Download Physico-chemical and computational approaches to drug by F Javier Luque; Xavier Barril PDF

By F Javier Luque; Xavier Barril

Content material: Preface; acceptance of ligands by way of macromolecular ambitions; thermodynamics of ligand binding; continuum solvation in biomolecular structures; bioavailability prediction at early drug discovery phases: in vitro assays and easy physicochemical principles; computational ideas in drug layout; molecular descriptors for database mining; pharmacophore versions in drug layout; docking and digital screening; binding loose power calculations and scoring in small-molecule docking; COMparative BINding power (COMBINE) research as a structure-based 3D-QSAR procedure; accounting for goal flexibility in the course of ligand-receptor docking; more advantageous sampling tools in drug layout; exploring variety of drug objective websites; increasing the objective area: druggability review; computational thoughts and demanding situations for focusing on protein-protein interactions with small molecules; case reviews; utilizing molecular simulations and metadynamics to foretell binding loose energies and kinetics; the case of COX and CDK2; Computer-assisted layout of drug-like man made libraries; index

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Although biopolymers can act as protein ligands and are increasingly important therapeutic agents, the drug discovery aspects of their binding thermodynamics are less explored and are not considered here. 1 Basic Equations of Ligand–Protein Binding Thermodynamics The binding affinity of a ligand (L) to a protein (P) can be characterized by the dissociation constant, Kd: Kd ~ ½LŠ½PŠ ½LPŠ ð2:1Þ corresponding to the process LP

Thus, the ligand is treated quantum mechanically and is polarized by the point charges of the target protein, and the induced dipole at a given target atom is then reformulated as an induced charge in an iterative manner. The final set of polarized charges was evaluated for 12 protein–ligand systems. Although inclusion of polarization does not always led to the lowest energy pose having a lower rmsd, it was found that the polarized charges resulted in an increased cluster size and a concomitant decrease in the rmsd of the docked pose with regard to the crystallographic solution.

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