Two Crystal Structures of Human Neutrophil Collagenase, One Complexed with a Primed- and the Other with an Unprimed-Side Inhibitor:  Implications for Drug Design

Abstract

Two crystal structures of human neutrophil collagenase (HNC, MMP-8), one complexed with a primed- and the other with an unprimed-side inhibitor, were determined using synchrotron radiation at 100 K. Both inhibitors contain non-hydroxamate zinc-binding functions. The Pro-Leu-L-Trp(P)(OH)(2) occupies the unprimed region of the active site, furnishes new structural information regarding interaction between the catalytic zinc ion and the phosphonate group, and is the only example of occupation of the S(1) subsite of MMP-8 by the bulky tryptophan side chain. The (R)-2-(biphenyl-4-ylsulfonyl)-1,2,3, 4-tetrahydroisochinolin-3-carboxylic acid, a conformationally constrained D-Tic derivative, accommodates its biphenyl substituent into the deep primary specificity S(1)' subsite, inducing a widening of the entrance to this pocket; this modification of the protein, mainly consisting in a shift of the segment centered at Pro217, is observed for the first time in MMP-8 complexes. Cation-aromatic interactions can stabilize the formation of both complexes, and the beneficial effect of aromatic substituents in proximity of the catalytic zinc ion is discussed. The phosphonate group bound to either a primed- or unprimed-side inhibitor maintains the same relative position with respect to the catalytic zinc ion, suggesting that this binding function can be exploited for the design of combined inhibitors assembled to interact with both primed and unprimed regions of the active cleft.

Insight into autoproteolytic activation from the structure of cephalosporin acylase: A protein with two proteolytic chemistries

“…4). Similar interactions are recognized as crucial for the structural stabilization of caspase BIR domain (28) and neutrophil collagenase (29). Moreover, (Phe-177) is the only residue of 682 modeled amino acid residues in a disallowed region of the Ramachandran plot in all mutant crystal structures as well as in precursor and mature CA (see Fig.…”

PRODRG: a tool for high-throughput crystallography of protein–ligand complexes

“…(b) As (a) for Triton X-100 in SCP-2L (Haapalainen et al, 2001). (c) Ligand from a high-resolution structure (cyan molecule) of human neutrophil collagenase (Gavuzzo et al, 2000) re-re®ned at lower resolution with topologies generated either with PRODRG (green molecule) or with LIBCHECK (orange molecule). Again, the protein is shown as a semitransparent cartoon.…”

“…values are given for the unperturbed and perturbed case separated by a slash. HGPRT, Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase (Heroux et al, 2000); CBM29-2, Piromyces equi family 29 carbohydratebinding module (Charnock et al, 2002); HNC, human neutrophil collagenase (Gavuzzo et al, 2000); DERA, E. coli d-2-deoxyribose-5-phosphate aldolase (Heine et al, 2001); DHFR, human dihydrofolate reductase (Klon et al, 2002); EAPA, Cryphonectria parasitica endothiapepsin (Erskine et al, 2003); PRPP, phosphoribosylpyrophosphate; BSI, 2-(biphenyl-4-sulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid; LIH, 6-[(5-quinolylamino)methyl]-2,4-diamino-5-methylpyrido(2,3-d)pyrimidine; LOV, 5-amino-4-hydroxy-2-isoproyl-7-methyl-octanoic acid; SUI, (3-amino-2,5-dioxo-1-pyrrolidinyl)-acetic acid. which, after inspection by the user, can be used in re®nement.…”

“…In the remaining two cases [HNC (Gavuzzo et al, 2000) and EAPA (Erskine et al, 2003)] the re®nement using PRODRG topologies gives signi®cantly better ligand conformations, with r.m.s.d. LIBCHECK /r.m.s.d.…”

Phosphorus based inhibitors of matrix metalloproteinases

“…An Italian-German collaborative project has reported the crystal structure of 28 complexed with MMP-8, where it occupies the unprimed region of active site [65]. Scientists from the same laboratory prepared a series of phosphonic acid analogs by replacing the terminal Lproline with other amino acid residues to yield compounds of increased affinity towards MMP-2 and MMP-8.…”