Computational Docking Study of P7 Ion Channel from HCV Genotype 3 and Genotype 4 and Its Interaction with Natural Compounds
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RESEARCH ARTICLE Computational Docking Study of p7 Ion Channel from HCV Genotype 3 and Genotype 4 and Its Interaction with Natural Compounds Shilu Mathew1,2,3, Kaneez Fatima4, M. Qaiser Fatmi5, Govindaraju Archunan3, Muhammad Ilyas6, Nargis Begum1, Esam Azhar7, Ghazi Damanhouri7, Ishtiaq Qadri7* 1 Department of Biotechnology, Jamal Mohamed College, Tiruchirappalli, India, 2 Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia, 3 Department of Animal Science, Bharathidasan University, Tiruchirappalli, India, 4 IQ Institute of Infection and Immunity, Lahore, Punjab, Pakistan, 5 Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad, Pakistan, 6 Department of Botany, Jamal Mohamed College, Tiruchirappalli, Tamil Nadu, India, 7 King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia * [email protected] Abstract OPEN ACCESS Citation: Mathew S, Fatima K, Fatmi MQ, Archunan G, Ilyas M, Begum N, et al. (2015) Computational Background Docking Study of p7 Ion Channel from HCV Genotype 3 and Genotype 4 and Its Interaction with The current standard care therapy for hepatitis C virus (HCV) infection consists of two re- Natural Compounds. PLoS ONE 10(6): e0126510. gimes, namely interferon-based and interferon-free treatments. The treatment through the doi:10.1371/journal.pone.0126510 combination of ribavirin and pegylated interferon is expensive, only mildly effective, and is Academic Editor: Shama Ahmad, University of associated with severe side effects. In 2011, two direct-acting antiviral (DAA) drugs, boce- Alabama at Birmingham, UNITED STATES previr and telaprevir, were licensed that have shown enhanced sustained virologic re- Received: December 8, 2014 sponse (SVR) in phase III clinical trial, however, these interferon-free treatments are more Accepted: April 2, 2015 sensitive to HCV genotype 1 infection. The variable nature of HCV, and the limited number of inhibitors developed thus aim in expanding the repertoire of available drug targets, result- Published: June 1, 2015 ing in targeting the virus assembly therapeutically. Copyright: © 2015 Mathew et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits Aim unrestricted use, distribution, and reproduction in any medium, provided the original author and source are We conducted this study to predict the 3D structure of the p7 protein from the HCV geno- credited. types 3 and 4. Approximately 63 amino acid residues encoded in HCV render this channel Data Availability Statement: All relevant data are sensitive to inhibitors, making p7 a promising target for novel therapies. HCV p7 protein within the paper and its Supporting Information files. forms a small membrane known as viroporin, and is essential for effective self-assembly of Funding: Financial support of this work was provided large channels that conduct cation assembly and discharge infectious virion particles. by the King Abdulaziz City for Science and Technology, (KACST)-Large grant 162-34, to Ishtiaq Qadri. Method Competing Interests: The authors have declared In this study, we screened drugs and flavonoids known to disrupt translation and production that no competing interests exist. of HCV proteins, targeted against the active site of p7 residues of HCV genotype 3 (GT3) PLOS ONE | DOI:10.1371/journal.pone.0126510 June 1, 2015 1/26 Computational Docking Study of HCVp7 Ion Channel from Genotype 3 and 4 (isolatek3a) and HCV genotype 4a (GT4) (isolateED43). Furthermore, we conducted a quantitative structure–activity relationship and docking interaction study. Results The drug NB-DNJ formed the highest number of hydrogen bond interactions with both mod- eled p7 proteins with high interaction energy, followed by BIT225. A flavonoid screen dem- onstrated that Epigallocatechin gallate (EGCG), nobiletin, and quercetin, have more binding modes in GT3 than in GT4. Thus, the predicted p7 protein molecule of HCV from GT3 and GT4 provides a general avenue to target structure-based antiviral compounds. Conclusions We hypothesize that the inhibitors of viral p7 identified in this screen may be a new class of potent agents, but further confirmation in vitro and in vivo is essential. This structure-guided drug design for both GT3 and GT4 can lead to the identification of drug-like natural com- pounds, confirming p7 as a new target in the rapidly increasing era of HCV. Introduction Hepatitis C virus (HCV) is chronically affecting approximately 180 million people worldwide. HCV infected individuals are at risk for liver cirrhosis as well as hepatocellular carcinoma [1, 2]. The enveloped HCV belongs to family Flaviviridae with seven main genotypes and roughly about 100 subtypes according to the wide geographical distribution of the HCV [3, 4]. HCV ge- notypes (GTs) 1–3 are distributed worldwide. The most common subtypes are 1a and 1b, ac- counting for about 60% of global HCV infections. These HCV subtypes prevail in Eastern Europe, Japan, and North America. GT2 remains less frequently reported than GT1. GT3 is en- demic in Southeast Asia, and is unevenly distributed in various other countries around the world. GT4 is largely found in the Middle East, Central Africa, and Egypt, GT5 is almost exclu- sively found in South Africa, and GTs 6–11 are scattered across Asia [5–8]. The current treat- ment routes are limited to interferon-based and interferon-free regimens. Ribavirin and IFN- alpha-2 combination therapy has limited, but variable, effectiveness, depending on the HCV genotype and the host immune response [9, 10]. In the USA, simeprevir, an FDA approved NS3/4A protease inhibitor, is also dosed along with peg-IFN and ribavirin as triple therapy. Re- cently in 2011, Food and Drug Administration (FDA) and European Medicines Agency (EMEA) have approved two direct-acting antivirals (DAAs) namely boceprevir and telaprevir; these NS3/4A protease inhibitors have shown promising sustained virologic response (SVR) in phase III clinical trial, however, they are genotype specific [11]. Some combination therapies of some oral drugs have been also licensed by FDA during 2013 and 2014, which include sofosbu- vir, a nucleotide analog that inhibits RNA polymerase, in combination with ribavirin for oral dual therapy of HCV GT2 and GT3 as well as sofosbuvir in combination with the viral NS5A inhibitor ledipasvir for the treatment of GT1 infection, respectively [12]. During 2012, at least 30 additional DAAs were in various stages of clinical development. The HCV genome is expressed as large as a polyprotein and cleaved by proteases into an array of proteins. The single-stranded RNA genome encodes structural proteins, including core, glycoproteins E1 and E2, and p7, along with non-structural proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B [13]. The p7 ion channel is positioned in the middle of both the PLOS ONE | DOI:10.1371/journal.pone.0126510 June 1, 2015 2/26 Computational Docking Study of HCVp7 Ion Channel from Genotype 3 and 4 structural protein E2 and non-structural proteins [14]. HCV p7 is a viral channel-forming pro- tein comprised of two elongated hydrophobic transmembrane (TM) domains linked by a cyto- solic loop [15]. However, the structural information for p7 ion channel is known, including protein oligomerization as well as folding of the helices [16, 17]. The hexameric bundle struc- ture was reported for the first time in a Nuclear Magnetic Resonance (NMR) spectroscopic study; the three-dimensional structure of the hexamer was generated using computational methods [18]. The recent advances in computational techniques have enabled us to build small protein molecules and portions of larger protein molecules with reasonably good resolution. Various approaches have been developed and adopted, including a combination of modeling, molecular docking, and molecular dynamics simulations [19]. Computer-modeling of proteins is guided by the knowledge of how membrane proteins are folded or inserted into the lipid membrane. Membrane proteins are translated with the aid of translocons [20–22]. Translocons are membrane-spanning proteins that enable the primary sequence of the membrane protein to form secondary structure within the hydrophobic region of the lipid membrane. The final topology of the membrane protein is dictated by the prime amino acid sequence of the protein [23–25]. The protein is finally released into lipid bilayer. Thus, once the secondary structure is formed, the protein retains this folded structure. These viral channel-forming proteins can also be built alone using computational techniques [26, 27]. Apart from forming a self-assembled, sophisticated, funnel-like architecture that selectively conducts cations, the p7 protein also plays a crucial role in viral assembly and envelopment processes in coordination with NS2 protein [14, 28, 29]. Steinmann and co-workers have shown that the production of viral particle by p7 is genotype-specific due to its interaction with other viral factors. However, the interaction pattern of p7 protein with other viral and host fac- tors as well as its exact contribution in viral production remains uncertain [29]. Recently, a co- immunoprecipitation study using a replication-competent virus containing a double HA- tagged p7 was performed by Vieyres and co-workers that endorsed the formation of specific in- teraction between p7 and NS2, and highlighted its importance in virus production in cell cul- ture [30]. Although