• Zumaana Rafiq Department of Biotechnology, Dr. M. G. R. Educational and Research Institute, E. V. R. Periyar Salai, Maduravoyal, Chennai 600095,
  • Saranya Sivaraj Department of Biotechnology, Dr. M. G. R. Educational and Research Institute, E. V. R. Periyar Salai, Maduravoyal, Chennai 600095,
  • Rama Vaidyanathan Dr. A. P. J. Abdul Kalam Centre for Innovation and Entrepreneurship, Dr. M. G. R. Educational and Research Institute, I Year Campus, E. V. R. Periyar Salai, Adayalampattu, Chennai 600095



Punigratane, EPI, AcrB efflux pump, Drug candidate, Docking


Objective: Efflux-mediated resistance is a growing therapeutic complication as it reduces the efficacy of antibiotics. In gram-negative bacteria like E. coli and K. pneumoniae, this can be overcome with the help of efflux pump inhibitors (EPI) targeted at the transporter protein AcrB that plays a key role in binding to antibiotics. Our study focuses on the potential EPI Punigratane isolated from the rind of Punica granatum. Using computational docking analysis and in silico analysis, our aim is to determine whether Punigratane has the ability to interact and inhibit the AcrB pump and whether it has drug viability.

Materials: Computational docking analyses were carried out using the online platforms Mcule and PatchDock. Drug-likeness and classification of Punigratane was predicted using online tools PreADMET and SuperPred. Admet SAR and Toxicity Checker at Mcule were used to predict ADME (absorption, distribution, metabolism, and excretion) and overt toxicity properties.

Results: Punigratane was computationally docked with 57 AcrB crystal structures available at the PDB database to determine whether it could bind to the active site regions. It was found to bind in the periplasmic region close to the substrate bile acid where it is thought to bring about inhibition by steric hindrances. When docked with AcrB mutant (AcrB N109A), it was found to bind in the same periplasmic site as the substrates (EtBr, Rhodamine 6G, Ciprofloxacin, Bile acid) as well as the inhibitor (phenylalanine-arginine β-naphthylamide-PaβN). When docked in the active site of the inhibitor MBX2319, it was found to have a comparable docking score as well as the same hydrophobic interactions as the inhibitor. In silico analysis showed that Punigratane exhibited a drug-likeness to the inhibitor MBX2319 and that its drug classification is similar to antimicrobial agents. It was also found be a potential drug due to its intestinal absorption, increased bioavailability and non-toxic nature.

Conclusion: Therefore our report shows that Punigratane could be a potential drug candidate that inhibits efflux activity by interacting and inhibiting the AcrB efflux pump. 


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How to Cite

Rafiq, Z., S. Sivaraj, and R. Vaidyanathan. “COMPUTATIONAL DOCKING AND IN SILICO ANALYSIS OF POTENTIAL EFFLUX PUMP INHIBITOR PUNIGRATANE”. International Journal of Pharmacy and Pharmaceutical Sciences, vol. 10, no. 3, Mar. 2018, pp. 27-34, doi:10.22159/ijpps.2018v10i3.21629.



Original Article(s)