Modeling the value of predictive affinity scoring in preclinical drug discovery.

Drug discovery is widely recognized to be a difficult and costly activity in large part due to the challenge of identifying chemical matter which simultaneously optimizes multiple properties, one of which is affinity for the primary biological target. Further, many of these properties are difficult to predict ahead of expensive and time-consuming compound synthesis and experimental testing. Here we highlight recent work to develop compound affinity prediction models, and extensively investigate the value such models may provide to preclinical drug discovery.

Docking covalent inhibitors: a parameter free approach to pose prediction and scoring.

Although many popular docking programs include a facility to account for covalent ligands, large-scale systematic docking validation studies of covalent inhibitors have been sparse. In this paper, we present the development and validation of a novel approach for docking and scoring covalent inhibitors, which consists of conventional noncovalent docking, heuristic formation of the covalent attachment point, and structural refinement of the protein-ligand complex. This approach combines the strengths of the docking program Glide and the protein structure modeling program Prime and does not require any parameter fitting for the study of additional covalent reaction types.

Bonded exciplex formation: electronic and stereoelectronic effects.

As recently proposed, the singlet-excited states of several cyanoaromatics react with pyridine via bonded-exciplex formation, a novel concept in photochemical charge transfer reactions. Presented here are electronic and steric effects on the quenching rate constants, which provide valuable support for the model. Additionally, excited-state quenching in poly(vinylpyridine) is strongly inhibited both relative to that in neat pyridine and also to conventional exciplex formation in polymers, consistent with a restrictive orientational requirement for the formation of bonded exciplexes.

Bonded exciplexes. A new concept in photochemical reactions.

Charge-transfer quenching of the singlet excited states of cyanoaromatic electron acceptors by pyridine is characterized by a driving force dependence that resembles those of conventional electron-transfer reactions, except that a plot of the log of the quenching rate constants versus the free energy of electron transfer is displaced toward the endothermic region by 0.5-0.8 eV.

Mimicking photosynthesis in a computationally designed synthetic metalloprotein.

While advances in protein design have made possible the construction of protein architectures with nativelike properties and predictable structures and function, there are as of yet no examples of functional, protein-based, solar energy conversion systems. This communication describes the design and characterization of an artificial reaction center (RC) protein that closely resembles the function of the natural photosynthetic RC. The synthetic protein, designed by the protein design program CORE, participates in multiple reduction/oxidation cycles with exogenous acceptors/donors following photoexcitation.