Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: Computational screening of inhibitors to HIV-1 entry

BMC Bioinformatics

Volumn 9, Issue SUPPL. 12, 2008, Pages

  Gowthaman, Uthaman ^a   Jayakanthan, Mannu ^a   Sundar, Durai ^a,b  

^a PONDICHERRY UNIVERSITY   (India)

^b INDIAN INSTITUTE OF TECHNOLOGY DELHI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SURFACE PROTEINS; ENVELOPE GLYCOPROTEINS; FAVORABLE INTERACTIONS; HYDROPHOBIC AMINO ACIDS; INTERCHANGE REACTIONS; LABORATORY EXPERIMENTS; MOLECULAR DOCKING SIMULATIONS; PROTEIN DISULFIDE ISOMERASES; ACTIVE SITE; ANTI-HIV; BINDING SPECIFICITIES; CELL SURFACES; CHEMOKINES; CONFORMATIONAL CHANGE; DISULFIDE BONDS; DRUG DESIGN; IN-SILICO; INHIBITOR MOLECULES; MODE OF BINDING; MOLECULAR DOCKING; REDOX-ACTIVE SITES; RELATED COMPOUNDS; THIOL-DISULFIDE; VIRUS ENTRY;

AMINO ACIDS; CELL MEMBRANES; COMPUTER SIMULATION; COVALENT BONDS; ENZYME ACTIVITY; EXPERIMENTS; HYDROGEN BONDS; LIGANDS; MOLECULAR MODELING; PROTEINS; VIRUSES; BIOINFORMATICS; CARBOXYLIC ACIDS;

DISEASES;

2 (2 CARBOXY 4 NITROPHENYL)DISULFONYL 5 NITROBENZOIC ACID; 2 NITRO 5 SULFOSULFONYLBENZOIC ACID; 2 NITRO 5 THIOCYANATOBENZOIC ACID; 5 (3 CARBOXY 4 NITROPHENYL)SULFONYL 2 NITROBENZOIC ACID; 5,5' DITHIOBIS(2 NITROBENZOIC ACID); ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; NITROBENZENE DERIVATIVE; NSC 517871; NSC 695265; PROTEIN DISULFIDE ISOMERASE; THIONITROBENZOIC ACID; UNCLASSIFIED DRUG; LIGAND;

COMPUTER MODEL; COMPUTER SIMULATION; CONFERENCE PAPER; CONTROLLED STUDY; DISULFIDE BOND; DRUG DESIGN; DRUG SCREENING; DRUG STRUCTURE; ENZYME ACTIVITY; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DOCKING; NONHUMAN; OXIDATION REDUCTION REACTION; VIRUS ENTRY; ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; CONFORMATION; ENZYME ACTIVE SITE; METABOLISM; METHODOLOGY; PHARMACEUTICS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

ALGORITHMS; ANTI-HIV AGENTS; CATALYTIC DOMAIN; CHEMISTRY, PHARMACEUTICAL; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DITHIONITROBENZOIC ACID; DRUG DESIGN; HIV-1; LIGANDS; MOLECULAR CONFORMATION; OXIDATION-REDUCTION; PROTEIN DISULFIDE-ISOMERASES; TECHNOLOGY, PHARMACEUTICAL;

EID: 57649166525     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S12-S14     Document Type: Conference Paper

References (17)

1. Chan DC Kim PS HIV entry and its inhibition Cell 1998, 93:681-684 10.1016/S0092-8674(00)81430-0 9630213
2. Ryser HJ Levy EM Mandel R DiSciullo GJ Inhibition of human immunodeficiency virus infection by agents that interfere with thiol-disulfide interchange upon virus-receptor interaction Proc Natl Acad Sci USA 1994, 91:4559-4563 43825 8183947 10.1073/pnas.91.10.4559
3. Gallina A Hanley TM Mandel R Trahey M Broder CC Viglianti GA Ryser HJ Inhibitors of protein-disulfide isomerase prevent cleavage of disulfide bonds in receptor-bound glycoprotein 120 and prevent HIV-1 entry J Biol Chem 2002, 277:50579-50588 10.1074/jbc.M204547200 12218051
4. Freedman RB Hirst TR Tuite MF Protein disulphide isomerase: Building bridges in protein folding Trends Biochem Sci 1994, 19:331-336 10.1016/ 0968-0004(94)90072-8 7940678
5. Yoshimori T Semba T Takemoto H Akagi S Yamamoto A Tashiro Y Protein disulfide-isomerase in rat exocrine pancreatic cells is exported from the endoplasmic reticulum despite possessing the retention signal J Biol Chem 1990, 265:15984-15990 2394756
6. Wlodawer A Vondrasek J Inhibitors of HIV-1 protease: A major success of structure-assisted drug design Annu Rev Biophys Biomol Struct 1998, 27:249-284 10.1146/annurev.biophys.27.1.249 9646869
7. Goodsell DS Olson AJ Automated docking of substrates to proteins by simulated annealing Proteins 1990, 8:195-202 10.1002/prot.340080302 2281083
8. Ryser HJ Fluckiger R Progress in targeting HIV-1 entry Drug Discov Today 2005, 10:1085-1094 10.1016/S1359-6446(05)03550-6 16182193
9. NCBI-PubChem Compound database http://pubchem.ncbi.nlm.nih.gov/
10. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V Church DM DiCuccio M Edgar R Federhen S Database resources of the National Center for Biotechnology Information Nucleic Acids Res 2007, 35:D5-D12 1781113 17170002 10.1093/nar/gkl1031
11. Protein Data Bank http://www.rcsb.org/pdb/home/home.do
12. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The Protein Data Bank Nucleic Acids Res 2000, 28:235-242 102472 10592235 10.1093/nar/28.1.235
13. Kemmink J Darby NJ Dijkstra K Nilges M Creighton TE Structure determination of the N-terminal thioredoxin-like domain of protein disulfide isomerase using multidimensional heteronuclear 13C/15N NMR spectroscopy Biochemistry 1996, 35:7684-7691 10.1021/bi960335m 8672469
14. Kemmink J Dijkstra K Mariani M Scheek RM Penka E Nilges M Darby NJ The structure in solution of the b domain of protein disulfide isomerase J Biomol NMR 1999, 13:357-368 10.1023/A:1008341820489 10383197
15. Morris GM Goodsell DS Halliday RS Huey R Hart WE Belew RK Olson AJ Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J Comput Chem 1998, 19:1639-1662 10.1002/ (SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
16. Cole JC Murray CW Nissink JW Taylo RD Taylor R Comparing protein-ligand docking programs is difficult Proteins 2005, 60:325-332 10.1002/ prot.20497 15937897
17. Woo HK Lau KC Wang XB Wang LS J Phys Chem A 2006, 110:12603-12606 10.1021/jp0643799 17107110