Pharmacophore-Based Virtual Screening to Aid in the Identification of Unknown Protein Function

Chemical Biology and Drug Design

Volumn 80, Issue 6, 2012, Pages 828-842

  Mallipeddi, Prema L ^a   Joshi, Manali ^a,b   Briggs, James M ^a  

^a University of Houston   (United States)

^b UNIVERSITY OF PUNE   (India)

Author keywords

Binding site prediction; Pharmacophore modeling; Protein function prediction; Tanimoto coefficient; Virtual screening

Indexed keywords

3 DEOXY 7 PHOSPHOHEPTULONATE SYNTHASE; ADENOSINE DEAMINASE; ARGINASE; DRUG; ENOLASE; FRUCTOSE BISPHOSPHATE ALDOLASE; MANDELATE RACEMASE;

ARTICLE; BINDING SITE; CASTP; DRUG SCREENING; ENZYME SPECIFICITY; HYDROGEN BOND; IONIZATION; METABOLITE; METHODOLOGY; MOLECULAR INTERACTION; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; THEMATICS;

ADENOSINE DEAMINASE; ARGINASE; BINDING SITES; DATABASES, FACTUAL; FRUCTOSE-BISPHOSPHATE ALDOLASE; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; PHOSPHOPYRUVATE HYDRATASE; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RACEMASES AND EPIMERASES; SMALL MOLECULE LIBRARIES; THERMODYNAMICS;

EID: 84868123535     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2012.01408.x     Document Type: Article

References (44)

1. Matthews B.W. (2007) Protein structure initiative: getting into gear. Nat Struct Mol Biol;14:459-460.
2. Norvell J.C., Berg J.M. (2007) Update on the protein structure initiative. Structure;15:1519-1522.
3. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. (2000) The protein data bank. Nucleic Acids Res;28:235-242.
4. Kim S.H., Shin D.H., Choi I.G., Schulze-Gahmen U., Chen S., Kim R. (2003) Structure-based functional inference in structural genomics. J Struct Funct Genomics;4:129-135.
5. Hegyi H., Gerstein M. (1999) The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol;288:147-164.
6. Ofran Y., Punta M., Schneider R., Rost B. (2005) Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discov Today;10:1475-1482.
7. Allali-Hassani A., Pan P.W., Dombrovski L., Najmanovich R., Tempel W., Dong A., Loppnau P., Martin F., Thornton J., Edwards A.M., Bochkarev A., Plotnikov A.N., Vedadi M., Arrowsmith C.H. (2007) Structural and chemical profiling of the human cytosolic sulfotransferases. PLoS Biol;5:e97.
8. Kalyanaraman C., Bernacki K., Jacobson M.P. (2005) Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry;44:2059-2071.
9. Song L., Kalyanaraman C., Fedorov A.A., Fedorov E.V., Glasner M.E., Brown S., Imker H.J., Babbitt P.C., Almo S.C., Jacobson M.P., Gerlt J.A. (2007) Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol;3:486-491.
10. Hermann J.C., Ghanem E., Li Y., Raushel F.M., Irwin J.J., Shoichet B.K. (2006) Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc;128:15882-15891.
11. Hermann J.C., Marti-Arbona R., Fedorov A.A., Fedorov E., Almo S.C., Shoichet B.K., Raushel F.M. (2007) Structure-based activity prediction for an enzyme of unknown function. Nature;448:775-779.
12. Shin D.H., Yokota H., Kim R., Kim S.H. (2002) Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Proc Natl Acad Sci U S A;99:7980-7985.
13. Wilson D., Madera M., Vogel C., Chothia C., Gough J. (2007) The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res;35(Database issue):D308-D313.
14. Sun H (2008) Pharmacophore-based virtual screening. Curr Med Chem;15:1018-1024.
15. Gerlt J.A., Allen K.N., Almo S.C., Armstrong R.N., Babbitt P.C., Cronan J.E., Dunaway-Mariano D., Imker H.J., Jacobson M.P., Minor W., Poulter C.D., Raushel F.M., Sali A., Shoichet B.K., Sweedler J.V. (2011) The enzyme function initiative. Biochemistry;50:9950-9962.
16. Dundas J., Ouyang Z., Tseng J., Binkowski A., Turpaz Y., Liang J. (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res;34(Web Server issue):W116-W118.
17. Ondrechen M.J., Clifton J.G., Ringe D. (2001) THEMATICS: a simple computational predictor of enzyme function from structure. Proc Natl Acad Sci U S A;98:12473-12478.
18. Goodford P.J. (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem;28:849-857.
19. Wilson D.K., Quiocho F.A. (1993) A pre-transition-state mimic of an enzyme: X-ray structure of adenosine deaminase with bound 1-deazaadenosine and zinc-activated water. Biochemistry;32:1689-1694.
20. Dalby A., Dauter Z., Littlechild J.A. (1999) Crystal structure of human muscle aldolase complexed with fructose 1, 6-bisphosphate: mechanistic implications. Protein Sci;8:291-297.
21. Bewley M.C., Jeffrey P.D., Patchett M.L., Kanyo Z.F., Baker E.N. (1999) Crystal structures of Bacillus caldovelox arginase in complex with substrate and inhibitors reveal new insights into activation, inhibition and catalysis in the arginase superfamily. Structure;7:435-448.
22. Lebioda L., Stec B. (1991) Mechanism of enolase: the crystal structure of enolase-Mg2(+)-2-phosphoglycerate/phosphoenolpyruvate complex at 2.2-A resolution. Biochemistry;30:2817-2822.
23. Landro J.A., Gerlt J.A., Kozarich J.W., Koo C.W., Shah V.J., Kenyon G.L., Neidhart D.J., Fujita S., Petsko G.A. (1994) The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate. Biochemistry;33:635-643.
24. Madura J.D., Briggs J.M., Wade R.C., Davis M.E., Luty B.A., Ilin A., Antosiewicz J., Gilson M.K., Bagheri B., Scott L.R., McCammon J.A. (1995) Electrostatics and diffusion of molecules in solution: simulations with the university of Houston Brownian dynamics program. Comp Phys Commun;91:57-95.
25. Antosiewicz J., Briggs J.M., Elcock A.H., Gilson M.K., Andrew M. (1996) Computing ionization states of proteins with a detailed charge model. J Comput Chem;17:1633-1644.
26. Goto S., Okuno Y., Hattori M., Nishioka T., Kanehisa M. (2002) LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res;30:402-404.
27. Arias H.R., Trudell J.R., Bayer E.Z., Hester B., McCardy E.A., Blanton M.P. (2003) Noncompetitive antagonist binding sites in the torpedo nicotinic acetylcholine receptor ion channel. Structure-activity relationship studies using adamantane derivatives. Biochemistry;42:7358-7370.
28. Humphrey W., Dalke A., Schulten K. (1996) VMD: visual molecular dynamics. J Mol Graph;14:33-38, 27-8.
29. Thieleczek R., Mayr G.W., Brandt N.R. (1989) Inositol polyphosphate-mediated repartitioning of aldolase in skeletal muscle triads and myofibrils. J Biol Chem;264:7349-7356.
30. Pan Y., Ayani T., Nadas J., Wen S., Guo Z. (2004) Accessibility of N-acyl-D-mannosamines to N-acetyl-D-neuraminic acid aldolase. Carbohydr Res;339:2091-2100.
31. Larsen T.M., Wedekind J.E., Rayment I., Reed G.H. (1996) A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution. Biochemistry;35:4349-4358.
32. Wold F., Barker R. (1964) D-erythronic acid 3-phosphate. A substrate for enolase. Biochim Biophys Acta;85:475-479.
33. Manneck T., Keiser J., Muller J. (2012) Mefloquine interferes with glycolysis in schistosomula of Schistosoma mansoni via inhibition of enolase. Parasitology;139:1-9.
34. Babbitt P.C., Hasson M.S., Wedekind J.E., Palmer D.R., Barrett W.C., Reed G.H., Rayment I., Ringe D., Kenyon G.L., Gerlt J.A. (1996) The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry;35:16489-16501.
35. Hendlich M., Rippmann F., Barnickel G. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graphics Model;15:359-363, 389.
36. Glaser F., Morris R.J., Najmanovich R.J., Laskowski R.A., Thornton J.M. (2006) A method for localizing ligand binding pockets in protein structures. Proteins;62:479-488.
37. Hetenyi C., van der Spoel D. (2006) Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Lett;580:1447-1450.
38. Elcock A.H. (2001) Prediction of functionally important residues based solely on the computed energetics of protein structure. J Mol Biol;312:885-896.
39. Brylinski M., Konieczny L., Roterman I. (2006) Ligation site in proteins recognized in silico. Bioinformation;1:127-129.
40. Brylinski M., Skolnick J. (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A;105:129-134.
41. Martin Y.C., Kofron J.L., Traphagen L.M. (2002) Do structurally similar molecules have similar biological activity? J Med Chem;45:4350-4358.
42. Hindle S.A., Rarey M., Buning C., Lengaue T. (2002) Flexible docking under pharmacophore type constraints. J Comput Aided Mol Des;16:129-149.
43. Jansen J.M., Martin E.J. (2004) Target-biased scoring approaches and expert systems in structure-based virtual screening. Curr Opin Chem Biol;8:359-364.
44. Carlson H.A., Masukawa K.M., Rubins K., Bushman F.D., Jorgensen W.L., Lins R.D., Briggs J.M., McCammon J.A. (2000) Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem;43:2100-2114.