Ligand atom partial charges assignment for complementary electrostatic potentials

Synergy between combinatorial chemistry and de novo design

Traditional de novo design algorithms are able to generate many thousands of ligand structures that meet the constraints of a protein structure, but these structures are often not synthetically tractable. In this article, we describe how concepts from structure-based de novo design can be used to explore the search space in library design. A key feature of the approach is the requirement that specific templates are included within the designed structures. Each template corresponds to the "central core" of a combinatorial library. The template is positioned within an acyclic chain whose length and bond orders are systematically varied, and the conformational space of each structure that results (core plus chain) is explored to determine whether it is able to link together two or more strongly interacting functional groups or pharmacophores located within a protein binding site. This fragment connection algorithm provides "generic" 3D molecules in the sense that the linking part (minus the template) is built from an all-carbon chain whose synthesis may not be easily achieved. Thus, in the second phase, 2D queries are derived from the molecular skeletons and used to identify possible reagents from a database. Each potential reagent is checked to ensure that it is compatible with the conformation of its parent 3D conformation and the constraints of the binding site. Combinations of these reagents according to the combinatorial library reaction scheme give product molecules that contain the desired core template and the key functional/pharmacophoric groups, and would be able to adopt a conformation compatible with the original molecular skeleton without any unfavorable intermolecular or intramolecular interactions. We discuss how this strategy compares with and relates to alternative approaches to both structure-based library design and de novo design.

A branch-and-bound method for optimal atom-type assignment in de novo ligand design

This paper investigates a computational procedure for the determination of the atom types on the vertices of a molecular skeleton to optimize interaction with the receptor site whilst maintaining a synthetically reasonable structure. The connectivity of the skeleton is analysed and appropriate atom types are compiled for each vertex. Receptor ionization and conformational states are generated by varying the positions of hydrogen atoms and electron lone pairs in the carboxyl, rotatable hydroxyl and amino groups. The structure is divided into small non-overlapping substructures. Atom types are assigned exhaustively onto each of the substructures using a depth-first search method; chemical rules are applied to reject unacceptable atom combinations early on. An empirical interaction score is calculated and the representatives of each partial structure are stored in ascending order according to their scores. The branch-and-bound procedure is then used to find the structures with the lowest scores. The method is illustrated using five protein-ligand complexes.

The estradiol pharmacophore: ligand structure-estrogen receptor binding affinity relationships and a model for the receptor binding site

The accumulated knowledge on the binding of estradiol (E2) and its analogs and the results of affinity-labeling studies have been reviewed and are used herein to derive a binding site model for the estrogen receptor (ER). Estradiol is nonpolar and hydrophobic, except at its molecular termini. Most of its skeletal flexibility resides in the B-ring, and it probably binds in a low-energy conformation. The phenolic OH group in the A-ring contributes about 1.9 kcal/mol to the binding free energy and probably acts primarily as a hydrogen bond donor. The 17 beta-hydroxyl group in the D-ring contributes approximately 0.6 kcal/mol to the binding and probably acts as a hydrogen bond acceptor, either directly or via a water molecule. There also seems to be a degree of flexibility in the region of the receptor that encompasses the D-ring. The aromatic ring contributes about 1.5 kcal/mol, probably through weak polar interactions with receptor residues that contact the beta-face of the steroid. The receptor seems to surround the ligand, so that all four rings contribute significantly to binding. Small hydrophobic substituents enhance binding affinity at positions 4, 12 beta, 14, and 16 alpha; whereas, larger hydrophobic substituents are tolerated at positions 7 alpha, 11 beta, and 17 alpha. In general, the ER is intolerant of polar substituents. Based on E2 analogs bearing affinity-labeling groups, cysteine residues might be present in the binding site in the area of C-4, C-17 alpha, and C-17 beta, and a lysine residue might be located near C-16. Models that represent the limits of deformability of the ligand binding site, the position of preformed pockets, and space occupied by the receptor are presented. The various elements in this model for the binding of steroidal estrogens by the estrogen receptor are consistent with evidence emerging from the crystal structures of related nuclear hormone receptor ligand complexes.

The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties

This paper is the first of a series which examines the problems of atom assignment in automated de novo drug design. In subsequent papers, a combinatoric optimization method for fragment placement onto 3D molecular graphs is provided. Molecules are built from molecular graphs by placing fragments onto the graph. Here we examine the transferability of atomic residual charge, by fragment placement, with respect to the electrostatic potential. This transferability has been tested on 478 molecular structures extracted from the Cambridge Structural Database. The correlation found between the electrostatic potential computed from composite fragments and that computed for the whole molecule was encouraging, except for extended conjugated systems.