Quantitative measures of molecular similarity

Methods to analyze transition-state analogs for enzymatic reactions

Carey K. Bagdassarian, Benjamin B. Braunheim, Vern L. Schramm, Steven D. Schwartz

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

A formalism is presented for quantifying the similarity between any two molecules. The chemical descriptor used for comparison is the molecular electrostatic potential at the van der Waals surface. Thus, both the spatial properties of a molecule and its chemical features are captured in this approach. For molecules that are geometrically alike, the most useful similarity measure stems from orienting the two species so that their physical surfaces are aligned as well as possible, without regard to chemical patterns. After this alignment is achieved, a single measure sensitive to the spatial distribution of the electrostatic potential is used to rank the electronic similarity. Molecular similarity measures are applied to the enzyme systems AMP deaminase and AMP nucleosidase in order to understand quantitatively why their respective transition-state inhibitors bind more tightly than do their substrates.

Original languageEnglish (US)
Pages (from-to)1797-1804
Number of pages8
JournalInternational Journal of Quantum Chemistry
Volume60
Issue number8
StatePublished - Dec 20 1996

Fingerprint

AMP nucleosidase
analogs
adenosine monophosphate
Molecules
Electrostatics
AMP Deaminase
electrostatics
molecules
Spatial distribution
stems
inhibitors
enzymes
spatial distribution
alignment
Substrates
Enzymes
formalism
electronics

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Quantitative measures of molecular similarity : Methods to analyze transition-state analogs for enzymatic reactions. / Bagdassarian, Carey K.; Braunheim, Benjamin B.; Schramm, Vern L.; Schwartz, Steven D.

In: International Journal of Quantum Chemistry, Vol. 60, No. 8, 20.12.1996, p. 1797-1804.

Research output: Contribution to journalArticle

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