Molecular dynamics and computational study of Mannich-based coumarin derivatives: potent tyrosine kinase inhibitor

The manifestation of bacterial UTI (Urinary Tract Infection) has been predominantly endemic, globally; eventually, the development of new UTI antibacterial agent(s) remains the call of the day. Herein, two series of Mannich-based 4-hydroxy coumarin derivatives, 7a-m and 8a-m were designed by suitable heterocyclic amines condensed with aldehydes. The synthesised molecules were interpreted by ¹H-NMR and ¹³C-NMR spectral analyses with in vitro antibacterial studies. The compound, 4-hydroxy-3-((4-hydroxy-3-methoxyphenyl)(morpholino)methyl)-2H-chromen-2-one 8l was the significant derivative against pathogenic bacteria Staphylococcus aureus and Escherichia coli with MIC values 12.50 and 25 µM, respectively. Computational assessments with the Lipinski’s rule of five, ADMET properties and molecular docking studies revealed that analogues, 7f, 7l, 8d, 8j and 8k could be potent druggable molecules with significant binding affinity towards bacterial tyrosine kinase, as target. To understand the mode of binding and intrinsic stabilities of potent receptor-ligand complexes, each system was subjected molecular dynamics simulations for 100 ns. Inter-molecular contact analysis and intrinsic hydrogen-bond stability portrayed the analogues 8l form a number of non-bonded contacts with the receptor tyrosine kinase being mostly dominated by electrostatic and hydrophobic contacts. The results from the present structure-based designing approach might be a valuable tool towards identification of a new antibacterial drug candidate(s) against UTI in near future.

Abbreviations4-HC

4-hydroxy coumarin

ADMET

absorption, distribution, metabolism, excretion, toxicity

DCE

1,2-dichloroethane

DCM

dichloromethane

DMSO

dimethyl sulfoxide

MD

molecular dynamics

MIC

minimum inhibitory concentration

NMR

nuclear magnetic resonance

NPT

isothermal isobaric ensembles

NVT

canonical ensembles

PCA

principal component analysis

PDB

protein data bank

Rg

radius gyration

RMSF

root-mean-square fluctuations

RSMD

root-mean-square deviation

UTI

urinary Tract Infection

4-hydroxy coumarin

absorption, distribution, metabolism, excretion, toxicity

1,2-dichloroethane

dichloromethane

dimethyl sulfoxide

molecular dynamics

minimum inhibitory concentration

nuclear magnetic resonance

isothermal isobaric ensembles

canonical ensembles

principal component analysis

protein data bank

radius gyration

root-mean-square fluctuations

root-mean-square deviation

urinary Tract Infection

Communicated by Ramaswamy H. Sarma