QM/MM study of the cyclization reaction mechanism for pimelic o-aminobenzamide Histone deacetylase (HDAC) inhibitor 4b

Abstract

The detailed mechanism of the intramolecular cyclization reaction of pimelic o-aminobenzamide histone deacetylase (HDAC) inhibitor 4b (N1-(2-aminophenyl)-N7-phenylheptanediamide) was studied using Molecular Dynamics (MD) simulations for conformational sampling and a hybrid quantum mechanical/molecular mechanical (QM/MM) method for the energy profiling during the reaction progress, as well as for verifying the topology of the intermediates.

Author (co-authors)
First name Last name Institutional affiliation E-mail Phone number ORCID ID Academic status, position Institution address Author contribution(s) Institutional affiliation
Olena
Klenina
olena_klenina@yahoo.com
0000-0002-8946-3698
Associate Professor
Pekarska Str., 69
Investigation
Methodology
Writing – Original Draft Preparation
Danylo Halytsky Lviv National Medical University
Laura
Márquez Cantudo
laura.marquezcantudo@ceu.es
0000-0002-1618-1366
PhD student
Boadilla del Monte, Urbanización Montepríncipe, 28668, Spain
Investigation
Methodology
Universidad San Pablo CEU
Claire
Coderch
claire.coderchboue@ceu.es
0000-0001-7229-8289
Profesor Titular
Boadilla del Monte, Urbanización Montepríncipe, 28668, Spain
Data Curation
Methodology
Supervision
Writing – Review & Editing
Universidad San Pablo CEU
Beatriz
de Pascual-Teresa Fernandez
bpaster@ceu.es
0000-0002-1101-0373
Profesor Catedrático
Boadilla del Monte, Urbanización Montepríncipe, 28668, Spain
Conceptualization
Project Administration
Supervision
Writing – Review & Editing
Universidad San Pablo CEU