Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40

• Published in: International journal of molecular sciences 2016-11, Vol.17 (11), p.1748-1748
• Main Authors: Mirza, Muhammad Usman, Ikram, Nazia
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Computer-Aided Design; Drug Design; Ebola virus; Ebolavirus; Ebolavirus - drug effects; Ebolavirus - metabolism; Hemorrhagic Fever, Ebola - drug therapy; Hemorrhagic Fever, Ebola - virology; Humans; Molecular biology; molecular docking; Molecular Docking Simulation; Phytochemicals; Proteins; retrospective validation; Sequence Alignment; Viral Matrix Proteins - antagonists & inhibitors; Viral Matrix Proteins - chemistry; Viral Matrix Proteins - metabolism; Viral Regulatory and Accessory Proteins - antagonists & inhibitors; Viral Regulatory and Accessory Proteins - chemistry; Viral Regulatory and Accessory Proteins - metabolism; virtual screening; VP35; VP40
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms17111748

The Ebola virus (EBOV) has been recognised for nearly 40 years, with the most recent EBOV outbreak being in West Africa, where it created a humanitarian crisis. Mortalities reported up to 30 March 2016 totalled 11,307. However, up until now, EBOV drugs have been far from achieving regulatory (FDA) approval. It is therefore essential to identify parent compounds that have the potential to be developed into effective drugs. Studies on Ebola viral proteins have shown that some can elicit an immunological response in mice, and these are now considered essential components of a vaccine designed to protect against Ebola haemorrhagic fever. The current study focuses on chemoinformatic approaches to identify virtual hits against Ebola viral proteins (VP35 and VP40), including protein binding site prediction, drug-likeness, pharmacokinetic and pharmacodynamic properties, metabolic site prediction, and molecular docking. Retrospective validation was performed using a database of non-active compounds, and early enrichment of EBOV actives at different false positive rates was calculated. Homology modelling and subsequent superimposition of binding site residues on other strains of EBOV were carried out to check residual conformations, and hence to confirm the efficacy of potential compounds. As a mechanism for artefactual inhibition of proteins through non-specific compounds, virtual hits were assessed for their aggregator potential compared with previously reported aggregators. These systematic studies have indicated that a few compounds may be effective inhibitors of EBOV replication and therefore might have the potential to be developed as anti-EBOV drugs after subsequent testing and validation in experiments in vivo.