Computer Simulation in Molecular Medicine and Drug Design

Paper by RAS Corresponding Member S. D. Varfolomeev^a,b,
Candidate of Science (Chemistry) S. V. Lushchekina^a,
and Doctor of Science (Chemistry) A. V. Nemukhin^a,b*

^a Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia

^b Moscow State University, Moscow, Russia

e-mail: sdvarf@sky.chph.ras.ru, sofya.lushchekina@gmail.com, anem@lcc.chem.msu.ru

Received January 24, 2016

Abstract—Achievements in genomics and proteomics, as well as the exponential growth of computing power,
ensure qualitatively new opportunities in understanding the molecular nature of “living matter” and, as a con-
sequence, the extension of the capabilities of medicine. This paper considers two scientific fields in which high-
throughput computing is especially effective. The first is computer-aided design of drugs, and the second is
analysis of human molecular polymorphism and individual sensitivity to drugs. General provisions are illus-
trated with specific examples, including the development of a new class of antimyasthenic drugs—cholinest-
erase inhibitors, research in the molecular polymorphism of brain aspartoacylase, the clarification of the nature
of Canavan disease, and the study of individual sensitivity to drugs—cholinesterase inhibitors.

Keywords: personalized medicine, molecular medicine, human molecular polymorphism, supercomputer tech-
nologies, molecular simulation, highly productive computing, molecular dynamics, quantum chemistry, com-
puter-aided drug design, individual sensitivity to drugs.

DOI: 10.1134/S101933161603014X

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