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A. B. Rozhenko
EPS
electrostatic potential surface
FAAH
fatty acid amide hydrolase
FEP
free energy perturbation
HIV
human immunodeficiency virus
HMGR
3-hydroxy-3-methylglutaryl-coenzyme A reductase
HOMO
highest occupied molecular orbital
IC 50
half maximal inhibitory concentration
IEF
integral equation formalism
IN
integrase
LUMO
lowest unoccupied molecular orbital
MD
molecular dynamics
MD/MM
molecular mechanics/molecular dynamics
MEP
molecular electrostatic potential
MFCC
molecular fractionation with conjugate caps approach
MMP
matrix metalloproteinase
MNDO
modified neglect of diatomic overlap
MO
molecular orbital
MP2
second-order Møller-Plesset perturbation theory
PCM
polarizable continuum model
PDE
phosphodiesterase
PES
potential energy surfaces
PLA 2
phospholipases A 2 enzymes
PM3
parameterized model number 3 (Stewart’s semi-empirical approach)
PMF
potential of mean force
QM/MM
quantum mechanic/molecular mechanics hybrid approach
QSAR
quantitative structure–activity relationship
RHF
restricted Hartree-Fock method
RI
resolution of the identity
RNA
ribonucleic acid
SCC-DFTB self-consistent charge-density functional tight binding
SCRFPCM self-consistent reaction field polarizable continuum model
SIBFA
sum of interactions between fragments ab initio computed
TSS
transition state structures
XO
xanthine oxidase
7.1 Introduction
Over the last few decades, quantum chemical calculations became a powerful alternative to experimental methods in medicinal and drug chemistry in creating novel
drug candidates [1–3]. One of these modern approaches is based on elaboration of
small molecules, binding to the active site of an enzyme and inhibiting the reaction catalyzed by the enzyme [4]. These chemical substances should also exhibit