In silico investigation of the interactions of certain drugs proposed for the treatment of Covid-19 with the paraoxonase-1

Abstract

Coronavirus disease 2019 (Covid-19) has caused one of the biggest pandemics of modern times, infected over 240 million people and killed over 4.9 million people, and continues to do so. Although many drugs are widely recommended in the treatment of this disease, the interactions of these drugs with an anti-atherosclerotic enzyme, paraoxonase-1 (PON1), are not well known. In our study, we investigated the interactions of 18 different drugs, which are claimed to be effective against covid-19, with the PON1 enzyme and its genetics variants L55M and Q192R with molecular docking, molecular dynamics simulation and free energy calculation method MM/PBSA. We found that ruxolitinib, dexamethasone, colchicine; dexamethasone, sitagliptin, baricitinib and galidesivir, ruxolitinib, hydroxychloroquine were the most effective compounds in binding PON1-w, PON1L55M and PON1Q192R respectively. Mainly, sitagliptin, galidesivir and hydroxychloroquine have attracted attention by showing very high affinity (<-300 kJ/mol) according to the MM/PBSA method. We concluded that the drug interactions should be considered and more attention should be paid in the use of these drugs.

Communicated by Ramaswamy H. Sarma

Keywords:

• Covid-19
• paraoxonase-1
• molecular dynamic simulation
• molecular docking
• MM/PBSA

Acknowledgments

The numerical calculations reported in this paper were partially performed at TUBITAKULAKBIM, High Performance, and Grid Computing Center (TRUBA resources).

Disclosure statement

No potential conflict of interest was reported by the authors.

Authors' contributions

ZD is responsible for the preparation and implementation of the methodology and writing the manuscript. BVK and AO are responsible for designing the concept and reviewing the manuscript. IK is responsible for the analysis of data and critical evaluation of the manuscript.

Availability of data

All data are available with reasonable request.

Code availability

N/A