2D-3D Migration of Large Chemical Inventories with Conformational Multiplication. Application of the Genetic Algorithm

• Published in: Journal of chemical information and modeling 2005-03, Vol.45 (2), p.283-292
• Main Authors: Mekenyan, Ovanes, Pavlov, Todor, Grancharov, Vanjo, Todorov, Milen, Schmieder, Patricia, Veith, Gilman
• Format: Article
• Language: English
• Subjects: Algorithms; Automation; Chemicals; Databases, Factual; Dimensional analysis; Drug Design; Genetics; Models, Chemical; Molecular Conformation; Quantitative Structure-Activity Relationship; Steroids - chemistry
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/ci0498463

Mathematical chemistry has afforded a variety of research areas with important tools to understand and predict the behavior of chemicals without having to consider the complexities of three-dimensional conformations of molecules. Predictive toxicology, an area of increasing importance to toxicity assessments critical to molecular design and risk management, must be based on more explicit descriptions of structure, however. Minimum energy conformations are often used for convenience due, in part, to the difficulty of computing a representative population of conformers in all but rigid structures. Such simplifying assumptions fail to reveal the variance of the stereoelectronic nature of molecules as well as the misclassification of chemicals which initiate receptor-based toxicity pathways. Because these errors impact both the success in discovering new lead and the identification of possible hazards, it is important that mathematical chemistry develop additional tools for conformational analysis. This paper presents a new system for automated 2D-3D migration of chemicals in large databases with conformer multiplication. The main advantages of this system are its straightforward performance, reasonable execution time, simplicity and applicability to building large 3D chemical inventories. The module for conformer multiplication within the 2D-3D migration system is based on a new formulation of the genetic algorithm for computing populations of possible conformers. The performance of the automated 2D-3D migration system in building a centralized 3D database for all chemicals in commerce worldwide is discussed. The applicability of the 3D database in assessing the impact of molecular flexibility on identifying active conformers in QSAR analysis and assessing similarity between chemicals is illustrated.