Research Article Mutational studies of novel screened molecules against wild and mutated HIV-1 integrase using molecular docking studies Pawan Gupta1,2*, Prabha Garg2 ABSTRACT Background and Aim: The screened molecules which proposed novel HIV-1 integrase inhibitors were collected from the literature. Mutational studies were performed to check whether these molecules are having good binding affinity against mutated HIV-1 IN or not using molecular docking technique. Materials and Methods: First, homology models of the mutated HIV-1 IN were prepared and subsequently all the models were refined and optimized in MODELLER program. Next, molecular docking studies were performed into the active site of mutated HIV-1 IN models using the proposed inhibitors in AutoDock 4.1 program. The results of these studies were compared with the wild type docking studies. Results: The docking studies were found that some of the screened molecules (ZINC1245110, 131614, 92749, ZINC05181828, and ZINC13147504) followed the same binding patterns (in term of locations, interactions, and binding score) as found with wild type HIV-1 IN. Conclusions: Computationally, the same binding patterns were exhibited by these molecules (ZINC1245110, 131614, 92749, ZINC05181828, and ZINC13147504) against mutated models as wild type. This elucidated that these molecules having susceptibility against the drug-resistant HIV-1 IN. Hence, these molecules may be used as a starting point to design novel inhibitors against mutated HIV-1 IN, which need to be confirmed experimentally. KEY WORDS: Docking, Drug resistance, Homology modeling, HIV-1 integrase, Mutation INTRODUCTION Drug resistance is the inevitable consequence of incomplete suppression of HIV-1 replication. The Human immuno-virus (HIV) causes AIDS. Three rapid replication rate of HIV and its inherent genetic essential enzymes required for HIV replication variation have led to the identification of many encoded by pol gene: Reverse transcriptase (nucleoside HIV-1 variants that exhibit altered drug susceptibility. and non-nucleoside), protease, and integrase (IN). Numbers of mutational studies have been published Last few decades, all of them are considered to be on HIV-1 IN which found to be important aspect to promising targets for the development of anti-HIV understand the drug resistance studies.[4,16-18] More [1-6] drugs. Among them, IN has been identified as a than 60 mutations have been specifically associated unique and validated HIV target for drug design and with resistance to HIV-1 IN inhibitors in vitro and [7,8] discovery as IN having no ortholog in human. In in vivo. The primary mutations are associated in the past decade, only few drugs have been approved active site and greatly affected the HIV-1 IN activity. [9] [10] and in clinical trial against HIV-1 IN: raltegravir Other mutations are not found in active site, but exert [11] (FDA-2007), elvitegravir (FDA-2012), their effect along with other mutations (Table 1).[16,17] [12] dolutegravir (FDA-2013), BI 224436, bictegravir These mutations sometime alleviate the effect of other [12-15] (GS-9883), cabotegravir, and MK-2048. mutations or enhanced it. The conformational changes which occurs due to mutations at the active site of Access this article online target protein causes alteration in the drug binding ability of the protein. At instances when the mutations Website: jprsolutions.info ISSN: 0974-6943 are severe, the binding ability gets diminished 1Department of Research and Development and School of Pharmaceutical Sciences, Lovely Professional University, Phagwara - 144 411, Punjab, India, Tel. :+91-1824-444022, Fax. +91-1824-506111, 2Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, Mohali - 160 062, Punjab, India, Tel.: +91- 172-2214 682; fax: +91-172-2214 692 *Corresponding author: Pawan Gupta, Department of Research and Development (Research Coordinator) and School of Pharmaceutical Sciences (Assistant Professor), Block-38, Room No. 203, Lovely Professional University, Phagwara, Punjab, India - 144 411, E-mail: [email protected] Received on: 17-05-2017; Revised on: 28-06-2017; Accepted on: 15-07-2017 Journal of Pharmacy Research | Vol 11 • Issue 9 • 2017 1067 Pawan Gupta and Prabha Garg resulting in survival of the organism in the presence Table 1: HIV-1 integrase residues involved in drug of drug, leading to drug resistance. Therefore, it is resistance[16] necessary that drug resistance studies need to be done Raltegravir Elvitagravir for novel inhibitors to confirm their activity against N155H, L74M, E92Q, T66I, E92Q, S147G, mutated HIV-1 IN as well. T97A, V151I, Y143H, Q146P, H51Y, E157Q, G163R D232N, Q148K/ Q95K, E138K, R263K, To evaluate the drug resistance profile of inhibitors, R/H, L74M, E138K, F121Y, S153Y, S147G molecular docking is very suitable technique to analyze G140S/A, Y143R/C, L74A, the binding modes into the active site of mutated E92Q, I203M, S230R protein and compared with wild type proteins.[19] This Primary resistance mutations are indicated in bold. HIV-1: Human can enable to depict what is actually happened after immuno-virus - 1 mutation into active site of protein and how binding MATERIALS AND METHODS affinity is changed. The relationship between the binding affinity of drug and drug resistance is inverse; Data Set Collection and Preparation [19] higher the affinity – lower will be the resistance. The data sets: Benzodithiazine, curcumine, and screened Although, binding affinity is measured by docking molecules[20-22,24] and HIV-1 IN (PDB ID: 1QS4 and 1BL3) score (high score leads to high affinity). However, were used in these studies. AutoDock tool (ADT)[25] was this is not sole factor for binding mode analysis. used to prepare these data sets (adding polar hydrogen’s Altogether, docking score and binding interactions are and loading Kollman United Atoms charges). For getting [20] best criteria for binding mode selection. PDBQT file format for AutoDock docking protocol, all the data sets were processed in MGL tool. In previous work, two series (benzodithiazine and curcumine series) of molecules were collected. To Mutational Model Development identify the novel lead molecules, docking, QSAR, and The mutational models (mutated homology models) for shape-based screening (SBS) were performed against HIV-1 IN were performed using Modeller9v7 program[26] HIV-1 IN (protein data bank [PDB] ID: 1QS4 and for wild type HIV-1 IN (PDB IDs: 1QS4, 1BL3). As 1BL3) using these series (benzodithiazine for 1QS4 evident from the literature,[4,17,18] important primary and curcumine series for 1BL3).[20-23] In these studies, mutations (highlighted in Table 1) were identified and first important structural features were identified selected for building of the mutational models of HIV-1 which were responsible for IN inhibitory activity. IN. These models are designated as follow: Second, results of the SBS of ZINC and SPECS • Model-1:Gln148Arg and Asn155His databases[24] and absorption, distribution, metabolism, • Model-2: Thr66Ile and Glu92Gln. and excretion studies were gave novel molecules (for benzodithiazine series Mol ID: ZINC07558742, For both IN proteins, only A chain of 1QS4 and C [22] ZINC07795482, ZINC11153210, ZINC12485110, chain of 1BL3 were taken as this is having full defined 131614, and 131621; for curcumine series Mol ID: active site of IN protein.[20,21] Complete sequences of ZINC05181828, ZINC13147504, ZINC14672476, PDB IDs: 1QS4 and 1BL3 were collected from PDB [24] 92749, 92770, 92827, and 146610) which satisfied and inserted the primary mutations in them. After that, and followed the same trend as best active molecules sequence alignments of mutated and wild types were (benzodithiazine and curcumine derivatives) using carried out using sequence alignment tool (ClustalX 2.1 in silico predictions (through QSAR equations program). Figure 2 is showing the sequence alignments [20-24] and docking analysis). It was revealed that between wild type (1QS4A and 1BL3C) and mutated these molecules may have potential against HIV- (Mut) protein of 1QS4 and 1BL3, respectively. 1 IN. In the presented work, mutational models for HIV-1 IN (PDB ID: 1QS4 and 1BL3)) were build Next, Model 1 and Model 2 were built using the using Modeller9v7 tool for the reported mutations Modeller9v7 program. It was given five best (Gln148Arg, Asn155His, Thr66Ile, and Glu92Gln, models on the basis of Discrete Optimized Protein highlighted in Table 1). The binding mode analysis Energy (DOPE) score and molecular probability of the best active molecules of the benzodithiazine, density function (molpdf). The lowest score of these curcumine, and screened molecules (Figure 1) were parameters are considered to be significant for good performed against mutated HIV-1 IN using docking model. The least energy model cannot be a good idea methodologies for drug resistance studies and for considering a best model. compared the results with wild type results. These studies will give the idea about which screened Model Validation and Refinement molecules are also computationally active against The developed models have to follow the model mutated HIV-1 IN, but biological assay need to be validation criteria significantly using structural done to confirm their in vitro activity against both analysis and verification server (SAVES) web-based mutated and wild type strain of HIV-1 IN. tools (PROCHECK [Ramachandran plot] and ERRAT 1068 Journal of Pharmacy Research | Vol 11 • Issue 9 • 2017 Pawan Gupta