Keywords Binding free energy calculations, Computational chemistry, Epigenetic
inhibitors, Histone deacetylases, Histone demethylases, Histone methyltransferases,
Homology modeling, Molecular docking, Molecular modeling, Structure-based
drug design, Virtual screening
Abbreviations
3D
Three-dimensional
α-KG
α-Ketoglutarate
ADMET
Absorption, distribution, metabolism, excretion, and toxicity
AML
Acute myeloid leukemia
AOD
Amine oxidase domain
CARM1
Coactivator-associated arginine methyltransferase 1
CoMFA
Comparative molecular field analysis
CoMSIA
Comparative molecular similarity indices analysis
DOT1L
Disruptor of telomeric silencing 1-like
DNA
Deoxyribonucleic acid
DNMT
DNA methyltransferase
EZH
Enhancer of Zeste homologue
FAD
Flavin adenine dinucleotide
FDH
Formaldehyde dehydrogenase
FEP
Free energy perturbation
FIH
Factor inhibiting hypoxia-inducible factor
G9a/EHMT2 Euchromatic histone-lysine N-methyltransferase 2
GLP
G9a-like protein
H3K4
Lysine 4 of histone 3
H3K4me3
Trimethylated lysine 4 of histone 3
H3K9me2
Dimethylated lysine 9 of histone 3
HDAC
Histone deacetylase
HTS
High-throughput screening
IC 50
The half maximal inhibitory concentration
ICM
Internal coordinate modeling
JARID
Jumonji and AT-rich interaction domain
Jmj
Jumonji
JMJD
Jumonji domain-containing protein
KDM
Lysine demethylase
KMT
Lysine methyltransferase
LIE
Linear interaction energy
LSD
Lysine-specific demethylase
MAO
Monoamine oxidase
MDS
Myelodysplastic syndromes
MM-GBSA
Molecular mechanics generalized Born surface area
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D. Robaa et al.