An investigation into the construction of molecular models by the template joining method

Applications and limitations of in silico models in drug discovery

Drug discovery in the late twentieth and early twenty-first century has witnessed a myriad of changes that were adopted to predict whether a compound is likely to be successful, or conversely enable identification of molecules with liabilities as early as possible. These changes include integration of in silico strategies for lead design and optimization that perform complementary roles to that of the traditional in vitro and in vivo approaches. The in silico models are facilitated by the availability of large datasets associated with high-throughput screening, bioinformatics algorithms to mine and annotate the data from a target perspective, and chemoinformatics methods to integrate chemistry methods into lead design process. This chapter highlights the applications of some of these methods and their limitations. We hope this serves as an introduction to in silico drug discovery.

Simple estimation of absolute free energies for biomolecules

One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is irrelevant, however, if the absolute free energy of each state can be computed. We present a method for calculating the absolute free energy that employs a simple construction of an exactly computable reference system which possesses high overlap with the state of interest. The approach requires only a physical ensemble of conformations generated via simulation and an auxiliary calculation of approximately equal central-processing-unit cost. Moreover, the calculations can converge to the correct free energy value even when the physical ensemble is incomplete or improperly distributed. As a "proof of principle," we use the approach to correctly predict free energies for test systems where the absolute values can be calculated exactly and also to predict the conformational equilibrium for leucine dipeptide in implicit solvent.

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.

BUILDER v.2: improving the chemistry of a de novo design strategy

Significant improvements have been made to the de novo drug design program BUILDER. The BUILDER strategy is to find molecule templates that bind tightly to 'hot spots' in the target receptor, and then generate bridges to join these templates. In this paper, the bridging algorithm has been further developed to improve the chemical sense and diversity of the bridges, as well as the robustness of the technique. The improved algorithm is then applied to rebuild known bridges in methotrexate and HIV protease. Finally, the entire BUILDER approach is tested by rebuilding methotrexate de novo.

A fast and efficient method to generate biologically relevant conformations

Mutual binding between a ligand of low molecular weight and its macromolecular receptor demands structural complementarity of both species at the recognition site. To predict binding properties of new molecules before synthesis, information about possible conformations of drug molecules at the active site is required, especially if the 3D structure of the receptor is not known. The statistical analysis of small-molecule crystal data allows one to elucidate conformational preferences of molecular fragments and accordingly to compile libraries of putative ligand conformations. A comparison of geometries adopted by corresponding fragments in ligands bound to proteins shows similar distributions in conformations space. We have developed an automatic procedure that generates different conformers of a given ligand. The entire molecule is decomposed into its individual ring and open-chain torsional fragments, each used in a variety of favorable conformations. The latter ones are produced according to the library information about conformational preferences. During this building process, an extensive energy ranking is applied. Conformers ranked as energetically favorable are subjected to an optimization in torsion angle space. During minimization, unfavorable van der Waals interactions are removed while keeping the open-chain torsion angles as close as possible to the experimentally most frequently observed values. In order to assess how well the generated conformers map conformation space, a comparison with experimental data has been performed. This comparison gives some confidence in the efficiency and completeness of this approach. For some ligands that had been structurally characterized by protein crystallography the program was used to generate sets of some 10 to 100 conformers. Among these, geometries are found that fall convincingly close to the conformations actually adopted by these ligands at the binding site.

Current methods for site-directed structure generation

There has been a rapid growth of interest in techniques for site-directed drug design, fueled by the increasing availability of structural models of proteins of therapeutic importance, and by studies reported in the literature showing that potent chemical leads can be obtained by these techniques. Structure generation programs offer the prospect of discovering highly original lead structures from novel chemical families. Due to the fact that this technique is more-or-less still in its infancy, there are no case studies available that demonstrate the use of structure generation programs for site-directed drug design. Such programs were first proposed in 1986, and became commercially available in early 1992. They have shown their ability to reproduce, or suggest reasonable alternatives for, ligands in well-defined binding sites. This brief review will discuss the recent advances that have been made in the field of site-directed structure generation.

Constitutional, configurational and conformational analysis of transition metal coordination complexes

A computational approach to conformational analysis is applied to the study of transition metal coordination complexes. The method provides a means of rapidly exploring conformational space without any inherent reliance on energy calculations and is therefore applicable to a wide variety of systems. It has been incorporated into an algorithm which explores the constitutional, configurational and conformational degrees of freedom for a metal ion and a number of potential ligands. The program determines which of the possible coordination complex products could form stable conformations and can therefore be used to rationalise the products obtained from the mixture. The method is illustrated using two cases: the cobalt(III)-triethylenetetramine-glycine system and complexes of diindolopyridine derivatives.

Automated conformational analysis: algorithms for the efficient construction of low-energy conformations

The method of constructing low-energy conformations using template joining can provide an efficient means of searching the conformational space of molecules. The simplest algorithm to perform this task would construct each potential conformation from scratch. However, new algorithms, some of which use techniques from Artificial Intelligence, have been developed which can greatly improve the efficiency of this approach.