The structural basis of matrix metalloproteinase inhibition

Current Opinion in Drug Discovery and Development

Volumn 2, Issue 5, 1999, Pages 449-462

  Borkakoti, Neera ^a  

^a ROCHE PRODUCTS LTD   (United Kingdom)

Author keywords

Active site; Inhibitors; Matrix metalloproteinase; Zinc binding domain

Indexed keywords

CARBOXYLIC ACID DERIVATIVE; COLLAGENASE; GELATINASE A; HYDROXAMIC ACID DERIVATIVE; MATRILYSIN; MATRIX METALLOPROTEINASE; MATRIX METALLOPROTEINASE INHIBITOR; NEUTROPHIL COLLAGENASE; RO 31 4724; RO 32 0554; RO 32 7904; STROMELYSIN; TISSUE INHIBITOR OF METALLOPROTEINASE 1; TISSUE INHIBITOR OF METALLOPROTEINASE 2; UNCLASSIFIED DRUG;

COMPUTER SIMULATION; DRUG DESIGN; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME INHIBITOR INTERACTION; HUMAN; HYDROGEN BOND; LIGAND BINDING; MOLECULAR INTERACTION; NONHUMAN; PROTEIN DOMAIN; REVIEW;

EID: 0032722577     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (51)

1. Woessner Jr JF: Matrix metalloproteinases and their inhibitors in connective tissue remodeling. F/lSEB J(1991) 5:2145-2154.
2. Birkedal-Hansen H: Proteolytic remodeling of extracellular matrix. CurrOpin Cell Biol(1995) 7(5):728-735.
3. Nagase H: Matrix metalloproteinases. In: Zinc metalloproteases in health and disease, Hooper NM (Ed). Taylor and Francis, London (1996):153-204.
4. Nagase H: Activation mechanisms of matrix metalloproteinases. Biol Chem (1997) 378:151-160.
5. Willenbrock F, Murphy G: Structure-function relationships in the tissue inhibitors of metalloproteinases. Am J Resp Crit Care Med(1994) 150:5165-5170.
6. Peress N, Perillo E, Zucker S: Localization of tissue Inhibitor of matrix metalloproteinases in Alzheimer's disease and normal brain. J Neuropathol Exp Neurol (1995) 54(1 ):16-22.
7. Wemicke D, Seyfert C, Hinzmann B, Gromnica-lhle E: Cloning of collagenase 3 from the synovial membrane and its expression in rheumatoid arthritis and osteoarthritis. •J Rheumato! (1996) 23(4):590-595.
8. Stetler-Stevenson WG, Hewitt R, Corcoran M: Matrix metalloproteinases and tumor invasion: From correlation and causality to the clinic. Semin Cancer Biol (1996) 7(3): 147-154.
9. Steinman L: Multiple sclerosis: a coordinated immunological attack against myelin in the central nervous system. Cell (1996) 85(3):299-302.
10. Ahrens D, Koch AE, Pope RM, Stein-Picarella M, Niedbala MJ: Expression of matrix metalloproteinase 9 (96-kd gelatinase B) in human rheumatoid arthritis. Arthritis Rheum (1996) 39(9): 1576-1587.
11. Johnson WH, Roberts NA, Borkakoti N: Collagenase inhibitors: Their design and potential therapeutic use. J Enzyme Inhib (1987) 2:1-22.
12. Whittaker M, Brown P: Recent advances in matrix metailoproteinase inhibitor research and development. CurrOpin Drug D/scovDev(1998) 1(2):157-164.
13. Bottomley KM, Johnson WH, Walter DS: Matrix metalloproteinase inhibitors in arthritis. J Enzyme Inhibition (1998)13:79-101.
14. Babine RE, Bender SL: Molecular recognition of proteinligand complexes: Applications to drug design. Chem Rev (1997)97:1359-1472. • This paper gives a comprehensive account of structure-based design and includes structural data not available in public databases.
15. Borkakoti N: Matrix metalloproteases: Variations on a theme. Prog Biophys Mol Biol (1998) 70:73-94.
16. Murphy GJ, Murphy G, Reynolds JJ: The origin of matrix metalloprotelnases and their familial relationships. FEBS Lett (1991) 289(1):4-7.
17. Pendas AM, Knauper V, Puente XS, Uano E, Mattei MG, Apte S, Murphy G, Lopez Otin C: Identification and characterization of a novel human matrix metalloproteinase with unique structural characteristics, chromosomal location, and tissue distribution. J Biol Chem (1997) 272(7):4281 -4286.
18. Velasco G, Pendas AM, Fueyo A, Knauper V, Murphy G, LopezOtin C: Cloning and characterization of human MMP-23, a new matrix metalloproteinase predominantly expressed in reproductive tissues and lacking conserved domains in other family members. J Biol Chem (1999) 274(8):4570-4576. • This paper suggests that MMP-23, which has a unusual domain structure, plays a specialized role in the reproductive process.
19. Becker JW, Marcy AI, Rokosz LL, Axel MG, Burbaum JJ, Fitzgerald PM, Cameron PM, Esser CK, Hagmann WK, Hermes JD, Springer JP: Stromelysin-1 : Three-dimensional structure of the inhibited catalytic domain and of the Ctruncated proenzyme. Protein Sc/(1995) 4{10):1966-1976.
20. Li J, Brick P, O'Hare MC, Skarzynski T, Lloyd LF, Curry VA, Clark IM, Bigg HF, Hazleman BL, Cawston TE, Blow DM: Structure of full length porcine synovial collagenase reveals a C-terminal domain containing a calcium-linked, four bladed propeller. Structure (1995) 3:541-549.
21. Morgunova E, Tuuttila A, Bergmann U, Isupov M, Lindqvist Y, Schneider G, Tryggvason K: Structure of human pro-matrix metalloproteinase-2: Activation mechanism revealed. Science (1999) 284:1667-1670. • This paper is the first to provide three-dimensional structural data on a MMP-2, and also the only structure representing the full length proform of any MM P.
22. Springman EB, Angelton EL, Birkedal-Hansen H, Van Wart HE: Multiple modes of activation of latent fibroblast collagenase: evidence for the role of a cys-73 active site zinc complex in latency and a 'cysteine switch1 mechanism for activation. Proc Natl Acad Sei USA (1990) 87:364-368. • Paper postulating the mode of activation of MMPs on biochemical evidence.
23. Fernandez-Catalan C, Bode W, Huber R, Turk D, Calvete JJ, Lichte A, Tschesche H, Maskos K: Crystal structure of the complex formed by the membrane type 1-matrix metalloproteinase with the tissue inhibitor of metalloproteinases-2, the soluble progelatinase A receptor. EMBO J(1998) 17(17):5238-5248. • First structure of the catalytic domain of a membrane-bound MMP.
24. Gomis-Ruth FX, Maskos K, Betz M, Bergner A, Huber R, Suzuki K, Yoshida N, Nagase H, Brew K, Bourenkov GP, Bartunik H, Bode W: Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1. Nature (1997)389:77-81. •• First structural data on any member of the MMP family complexed with physiological inhibitor TIMP.
25. Nagase H, Fields GB: Human matrix metalloproteinase specificity studies using collagen sequence-based synthetic peptides. Biopolymers (1996) 40(4):399-416.
26. Borkakoti N, Winkler FK, Williams DH, D'Arcy A, Broadhurst MJ, Brown PA, Johnson WH, Murray EJ: Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor. Nature Struct Biol (1994) 1:106-110. • Structural data illustrating the substrate-like binding mode of a typical prime side MMP inhibitor.
27. Brandstetter H, Engh RA, Von Roedem EG, Moroder L, Huber R, Bode W, Grams F: Structure of malonic acid-based inhibitors bound to human neutrophil collagenase. A new binding mode explains apparently anomalous data. Protein Sc/(1998)7(6):1303-1309. • Crystallographic data explaining the differences in the affinity for different classes of hydroxamate-containing MMP inhibitors.
28. Bode W, Reinemer P, Huber R, Kleine T, Schnierer S, Tschesche H: The X-ray crystal structure of the catalytic domain of human neutrophil collagenase inhibited by a substrate analogue reveals the essentials for catalysis and specificity. EMBO J(1994) 13(6):1263-1269.
29. Lovejoy B, Cleasby A, Hassell AM, Longley K, Luther MA, Weigl D, McGeehan G, McElroy AB, Drewry D, Lambert MH, Jordan SR: Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor. Science (1994) 263(5145):375-377. .
30. Browner MF, Smith WW, Castelhano AL: Matrilysin-inhibitor complexes: Common themes among metalloproteases. Biochemistry (1995) 34(20):6602-6610.
31. Esser CK, Bugianesi RL, Caldwell CG, Chapman KT, Durette PL, Girotra NN, Kopka IE, Lanza TJ, Levorse DA, MacCoss M, Owens KA, Ponpipom MM, Simeone JP, Harrison RK, Niedzwiecki L, Becker JW, Marcy AI, Axel MG, Christen AJ, McDonnell J, Moore VL, Olszewski JM, Saphos C, Visco DM, Shen F, Colletti A, Krieker PA, Hagmann WK: Inhibition of stromelysin-1 (MMP-3) by PV-biphenylylethyl carboxyalkyl dipeptides. J Med Chem (1997) 40(6):1026-1040.
32. Grams F, Reinemer P, Powers JC, Kleine T, Pieper M, Tschesche H, Huber R, Bode W: X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design. Eur J Biochem (1995)228(3):830-841.
33. Finzel BC, Baldwin ET, Bryant Jr GL, Hess GF, Wilks JW, Trepod CM, Mort JE, Marshall VP, Petzold GL, Poorman RA, O'Sullivan TJ, Schostarez HJ, Mitchell MA: Structural characterizations of nonpeptidic thiadiazole inhibitors of matrix metalloproteinases reveal the basis for stromelysin selectivity. Protein Sc/(1998) 7(10):2118-2126. • Interesting details of a non-peptidic inhibitor binding to the nonprime side of MMP-3.
34. Reiter LA, Rizzi JP, Pandit J, Lasut MJ, McGahee SM, Parikh VD, Blake JF, Danley DE, Laird ER, Lopez-Anaya A, Lopresti-Morrow LL, Mansour MN, Martinelli GJ, Mitchell PG, Owens BS, Pauly TA, Reeves LM, Schulte GK, Yocum SA: Inhibition of MMP-1 and MMP-13 with phosphinic acids that exploit binding In the S2 pocket Bioorg Med Chem Lett (1999) 9(2):127-132. Structural data on MMP inhibitors that interact at both the primed and non-primed subsites.
35. Lovejoy B, Hassell AM, Luther MA, Weigl D, Jordan SR: Crystal structures of recombinant 19-kDa human fibroblast collagenase complexed to itself. Biochemistry (1994) 33(27):8207-8217.
36. Li YC, Zhang X, Melton R, Ganu V, Gonnella NC: Solution structure of the catalytic domain of human stromelysin-1 complexée! to a potent, nonpeptidic inhibitor. Biochemistry (1998) 37(40):14048-14056. •• NMR data on the mode of binding of a non-peptidic sulfonamide inhibitor. Also illustrates the flexiblility of the VR2 region of the proteins.
37. Lovejoy B, Welch AR, Carr S, Luong C, Broka C, Hendricks RT, Campbell JA, Walker KA, Martin R, Van Wart H, Browner MF: Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors. Nature Struct Biol (1999) 6(3):217-221. •• Crystal data on sulfone inhibitors illustrating the inhibitor induced changes to the P1'pocket of MMP-1.
38. Pikul S, McDow-Dunham KL, Almstead NG, De B, Natchus MG, Anastasio MV, McPhai! SJ, Snider CE, Taiwo YO, Chen L, Dunaway CM, Gu F, Mieling GE: Design and synthesis of phosphlnamide-based hydroxamic acids as inhibitors of matrix metalloproteinases. J Med Chem (1999) 42(1):87-94.
39. Pavlovsky AG, Williams MG, Ye Q-Z, Ortwine DF, Purchase III CF, White AD, Dhanaraj V, Roth BD, Johnson LL, Hupe D, Humblet C, Blundell TL: X-ray structure of human stromelysin catalytic domain complexed with nonpeptide inhibitors: Implications for inhibitor selectivity. Protein Sc/ence(1999) 8:1455-1462.
40. Szardenings AK, Harris D, Lam S, Shi L, Tien D, Wang Y, Patel DV, Navre M, Campbell DA: Rational design and combinatorial evaluation of enzyme inhibitor scaffolds: identification of novel inhibitors of matrix metalloproteinases. J Med Chem (1998) 41 (13):2194-2200.
41. Porter JR, Beeley NRA, Boyce B, Mason B, Millican A, Millar K, Leonard J, Morphy JR, O'Connell JP: Potent and selective inhibitors of gelatinase-A. 1. Hydroxamic acid derivatives. Bioorg Med Chem Lett (1994) 4:2741 -2746.
42. Dhanaraj V, Ye Q-Z, Johnson LL, Hupe DJ, Ortwine DF, Dunbar JB, Rubin JR, Pavlovsky A, Humblet C, Blundell TL: Xray structure of stromelysin catalytic domain and its comparison with members of the zinc metalloproteinase superfamily. Structure (1996) 4:375-386.
43. Borkakoti N: Zinc endoproteases: A structural superfamily. In: Structure based ligand design, Bonm HJ, Gubemator K (Eds). Wiley/VCH, Germany (1997):73-87.
44. Szardenings AK, Antonenko V, Campbell DA, DeFrancisco N, Ida S, Shi L, Sharkov N, Tien D, Wang Y, Navre M: Identification of highly selective Inhibitors of collagenase1 from combinatorial libraries of diketopiperazines. J Med Chem (1999) 42(8):1348-1357.
45. Rockwell A, Melden M, Copeland RA, Hardman K, Decicco CP, DeGrado WF: Complementarity of combinatorial chemistry and structure-based ligand design: Application to the discovery of novel inhibitors of matrix metalloproteinases. J Am Chem Soc (1996) 118:1033710338.
46. Broadhurst MJ, Brown PA, Lawton G, Ballantyne N, Borkakoti N, Bottomley K, Cooper Ml, Eatherton AJ, Kilford IR, Malsher PJ, Nixon JS, Lewis EJ, Sutton BM, Johnson WH: Design and synthesis of the cartilage protective agent (CPA, Ro323555). Bioorg Med Chem Lett (1997) 7(17):2299-2302.
47. Beckett RP, Whittaker M: Matrix metalloproteinase inhibitors 1998. Exp Opin Ther Patents (1998) 8:259-282. • A recent review of the patent literature on MMP inhibitors.
48. Carson M: Ribbon models of macromolecules. J Mol Graphics (1987) 5:103-106.
49. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M: The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol (1977) 112:535-542.
50. Gerber PR, Muller K: MAB, a generally applicable molecular force field for structure modeling in medicinal chemistry. J Comput-Aided Molec Des (1995) 9(3):251 -268.
51. Nicholls A, Bharadwaj R, Honig B: Grasp-graphical representation and analysis of surface properties. Biophys J (1993) 64:166-169.