Discovery of the first SecA inhibitors using structure-based virtual screening

Biochemical and Biophysical Research Communications - Tập 368 - Trang 839-845 - 2008
Minyong Li1, Ying-Ju Huang2, Phang C. Tai2, Binghe Wang1
1Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Campus Box 4098, Atlanta, GA 30302-4098, USA
2Department of Biology, Georgia State University, Atlanta, GA 30302-4010, USA

Tài liệu tham khảo

Mori, 2001, The Sec protein-translocation pathway, Trends Microbiol., 9, 494, 10.1016/S0966-842X(01)02174-6 Saier, 2006, Protein secretion and membrane insertion systems in Gram-negative bacteria, J. Membr. Biol., 214, 75, 10.1007/s00232-006-0049-7 van Klompenburg, 1997, In vitro membrane integration of leader peptidase depends on the Sec machinery and anionic phospholipids and can occur post-translationally, FEBS Lett., 413, 109, 10.1016/S0014-5793(97)00888-0 Lill, 1990, The ATPase activity of SecA is regulated by acidic phospholipids, SecY, and the leader and mature domains of precursor proteins, Cell, 60, 271, 10.1016/0092-8674(90)90742-W Knott, 1994, The SecA inhibitor, azide, reversibly blocks the translocation of a subset of proteins across the chloroplast thylakoid membrane, J. Biol. Chem., 269, 7843, 10.1016/S0021-9258(17)37125-9 Oliver, 1990, Azide-resistant Mutants of Escherichia coli Alter the SecA Protein, An Azide-sensitive Component of the Protein Export Machinery, Proc. Natl. Acad. Sci. USA, 87, 8227, 10.1073/pnas.87.21.8227 Yoshikawa, 1998, Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase, Science, 280, 1723, 10.1126/science.280.5370.1723 Bowler, 2006, How azide inhibits ATP hydrolysis by the F-ATPases, Proc. Natl. Acad. Sci. USA, 103, 8646, 10.1073/pnas.0602915103 Stoddard, 1990, The structure of iron superoxide dismutase from Pseudomonas ovalis complexed with the inhibitor azide, Protein Eng., 4, 113, 10.1093/protein/4.2.113 Yound, 1971, The nature of binding of competitive inhibitors to alcohol dehydrogenases, J. Biol. Chem., 246, 2815, 10.1016/S0021-9258(18)62255-0 Zaitsev, 1999, An X-ray crystallographic study of the binding sites of the azide inhibitor and organic substrates to ceruloplasmin, a multi-copper oxidase in the plasma, J. Biol. Inorg. Chem., 4, 579, 10.1007/s007750050380 Sugie, 2002, CJ-21,058, a new SecA inhibitor isolated from a fungus, J. Antibiot., 55, 25, 10.7164/antibiotics.55.25 Papanikolau, 2007, Structure of dimeric SecA, the Escherichia coli preprotein translocase motor, J. Mol. Biol., 366, 1545, 10.1016/j.jmb.2006.12.049 Schneider, 2002, Virtual screening and fast automated docking methods, Drug Discov. Today, 7, 64, 10.1016/S1359-6446(01)02091-8 Lyne, 2002, Structure-based virtual screening: an overview, Drug Discov. Today, 7, 1047, 10.1016/S1359-6446(02)02483-2 Bajorath, 2002, Integration of virtual and high-throughput screening, Nat. Rev. Drug Discov., 1, 882, 10.1038/nrd941 Bologa, 2006, Virtual and biomolecular screening converge on a selective agonist for GPR30, Nat. Chem. Biol., 2, 207, 10.1038/nchembio775 Pearlman, 1987, CONCORD: rapid generation of high quality approximate 3D molecular structures, Chem. Des. Autom. News, 2, 1 SYBYL 7.1, Tripos Inc., St. Louis, MS, 2005. Jakalian, 2000, Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method, J. Comput. Chem., 21, 132, 10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P Jakalian, 2002, Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation, J. Comput. Chem., 23, 1623, 10.1002/jcc.10128 QuACPAC, OpenEye Scientific Software, Inc., Santa Fe, NM, Quality Atomic Charges, Proton Assignment and Canonicalization, 2007. Ewing, 2001, DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases, J. Comput. Aided Mol. Des., 15, 411, 10.1023/A:1011115820450 Moustakas, 2006, Development and validation of a modular, extensible docking program: DOCK 5, J. Comput. Aided Mol. Des., 20, 601, 10.1007/s10822-006-9060-4 Muegge, 2003, Selection criteria for drug-like compounds, Med. Res. Rev., 23, 302, 10.1002/med.10041 FRED, OpenEye Scientific Software, Inc., Santa Fe, NM, Fast Rigid Exhaustive Docking, 2007. Feher, 2006, Consensus scoring for protein–ligand interactions, Drug Discov. Today, 11, 421, 10.1016/j.drudis.2006.03.009 Eldridge, 1997, Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes, J. Comput. Aided Mol. Des., 11, 425, 10.1023/A:1007996124545 Murray, 1998, Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand–receptor binding affinities and the use of Bayesian regression to improve the quality of the model, J Comput. Aided Mol. Des., 12, 503, 10.1023/A:1008040323669 Verkhivker, 2000, Deciphering common failures in molecular docking of ligand–protein complexes, J. Comput. Aided Mol. Des., 14, 731, 10.1023/A:1008158231558 Stahl, 2001, Detailed analysis of scoring functions for virtual screening, J. Med. Chem., 44, 1035, 10.1021/jm0003992 McGann, 2003, Gaussian docking functions, Biopolymers, 68, 76, 10.1002/bip.10207 IDEA, Breadth Technology, Taipei, Taiwan, 2007. Li, 2006, Computational studies of H5N1 hemagglutinin binding with SA-alpha-2, 3-Gal and SA-alpha-2, 6-Gal, Biochem. Biophys. Res. Commun., 347, 662, 10.1016/j.bbrc.2006.06.179 Li, 2007, Homology modeling and examination of the effect of the D92E mutation on the H5N1 nonstructural protein NS1 effector domain, J. Mol. Model., 13, 1237, 10.1007/s00894-007-0245-0 Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79, 926, 10.1063/1.445869 Case, 2005, The Amber biomolecular simulation programs, J. Comput. Chem., 26, 1668, 10.1002/jcc.20290 W.L. DeLano, The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA, USA. Available from: http://www.pymol.org, 2006. McDonald, 1994, Satisfying hydrogen bonding potential in proteins, J. Mol. Biol., 238, 777, 10.1006/jmbi.1994.1334 Wallace, 1995, LIGPLOT: a program to generate schematic diagrams of protein–ligand interactions, Protein Eng., 8, 127, 10.1093/protein/8.2.127 Schmidt, 1989, SecA protein autogenously represses its own translation during normal protein secretion in Escherichia coli, J. Bacteriol., 171, 643, 10.1128/jb.171.2.643-649.1989 Karamanou, 1999, A molecular switch in SecA protein couples ATP hydrolysis to protein translocation, Mol. Microbiol., 34, 1133, 10.1046/j.1365-2958.1999.01686.x Chen, 1996, A significant fraction of functional SecA is permanently embedded in the membrane. SecA cycling on and off the membrane is not essential during protein translocation, J. Biol. Chem., 271, 29698, 10.1074/jbc.271.47.29698 Chen, 1998, Identification and characterization of protease-resistant SecA fragments: SecA has two membrane-integral forms, J. Bacteriol., 180, 527, 10.1128/JB.180.3.527-537.1998 Dempsey, 2002, The ATPase domain of SecA can form a tetramer in solution, J. Mol. Biol., 315, 831, 10.1006/jmbi.2001.5279