Inhibition of Primed Ebola Virus Glycoprotein by Peptide Compound Conjugated to HIV-1 Tat Peptide Through a Virtual Screening Approach

Ahmad Husein Alkaff, Mutiara Saragih, Mochammad Arfin Fardiansyah Nasution, Usman Sumo Friend Tambunan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

A higher prevalence of Ebola hemorrhagic fever is caused by Ebola virus (EBOV). It enters into the host cell through macropinocytosis mechanism. During the entry process, the primed viral glycoprotein (GPcl) interacts with a lysosomal cholesterol transporter, Niemann Pick C1 (NPC1), leading to the fusion of the viral envelope and the host endosomal membrane. Hence, disrupting the interaction between EBOV GPcl and host NPC1 is a promising way to prevent the viral nucleocapsid content entering the cytoplasm. In this study, a virtual screening approach has been used to investigate peptide compounds conjugated to HIV-1 Tat peptide as drug lead candidate inhibiting EBOV GPcl. About 50,261 peptides from NCBI PubChem database, which acts as ligands, were subjected to initial toxicological screening to omit ligands with undesired properties. The remaining ligands underwent a pharmacophore search, rigid docking, and flexible docking simulation to discover ligands with favorable inhibition activities. Calfluxin, SNF 8906, grgesy, phosphoramidon, and endothelin (16-21) were five ligands which have lower ΔGbinding value compared to the standard ligand. The chosen ligands were subjected to absorption, distribution, metabolism, excretion, and toxicity (ADME-Tox) analysis, which was accomplished by pkCSM software. Subsequently, they were conjugated to HIV-1 Tat peptide to accumulate them inside the endosome. The inhibition activity was reevaluated by the second flexible molecular docking simulation. As a result, only C-Calfluxin showed improved affinity while managing minimal conformational changes in protein-peptide interaction compared to its respective unconjugated ligand.

Original languageEnglish
Title of host publicationComputational Intelligence Methods for Bioinformatics and Biostatistics - 15th International Meeting, CIBB 2018, Revised Selected Papers
EditorsMaria Raposo, Paulo Ribeiro, Susana Sério, Antonino Staiano, Angelo Ciaramella
PublisherSpringer
Pages153-165
Number of pages13
ISBN (Print)9783030345846
DOIs
Publication statusPublished - 1 Jan 2020
Event15th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2018 - Caparica, Portugal
Duration: 6 Sep 20188 Sep 2018

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume11925 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference15th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2018
Country/TerritoryPortugal
CityCaparica
Period6/09/188/09/18

Keywords

  • Ebola
  • Flexible molecular docking simulation
  • GPcl
  • HIV-1 Tat
  • NPC1
  • Peptide
  • Virtual pharmacophore screening

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