Molecular Docking Studies of Sesquiterpenoids against Helicobacter pylori Peptide Deformylase
Muhammad Dawood
Department of Pharmacy, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
Nighat Fatima *
Department of Pharmacy, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
Amara Mumtaz
Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
Sidra Rehman
Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
Irum Shazadi
Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
Qaisar Mahmood
Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
Syed Aun Muhammad *
Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan.
*Author to whom correspondence should be addressed.
Abstract
Helicobacter pylori is a gastric mucosal pathogen and is a major causative factor for gastrointestinal diseases like peptic ulcer and gastric cancer. New molecules are required for effective treatment due to emerging issues of antibiotic resistance. However, the recognition of anti-Helicobacter pylori agent is a difficult task due to inadequacy of perfect protein target sites. Peptide deformylase is a significant and essential enzyme for bacterial growth due to its vital role in peptide chain elongation. In human cells peptide deformylase has no effect on the synthesis of protein therefore it can be an effective and selective drug target against Helicobacter pylori infections. In this study, binding mode of five sesquiterpenoids against the peptide deformylase was determined. The 3-dimensional structure of peptide deformylase for in-sillico study was accessed from the Protein Data Bank. Pharmacokinetics profile of sesquiterpenoids derivatives was determined by applying Lipinski’s rule of 5. The binding energies of molecular docking for 1 to 5 ligands are: -13, -15, -11, -13, and -11 kcal/mol respectively. The compound 2 exhibited reasonably good binding affinity (-15 kcal/mol) when compared with other ligands. This study could pave the ways for in-vitro analysis to establish these compounds as potential anti-Helicobacter pylori drugs.
Keywords: Helicobacter pylori, peptide deformylase, sesquiterpenoids