Structure of a Retro-binding Peptide Inhibitor Complexed with Human α-Thrombin

Tabernero, Lydia; Chang, Chong-Hwan; Ohringer, S. L.; Lau, Wan F.; Iwanowicz, Edwin J.; Han, Wen-Ching; Wang, T. C.; Seiler, Steven M.; Roberts, Daniel G.; Sack, John S.

doi:10.1006/jmbi.1994.0060

Cited by 41 publications

(21 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The remaining three involve nonpolar fragments in the $3 pocket, $2 pocket, or on the solvent-exposed surface of the Trp 6°D indole. This is in agreement with the binding modes of known thrombin inhibitors [25,26,52,54]. A CCLD run, which utilized the 875 MCSS minima with favorable free energy of binding, generated several ligands showing the same interaction patterns as those of the PPACK thrombin complex.…”

Section: Discussionsupporting

confidence: 52%

“…4g), where its N n donates to the Asp t89 carboxylate oxygens (2.60 and 3.42 A), and both N q and N w are involved in hydrogen bonds with the backbone CO of Gly 219 (2.64 and 2.70 A_). A similar binding mode for the guanidino group has recently been found in a retro-binding peptide inhibitor of thrombin, Phe-allo-Thr-Phe-O-CH 3 acylated at its N-terminus with 4-guanidino butanoic acid [54]. Methylguanidinium minima 5 and 6 have the same orientation and interactions with the protein as minimum 4, despite slightly different orientations of the methyl group (not shown).…”

Section: Charged Group Minimamentioning

confidence: 76%

See 1 more Smart Citation

Computational combinatorial ligand design: Application to human ?-thrombin

Caflisch¹

1996

J Computer-Aided Mol Des

View full text Add to dashboard Cite

A new method is presented for computer-aided ligand design by combinatorial selection of fragments that bind favorably to a macromolecular target of known three-dimensional structure. Firstly, the multiple-copy simultaneous-search procedure (MCSS) is used to exhaustively search for optimal positions and orientations of functional groups on the surface of the macromolecule (enzyme or receptor fragment). The MCSS minima are then sorted according to an approximated binding free energy, whose solvation component is expressed as a sum of separate electrostatic and nonpolar contributions. The electrostatic solvation energy is calculated by the numerical solution of the linearized Poisson-Boltzmann equation, while the nonpolar contribution to the binding free energy is assumed to be proportional to the loss in solvent-accessible surface area. The program developed for computational combinatorial ligand design (CCLD) allows the fast and automatic generation of a multitude of highly diverse compounds, by connecting in a combinatorial fashion the functional groups in their minimized positions. The fragments are linked as two atoms may be either fused, or connected by a covalent bond or a small linker unit. To avoid the combinatorial explosion problem, pruning of the growing ligand is performed according to the average value of the approximated binding free energy of its fragments. The method is illustrated here by constructing candidate ligands for the active site of human alpha-thrombin. The MCSS minima with favorable binding free energy reproduce the interaction patterns of known inhibitors. Starting from these fragments, CCLD generates a set of compounds that are closely related to high-affinity thrombin inhibitors. In addition, putative ligands with novel binding motifs are suggested. Probable implications of the MCSS-CCLD approach for the evolving scenario of drug discovery are discussed.

show abstract

Section: Discussionsupporting

confidence: 52%

Section: Charged Group Minimamentioning

confidence: 76%

Computational combinatorial ligand design: Application to human ?-thrombin

Caflisch¹

1996

J Computer-Aided Mol Des

View full text Add to dashboard Cite

show abstract

“…The binding of the small molecule inhibitor BMS-183507 (Tabernero et al, 1995) exhibits some of the features of each class. In this complex, the Phe 1 -d o Thr 2-Phe 3 portion of the inhibitor binds like the first three N-terminal residues of hirudin with the inhibitor backbone forming a parallel @-strand to the main-chain segment Ser 214-Gly 219.…”

Section: Resultsmentioning

confidence: 99%

“…The coordinates for the hirudin peptide were extracted from the C-terminal region of the thrombin-hirugen structure (Rydel et al, 1990) and added to the thrombin model with the computer graphics program CHAIN (Sack, 1988). Two models of the BMS-186282 complex were constructed by Dr. Wan Lau as described previously (Tabernero et al, 1995). Refinement of both models of the bound conformation of BMS-186282 were attempted; one of these models could not be made to fit the observed density and was discarded.…”

Section: Structure Solution and Refinementmentioning

confidence: 99%

“…These polypeptides, like hirudin itself, also form a pair of hydrogen bonds to Gly216, but the P-strand arrangement is parallel. A novel series of tri-J ",.A," peptide analogues, typified by BMS-183507, which were initially modeled after the Phe-Pro-Arg peptides but were found to bind to thrombin in the parallel or "retro" fashion observed for hirudin, have also been reported (Iwanowicz et al, 1994;Tabernero et al, 1995).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Crystallographic determination of the structures of human α‐thrombin complexed with BMS‐186282 and BMS‐189090

Malley¹,

Tabernero²,

Chang³

et al. 1996

Protein Science

Self Cite

View full text Add to dashboard Cite

The crystallographic structures of the ternary complexes of human a-thrombin with hirugen (a sulfated hirudin fragment) and the small-molecule active site thrombin inhibitors BMS-186282 and BMS-189090 have been determined at 2.6 and 2.8 A. In both cases, the inhibitors, which adopt verysimilar bound conformations, bind in an antiparallel P-strand arrangement relative to the thrombin main chain in a manner like that reported for PPACK, D-Phe-Pro-Arg-CH,Cl. They do, however, exhibit differences in the binding of the alkyl guanidine moiety in the specificity pocket. Numerous hydrophilic and hydrophobic interactions serve to stabilize the inhibitors in the binding pocket. Although PPACK forms covalent bonds to both serine and the histidine of the catalytic triad of thrombin, neither BMS-186282 nor BMS-189090 bind covalently and only BMS-186282 forms a hydrogen bond to the serine of the catalytic triad. Both inhibitors bind with high affinity (K, = 79 nM and 3.6 nM, respectively) and are highly selective for thrombin over trypsin and other serine proteases.Keywords: crystallography; human a-thrombin-inhibitor complexes; structure-based drug designThe serine protease thrombin occupies a central position in the blood coagulation cascade. It cleaves circulating fibrinogen to fibrin monomers, which then polymerize and are covalently linked by thrombin-activating factor XIIIa, which is also a prodReprint requests to: Mary E Malley, Department of Solid State Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, P.O. Box 4000, Princeton, New Jersey 08543-4000; e-mail: malley@bms.com.Present address: Department of Biological Sciences, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana 47907. uct of thrombin activation. In addition, thrombin activates several other coagulation and plasma factors, such as factors V, VIII, protein C, and protein S. Thrombin also induces platelet aggregation and promotes the proliferation of endothelial cells, the liberation of tissue plasminogen activator, and the contraction and dilation of blood vessels. Selective inhibition of thrombin may result in efficient control of various pathophysiologic states, such as thrombosis and arteriosclerosis, and aid in the prevention of myocardial infarction (Berliner 1992; Fenton, 1986; Fenton et al., 1991). Abbreviations: BMS-186282, [S-(R*,R*)]-4-[Aminoiminomethyl)-amino]-N-[[l-[3-hydy-2-[(2-naphthalenyls~fony~)~no]-l-oxopropyl]- 2-pyrrolidinyl]methyI]butanamide; BMS-189090, [S-(R*,R*)]-l-(Aminoiminomethyl)-N-[[l-[N-[(2-naphthalenylsulfonyl)-~-seryl]-2-pyrrolidinyl]-Human a-thrombin consists of two polypeptide chains, A and B, connected through a single disulfide bond. The A chain has 36 residues (after the loss of a tridecapeptide during activation with prothrombin) and the B chain has 259 residues. The B chain is glycosylated at Asn 60G and contains the active site residues His 57, Asn 102, and Ser 195. The numbering scheme for the thrombin residues in this paper are assigned by homology with chymotrypsin as d...

show abstract