Free Access
J. Chim. Phys.
Volume 95, Number 2, February 1998
Page(s) 443 - 446
DOI: 10.1051/jcp:1998158

J. Chim. Phys. Vol. 95, N°2  p. 443-446

A NMR and MD study of the active site of factor Xa by selective inhibitors

B.T. Doan1, 2, F. Fraternali1, 3, Q.T. Do1, 4, R.A. Atkinson1, 5, P. Palmas1, 6, V. Sklenar1, 7, P. Wildgoose8, P. Strop9 and V. Saudek1, 10

1  Marion Merrell Research Institute, HMR, 67080 Strasbourg, France
2  LCSOB, RMN, UPMC Paris 6, 75252 Paris, France
3  EMBL, 6900 Heidelberg, Germany
4  Tripos Associates, 92167 Antony, France
5  ESBS, 67400 Illkirch, France
6  CEA, 37260 Monts, France
7  Masaryck University, 611 37, Brno, Czech Republic
8  Hoechst AG, HMR, Central Pharma Research, 65926 Frankfurt, Germany
9  Selectide Corporation, HMR, Tucson, AZ 85737, U.S.A.
10  Synthélabo Biomoléculaire, 67080 Strasbourg, France

The structure of two selective inhibitors obtained by the screening of a vast combinatorial library, Ac-Tyr-Ile-Arg-Ile-NH 2 and Ac-(4-amino-Phe)-(Cyc.-Gly)-NH 2, in the active site of the blood clotting enzyme factor Xa was determined using transferred NOE NMR and simulated annealing (SA) under NMR constraints. The refined structures of the inhibitors were docked in the active site and SA was performed inside the enzyme which has been kept as a rigid charged template. The final structures were optimised by molecular dynamics simulation of the complexes in water. The inhibitors assume a compact, very well defined conformation embedded in the binding site without blocking the catalysis. The model allows to explain the mode of action, affinity and specificity.

L'étude structurale d'inhibiteurs du facteur Xa, une enzyme de coagulation, obtenus par chimie combinatoire : Ac-Tyr-Ile-Arg-Ile-NH2, Ac-(4-amino-Phe)-(Cyc.-Gly)-NH 2, a été réalisée par RMN NOE de transfert et modélisation moléculaire. Les structures ont été calculées sous contraintes RMN : géométrie de distance, recuit simulé et minimisation, affinées par une recherche conformationnelle et recuit de l'inhibiteur placé dans le site actif et optimisées par simulation de dynamique moléculaire du complexe dans l'eau. L'inhibiteur présente une structure compacte positionnée dans le site d'interaction hors d'accès du site catalytique. Ce modèle permet d'expliquer le mode d'action, l'affinité et la spécificité des peptides.

Key words: transfer NOE -- Simulated Annealing -- Factor Xa -- inhibitors

© EDP Sciences 1998

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