Alignment-independent QSAR analysis of SecA inhibitors

Protein and Peptide Letters

Volumn 20, Issue 7, 2013, Pages 802-807

  Xu, Min ^a   Bi, Yiling ^b   Zhu, Mengyuan ^b   Li, Minyong ^b  

^a Chinese People's Armed Police Forces   (China)

^b SHANDONG UNIVERSITY   (China)

Author keywords

3D QSAR; Antimicrobial drug; Inhibitors; SecA ATPase

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; ANTIINFECTIVE AGENT; BTB 06881; CD 09529; CJ 21058; HTS 12302; HYDROGEN; KM 03277; MONOMER; PROTEIN SECA; SECA INHIBITOR; SEW 05929; SP 00943; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DRUG STRUCTURE; DRUG SYNTHESIS; ESCHERICHIA COLI; HYDROGEN BOND; HYDROPHOBICITY; IC 50; LIGAND BINDING; MOLECULAR DOCKING; NONHUMAN; PROTEIN BINDING; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SEQUENCE ALIGNMENT;

ADENOSINE TRIPHOSPHATASES; ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; ENZYME INHIBITORS; MEMBRANE TRANSPORT PROTEINS; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84882333152     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/0929866511320070010     Document Type: Article

References (25)

1. Wang, L.; Wang, Y.; Jin, S.; Wu, Z.; Chin, D.P.; Koplan, J.P.; Wilson, M.E. Emergence and control of infectious diseases in China. Lancet, 2008, 372, 1598-1605.
2. Heddini, A.; Cars, O.; Qiang, S.; Tomson, G. Antibiotic resistance in China-A major future challenge. Lancet, 2009, 373, 30.
3. Cabelli, R.J.; Dolan, K.M.; Qian, L.P.; Oliver, D.B. Characterization of membrane-Associated and soluble states of SecA protein from wild-Type and SecA51(TS) mutant strains of Escherichia coli. J. Biol. Chem., 1991, 266, 24420-24427.
4. Economou, A. Sec, drugs and rock'n'roll: antibiotic targeting of bacterial protein translocation. Expert Opin. Ther. Targets, 2001, 5, 141-153.
5. Saier, M.H. Protein secretion and membrane insertion systems in gram-negative bacteria. J. Membr. Biol., 2006, 214, 75-90.
6. Driessen, A.J.; Fekkes, P.; van der Wolk, J.P. The Sec system. Curr. Opin. Microbiol., 1998, 1, 216-222.
7. Mori, H.; Ito, K. The Sec protein-Translocation pathway. Trends Microbiol., 2001, 9, 494-500.
8. van Klompenburg, W.; Ridder, A.N.; van Raalte, A.L.; Killian, A.J.; von Heijne, G.; de Kruijff, B. In vitro membrane integration of leader peptidase depends on the Sec machinery and anionic phospholipids and can occur post-Translationally. FEBS Lett., 1997, 413, 109-114.
9. Lill, R.; Dowhan, W.; Wickner, W. The ATPase activity of SecA is regulated by acidic phospholipids, SecY, and the leader and mature domains of precursor proteins. Cell, 1990, 60, 271-280.
10. Papanikou, E.; Karamanou, S.; Economou, A. Bacterial protein secretion through the translocase nanomachine. Nat. Rev. Microbiol., 2007, 5, 839-851.
11. Driessen, A.J.; Nouwen, N. Protein translocation across the bacterial cytoplasmic membrane. Annu. Rev. Biochem., 2008, 77, 643-667.
12. Erlandson, K.J.; Miller, S.B.; Nam, Y.; Osborne, A.R.; Zimmer, J.; Rapoport, T.A. A role for the two-helix finger of the SecA ATPase in protein translocation. Nature, 2008, 455, 984-987.
13. Papanikolau, Y.; Papadovasilaki, M.; Ravelli, R.B.; McCarthy, A.A.; Cusack, S.; Economou, A.; Petratos, K. Structure of dimeric SecA, the Escherichia coli preprotein translocase motor. J. Mol. Biol., 2007, 366, 1545-1557.
14. Vrontou, E.; Economou, A. Structure and function of SecA, the preprotein translocase nanomotor. Biochim. Biophys. Acta, 2004, 1694, 67-80.
15. Li, M.; Huang, Y.J.; Tai, P.C.; Wang, B. Discovery of the first SecA inhibitors using structure-based virtual screening. Biochem. Biophys. Res. Commun., 2008, 368, 839-845.
16. Chen, W.; Huang, Y.J.; Gundala, S.R.; Yang, H.; Li, M.; Tai, P.C.; Wang, B. The first low microM SecA inhibitors. Bioorg. Med. Chem., 2010, 18, 1617-1625.
17. Huang, Y.J.; Wang, H.; Gao, F.B.; Li, M.; Yang, H.; Wang, B.; Tai, P.C. Fluorescein analogues inhibit SecA ATPase: the first submicromolar inhibitor of bacterial protein translocation. ChemMed-Chem, 2012, 7, 571-577.
18. Sugie, Y.; Inagaki, S.; Kato, Y.; Nishida, H.; Pang, C.H.; Saito, T.; Sakemi, S.; Dib-Hajj, F.; Mueller, J.P.; Sutcliffe, J.; Kojima, Y. CJ.-21,058, a new SecA inhibitor isolated from a fungus. J. Antibiot., 2002, 55, 25-29.
19. Jang, M. Y.; De Jonghe, S.; Segers, K.; Anne, J.; Herdewijn, P. Synthesis of novel 5-Amino-Thiazolo[4,5-d]pyrimidines as E. coli and S. Aureus SecA inhibitors. Bioorg. Med. Chem., 2011, 19, 702-714.
20. Akula, N.; Trivedi, P.; Han, F.Q.; Wang, N. Identification of small molecule inhibitors against SecA of Candidatus Liberibacter asiaticus by structure based design. Eur. J. Med. Chem., 2012, 54, 919-924.
21. Cramer, R.D.; Patterson, D.E.; Bunce, J.D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 1988, 110, 5959-5967.
22. Klebe, G.; Abraham, U. Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries. J. Comput. Aided Mol. Des., 1999, 13, 1-10.
23. Pastor, M.; Cruciani, G.; McLay, I.; Pickett, S.; Clementi, S. GRid-INdependent descriptors (GRIND): a novel class of alignment independent three-dimensional molecular descriptors. J. Med. Chem., 2000, 43, 3233-3243.
24. Goodford, P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem., 1985, 28, 849-857.
25. Kuntz, I.D.; Blaney, J.M.; Oatley, S.J.; Langridge, R.; Ferrin, T.E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol., 1982, 161, 269-288.