Modeling an active conformation for linear peptides and design of a competitive inhibitor for HMG-CoA reductase

Journal of Molecular Recognition

Volumn 21, Issue 4, 2008, Pages 224-232

  Pak, Valeriy V ^a   Koo, Minseon ^a   Kim, Min Jung ^a   Yang, Hye Jeong ^a   Yun, Lyubov ^b   Kwon, Dae Young ^a  

^a Korea Food Research Institute   (South Korea)

^b S Yu Yunusov Institute of the Chemistry of Plant Substances Uzbekistan Academy of Sciences   (Uzbekistan)

Author keywords

Active conformation; Circular dichroism; Design; HMG CoA reductase; Inhibitors; Peptides

Indexed keywords

HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; PEPTIDE; PEPTIDE LIBRARY;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; DRUG DESIGN; PROTEIN CONFORMATION;

CIRCULAR DICHROISM; DRUG DESIGN; HYDROXYMETHYLGLUTARYL-COA REDUCTASE INHIBITORS; MODELS, MOLECULAR; PEPTIDE LIBRARY; PEPTIDES; PROTEIN CONFORMATION;

GLYCINE MAX;

EID: 47649114218     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.889     Document Type: Article

References (32)

1. Becker OM. 1997. Geometric versus topological clustering: an insight into conformational mapping. Proteins 27: 213-226.
2. Becker OM, Levy Y, Ravitz O. 2000. Flexibility, conformation space, and bioactivity. J. Phys. Chem. 104: 2123-2135.
3. Beeman D. 1976. Some multistep methods for use in molecular dynamics calculations. J. Comput Phys. 20: 130-139.
4. Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye-binding. Anal. Biochem. 72: 248-254.
5. Burkert U, Allinger NL. 1982. Molecular Mechanics. ACS Monograph N. 177. ACS: Washington.
6. Caprino LA, Han GY. 1972. The 9-fluorenylmethyloxycarbonsy amino-protecting group. J. Org. Chem. 37: 3404-3409.
7. Casio M, Wallace BA. 1996. Effects of local environments on circular dichroism of polypeptides. Anal. Biochem. 227: 90-100.
8. Chang C, Meienhofer J. 1978. Solid-phase peptide synthesis using mild base cleavage of Nα-fluorenylmethyloxycarbonylamino acids, exemplified by a synthesis of dihydrosomatostatin. Int. J. Pept. Protein Res. 11: 246-249.
9. Dewar MJS, Zoebish EG, Healy EF, Stewart JJP. 1985. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 107: 3902-3909.
10. Eisenberg DA. 1998. Cholesterol lowering in the management of coronary artery disease: the clinical implications of recent trials. Am. J. Med. 104: 2S-5S.
11. Endo A. 1992. The discovery and development of HMG-CoA reductase inhibitors. J. Lipid Res. 33: 1569-1582.
12. Fields CG, Lloyd DH, Macdonald RL, Otteson KM, Noble RL. 1991. HBTU activation for automated Fmoc solid-phase peptide synthesis. Pept. Res. 4: 95-101.
13. Fisher R. 1935. The Design of Experiments. Oxford University Press: Oxford.
14. Gunasekaran K, Gomathi L, Ramakrishman C, Chandrasekhar J, Balaram P. 1998. Conformational interconversions in peptide β-turns: analysis of turns in proteins and computational estimates of barriers. J. Mol. Biol. 284: 1505-1516.
15. Hebert PR, Gaziano JM, Chan KS, Hennekens CH. 1997. Cholesterol lowering with statin drugs, risk of stroke and total mortality. an overview of randomized trials. J. Am. Med. Assoc. 278: 313-321.
16. Istvan E. 2003. Statin inhibition of HMG-CoA reductase: a 3-dimensional view. Atheroscler. Suppl. 4: 3-8.
17. Istvan ES, Deisenhofer J. 2001. Structural mechanism for statin inhibition of HMG-CoA reductase. Science 292: 1160-1164.
18. Johnson WCJr. 1990. Protein secondary structure and circular dichroism: a practical guide. Protein Struct. Funct. Genet. 7: 205-214.
19. Kalazsi A, Mezo G, Hudecz F, Farkas O. 2002. Conformation characterization of flexible oligopeptides. J. Pept. Sci. 8: S194.
20. Kollman PA. 1996. Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules. Acc. Chem. Res. 29: 461-469.
21. Krittanai C, Johnson WCJr. 1997. Correcting the circular dichroism spectra of peptides for contributions of absorbing side chains. Anal. Biochem. 253: 57-64.
22. Kwon DY, Oh SW, Lee JS, Yang HJ, Lee SH, Lee JH, Lee YB, Sohn HS. 2002. Amino acid substitution of hypocholesterolemic peptides originated from glycinin hydrolyzate. Food Sci. Biotechnol. 11: 55-61.
23. Pak W, Kim SH, Koo M, Lee N, Shakhidoyatov KM, Kwon DY. 2006. Peptide design of a competitive inhibitor for HMG-CoA reductase based on statin structure. Biopolymers (Pept. Sci.) 84: 586-594.
24. Pak W, Koo M, Kasimova TD, Kwon DY. 2004. Conformation analysis of Ile-Ala-Val-Pro peptide and its derivatives by circular dichroism. Chem. Nat. Comp. 40: 398-404.
25. Pak W, Koo M, Kim MJ, Yun L, Kwon DY. 2008. Binding effect and design of a competitive inhibitory peptide for HMG-CoA reductase through modeling of an active peptide backbone. Bioorg. Med. Chem. 16: 1309-1319.
26. Pak W, Koo M, Lee N, Lee JS, Kasimova TD, Kwon DY. 2005a. Isolation and identification of hypocholesterolemic peptide from 11S globulin of soy protein. Chem. Nat. Comp. 41: 710-714.
27. Pak W, Koo M, Lee N, Lee JS, Kasimova TD, Kwon DY. 2005b. Structure-activity relationship of Ile-Ala-Val-Pro peptide and its derivatives by using semi-empirical AM1 method. Chem. Nat. Comp. 41: 454-460.
28. Pak W, Koo M, Yun LM, Kwon DY. 2007. Recognized sequence and conformation in design of linear peptides as a competitive inhibitor for HMG-CoA reductase. J. Mol. Recognit. 20: 197-203.
29. Payne JW, Marshall NJ, Grail BM, Gupta S. 2002. Conformer profiles and biological activities of peptides. Curr. Org. Chem. 6: 1221-1246.
30. Pierschbacher MD, Ruoslahti E. 1987. Influence of stereochemistry of the sequence Arg-Gly-Asp-Xaa on binding specifity in cell adhesion. J. Biol. Chem. 262: 17294-17298.
31. Perkin-Elmer. 1995. Introduction to Cleavage Techniques. Perkin-Elmer Cooperation: Foster City; 9-17.
32. Segel IH. 1976. Biochemical Calculations. John Wiley & Sons: New York; 246-252.