
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Joseph D Bauman
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210,
| | - Eddy Arnold
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854,
| |
Collapse
|
42
|
Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E. Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet. ACS Chem Biol 2016; 11:2158-64. [PMID: 27192549 DOI: 10.1021/acschembio.6b00187] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
HIV-1 reverse transcriptase (RT) catalytically incorporates individual nucleotides into a viral DNA strand complementing an RNA or DNA template strand; the polymerase active site of RT adopts multiple conformational and structural states while performing this task. The states associated are dNTP binding at the N site, catalytic incorporation of a nucleotide, release of a pyrophosphate, and translocation of the primer 3'-end to the P site. Structural characterization of each of these states may help in understanding the molecular mechanisms of drug activity and resistance and in developing new RT inhibitors. Using a 38-mer DNA template-primer aptamer as the substrate mimic, we crystallized an RT/dsDNA complex that is catalytically active, yet translocation-incompetent in crystals. The ability of RT to perform dNTP binding and incorporation in crystals permitted obtaining a series of structures: (I) RT/DNA (P-site), (II) RT/DNA/AZTTP ternary, (III) RT/AZT-terminated DNA (N-site), and (IV) RT/AZT-terminated DNA (N-site)/foscarnet complexes. The stable N-site complex permitted the binding of foscarnet as a pyrophosphate mimic. The Mg(2+) ions dissociated after catalytic addition of AZTMP in the pretranslocated structure III, whereas ions A and B had re-entered the active site to bind foscarnet in structure IV. The binding of foscarnet involves chelation with the Mg(2+) (B) ion and interactions with K65 and R72. The analysis of interactions of foscarnet and the recently discovered nucleotide-competing RT inhibitor (NcRTI) α-T-CNP in two different conformational states of the enzyme provides insights for developing new classes of polymerase active site RT inhibitors.
Collapse
Affiliation(s)
- Kalyan Das
- Center
for Advanced Biotechnology and Medicine (CABM), Department of Chemistry
and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States
| | - Jan Balzarini
- Rega
Institute for Medical Research and Department of Microbiology and
Immunology, KU Leuven, B-3000 Leuven, Belgium
| | - Matthew T. Miller
- Center
for Advanced Biotechnology and Medicine (CABM), Department of Chemistry
and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States
| | - Anita R. Maguire
- Department
of Chemistry and School of Pharmacy, Analytical and Biological Chemistry
Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| | - Jeffrey J. DeStefano
- Department
of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, United States
| | - Eddy Arnold
- Center
for Advanced Biotechnology and Medicine (CABM), Department of Chemistry
and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States
| |
Collapse
|
43
|
Mullins ND, Maguire NM, Ford A, Das K, Arnold E, Balzarini J, Maguire AR. Exploring the role of the α-carboxyphosphonate moiety in the HIV-RT activity of α-carboxy nucleoside phosphonates. Org Biomol Chem 2016; 14:2454-65. [PMID: 26813581 PMCID: PMC4755898 DOI: 10.1039/c5ob02507a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 11/21/2022]
Abstract
As α-carboxy nucleoside phosphonates (α-CNPs) have demonstrated a novel mode of action of HIV-1 reverse transcriptase inhibition, structurally related derivatives were synthesized, namely the malonate 2, the unsaturated and saturated bisphosphonates 3 and 4, respectively and the amide 5. These compounds were evaluated for inhibition of HIV-1 reverse transcriptase in cell-free assays. The importance of the α-carboxy phosphonoacetic acid moiety for achieving reverse transcriptase inhibition, without the need for prior phosphorylation, was confirmed. The malonate derivative 2 was less active by two orders of magnitude than the original α-CNPs, while displaying the same pattern of kinetic behavior; interestingly the activity resides in the “L”-enantiomer of 2, as seen with the earlier series of α-CNPs. A crystal structure with an RT/DNA complex at 2.95 Å resolution revealed the binding of the “L”-enantiomer of 2, at the polymerase active site with a weaker metal ion chelation environment compared to 1a (T-α-CNP) which may explain the lower inhibitory activity of 2.
Collapse
Affiliation(s)
- Nicholas D Mullins
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland.
| | - Nuala M Maguire
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland.
| | - Alan Ford
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland.
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8020, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8020, USA
| | - Jan Balzarini
- KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Anita R Maguire
- Department of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland. and School of Pharmacy, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork, Ireland
| |
Collapse
|
44
|
Bauman JD, Harrison JJEK, Arnold E. Rapid experimental SAD phasing and hot-spot identification with halogenated fragments. IUCrJ 2016; 3:51-60. [PMID: 26870381 PMCID: PMC4704079 DOI: 10.1107/s2052252515021259] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/09/2015] [Indexed: 05/14/2023]
Abstract
Through X-ray crystallographic fragment screening, 4-bromopyrazole was discovered to be a 'magic bullet' that is capable of binding at many of the ligand 'hot spots' found in HIV-1 reverse transcriptase (RT). The binding locations can be in pockets that are 'hidden' in the unliganded crystal form, allowing rapid identification of these sites for in silico screening. In addition to hot-spot identification, this ubiquitous yet specific binding provides an avenue for X-ray crystallographic phase determination, which can be a significant bottleneck in the determination of the structures of novel proteins. The anomalous signal from 4-bromopyrazole or 4-iodopyrazole was sufficient to determine the structures of three proteins (HIV-1 RT, influenza A endonuclease and proteinase K) by single-wavelength anomalous dispersion (SAD) from single crystals. Both compounds are inexpensive, readily available, safe and very soluble in DMSO or water, allowing efficient soaking into crystals.
Collapse
Affiliation(s)
- Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA
| | - Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA
- Correspondence e-mail:
| |
Collapse
|
45
|
Neogi U, Häggblom A, Singh K, Rogers LC, Rao SD, Amogne W, Schülter E, Zazzi M, Arnold E, Sarafianos SG, Sönnerborg A. Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries. J Antimicrob Chemother 2015; 71:367-71. [PMID: 26518047 DOI: 10.1093/jac/dkv359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/02/2015] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES The use of the NNRTI rilpivirine in low- and middle-income countries (LMICs) is under debate. The main objective of this study was to provide further clinical insights and biochemical evidence on the usefulness of rilpivirine in LMICs. PATIENTS AND METHODS Rilpivirine resistance was assessed in 5340 therapy-naive and 13,750 first-generation NNRTI-failed patients from Europe and therapy-naive HIV-1 subtype C (HIV-1C)-infected individuals from India (n = 617) and Ethiopia (n = 127). Rilpivirine inhibition and binding affinity assays were performed using patient-derived HIV-1C reverse transcriptases (RTs). RESULTS Primary rilpivirine resistance was rare, but the proportion of patients with >100,000 HIV-1 RNA copies/mL pre-ART was high in patients from India and Ethiopia, limiting the usefulness of rilpivirine as a first-line drug in LMICs. In patients failing first-line NNRTI treatments, cross-resistance patterns suggested that 73% of the patients could benefit from switching to rilpivirine-based therapy. In vitro inhibition assays showed ∼ 2-fold higher rilpivirine IC50 for HIV-1C RT than HIV-1B RT. Pre-steady-state determination of rilpivirine-binding affinities revealed 3.7-fold lower rilpivirine binding to HIV-1C than HIV-1B RT. Structural analysis indicated that naturally occurring polymorphisms close to the NNRTI-binding pocket may reduce rilpivirine binding, leading to lower susceptibility of HIV-1C to rilpivirine. CONCLUSIONS Our clinical and biochemical findings indicate that the usefulness of rilpivirine has limitations in HIV-1C-dominated epidemics in LMICs, but the drug could still be beneficial in patients failing first-line therapy if genotypic resistance testing is performed.
Collapse
Affiliation(s)
- Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden
| | - Amanda Häggblom
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Kamalendra Singh
- Departments of Molecular Microbiology & Immunology and Biochemistry, Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Leonard C Rogers
- Departments of Molecular Microbiology & Immunology and Biochemistry, Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Shwetha D Rao
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden
| | | | - Eugen Schülter
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Eddy Arnold
- Department of Chemistry and Chemical Biology and Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Stefan G Sarafianos
- Departments of Molecular Microbiology & Immunology and Biochemistry, Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| |
Collapse
|
46
|
Abstract
Structures of L proteins from La Crosse orthobunyavirus and vesicular stomatitis virus reveal insights into RNA synthesis and distinctive mRNA capping mechanisms of segmented and non-segmented negative-sense single-strand RNA viruses.
Collapse
Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA.
| |
Collapse
|
47
|
John J, Kim Y, Bennett N, Das K, Liekens S, Naesens L, Arnold E, Maguire AR, Götte M, Dehaen W, Balzarini J. Pronounced Inhibition Shift from HIV Reverse Transcriptase to Herpetic DNA Polymerases by Increasing the Flexibility of α-Carboxy Nucleoside Phosphonates. J Med Chem 2015; 58:8110-27. [PMID: 26450273 DOI: 10.1021/acs.jmedchem.5b01180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpha-carboxynucleoside phosphonates (α-CNPs) are novel viral DNA polymerase inhibitors that do not need metabolic conversion for enzyme inhibition. The prototype contains a cyclopentyl linker between nucleobase and α-carboxyphosphonate and preferentially (50- to 100-fold) inhibits HIV-1 RT compared with herpetic DNA polymerases. A synthesis methodology involving three steps has been developed for the synthesis of a series of novel α-CNPs, including a Rh(II)-catalyzed O-H insertion that connects the carboxyphosphonate group to a linker moiety and an attachment of a nucleobase to the other end of the linker by a Mitsunobu reaction followed by final deprotection. Replacing the cyclopentyl moiety in the prototype α-CNPs by a more flexible entity results in a selectivity shift of ∼ 100-fold in favor of the herpetic DNA polymerases when compared to selectivity for HIV-1 RT. The nature of the kinetic interaction of the acyclic α-CNPs against the herpetic DNA polymerases differs from the nature of the nucleobase-specific kinetic interaction of the cyclopentyl α-CNPs against HIV RT.
Collapse
Affiliation(s)
| | | | - Nicholas Bennett
- Department of Medical Microbiology and Immunology, University of Alberta , 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08901, United States
| | | | | | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08901, United States
| | - Anita R Maguire
- Department of Chemistry and School of Pharmacy, Analytical and Biological Chemistry Research Facility, University College Cork , Cork, Ireland
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta , 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada
| | | | | |
Collapse
|
48
|
Miller MT, Tuske S, Das K, DeStefano JJ, Arnold E. Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer. Protein Sci 2015; 25:46-55. [PMID: 26296781 DOI: 10.1002/pro.2776] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/19/2015] [Accepted: 08/20/2015] [Indexed: 01/09/2023]
Abstract
The development of a modified DNA aptamer that binds HIV-1 reverse transcriptase (RT) with ultra-high affinity has enabled the X-ray structure determination of an HIV-1 RT-DNA complex to 2.3 Å resolution without the need for an antibody Fab fragment or RT-DNA cross-linking. The 38-mer hairpin-DNA aptamer has a 15 base-pair duplex, a three-deoxythymidine hairpin loop, and a five-nucleotide 5'-overhang. The aptamer binds RT in a template-primer configuration with the 3'-end positioned at the polymerase active site and has 2'-O-methyl modifications at the second and fourth duplex template nucleotides that interact with the p66 fingers and palm subdomains. This structure represents the highest resolution RT-nucleic acid structure to date. The RT-aptamer complex is catalytically active and can serve as a platform for studying fundamental RT mechanisms and for development of anti-HIV inhibitors through fragment screening and other approaches. Additionally, the structure allows for a detailed look at a unique aptamer design and provides the molecular basis for its remarkably high affinity for RT.
Collapse
Affiliation(s)
- Matthew T Miller
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| | - Steve Tuske
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| | - Jeffrey J DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, 20742
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| |
Collapse
|
49
|
Goswami D, Tuske S, Pascal BD, Bauman JD, Patel D, Arnold E, Griffin PR. Differential isotopic enrichment to facilitate characterization of asymmetric multimeric proteins using hydrogen/deuterium exchange mass spectrometry. Anal Chem 2015; 87:4015-4022. [PMID: 25763479 DOI: 10.1021/acs.analchem.5b00372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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
Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry has emerged as a powerful tool for analyzing the conformational dynamics of protein-ligand and protein-protein interactions. Recent advances in instrumentation and methodology have expanded the utility of HDX for the analysis of large and complex proteins; however, asymmetric dimers with shared amino acid sequence present a unique challenge for HDX because assignment of peptides with identical sequence to their subunit of origin remains ambiguous. Here we report the use of differential isotopic labeling to facilitate HDX analysis of multimers using HIV-1 reverse transcriptase (RT) as a model. RT is an asymmetric heterodimer of 51 kDa (p51) and 66 kDa (p66) subunits. The first 440 residues of p51 and p66 are identical. In this study differentially labeled RT was reconstituted from isotopically enriched ((15)N-labeled) p51 and unlabeled p66. To enable detection of (15)N-deuterated RT peptides, the software HDX Workbench was modified to follow a 100% (15)N model. Our results demonstrated that (15)N enrichment of p51 did not affect its conformational dynamics compared to unlabeled p51, but (15)N-labeled p51 did show different conformational dynamics than p66 in the RT heterodimer. Differential HDX-MS of isotopically labeled RT in the presence of the non-nucleoside reverse transcriptase inhibitor (NNRTI) efavirenz (EFV) showed subunit-specific perturbation in the rate of HDX consistent with previously published results and the RT-EFV cocrystal structure.
Collapse
Affiliation(s)
- Devrishi Goswami
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458.USA
| | - Steve Tuske
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Bruce D Pascal
- Informatics Core, The Scripps Research Institute, Jupiter, FL 33458.USA
| | - Joseph D Bauman
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Disha Patel
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458.USA
| |
Collapse
|
50
|
|