Towards Understanding the Structure, Dynamics and Bio-activity of Diabetic Drug Metformin

TL;DR

This study explores the structural, dynamical, and DNA-binding properties of metformin hydrochloride using experiments, quantum calculations, and molecular dynamics, revealing its stable tautomeric form and groove-binding mode.

Contribution

It provides a comprehensive analysis of metformin's structure, stability, solvation, and DNA interaction mechanisms, which were not fully understood before.

Findings

Non-planar tautomer is most stable

Metformin forms strong hydrogen bonds with water

Binds DNA via minor/major groove in a non-intercalating manner

Abstract

Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows anti-tumour activities and increases the survival rate of patients suffering from certain types of cancer namely colorectal, breast, pancreas and prostate cancer. However, theoretical studies of structure and dynamics of metformin have not yet been fully explored. In this work, we investigate the characteristic structural and dynamical features of three mono-protonated forms of metformin hydrochloride with the help of experiments, quantum chemical calculations and atomistic molecular dynamics simulations. We validate our force field by comparing simulation results to that of the experimental findings. Nevertheless, we discover that the non-planar tautomeric form is the most stable. Metformin forms strong hydrogen bonds with surrounding water molecules and its solvation dynamics show unique features. Because of an extended positive charge distribution, metformin possesses features of being a permanent cationic partner toward several targets. We study its interaction and binding ability with DNA using UV spectroscopy, circular dichroism, fluorimetry and metadynamics simulation. We find a non-intercalating mode of interaction. Metformin feasibly forms a minor/major groove-bound state within a few tens of nanoseconds, preferably with AT rich domains. A significant decrease in the free-energy of binding is observed when it binds to a minor groove of DNA.