Journal Article

How do physicochemical properties contribute to inhibitory activity of promising peptides against Zika Virus NS3 protease?

Lourenço, Felipe Rebello, Giarolla, Jeanine, da Silva Santos, Soraya, Silva, João Vitor, Savino, Débora Feliciano

2024

Overview

Context and results Flavivirus diseases’ cycles, especially Dengue and Yellow Fever, can be observed all over Brazilian territory, representing a great health concern. Additionally, there are no drugs available in therapy. In this scenario, in silico methodologies were applied to obtain physicochemical properties, as well as to better understand the ligand-biological target interaction mode of 20 previously reported NS2B/NS3 protease inhibitors of Dengue virus. Since catalytic site of flavivirus hold similarities, such as the same catalytic triad (His51, Asp75 e Ser135), the ability of this series of molecules to fit in Zika NS3 domains can be achieved. We performed an exploratory data analysis, using statistical methodologies, such as PCA (Principal Component Analysis) and HCA (Hierarchical Component Analysis), to assist the comprehension of how physicochemical properties impact the interaction observed by the docking studies, as well as to build a correlation between the respective ranked characteristics. Based on these previous studies, peptides were selected for the dynamics simulations, which were useful to better understand the ligand-protein interactions. Information relating to, for instance, energy, ΔG, average number of hydrogen bonds and distance from Ser135 (one of the main amino acids in the catalytic pocket) were discussed. In this sense, peptides 15 (considering ΔG value and Hbond number), 7 (ΔG and energy) and 1, 6, 7 and 15 (the proximity to Ser135 throughout the dynamics simulation) were highlighted as promising. Those interesting results could contribute to future studies regarding Zika virus drug design, since this infection represents a great concern in neglected populations. Methods The models were constructed in the ChemDraw software. The ligand parametrization was performed in the CHEM3D 17.0, UCSF Chimera. Docking simulations were carried out in the GOLD software, after the redocking validation. We used ASP as the function score. Additionally, for dynamics simulations we applied GROMACS software, exploring, mainly, free binding energy calculations. Exploratory analysis was carried out in Minitab 17.3.1 statistical software. Prior to the exploratory analysis, data of quantum chemical properties of the peptides were collected in Microsoft Excel spreadsheet and organized to obtain Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA).

• Publisher: Springer Berlin Heidelberg,Springer Nature B.V
• Subject: active sites / Amino acids / Characterization and Evaluation of Materials / Chemical properties / Chemistry / Chemistry and Materials Science / Chimeras / Cluster analysis / Computer Appl. in Life Sciences / Computer Applications in Chemistry / computer simulation / computer software / Computer viruses / Data analysis / dengue / Dengue fever / Dengue virus / Design / drug design / Drug development / energy / Enzymes / hydrogen / Hydrogen bonding / Infections / Ligands / Molecular Medicine / Original Paper / Parameterization / Peptides / Physicochemical properties / principal component analysis / Principal components analysis / Protease / Protease inhibitors / Protein interaction / Proteinase inhibitors / proteinases / Proteins / Quantum chemistry / quantum mechanics / Software / Statistics / Theoretical and Computational Chemistry / therapeutics / Tropical diseases / West Nile virus / Yellow fever / Zika virus