ABSTRACT
An ultrafast docking and virtual screening program, CRDOCK, is presented that contains (1) a search engine that can use a variety of sampling methods and an initial energy evaluation function, (2) several energy minimization algorithms for fine tuning the binding poses, and (3) different scoring functions. This modularity ensures the easy configuration of custom-made protocols that can be optimized depending on the problem in hand. CRDOCK employs a precomputed library of ligand conformations that are initially generated from one-dimensional SMILES strings. Testing CRDOCK on two widely used benchmarks, the ASTEX diverse set and the Directory of Useful Decoys, yielded a success rate of ~75% in pose prediction and an average AUC of 0.66. A typical ligand can be docked, on average, in just ~13 s. Extension to a representative group of pharmacologically relevant G protein-coupled receptors that have been recently cocrystallized with some selective ligands allowed us to demonstrate the utility of this tool and also highlight some current limitations. CRDOCK is now included within VSDMIP, our integrated platform for drug discovery.
Subject(s)
Drug Evaluation, Preclinical/methods , Ligands , Molecular Docking Simulation/methods , Proteins/metabolism , User-Computer Interface , Humans , Protein Conformation , Proteins/chemistry , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/metabolism , Thermodynamics , Time FactorsABSTRACT
A new family of pi-extended TTF analogues (3a-c) and D-pi-A chromophores (5a-c), in which the electroactive units (1,3-dithiole rings and 2,2-dicyanovinyl groups) are connected through a pyridine bridge with a meta substitution pattern, is reported. The redox behavior of these compounds has been investigated by cyclic voltammetry and theoretical calculations performed at the B3P86/6-31G** level. Unlike many pi-extended TTF derivatives, the 1,3-dithiole rings in compounds 3a-c do not behave independently and two oxidation processes are observed with an anodic separation ranging from 50 to 150 mV. Calculations show that electrons are equally extracted from both dithiole rings. A biradical structure is predicted for the dication state due to the near-degeneracy of the HOMO and HOMO - 1 orbitals. The presence of both donor (D) and acceptor (A) fragments in conjugates results in irreversible oxidation and reduction processes associated with the 1,3-dithiole ring and with the 2,2-dicyanovinyl moiety, respectively. An electrochemical-chemical-electrochemical (ECE) process takes place for all the compounds reported. The chemical process implies the dimerization of the radical cation for compounds 5 and the oligomerization of the biradical dication for compounds 3. The ECE process therefore generates new neutral dimeric (5) or oligomeric (3) species that incorporate the TTF vinylogue core.
