Statistical mechanics theory of molecular recognition and pharmaceutical design

Norio Yoshida, Yasuomi Kiyota, Saree Phongphanphanee, Yutaka Maruyama, Takashi Imai, Fumio Hirata

Research output: Contribution to journalReview article

1 Citation (Scopus)

Abstract

Molecular recognition (MR) is an essential elementary process allowing biomolecules to perform their function. MR can be defined as a molecular process in which one or several guest molecules are bound with a high probability at a particular site such as a cleft or a cavity, of a host molecule in a particular orientation. It is a thermodynamic process which is characterised by the difference of the free energies between two states of a host-guest system, bound and unbound. The process features an extremely heterogeneous atomic-environment around binding sites, which has turned away challenges by the conventional statistical mechanics of liquids, e.g. a mean field theory. We have been developing a new theory for MR in biomolecular systems, based on the statistical mechanics of liquids, or the 3D-reference interaction site model (RISM)/RISM theory. The theory has demonstrated its amazing capability of predicting the process from the first principle. In this article, we review our recent works on MR concerning protein and deoxyribonucleic acid. Some applications of the method to drug design are also presented.

Original languageEnglish
Pages (from-to)445-478
Number of pages34
JournalInternational Reviews in Physical Chemistry
Volume30
Issue number4
DOIs
Publication statusPublished - Oct 1 2011

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Molecular recognition
Statistical mechanics
statistical mechanics
Pharmaceutical Preparations
Mean field theory
Molecules
Liquids
Biomolecules
liquids
Free energy
molecules
drugs
deoxyribonucleic acid
free energy
Binding Sites
interactions
Thermodynamics
proteins
thermodynamics
cavities

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry

Cite this

Statistical mechanics theory of molecular recognition and pharmaceutical design. / Yoshida, Norio; Kiyota, Yasuomi; Phongphanphanee, Saree; Maruyama, Yutaka; Imai, Takashi; Hirata, Fumio.

In: International Reviews in Physical Chemistry, Vol. 30, No. 4, 01.10.2011, p. 445-478.

Research output: Contribution to journalReview article

Yoshida, Norio ; Kiyota, Yasuomi ; Phongphanphanee, Saree ; Maruyama, Yutaka ; Imai, Takashi ; Hirata, Fumio. / Statistical mechanics theory of molecular recognition and pharmaceutical design. In: International Reviews in Physical Chemistry. 2011 ; Vol. 30, No. 4. pp. 445-478.
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