Structural analysis of protein-ligand interactions: The binding of endogenous compounds and of synthetic drugs

Journal of Molecular Recognition

Volumn 27, Issue 2, 2014, Pages 65-72

  Gallina, Anna M ^a   Bork, Peer ^b   Bordo, Domenico ^a  

^a UNIVERSITY OF GENOA   (Italy)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

drug discovery; lead optimization; protein ligand interaction; secondary target

Indexed keywords

AMINO ACID; LIGAND; PEPTIDE FRAGMENT; PROTEIN;

ARTICLE; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; DRUG DEVELOPMENT; HUMAN; HYDROGEN BOND; LEAD OPTIMIZATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN-LIGAND INTERACTION; SECONDARY TARGET; STRUCTURE ACTIVITY RELATION;

DRUG DISCOVERY; LEAD OPTIMIZATION; PROTEIN-LIGAND INTERACTION; SECONDARY TARGET;

AMINO ACIDS; DATABASES, PROTEIN; DRUG DESIGN; HUMANS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGANDS; MOLECULAR STRUCTURE; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84892573390     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.2332     Document Type: Article

References (25)

1. Bartlett GJ, Porter CT, Borkakoti N, Thornton JM,. 2002. Analysis of catalytic residues in enzyme active sites. J. Mol. Biol. 324: 105-121.
2. Benson ML, Smith RD, Khazanov NA, Dimcheff B, Beaver J, Dresslar P, Nerothin J, Carlson HA,. 2007. Binding MOAD, a high-quality protein-ligand database. Nucleic Acid Res. 36: D674-D678.
3. Bogan AA, Thorn KS,. 1998. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280: 1-9.
4. Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P,. 2008. Drug target identification using side-effect similarity. Science 321: 263-266.
5. Creighton TE,. 1993. Proteins. Structures and molecular properties. 2nd Edn. W.H. Freeman and Company: New York.
6. Dakshanamurthy S, Issa NT, Assefnia S, Seshasayee A, Peters OJ, Madhavan S, Uren A, Brown ML, Byers SW,. 2012. Predicting new indications for approved drugs using a proteochemometric method. J. Med. Chem. 9: 6832-6848.
7. Dutta S, Burkhardt K, Young J, Swaminathan GJ, Matsuura T, Hendrick K, Nakamura H, Berman HM,. 2009. Data deposition and annotation at the worldwide Protein Data Bank. Mol. Biotechnol. 42: 1-13.
8. Ekins S, Williams AJ, Krasowski MD, Freundlich JS,. 2011. In silico repositioning of approved drugs for rare and neglected diseases. Drug Discov. Today 16: 298-310.
9. Fersht A,. 1993. Enzyme structure and mechanism. 2nd Edn. W.H. Freeman and Company: New York; 452-459.
10. Fuller JC, Burgoyne NJ, Jackson RM,. 2009. Predicting druggable binding sites at the protein-protein interface. Drug Discov. Today 14: 155-161.
11. Gallina AM, Bisignano P, Bergamino M, Bordo D,. 2013. PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures. Bioinformatics 29: 395-397.
12. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M,. 2012. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40: D109-D114.
13. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS,. 2011. DrugBank 3.0: a comprehensive resource for "omics" research on drugs. Nucleic Acids Res. 39: D1035-D1041.
14. Laskowski RA, Chistyakov VV, Thornton JM,. 2005. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res. 33: D266-D268.
15. Pearson WR, Lipman DJ,. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U. S. A. 85: 2444-2448.
16. Pyrkov TV, Pyrkova DV, Balitskava ED, Efremov RG,. 2009. The role of stacking interactions in complexes of proteins with adenine and guanine fragments of ligands. Acta Naturae. 1: 124-127.
17. Reddy AS, Amarnath HS, Bapi RS, Sastry GM, Sastry GN,. 2008. Protein ligand interaction database (PLID). Comput. Biol. Chem. 32: 387-390.
18. Sardana D, Zhu C, Zhang M, Gudivada RC, Yang L, Jegga AG,. 2011. Drug repositioning for orphan diseases. Brief. Bioinform. 12: 346-356.
19. Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA,. 2013. New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res. 41: D490-D498.
20. Singh J, Petter RC, Baillie TA, Whitty A,. 2011. The resurgence of covalent drugs. Nat. Rev. Drug Discov. 10: 307-317.
21. Soga S, Shirai H, Kobori M, Hirayama N,. 2007. Use of amino acid composition to predict ligand-binding sites. J. Chem. Inf. Model. 47: 400-406.
22. Tewari AK, Durbey R,. 2008. Emerging trends in molecular recognition: utility of weak aromatic interactions. Bioorg. Med. Chem. 16: 126-143.
23. Wallace AC, Laskowski RA, Thornton JM,. 1995. LIGPLOT: a program to generate schematic. Protein Eng. 8: 127-134.
24. Wang R, Fang X, Lu Y, Yang C-Y, Wang S,. 2005. The PDBbind database: methodologies and updates. J. Med. Chem. 48: 4111-4119.
25. Zvelebil M, Sternberg M,. 1988. Analysis and prediction of the location of catalytic residues in enzymes. Prot. Eng. 2: 127-138.