Structure of a Dihydroxycoumarin Active-Site Inhibitor in Complex with the RNase H Domain of HIV-1 Reverse Transcriptase and Structure-Activity Analysis of Inhibitor Analogs

被引:33
作者
Himmel, Daniel M. [1 ,2 ]
Myshakina, Nataliya S. [3 ]
Ilina, Tatiana [3 ]
Van Ry, Alexander [3 ]
Ho, William C. [1 ,2 ]
Parniak, Michael A. [3 ]
Arnold, Eddy [1 ,2 ]
机构
[1] Rutgers State Univ, Ctr Adv Biotechnol & Med, Piscataway, NJ 08854 USA
[2] Rutgers State Univ, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA
[3] Univ Pittsburgh, Sch Med, Dept Microbiol & Mol Genet, Pittsburgh, PA 15219 USA
基金
美国国家卫生研究院;
关键词
RIBONUCLEASE-H; CRYSTAL-STRUCTURES; RNA/DNA HYBRID; BINDING-SITES; RESISTANCE; ACID; RESOLUTION; MUTATIONS; IDENTIFICATION; MECHANISM;
D O I
10.1016/j.jmb.2014.05.006
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Human immunodeficiency virus (HIV) encodes four essential enzymes: protease, integrase, reverse transcriptase (RT)-associated DNA polymerase, and RT-associated ribonuclease H (RNase H). Current clinically approved anti-AIDS drugs target all HIV enzymatic activities except RNase H, which has proven to be a very difficult target for HIV drug discovery. Our high-throughput screening activities identified the dihydroxycoumarin compound F3284-8495 as a specific inhibitor of RT RNase H, with low micromolar potency in vitro. Optimization of inhibitory potency can be facilitated by structural information about inhibitor-target binding. Here, we report the crystal structure of F3284-8495 bound to the active site of an isolated RNase H domain of HIV-1 RI at a resolution limit of 1.71 angstrom. From predictions based on this structure, compounds were obtained that showed improved inhibitory activity. Computational analysis suggested structural alterations that could provide additional interactions with RT and thus improve inhibitory potency. These studies established proof of concept that F3284-8495 could be used as a favorable chemical scaffold for development of HIV RNase H inhibitors. (C) 2014 Elsevier Ltd. All rights reserved.
引用
收藏
页码:2617 / 2631
页数:15
相关论文
共 54 条
[1]   Nonnucleoside Reverse Transcriptase Inhibitor Resistance and the Role of the Second-Generation Agents [J].
Adams, Jessica ;
Patel, Nimish ;
Mankaryous, Nancy ;
Tadros, Mariam ;
Miller, Christopher D. .
ANNALS OF PHARMACOTHERAPY, 2010, 44 (01) :157-165
[2]   PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].
Adams, Paul D. ;
Afonine, Pavel V. ;
Bunkoczi, Gabor ;
Chen, Vincent B. ;
Davis, Ian W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Hung, Li-Wei ;
Kapral, Gary J. ;
Grosse-Kunstleve, Ralf W. ;
McCoy, Airlie J. ;
Moriarty, Nigel W. ;
Oeffner, Robert ;
Read, Randy J. ;
Richardson, David C. ;
Richardson, Jane S. ;
Terwilliger, Thomas C. ;
Zwart, Peter H. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221
[3]   Towards automated crystallographic structure refinement with phenix.refine [J].
Afonine, Pavel V. ;
Grosse-Kunstleve, Ralf W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Moriarty, Nigel W. ;
Mustyakimov, Marat ;
Terwilliger, Thomas C. ;
Urzhumtsev, Alexandre ;
Zwart, Peter H. ;
Adams, Paul D. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2012, 68 :352-367
[4]   Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design [J].
Bauman, Joseph D. ;
Das, Kalyan ;
Ho, William C. ;
Baweja, Mukta ;
Himmel, Daniel M. ;
Clark, Arthur D., Jr. ;
Oren, Deena A. ;
Boyer, Paul L. ;
Hughes, Stephen H. ;
Shatkin, Aaron J. ;
Arnold, Eddy .
NUCLEIC ACIDS RESEARCH, 2008, 36 (15) :5083-5092
[5]  
Bell JA, 2012, International Tables for Crystallography, VA-G, P534
[6]   Inhibition of the ribonuclease H and DNA polymerase activities of HIV-1 reverse transcriptase by N-(4-tert-butylbenzoyl)-2-hydroxy-1-naphthaldehyde hydrazone [J].
Borkow, G ;
Fletcher, RS ;
Barnard, J ;
Arion, D ;
Motakis, D ;
Dmitrienko, GI ;
Parniak, MA .
BIOCHEMISTRY, 1997, 36 (11) :3179-3185
[7]   Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].
Brunger, AT ;
Adams, PD ;
Clore, GM ;
DeLano, WL ;
Gros, P ;
Grosse-Kunstleve, RW ;
Jiang, JS ;
Kuszewski, J ;
Nilges, M ;
Pannu, NS ;
Read, RJ ;
Rice, LM ;
Simonson, T ;
Warren, GL .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921
[8]   Synthesis, Activity, and Structural Analysis of Novel α-Hydroxytropolone Inhibitors of Human Immunodeficiency Virus Reverse Transcriptase-Associated Ribonuclease H [J].
Chung, Suhman ;
Himmel, Daniel M. ;
Jiang, Jian-Kang ;
Wojtak, Krzysztof ;
Bauman, Joseph D. ;
Rausch, Jason W. ;
Wilson, Jennifer A. ;
Beutler, John A. ;
Thomas, Craig J. ;
Arnold, Eddy ;
Le Grice, Stuart F. J. .
JOURNAL OF MEDICINAL CHEMISTRY, 2011, 54 (13) :4462-4473
[9]   High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: Strategic flexibility explains potency against resistance mutations [J].
Das, Kalyan ;
Bauman, Joseph D. ;
Clark, Arthur D., Jr. ;
Frenkel, Yulia V. ;
Lewi, Paul J. ;
Shatkin, Aaron J. ;
Hughes, Stephen H. ;
Arnold, Eddy .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (05) :1466-1471
[10]   CRYSTAL-STRUCTURE OF THE RIBONUCLEASE-H DOMAIN OF HIV-1 REVERSE-TRANSCRIPTASE [J].
DAVIES, JF ;
HOSTOMSKA, Z ;
HOSTOMSKY, Z ;
JORDAN, SR ;
MATTHEWS, DA .
SCIENCE, 1991, 252 (5002) :88-95