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A Novel Technique for Virtual Discovery for Study of Multistage Bioprocesses

Vladimir Potemkin, Dean of Chemical Department, Head of Laboratory of Theoretical Problems of Organic Chemistry, Chelyabinsk State University

Date Posted: Thursday, May 22, 2008

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About the speaker

Vladimir Potemkin was born in 1962. In 1985 he graduated with honour from Chelybinsk State University. From 1987 he was a Scientist at Chelybinsk State University and was appointed Senior Scientist in 1989. In 1998 he undertook a Ph.D. degree in Physical Chemistry and became a Senior Lecturer. In 2000 he was appointed Head of Laboratory of Theoretical Problems of Organic Chemistry. In 2006 he worked at the Computer Chemistry Center in Erlangen (Germany) under supervision of Prof. Dr. Clark. Since 2006 he has held the position of Dean of Chemical Department at Chelyabinsk State University. Vladimir Potemkin is an author of more than 150 papers. He is a winner of Grand Prixes of Russian Academy of Sciences in the field of modelling in chemistry.

Abstract

A lot of modern methods for virtual discovery predict a bioactivity at the stage of receptor – ligand interaction. At the same time a biological action of a drug includes more than one stage of action even in cases of in vitro experiments. Therefore, a new method for virtual discovery is proposed. The method creates pseudo-atomic receptor model and allows to simulate a movement of a drug molecule to the receptor through water and membrane. The interaction with competitive sites is taken into account. Also the method allows to presuppose a metabolism of drug. The method has been used for detailed elucidation of stages of action for membranotropic dihydrofolatereductase inhibitors. It has been shown that the process of biological action of the drugs includes 3 critical stages: penetration through membrane, diffusion and interaction with the target. Some of the compounds play a role of pro-drugs and their metabolism yields to an active molecule. The quantitative relationships for each of the stages are obtained. The importance of every stage is estimated for each molecule. Now the algorithm is used for virtual screening of more than 20 kinds of biological activities.

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