title: Efficient estimation of MMGBSA-based BEs for DNA and aromatic furan amidino derivatives.
abstract: Molecular mechanics with Generalized Born surface area (MMGBSA) based binding energies (BEs) derived from the molecular dynamics (MD) trajectories are highly reliable and extensively used standards to estimate the strength of interactions between ligands and their receptor. MD simulations (5 ns) for 30 aromatic furan aminidino derivatives (anti-Pneumocystis carnii agents) have been carried out by using Amber program and BEs have been calculated by using Generalized Born (GB) method. Based on the generated data, we present a simple and effective method for the approximation of BEs without performing MD simulations and MMGBSA calculations. Quantum chemical (density functional theory based) and geometrical descriptors are used for the prediction of the BE values. All the developed models are statistically significant with high values of correlation and cross-validation coefficients. The prediction ability and effectiveness of the models are tested by the division of the data-set into four different training and test sets and the average error was only 4-7% (1.56-2.61 kcal/mol) of the actual BEs.
authors.affiliation: Molecular Modelling Group, Indian Institute of Chemical Technology, Uppal Road, Taranaka, Hyderabad 500 607, India. hemantkrsri@gmail.com
authors.forename: Hemant Kumar
authors.initials: HK
authors.lastname: Srivastava
authors.forename: G Narahari
authors.initials: GN
authors.lastname: Sastry
mesh_terms: D000465:Algorithms; D000578:Amidines / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D005663:Furans / Q000737:chemistry*; D006860:Hydrogen Bonding; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D021281:Quantitative Structure-Activity Relationship; D044366:Transition Temperature
chemical_list: D000578:Amidines; D005663:Furans; D008024:Ligands; D004247:DNA