Resisting resistant Mycobacterium tuberculosis naturally: Mechanistic insights into the inhibition of the parasite's sole signal peptidase Leader peptidase B

Biochemical and Biophysical Research Communications

Volumn 433, Issue 4, 2013, Pages 552-557

  Dhiman, Heena ^a   Dhanjal, Jaspreet Kaur ^a   Sharma, Sudhanshu ^a   Chacko, Sajeev ^b   Grover, Sonam ^c   Grover, Abhinav ^c  

^a DELHI TECHNOLOGICAL UNIVERSITY   (India)

^b INTER UNIVERSITY ACCELERATOR CENTRE   (India)

^c JAWAHARLAL NEHRU UNIVERSITY   (India)

Author keywords

Inhibition; LepB; Mycobacterium; Screening; Signal peptidase; Tuberculosis

Indexed keywords

LEADER PEPTIDASE B; PEPTIDASE; TUBERCULOSTATIC AGENT; UNCLASSIFIED DRUG; ZINC 08234345; ZINC 70454376;

ARTICLE; BACTERIAL GROWTH; CATALYSIS; DRUG BINDING; DRUG SCREENING; DRUG STRUCTURE; ENZYME INHIBITION; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; ANTITUBERCULAR AGENTS; BACTERIAL PROTEINS; BIOLOGICAL AGENTS; CAFFEIC ACIDS; CATALYTIC DOMAIN; CHROMONES; DATABASES, PHARMACEUTICAL; DISACCHARIDES; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ENZYME ACTIVATION; HIGH-THROUGHPUT SCREENING ASSAYS; LIGANDS; MEMBRANE PROTEINS; MOLECULAR DYNAMICS SIMULATION; MYCOBACTERIUM TUBERCULOSIS; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEIN STABILITY; PROTEIN STRUCTURE, TERTIARY; SERINE ENDOPEPTIDASES;

MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS;

EID: 84876497910     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2013.03.013     Document Type: Article

References (33)

1. Sassetti C.M., Boyd D.H., Rubin E.J. Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003, 48:77-84.
2. Feltcher M.E., Sullivan J.T., Braunstein M. Protein export systems of Mycobacterium tuberculosis: novel targets for drug development?. Future Microbiol. 2010, 5:1581-1597.
3. Economou A., Wickner W. SecA promotes preprotein translocation by undergoing ATP-driven cycles of membrane insertion and deinsertion. Cell 1994, 78:835-843.
4. Braun V., Wu H.C. Lipoproteins, structure, function, biosynthesis and models for protein export. Bacterial Cell Wall 1993, 319-342. Elsevier, Amsterdam. M. Ghuysen, R. Hakenback (Eds.).
5. Ollinger J., O'Malley T., Ahn J., Odingo J., Parish T. Inhibition of the sole type I signal peptidase of Mycobacterium tuberculosis is bactericidal under replicating and nonreplicating conditions. J. Bacteriol. 2012, 194:2614-2619.
6. Tuteja R. Type I signal peptidase: an overview. Arch. Biochem. Biophys. 2005, 441:107-111.
7. Paetzel M., Karla A., Strynadka N.C., Dalbey R.E. Signal peptidases. Chem. Rev. 2002, 102:4549-4580.
8. Barbosa M.D.F.S., Lin S., Markwalder J.A., Mills J.A., DeVito J.A., Teleha C.A., Garlapati V., Liu C., Thompson A., Trainor G.L., Kurilla M.G., Pompliano D.L. Regulated expression of the Escherichia coli lepB gene as a tool for cellular testing of antimicrobial compounds that inhibit signal peptidase I in vitro. Antimicrob. Agents Chemother. 2002, 46:3549-3554.
9. Paetzel M., Dalbey R.E., Strynadka N.C. Crystal structure of a bacterial signal peptidase in complex with a beta-lactam inhibitor. Nature 1998, 396:186-190.
10. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21:951-960.
11. Jefferys B.R., Kelley L.A., Sternberg M.J. Protein folding requires crowd control in a simulated cell. J. Mol. Biol. 2010, 397:1329-1338.
12. Eisenberg D., Luthy R., Bowie J.U. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 1997, 277:396-404.
13. Luthy R., Bowie J.U., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992, 356:83-85.
14. Schrodinger Schrodinger Suite 2009, Schrodinger, LLC, New York.
15. Irwin J.J., Shoichet B.K. ZINC - a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 2005, 45:177-182.
16. Laurie A.T., Jackson R.M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21:1908-1916.
17. Friesner R.A., Banks J.L., Murphy R.B., Halgren T.A., Klicic J.J., Mainz D.T., Repasky M.P., Knoll E.H., Shelley M., Perry J.K., Shaw D.E., Francis P., Shenkin P.S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47:1739-1749.
18. Halgren T.A., Murphy R.B., Friesner R.A., Beard H.S., Frye L.L., Pollard W.T., Banks J.L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47:1750-1759.
19. Van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J.C. GROMACS: Fast, flexible, and free. J. Comput. Chem. 2005, 26:1701-1718.
20. Lindorff-Larsen K., Piana S., Palmo K., Maragakis P., Klepeis J.L., Dror R.O., Shaw D.E. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins: Struct., Funct., Bioinf. 2010, 78:1950-1958.
21. Wang J.M., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25:1157-1174.
22. Case D.A., Darden T.A., Cheatham T.E., Simmerling C.L., Wang J., Duke R.E., Luo R., Walker R.C., Zhang W., Merz K.M., Roberts B., Hayik S., Roitberg A., Seabra G., Swails J., Goetz A.W., Kolossváry I., Wong K.F., Paesani F., Vanicek J., Wolf R.M., Liu J., Wu X.Y., Brozell S.R., Steinbrecher T., Gohlke H., Cai Q., Ye X., Wang J., Hsieh M.J., Cui G., Roe D.R., Mathews D.H., Seetin M.G., Salomon-Ferrer R., Sagui C., Babin V., Luchko T., Gusarov S., Kovalenko A., Kollman P.A. AMBER 12 2012, University of California, San Francisco.
23. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79:926-935.
24. Parrinello M., Rahman A. Polymorphic transitions in single-crystals - a new molecular-dynamics method. J. Appl. Phys. 1981, 52:7182-7190.
25. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103:8577-8593.
26. Ollinger J., O'Malley T., Ahn J., Odingo J., Parish T. Inhibition of the sole type I signal peptidase of Mycobacterium tuberculosis is bactericidal under replicating and nonreplicating conditions. Journal of Bacteriology 2012, 194:2614-2619.
27. Paetzel M., Dalbey R.E., Strynadka N.C. The structure and mechanism of bacterial type I signal peptidases. A novel antibiotic target. Pharmacol. Ther. 2000, 87:27-49.
28. Bytheway I., Cochran S. Validation of molecular docking calculations involving FGF-1 and FGF-2. J. Med. Chem. 2004, 47:1683-1693.
29. Pugsley A.P. The complete general secretory pathway in gram-negative bacteria. Microbiol. Rev. 1993, 57:50-108.
30. Mori H., Ito K. The Sec protein-translocation pathway. Trends Microbiol. 2001, 9:494-500.
31. Dalbey R.E., Wickner W. Leader peptidase catalyzes the release of exported proteins from the outer surface of the Escherichia coli plasma membrane. J. Biol. Chem. 1985, 260:15925-15931.
32. Fikes J.D., Bassford P.J. Export of unprocessed precursor maltose-binding protein to the periplasm of Escherichia coli cells. J. Bacteriol. 1987, 169:2352-2359.
33. Auclair S.M., Bhanu M.K., Kendall D.A. Signal peptidase I: cleaving the way to mature proteins. Protein Sci. 2012, 21:13-25.