Genetic algorithm for molecular 3D drug design

Potemkin V.A.1 , Grishina M.A.1, Pozhilenkova G.V.1, Mikuchina K.M.2, Laufer S.2

1. Chelyabinsk State University
2. Universität Tübingen
Section: Experimental/Clinical Study
Year: 2004
A new algorithm DesPot for 3D design of new perspective biological active compounds is suggested. The algorithm includes the following procedures: a genetic construction of new molecular structures, their geometry optimization using the global minimum search along the Hessian modes and evaluation their biological activity within 3D-QSAR algorithm BiS. For the design of new structures it has been suggested to use the genetic algorithm. This algorithm takes a less time in order to achieve the optimum in a number of discrete optimization problems. The probability of biological activity has been used as a criteria of optimum. The design of new molecules is carried out using the set of the known drugs. The geometry of new designed molecules is optimized in MM3 force field. Then the orientation of each new molecule in the model receptor is defined using BiS algorithm. The characteristics of “model receptor – ligand” interactions and the probability of biological activity are computed. Algorithm DesPot has been used for design of new compounds of 40 types of biological activity
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Potemkin, V. A., Grishina, M. A., Pozhilenkova, G. V., Mikuchina, K. M., Laufer, S. (2004). Genetic algorithm for molecular 3D drug design. Biomeditsinskaya Khimiya, 50(application 1), 42-48.
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