Molecular analysis of dUTPase of Helicobacter pylori for identification of novel inhibitors using in silico studies

Abstract

The human gastric pathogen Helicobacter pylori chronically affects the gastric mucosal layer of approximately half of world’s population. The emergence of resistant strains urges the need for identification of novel and selective drug against new molecular targets. A ubiquitous enzyme, Deoxyuridine 5’-triphosphate nucleotidohydrolase (dUTPase), is considered as first line of defense against uracil mis-incorporation into DNA, and essential for genome integrity. Lack of dUTPase triggers an elevated recombination frequency, DNA breaks and ultimately cell death. Hence, dUTPase can be considered as a promising target for development of novel lead inhibitor compounds in H. pylori treatment. Herein, we report the generation of three-dimensional model of the target protein using comparative modelling and its validation. To identify dUTPase inhibitors, a high throughput virtual screening approach utilizing Knowledge-based inhibitors and DrugBank database was implemented. Top ranked compounds were scrutinized based on investigations of the protein-ligand interaction fingerprints, molecular interaction maps and binding affinities and the drug potentiality. The best ligands were studied further for complex stability and intermolecular interaction profiling with respect to time under 100 ns classical molecular dynamic stimulation, establishing significant stability in dynamic states as observed from RMSD and RMSF parameters and interactions with the catalytic site residues. The binding free energy calculation computed using MM-GBSA method from the MD simulation trajectories demonstrated that our molecules possess strong binding affinity towards the Helicobacter pylori dUTPase protein. We conclude that our proposed molecules may be potential lead molecules for effective inhibition against the H. pylori dUTPase protein subject to experimental validation.

Communicated by Ramaswamy H. Sarma

Keywords:

• Helicobacter pylori
• MD stimulations
• MM-GBSA
• virtual screening
• docking

Acknowledgements

R.S. thanks the CSIR-HRDG for the fellowship (grant no. 09/995(0004)/2019-EMR-1). C.M. and R.S. thank Schrodinger team especially Ms. Shelvia Malik, Mr. Prajwal Nandekar, Mr. Pritesh Bhat, Mr. Kishore Venkatesh for facilitating quick access and providing excellent training sessions. R.S. thanks Dr. Ramakrishnan Sitaraman, Dr. Anandita Singh, Dr. Shashi Bhushan Tripathi, Dr. Udit Soni and Dr. Som Mondal for project related inputs and discussions as part of Student Research Committee (SRC), TERI SAS.

Author contributions

R.S. designed and conducted experiments, analysed and drafted the results. D. S conducted MDS experiment. S.A provided expertise of MDS. P.Am provided intellectual inputs, contributed to experimental design and analyses. C.M. conceived, designed, and coordinated the study, analysed the results, and drafted the manuscript. All authors edited and reviewed the final manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

Any data that is generated within the report will be available if required from the corresponding authors (C.M and S.A.).

Additional information

Funding

The study is supported by the grants received from the Indian Council of Medical Research (ICMR), New Delhi, India [Grant ID: ISRM/12(03)/2017] and the Department of Biotechnology (DBT), New Delhi, India [Grant ID: No. BT/RLF/Re-entry/47/2014].