Biocatalysis and Agricultural Biotechnology 35 (2021) 102042 Available online 24 May 2021 1878-8181/© 2021 Elsevier Ltd. All rights reserved. Structure based virtual screening of natural compounds and molecular dynamics simulation: Butirosin as Dipeptidyl peptidase (DPP-IV) inhibitor Rakesh Kumar Paul, Virendra Nath, Vipin Kumar * Department of Pharmacy, School of Chemical Sciences & Pharmacy, Central University of Rajasthan, Ajmer, 301817, India A R T I C L E INFO Keywords: Type II diabetes Mellitus Natural compounds DPP-IV Virtual screening MD simulation ABSTRACT Type II diabetes mellitus (T2DM) is a major metabolic disorder resulting in increase in morbidity and mortality rates. Dipeptidyl peptidase-IV (DPP-IV) is a validated and interesting target to develop novel and effective antihyperglycemic agents. Herein, we performed virtual screening of Prestwick library of natural compounds using structure based hierarchical methods to screen the potent compounds. Further, evaluations of dock score along with protein ligand interactions studies were performed. The topmost ranked compound was processed for molecular dynamic simulations (MD simulation) studies for 20 ns. In addition, in silico ADME analysis for the selection of compounds having admissible pharmacokinetic properties has been studied. The results of molecular docking suggest that compound Butirosin showed maximum dock score and binding energy as compared to the standard Alogliptin. MD simulation of DPP-IV-Alogliptin and DPP-IV-Butirosin complexes showed good stability throughout the simulation and RMSD values were 2.25 Å and 2.6 Å respectively. Thus, Butirosin could be the potential drug candidate for DPP-IV inhibition. 1. Introduction Type 2 Diabetes mellitus (T2DM) is a major metabolic disorder, characterized by insulin resistance and hyperglycaemia with the rise of other serious complications like ketoacidosis, kidney failure, foot ulcers, etc (Behera et al., 2015; Huang et al., 2019). As per International Dia- betes Federation (IDF) it is estimated that by 2040, there will be an increase in rates of diabetic patients around the globe (Ogurtsova et al., 2017). Based on the projection of World Health Organization (WHO), it was estimated that by 2025 there will be around 300 million cases of diabetes patient throughout the globe (Hung et al., 2012). In the current scenario, drugs acting on different targets are approved to combat dia- betes such as Exenatide as glucagon-like peptide 1 (GLP 1) mimetic agents, Gliptins as Dipeptidyl peptidase IV (DPP-IV) inhibitors, Glita- zones as Peroxisome proliferator-activated receptor agonists (PPAR-γ), carbenoxolone as 11β-Hydroxysteroid dehydrogenase-1 (11β HSD-1) inhibitor, Glifozin as Sodium/glucose cotransporters inhibitors (SGLTs), etc. (Kshirsagar et al., 2020). Among all the respective targets, DPP-IV is characterized as one of the enzymatic targets for Type 2 DM. DPP-IV is the key enzyme responsible for catalytic degradation of incretins like gastric inhibitory polypeptide (GIP) and the glucagon-like peptide-1 (GLP-1) (Ahren, 2007; Thornberry and Gallwitz, 2009; Uchida et al., 2018). The crystal structure of human DPP-IV (PDB ID: 2ONC) is of 2.55 Å resolution and observed active site is at S1 pocket with key residues Try547, Glu205, Glu206, Arg125 and Tyr631 (Feng et al., 2007). Therefore, inhibition of such enzyme can prolong the proportion of active GLP-1. Unfortunately, some serious adverse events of gliptins were found as respiratory tract infection, fu syndrome, gastrointestinal problems and skin reactions. Several compounds in different phytochemical classes were reported as DPP-IV inhibitors and these natural compounds play key role in the management of T2DM. Diverse isolated compounds from natural origin having wide range of DPP-IV inhibitory activity were favanoids, phe- nols, alkaloids, terpenoids, polypeptides, etc. (Gao et al., 2015). To minimize the adverse effects from synthetic compounds, natural prod- ucts are in use to treat various diseases from the ancestral era, therefore natural lead molecules are required for effective medication therapy in the management of type 2 diabetes mellitus. In the present study, we performed virtual screening to identify the potential DPP-IV inhibitors from Prestwick phytochemical library. Hi- erarchical structure-based screening using standard precision (SP) docking, extra precision (XP) docking and a druglike flter was applied to identify the best natural molecule as DPP-IV inhibitor. Further, binding energy calculations and molecular dynamics simulations (MD Simulation) were performed to study the dynamic behaviour of protein- * Corresponding author. E-mail address: vipbhardwaj@rediffmail.com (V. Kumar). Contents lists available at ScienceDirect Biocatalysis and Agricultural Biotechnology journal homepage: www.elsevier.com/locate/bab https://doi.org/10.1016/j.bcab.2021.102042 Received 16 March 2021; Received in revised form 18 May 2021; Accepted 19 May 2021