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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.
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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.
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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.
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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
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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.
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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
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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.
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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
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5
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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.
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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
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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.
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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.
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7
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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]
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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).
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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
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9
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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.
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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:
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10
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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.
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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
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11
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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.
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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
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12
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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.
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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
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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.
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14
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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.
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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
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Crespo I, Giménez-Dejoz J, Porté S, Cousido-Siah A, Mitschler A, Podjarny A, Pratsinis H, Kletsas D, Parés X, Ruiz FX, Metwally K, Farrés J. Design, synthesis, structure-activity relationships and X-ray structural studies of novel 1-oxopyrimido[4,5-c]quinoline-2-acetic acid derivatives as selective and potent inhibitors of human aldose reductase. Eur J Med Chem 2018; 152:160-174. [DOI: 10.1016/j.ejmech.2018.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/18/2018] [Accepted: 04/08/2018] [Indexed: 12/01/2022]
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16
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Ruiz FX, Crespo I, Álvarez S, Porté S, Giménez-Dejoz J, Cousido-Siah A, Mitschler A, de Lera ÁR, Parés X, Podjarny A, Farrés J. Structural basis for the inhibition of AKR1B10 by the C3 brominated TTNPB derivative UVI2008. Chem Biol Interact 2017; 276:174-181. [DOI: 10.1016/j.cbi.2017.01.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/02/2017] [Accepted: 01/30/2017] [Indexed: 10/20/2022]
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17
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Cousido-Siah A, Ruiz FX, Fanfrlík J, Giménez-Dejoz J, Mitschler A, Kamlar M, Veselý J, Ajani H, Parés X, Farrés J, Hobza P, Podjarny AD. IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors. ACS Chem Biol 2016; 11:2693-2705. [PMID: 27359042 DOI: 10.1021/acschembio.6b00382] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human enzyme aldo-keto reductase family member 1B10 (AKR1B10) has evolved as a tumor marker and promising antineoplastic target. It shares high structural similarity with the diabetes target enzyme aldose reductase (AR). Starting from the potent AR inhibitor IDD388, we have synthesized a series of derivatives bearing the same halophenoxyacetic acid moiety with an increasing number of bromine (Br) atoms on its aryl moiety. Next, by means of IC50 measurements, X-ray crystallography, WaterMap analysis, and advanced binding free energy calculations with a quantum-mechanical (QM) approach, we have studied their structure-activity relationship (SAR) against both enzymes. The introduction of Br substituents decreases AR inhibition potency but improves it in the case of AKR1B10. Indeed, the Br atoms in ortho position may impede these drugs to fit into the AR prototypical specificity pocket. For AKR1B10, the smaller aryl moieties of MK181 and IDD388 can bind into the external loop A subpocket. Instead, the bulkier MK184, MK319, and MK204 open an inner specificity pocket in AKR1B10 characterized by a π-π stacking interaction of their aryl moieties and Trp112 side chain in the native conformation (not possible in AR). Among the three compounds, only MK204 can make a strong halogen bond with the protein (-4.4 kcal/mol, using QM calculations), while presenting the lowest desolvation cost among all the series, translated into the most selective and inhibitory potency AKR1B10 (IC50 = 80 nM). Overall, SAR of these IDD388 polyhalogenated derivatives have unveiled several distinctive AKR1B10 features (shape, flexibility, hydration) that can be exploited to design novel types of AKR1B10 selective drugs.
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Affiliation(s)
- Alexandra Cousido-Siah
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
| | - Francesc X. Ruiz
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Joan Giménez-Dejoz
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - André Mitschler
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
| | - Martin Kamlar
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Jan Veselý
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Haresh Ajani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Xavier Parés
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Alberto D. Podjarny
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
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18
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Fadel F, Zhao Y, Cousido-Siah A, Ruiz FX, Mitschler A, Podjarny A. X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain. PLoS One 2016; 11:e0154190. [PMID: 27111557 PMCID: PMC4844120 DOI: 10.1371/journal.pone.0154190] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1) is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD). This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family) and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase) comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL) at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1) structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain.
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Affiliation(s)
- Firas Fadel
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
- * E-mail: (FF); (AP)
| | - Yuguang Zhao
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, United Kingdom
| | - Alexandra Cousido-Siah
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
| | - Francesc X. Ruiz
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
| | - André Mitschler
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
| | - Alberto Podjarny
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
- * E-mail: (FF); (AP)
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19
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Ruiz FX, Cousido-Siah A, Porté S, Domínguez M, Crespo I, Rechlin C, Mitschler A, de Lera ÁR, Martín MJ, de la Fuente JÁ, Klebe G, Parés X, Farrés J, Podjarny A. Cover Picture: Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10 (ChemMedChem 12/2015). ChemMedChem 2015. [DOI: 10.1002/cmdc.201500528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Francesc X. Ruiz
- Department of Integrative Biology; Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS, INSERM, UdS; rue Laurent Fries 67404 Illkirch CEDEX France
- Center for Advanced Biotechnology and Medicine; Department of Chemistry and Chemical Biology; Rutgers University; 08854-5627 Piscataway, NJ (USA)
| | - Alexandra Cousido-Siah
- Department of Integrative Biology; Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS, INSERM, UdS; rue Laurent Fries 67404 Illkirch CEDEX France
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; 08193 Bellaterra, Barcelona Spain
| | - Marta Domínguez
- Departmento de Química Orgánica and Centro de Investigaciones Biomédicas (CINBIO); Universidade de Vigo; 363100 Vigo Spain
| | - Isidro Crespo
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; 08193 Bellaterra, Barcelona Spain
| | - Chris Rechlin
- Institute of Pharmaceutical Chemistry; University of Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - André Mitschler
- Department of Integrative Biology; Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS, INSERM, UdS; rue Laurent Fries 67404 Illkirch CEDEX France
| | - Ángel R. de Lera
- Departmento de Química Orgánica and Centro de Investigaciones Biomédicas (CINBIO); Universidade de Vigo; 363100 Vigo Spain
| | - María Jesús Martín
- Biomar Microbial Technologies S.A.; Parque Tecnológico de León; 24009 León Spain
| | | | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry; University of Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; 08193 Bellaterra, Barcelona Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; 08193 Bellaterra, Barcelona Spain
| | - Alberto Podjarny
- Department of Integrative Biology; Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS, INSERM, UdS; rue Laurent Fries 67404 Illkirch CEDEX France
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20
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Ruiz FX, Cousido-Siah A, Porté S, Domínguez M, Crespo I, Rechlin C, Mitschler A, de Lera ÁR, Martín MJ, de la Fuente JÁ, Klebe G, Parés X, Farrés J, Podjarny A. Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10. ChemMedChem 2015; 10:1989-2003. [PMID: 26549844 DOI: 10.1002/cmdc.201500393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 12/15/2022]
Abstract
The human enzymes aldose reductase (AR) and AKR1B10 have been thoroughly explored in terms of their roles in diabetes, inflammatory disorders, and cancer. In this study we identified two new lead compounds, 2-(3-(4-chloro-3-nitrobenzyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetic acid (JF0048, 3) and 2-(2,4-dioxo-3-(2,3,4,5-tetrabromo-6-methoxybenzyl)-3,4-dihydropyrimidin-1(2H)-yl)acetic acid (JF0049, 4), which selectively target these enzymes. Although 3 and 4 share the 3-benzyluracil-1-acetic acid scaffold, they have different substituents in their aryl moieties. Inhibition studies along with thermodynamic and structural characterizations of both enzymes revealed that the chloronitrobenzyl moiety of compound 3 can open the AR specificity pocket but not that of the AKR1B10 cognate. In contrast, the larger atoms at the ortho and/or meta positions of compound 4 prevent the AR specificity pocket from opening due to steric hindrance and provide a tighter fit to the AKR1B10 inhibitor binding pocket, probably enhanced by the displacement of a disordered water molecule trapped in a hydrophobic subpocket, creating an enthalpic signature. Furthermore, this selectivity also occurs in the cell, which enables the development of a more efficient drug design strategy: compound 3 prevents sorbitol accumulation in human retinal ARPE-19 cells, whereas 4 stops proliferation in human lung cancer NCI-H460 cells.
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Affiliation(s)
- Francesc X Ruiz
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France. .,Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 08854-5627, Piscataway, NJ, (USA).
| | - Alexandra Cousido-Siah
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Marta Domínguez
- Departmento de Química Orgánica and Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 363100, Vigo, Spain
| | - Isidro Crespo
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Chris Rechlin
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - André Mitschler
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France
| | - Ángel R de Lera
- Departmento de Química Orgánica and Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 363100, Vigo, Spain
| | - María Jesús Martín
- Biomar Microbial Technologies S.A., Parque Tecnológico de León, 24009, León, Spain
| | | | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Alberto Podjarny
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France.
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21
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Giménez-Dejoz J, Kolář MH, Ruiz FX, Crespo I, Cousido-Siah A, Podjarny A, Barski OA, Fanfrlík J, Parés X, Farrés J, Porté S. Substrate Specificity, Inhibitor Selectivity and Structure-Function Relationships of Aldo-Keto Reductase 1B15: A Novel Human Retinaldehyde Reductase. PLoS One 2015; 10:e0134506. [PMID: 26222439 PMCID: PMC4519324 DOI: 10.1371/journal.pone.0134506] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/09/2015] [Indexed: 02/02/2023] Open
Abstract
Human aldo-keto reductase 1B15 (AKR1B15) is a newly discovered enzyme which shares 92% amino acid sequence identity with AKR1B10. While AKR1B10 is a well characterized enzyme with high retinaldehyde reductase activity, involved in the development of several cancer types, the enzymatic activity and physiological role of AKR1B15 are still poorly known. Here, the purified recombinant enzyme has been subjected to substrate specificity characterization, kinetic analysis and inhibitor screening, combined with structural modeling. AKR1B15 is active towards a variety of carbonyl substrates, including retinoids, with lower kcat and Km values than AKR1B10. In contrast to AKR1B10, which strongly prefers all-trans-retinaldehyde, AKR1B15 exhibits superior catalytic efficiency with 9-cis-retinaldehyde, the best substrate found for this enzyme. With ketone and dicarbonyl substrates, AKR1B15 also shows higher catalytic activity than AKR1B10. Several typical AKR inhibitors do not significantly affect AKR1B15 activity. Amino acid substitutions clustered in loops A and C result in a smaller, more hydrophobic and more rigid active site in AKR1B15 compared with the AKR1B10 pocket, consistent with distinct substrate specificity and narrower inhibitor selectivity for AKR1B15.
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Affiliation(s)
- Joan Giménez-Dejoz
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Michal H. Kolář
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Francesc X. Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire-Centre de Biologie Intégrative, CNRS, INSERM, UdS, Illkirch CEDEX, France
| | - Isidro Crespo
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire-Centre de Biologie Intégrative, CNRS, INSERM, UdS, Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire-Centre de Biologie Intégrative, CNRS, INSERM, UdS, Illkirch CEDEX, France
| | - Oleg A. Barski
- Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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22
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Fanfrlík J, Ruiz FX, Kadlčíková A, Řezáč J, Cousido-Siah A, Mitschler A, Haldar S, Lepšík M, Kolář MH, Majer P, Podjarny AD, Hobza P. The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition. ACS Chem Biol 2015; 10:1637-42. [PMID: 25919404 DOI: 10.1021/acschembio.5b00151] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effect of halogen-to-hydrogen bond substitution on the binding energetics and biological activity of a human aldose reductase inhibitor has been studied using X-ray crystallography, IC50 measurements, advanced binding free energy calculations, and simulations. The replacement of Br or I atoms by an amine (NH2) group has not induced changes in the original geometry of the complex, which made it possible to study the isolated features of selected noncovalent interactions in a biomolecular complex.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Francesc X. Ruiz
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404, Illkirch CEDEX, France
| | - Aneta Kadlčíková
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Alexandra Cousido-Siah
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404, Illkirch CEDEX, France
| | - André Mitschler
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404, Illkirch CEDEX, France
| | - Susanta Haldar
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Michal H. Kolář
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Institute
of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations
(IAS-5), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Pavel Majer
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Alberto D. Podjarny
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404, Illkirch CEDEX, France
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
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23
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Fadel F, Zhao Y, Cachau R, Cousido-Siah A, Ruiz FX, Harlos K, Howard E, Mitschler A, Podjarny A. New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. ACTA ACUST UNITED AC 2015; 71:1455-70. [PMID: 26143917 DOI: 10.1107/s139900471500783x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 10/30/2014] [Accepted: 04/21/2015] [Indexed: 11/10/2022]
Abstract
Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities.
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Affiliation(s)
- Firas Fadel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Raul Cachau
- Leidos Biomedical Research Inc. Advanced Biomedical Computer Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Francesc X Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Eduardo Howard
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Andre Mitschler
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
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24
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Cousido-Siah A, Ruiz FX, Crespo I, Porté S, Mitschler A, Parés X, Podjarny A, Farrés J. Structural analysis of sulindac as an inhibitor of aldose reductase and AKR1B10. Chem Biol Interact 2014; 234:290-6. [PMID: 25532697 DOI: 10.1016/j.cbi.2014.12.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 12/23/2022]
Abstract
Aldose reductase (AR, AKR1B1) and AKR1B10 are enzymes implicated in important pathologies (diabetes and cancer) and therefore they have been proposed as suitable targets for drug development. Sulindac is the metabolic precursor of the potent non-steroidal anti-inflammatory drug (NSAID) sulindac sulfide, which suppresses prostaglandin production by inhibition of cyclooxygenases (COX). In addition, sulindac has been found to be one of the NSAIDs with higher antitumoral activity, presumably through COX inhibition. However, sulindac anticancer activity could be partially mediated through COX-independent mechanisms, including the participation of AR and AKR1B10. Previously, it had been shown that sulindac and sulindac sulfone were good AR inhibitors and the structure of the ternary complex with NADP(+) and sulindac was described (PDB ID 3U2C). In this work, we determined the three-dimensional structure of AKR1B10 with sulindac and established structure-activity relationships (SAR) of sulindac and their derivatives with AR and AKR1B10. The difference in the IC50 values for sulindac between AR (0.36 μM) and AKR1B10 (2.7 μM) might be explained by the different positioning and stacking interaction given by Phe122/Phe123, and by the presence of two buried and ordered water molecules in AKR1B10 but not in AR. Moreover, SAR analysis shows that the substitution of the sulfinyl group is structurally allowed in sulindac derivatives. Hence, sulindac and its derivatives emerge as lead compounds for the design of more potent and selective AR and AKR1B10 inhibitors.
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Affiliation(s)
- Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire - Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Francesc X Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire - Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Isidro Crespo
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain
| | - André Mitschler
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire - Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire - Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain.
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Cousido-Siah A, Ruiz FX, Mitschler A, Porté S, de Lera ÁR, Martín MJ, Manzanaro S, de la Fuente JA, Terwesten F, Betz M, Klebe G, Farrés J, Parés X, Podjarny A. Identification of a novel polyfluorinated compound as a lead to inhibit the human enzymes aldose reductase and AKR1B10: structure determination of both ternary complexes and implications for drug design. ACTA ACUST UNITED AC 2014; 70:889-903. [PMID: 24598757 DOI: 10.1107/s1399004713033452] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/10/2013] [Indexed: 01/09/2023]
Abstract
Aldo-keto reductases (AKRs) are mostly monomeric enzymes which fold into a highly conserved (α/β)8 barrel, while their substrate specificity and inhibitor selectivity are determined by interaction with residues located in three highly variable external loops. The closely related human enzymes aldose reductase (AR or AKR1B1) and AKR1B10 are of biomedical interest because of their involvement in secondary diabetic complications (AR) and in cancer, e.g. hepatocellular carcinoma and smoking-related lung cancer (AKR1B10). After characterization of the IC50 values of both AKRs with a series of polyhalogenated compounds, 2,2',3,3',5,5',6,6'-octafluoro-4,4'-biphenyldiol (JF0064) was identified as a lead inhibitor of both enzymes with a new scaffold (a 1,1'-biphenyl-4,4'-diol). An ultrahigh-resolution X-ray structure of the AR-NADP(+)-JF0064 complex has been determined at 0.85 Å resolution, allowing it to be observed that JF0064 interacts with the catalytic residue Tyr48 through a negatively charged hydroxyl group (i.e. the acidic phenol). The non-competitive inhibition pattern observed for JF0064 with both enzymes suggests that this acidic hydroxyl group is also present in the case of AKR1B10. Moreover, the combination of surface lysine methylation and the introduction of K125R and V301L mutations enabled the determination of the X-ray crystallographic structure of the corresponding AKR1B10-NADP(+)-JF0064 complex. Comparison of the two structures has unveiled some important hints for subsequent structure-based drug-design efforts.
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Affiliation(s)
- Alexandra Cousido-Siah
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSER/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Francesc X Ruiz
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSER/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - André Mitschler
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSER/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Ángel R de Lera
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, Spain
| | - María J Martín
- Biomar Microbial Technologies S.A., Parque Tecnológico de León, 24009 León, Spain
| | - Sonia Manzanaro
- Biomar Microbial Technologies S.A., Parque Tecnológico de León, 24009 León, Spain
| | - Jesús A de la Fuente
- Biomar Microbial Technologies S.A., Parque Tecnológico de León, 24009 León, Spain
| | - Felix Terwesten
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Michael Betz
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Alberto Podjarny
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSER/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
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26
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Fanfrlík J, Kolář M, Kamlar M, Hurný D, Ruiz FX, Cousido-Siah A, Mitschler A, Řezáč J, Munusamy E, Lepšík M, Matějíček P, Veselý J, Podjarny A, Hobza P. Modulation of aldose reductase inhibition by halogen bond tuning. ACS Chem Biol 2013; 8:2484-92. [PMID: 23988122 DOI: 10.1021/cb400526n] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this paper, we studied a designed series of aldose reductase (AR) inhibitors. The series was derived from a known AR binder, which had previously been shown to form a halogen bond between its bromine atom and the oxygen atom of the Thr-113 side chain of AR. In the series, the strength of the halogen bond was modulated by two factors, namely bromine-iodine substitution and the fluorination of the aromatic ring in several positions. The role of the single halogen bond in AR-ligand binding was elucidated by advanced binding free energy calculations involving the semiempirical quantum chemical Hamiltonian. The results were complemented with ultrahigh-resolution X-ray crystallography and IC50 measurements. All of the AR inhibitors studied were shown by X-ray crystallography to bind in an identical manner. Further, it was demonstrated that it was possible to decrease the IC50 value by about 1 order of magnitude by tuning the strength of the halogen bond by a monoatomic substitution. The calculations revealed that the protein-ligand interaction energy increased upon the substitution of iodine for bromine or upon the addition of electron-withdrawing fluorine atoms to the ring. However, the effect on the binding affinity was found to be more complex due to the change of the solvation/desolvation properties within the ligand series. The study shows that it is possible to modulate the strength of a halogen bond in a protein-ligand complex as was designed based on the previous studies of low-molecular-weight complexes.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Michal Kolář
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Martin Kamlar
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - David Hurný
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Francesc X. Ruiz
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alexandra Cousido-Siah
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - André Mitschler
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Jan Řezáč
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Elango Munusamy
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Martin Lepšík
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Pavel Matějíček
- Department
of Physical and Macromolecular Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Jan Veselý
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Alberto Podjarny
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Pavel Hobza
- Institute of Organic
Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
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27
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Mory A, Ruiz FX, Dagan E, Yakovtseva EA, Kurolap A, Parés X, Farrés J, Gershoni-Baruch R. A missense mutation in ALDH1A3 causes isolated microphthalmia/anophthalmia in nine individuals from an inbred Muslim kindred. Eur J Hum Genet 2013; 22:419-22. [PMID: 23881059 DOI: 10.1038/ejhg.2013.157] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/19/2013] [Accepted: 05/27/2013] [Indexed: 11/09/2022] Open
Abstract
Nine affected individuals with isolated anophthalmia/microphthalmia from a large Muslim-inbred kindred were investigated. Assuming autosomal-recessive mode of inheritance, whole-genome linkage analysis, on DNA samples from four affected individuals, was undertaken. Homozygosity mapping techniques were employed and a 1.5-Mbp region, homozygous in all affected individuals, was delineated. The region contained nine genes, one of which, aldehyde dehydrogenase 1 (ALDH1A3), was a clear candidate. This gene seems to encode a key enzyme in the formation of a retinoic-acid gradient along the dorsoventral axis during an early eye development and the development of the olfactory system. Sanger sequence analysis revealed a missense mutation, causing a substitution of valine (Val) to methionine (Met) at position 71. Analyzing the p.Val71Met missense mutation using standard open access software (MutationTaster online, PolyPhen, SIFT/PROVEAN) predicts this variant to be damaging. Enzymatic activity, studied in vitro, showed no changes between the mutated and the wild-type ALDH1A3 protein.
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Affiliation(s)
- Adi Mory
- 1] Institute of Human Genetics, Rambam Health Care Campus, Haifa, Israel [2] The Ruth and Bruce Rappaport Faculty of Medicine, Technion Institute of Technology, Haifa, Israel
| | - Francesc X Ruiz
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Efrat Dagan
- 1] The Ruth and Bruce Rappaport Faculty of Medicine, Technion Institute of Technology, Haifa, Israel [2] Department of Nursing, University of Haifa, Haifa, Israel
| | - Evgenia A Yakovtseva
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alina Kurolap
- Institute of Human Genetics, Rambam Health Care Campus, Haifa, Israel
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ruth Gershoni-Baruch
- 1] Institute of Human Genetics, Rambam Health Care Campus, Haifa, Israel [2] The Ruth and Bruce Rappaport Faculty of Medicine, Technion Institute of Technology, Haifa, Israel
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28
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Golebiowski A, Paul Beckett R, Van Zandt M, Ji MK, Whitehouse D, Ryder TR, Jagdmann E, Andreoli M, Mazur A, Padmanilayam M, Cousido-Siah A, Mitschler A, Ruiz FX, Podjarny A, Schroeter H. 2-Substituted-2-amino-6-boronohexanoic acids as arginase inhibitors. Bioorg Med Chem Lett 2013; 23:2027-30. [DOI: 10.1016/j.bmcl.2013.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 01/26/2013] [Accepted: 02/01/2013] [Indexed: 11/17/2022]
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29
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Van Zandt MC, Whitehouse DL, Golebiowski A, Ji MK, Zhang M, Beckett RP, Jagdmann GE, Ryder TR, Sheeler R, Andreoli M, Conway B, Mahboubi K, D’Angelo G, Mitschler A, Cousido-Siah A, Ruiz FX, Howard EI, Podjarny AD, Schroeter H. Discovery of (R)-2-Amino-6-borono-2-(2-(piperidin-1-yl)ethyl)hexanoic Acid and Congeners As Highly Potent Inhibitors of Human Arginases I and II for Treatment of Myocardial Reperfusion Injury. J Med Chem 2013; 56:2568-80. [DOI: 10.1021/jm400014c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael C. Van Zandt
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Darren L. Whitehouse
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Adam Golebiowski
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Min Koo Ji
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Mingbao Zhang
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - R. Paul Beckett
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - G. Erik Jagdmann
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Todd R. Ryder
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Ryan Sheeler
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Monica Andreoli
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Bruce Conway
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Keyvan Mahboubi
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Gerard D’Angelo
- The Institutes for Pharmaceutical Discovery, LLC, 23 Business Park
Drive, Branford, Connecticut 06405, United States
| | - Andre Mitschler
- Department of Integrative Biology,
IGBMC, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Alexandra Cousido-Siah
- Department of Integrative Biology,
IGBMC, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Francesc X. Ruiz
- Department of Integrative Biology,
IGBMC, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Eduardo I. Howard
- Department of Integrative Biology,
IGBMC, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
- IFLYSIB, Conicet, UNLP, Calle 59 N° 789, La Plata, Argentina
| | - Alberto D. Podjarny
- Department of Integrative Biology,
IGBMC, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Hagen Schroeter
- Mars, Incorporated, 6885
Elm Street, McLean,Virginia 22101, United States
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30
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Cousido-Siah A, Petrova T, Hazemann I, Mitschler A, Ruiz FX, Howard E, Ginell S, Atmanene C, Van Dorsselaer A, Sanglier-Cianférani S, Joachimiak A, Podjarny A. Crystal packing modifies ligand binding affinity: the case of aldose reductase. Proteins 2012; 80:2552-61. [PMID: 22752989 DOI: 10.1002/prot.24136] [Citation(s) in RCA: 12] [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] [Received: 04/16/2012] [Revised: 06/05/2012] [Accepted: 06/13/2012] [Indexed: 01/06/2023]
Abstract
The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; K(d) = 6.5 nM) and IDD594 (594; K(d) = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used.
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Affiliation(s)
- Alexandra Cousido-Siah
- Department of Integrative Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, Illkirch, France
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