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

Abstract

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.

Abbreviations
4-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

Communicated by Ramaswamy H. Sarma

Keywords:

• MD simulation
• PCA
• 4-hydroxy coumarin
• Mannich-base

Acknowledgements

Authors are thankful to Department of Chemistry Ravenshaw University, for NMR facility.

Disclosure statement

Authors declared no conflict of interest.

Additional information

Funding

This study was supported by the PhD fellowship Grant 1781611002/2017 of Siksha O Anusandhan Deemed to be University, Bhubaneswar.