A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds

Molecules

Giuliano Malloci²  Attilio Vittorio Vargiu¹  Giovanni Serra²  Andrea Bosin²  Paolo Ruggerone²  Matteo Ceccarelli² 

[1]Dipartimento di Fisica, Università degli studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Cagliari), Italy

关键词: antimicrobial compounds;    molecular databases;    all-atom force fields;    molecular dynamics simulations;   

DOI  :  10.3390/molecules200813997

来源: mdpi

【 摘 要 】

We present an on-line database of all-atom force-field parameters and molecular properties of compounds with antimicrobial activity (mostly antibiotics and some beta-lactamase inhibitors). For each compound, we provide the General Amber Force Field parameters for the major species at physiological pH, together with an analysis of properties of interest as extracted from μs-long molecular dynamics simulations in explicit water solution. The properties include number and population of structural clusters, molecular flexibility, hydrophobic and hydrophilic molecular surfaces, the statistics of intra- and inter-molecular H-bonds, as well as structural and dynamical properties of solvent molecules within first and second solvation shells. In addition, the database contains several key molecular parameters, such as energy of the frontier molecular orbitals, vibrational properties, rotational constants, atomic partial charges and electric dipole moment, computed by Density Functional Theory. The present database (to our knowledge the first extensive one including dynamical properties) is part of a wider project aiming to build-up a database containing structural, physico-chemical and dynamical properties of medicinal compounds using different force-field parameters with increasing level of complexity and reliability. The database is freely accessible at http://www.dsf.unica.it/translocation/db/.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland.