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In Silico Screening of Sugar Alcohol Compounds to Inhibit Viral Matrix Protein VP40 of Ebola Virus

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In Silico Screening of Sugar Alcohol Compounds to Inhibit Viral Matrix Protein VP40 of Ebola Virus Molecular Biology Reports (2019) 46:3315–3324 https://doi.org/10.1007/s11033-019-04792-w ORIGINAL ARTICLE In silico screening of sugar alcohol compounds to inhibit viral matrix protein VP40 of Ebola virus Nagasundaram Nagarajan1 · Edward K. Y. Yapp2 · Nguyen Quoc Khanh Le1 · Hui‑Yuan Yeh1 Received: 28 December 2018 / Accepted: 28 March 2019 / Published online: 13 April 2019 © Springer Nature B.V. 2019 Abstract Ebola virus is a virulent pathogen that causes highly lethal hemorrhagic fever in human and non-human species. The rapid growth of this virus infection has made the scenario increasingly complicated to control the disease. Receptor viral matrix protein (VP40) is highly responsible for the replication and budding of progeny virus. The binding of RNA to VP40 could be the crucial factor for the successful lifecycle of the Ebola virus. In this study, we aimed to identify the potential drug that could inhibit VP40. Sugar alcohols were enrich with antiviral properties used to inhibit VP40. Virtual screening analysis was perform for the 48 sugar alcohol compounds, of which the following three compounds show the best binding afnity: Sorbitol, Mannitol and Galactitol. To understand the perfect binding orientation and the strength of non-bonded interactions, individual molecular docking studies were perform for the best hits. Further molecular dynamics studies were conduct to analyze the efcacy between the protein–ligand complexes and it was identify that Sorbitol obtains the highest efcacy. The best-screened compounds obtained drug-like property and were less toxic, which could be use as a potential lead compound to develop anti-Ebola drugs. Keywords Ebola · VP40 · Sugar alcohols · Molecular docking · Molecular dynamics simulations Introduction each named after the location where it first identified: Zaire (EBOV-Z), Sudan (EBOV-S), Thai forest (EBOV-T), Ebola is a flamentous, negative-stranded and highly patho- Bundibugyo (EBOV-B) and Reston (EBOV-R) with vary- genic RNA virus, which most often results in fatal illness ing fatality rates [3]. The RNA genome sequence length is in humans and other primates [1]. It typically causes hem- about ~ 19 Kb that encodes seven structural proteins such orrhagic fever that leads to severe bleeding from diferent as nucleoprotein (NP), viral matrix proteins VP24, VP30, parts of the body and causes death [2]. As of 30 March VP35, VP40, and RNA polymerase [3, 4]. A vaccine against 2016, 28,610 suspected cases and 11,307 deaths have been EBOV-Z has shown the potential of immune responses report in the most afected countries of Guinea, Liberia, and against surface glycoproteins and nucleoproteins [5]. Several Sierra Leone. The Ebola virus genus comprises fve species investigations on anti-Ebola drugs have carried out, but no efective drug has yet been approve by the FDA. * Nagasundaram Nagarajan Among the viral matrix protein, VP40 plays a crucial role [email protected] in the process of viral transcription at early stages of infec- * Hui-Yuan Yeh tion [6]. These studies strongly suggested that the binding [email protected] of RNA to VP40 could be the critical factor for the suc- Edward K. Y. Yapp cessful lifecycle of the Ebola virus. Drugs targeting VP40 [email protected] may alter the conformation of the protein and thus it could Nguyen Quoc Khanh Le afect the binding with RNA. The viral matrix protein VP40 [email protected] appears to be highly expressed in Ebola virus and plays a vital role in the budding of Ebola virus from the plasma 1 School of Humanities, Nanyang Technological University, membrane [7]. VP40 is made up of 326 amino acids and 14 Nanyang Dr, Singapore 637332, Singapore has two domains connected by a fexible linker, in which 2 Singapore Institute of Manufacturing Technology, 2 the N-terminal domain is responsible for oligomerization, Fusionopolis Way, Singapore 138634, Singapore Vol.:(0123456789)1 3 3316 Molecular Biology Reports (2019) 46:3315–3324 while the C-terminal domain is responsible for membrane Sugar alcohols are low digestible carbohydrates com- binding. Viral matrix proteinVP40 shows oligomerize monly found in plant products. These are hydrogenated in both hexamers and octamers, both of which consist of forms of carbohydrate in which the carbonyl group (alde- antiparallel viral matrix protein [VP40] dimers. It have to hyde or ketone) has reduced to a primary or secondary be noted that the formation of these diferent oligomeric hydroxyl group and can obtain by natural or synthetic form. forms was determined by diferences in the interdimeric The clinical efcacy and bioavailability of anti-viral drugs interface, while the monomer–monomer interface within are the important factors that have to taken in concern to intradimeric interface is similar in both octamers and hex- treat viral infections. Sugar alcohols have antiviral proper- amers. In most cases, it was noted that oligomeric VP40 ties [11] and it could be consider in combating Ebola. Sugar expressed in UV-inactivated virion’s and in mammalian alcohol are devoid of toxicity with high compatibility and cells expressing VP40, whereVP40 observed with high lipid biodegradability hence it can be used to enhance the efec- layers. Further VP40 octamer have shown to interact with tiveness against viral which improve the patient compliance RNA molecule at defned sequence pattern [8]. Although and decrease the adverse efect particularly by targeting the we know that octamerization of VP40 is vital for the Ebola specifc active sites for viral target. virus replication, the functions of both the octameric and In this study, we adopted a computational approach to hexameric forms of VP40 still under investigation. The Co- identify the potential lead molecules from the sugar alco- crystal 3D structure (PDB id: 1H2C) of VP40-RNA (Fig. 1) hols. Identifcation of the compounds based on the unique is an octamer shows that the two key amino acids PHE125 conformation, which may interact with specifc binding site and ARG134 of VP40 directly interacted with RNA [6]. The of the target to create a perfect molecular interaction. We RNA-protein structure is stabilised by 140 amino acid resi- used this platform to identify drug candidates that bind and dues of VP40 (including residues THR123, PHE125, and inhibit viral matrix protein VP40 of Ebola virus strains. This ARG134 of a fragment of the N-terminal domain) and UGA approach integrated with the retrieval of sugar alcohol com- (stop codon) of RNA. The crystal structure elucidate that pounds and virtual screening of compounds to identify the VP40 has to undergo two diferent conformational changes top ranking drug like candidates; molecular docking analysis in order to obtained oligomerization. This involves in the to identify the bind afnity of the screened lead compounds displacement of the N-terminal region (residues 31 to 70) and molecular dynamics simulation analysis to understand and the movement of the C-terminal domain, which then the efcacy of the best binding sugar alcohols. Our results forms the binding pocket for the specifc recognition of the explain the efciency of integrated molecular level inves- ssRNA motif U-G-A, Which could be consider as a potential tigation in prioritizing the compounds for further in vitro, target for antiviral drug design [9, 10]. in vivo and clinical testing. This approach will signifcantly Fig. 1 Surface view of Ebola VP40 bound with RNA showing the amino acid in RNA vicinity 1 3 Molecular Biology Reports (2019) 46:3315–3324 3317 reduce the time, risk, cost, and resources required to deter- position restrained dynamics simulations (NVT and NPT) mine efcacious therapies against future Ebola outbreaks. at 300 K for 300 ps. The equilibrated structures were then subject to molecular dynamics simulations for 50,000 ps at a constant temperature of 300 K and pressure of 1 atm, and the Materials and methods integration time step was set to 2 fs. The non-bonded list was created using an Atom-based threshold of 8 Å. Long-range Dataset electrostatic interactions were managed using the particle- mesh Ewald algorithm and Lennard-Jones mathematical The crystal structure of the matrix protein VP40 of Ebola model were applied with the threshold value of 0.9 nm for virus was retrieved from RCSB PDB database with the cor- interatomic potential calculation. During the simulations, the responding PDB ID 1H2C [8]. The three-dimensional struc- lengths of all bonds containing hydrogen atoms were con- tures of the sugar alcohols compounds were retrieve from strained by utilising the Lincs algorithm [17]; the trajectory PubChem database. The three-dimensional structures of the snapshots were stored for structural analysis every picosec- target protein was energy-minimized using the GROMACS ond. The RMSD, the hydrogen bonds, minimum distance 5.1.2 [12] adopting the GROMOS53a6 [13, 14] force feld were calculate using the Gromacs utilities g_rms, g_hbond parameters before performing the docking analysis. and g_mindist. Virtual screening and molecular docking analysis ADME and drug likeliness analysis Docking is often approximate to a lock and key process Lipinski’s rule of fve used to test the bioavailability char- where the confrmation of a ligand and receptor do not acteristics, such as the absorption, distribution, metabolism change during binding. Ligands are often fexible and occupy and elimination (ADME) of the ligands. In this present multiple conformations in solution, and although the confor- study, these molecular properties and the drug-likeness mation of receptors is better defned, they too can change, of the ligands were calculate using the Mol soft program particularly on ligand binding in the so-called “Induced ft (http://molso ft.com/mprop /). model”. VcPpt is the tool used for high throughput virtual screening; it was independently develop as an extension of Prediction of toxicity risk and oral toxicity (LD50) AutoDock vina. The top-ranked ligands further docked with molecular docking suit AutoDock Vina [15].
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