Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model.
A series of 27 benzamidine inhibitors covering a wide range of biological activity and chemical diversity was analysed to derive a Linear Interaction Energy in Continuum Electrostatics (LIECE) model for analysing the thrombin inhibitory activity. The main interactions occurring at the thrombin binding site and the preferred binding conformations of inhibitors were explicitly biased by including into the LIECE model 10 compounds extracted from X-ray solved thrombin-inhibitor complexes available from the Protein Data Bank (PDB). Supported by a robust statistics (r(2) = 0.698; q(2) = 0.662), the LIECE model was successful in predicting the inhibitory activity for about 76% of compounds (r (ext) (2) > or = 0.600) from a larger external test set encompassing 88 known thrombin inhibitors and, more importantly, in retrieving, at high sensitivity and with better performance than docking and shape-based methods, active compounds from a thrombin combinatorial library of 10240 mimetic chemical products. The herein proposed LIECE model has the potential for successfully driving the design of novel thrombin inhibitors with benzamidine and/or benzamidine-like chemical structure.
Nicolotti
Orazio
O
Dipartimento Farmaco-Chimico, University of Bari, Via Orabona 4, 70125, Bari, Italy. nicolotti@farmchim.uniba.it
Giangreco
Ilenia
I
Miscioscia
Teresa Fabiola
TF
Convertino
Marino
M
Leonetti
Francesco
F
Pisani
Leonardo
L
Carotti
Angelo
A
D001550:Benzamidines / Q000737:chemistry* / Q000494:pharmacology; D020650:Combinatorial Chemistry Techniques; D003198:Computer Simulation; D015195:Drug Design; D008958:Models, Molecular; D011485:Protein Binding / Q000187:drug effects; D021281:Quantitative Structure-Activity Relationship; D015842:Serine Proteinase Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D055672:Static Electricity; D013917:Thrombin / Q000037:antagonists & inhibitors* / Q000737:chemistry
D001550:Benzamidines; D015842:Serine Proteinase Inhibitors; D013917:Thrombin