Prediction of Toxoplasma gondii virulence factor ROP18 competitive inhibitors by virtual screening

• Published in: Parasites & vectors Vol. 12; no. 1; p. 98
• Main Authors: Yin, Kun, Zhao, Guihua, Xu, Chao, Qiu, Xiao, Wen, Biwei, Sun, Hui, Liu, Gongzhen, Liu, Ye, Zhao, Qingsong, Wei, Qingkuan, Huang, Bingcheng, Yan, Ge, Cao, Jianping
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 13-03-2019; BioMed Central; BMC
• Subjects: Activating transcription factor 6; Apoptosis; Aromatic compounds; ATP; Benzene; Binding; Binding sites; Bioinformatics; Bonds (Securities); Bridges; Care and treatment; Cations; Competition; Competitive inhibitors; Construction; Crystal structure; Drug development; Drugs; G proteins; Halogens; Hydrogen; Hydrogen bonding; Hydrogen bonds; Hydrophobicity; Identification; Immune response; Infections; Inhibitors; Interactions; Kinase inhibitors; Kinases; Mathematical models; Measurement; Molecular docking; Molecular structure; Operating systems (Software); Organic chemistry; Parasitological research; Pharmacology; Pharmacophore model; Phthalimide; Physiological effects; Physiological functions; Proteins; Protozoa; Rhoptry protein; Ring structures; Risk factors; ROP18; SAR (radar); Scaffolds; Screening; Structure-function relationships; Styrene; Substrates; Toxoplasma gondii; Toxoplasmosis; Transcription; Transcription factors; Virtual screening; Virulence; Virulence (Microbiology); Virulence factors; Virtual screening; ROP18; Toxoplasma gondii; Competitive inhibitors; Pharmacophore model
• ISSN: 1756-3305; 1756-3305
• DOI: 10.1186/s13071-019-3341-y

Rhoptry protein 18 (ROP18) is a key virulence factor of Toxoplasma gondii. The host's immune responses mediated by immune-related GTPases (IRGs) could be blocked by ROP18's kinase activity. ROP18 also interacts with various substrates, such as activating transcription factor 6 beta (ATF6β) and affects multiple physiological functions within host cells, thereby inducing intense virulence. In this study, competitive inhibitors targeted to ROP18 were subjected to virtual screening based on the principle of structure-based drug design (SBDD).
The preparation of the ROP18 structure was conducted using the "Structure Prepare" function of Molecular Operating Environment (MOE) software. The ATP-binding pocket was selected as the starting point for virtual screening. Construction of the pharmacophore model used Extended Hückel Theory (EHT) half-quantitative measurement and construction, as well as the characteristics of Type I kinase inhibitors. The pharmacophore model of ROP18 was imported into the Specs database for small molecule similarity screening using EHT pharmacophore measurement. Hit compounds were selected using the functions of London dG and generalized-born volume integral/weighted surface area (GBVI/WSA) scoring. The top 100 hits were analyzed by molecular docking and structure activity relationships (SAR) analysis.
The final pharmacophore comprised three typical characteristics: three hydrogen bond acceptors/donors, two ring aromatic features occupying the hydrophobic core, and one cation group feature targeted to the terminus of ATP. A total of 1314 hit compounds analogous to ROP18 pharmacophore were passed through the Specs. After two rounds of docking, 25 out of 100 hits were identified as belonging to two main scaffold types: phthalimide ring structure, thiazole ring and styrene structure. Additionally, the screen also identified 13 inhibitors with distinct scaffold types. The docking models and SAR analysis demonstrated that these hits could engage in multiple hydrogen bonds, salt bridges halogen bonds, and hydrophobic interactions with ROP18, and para-position halo substituents on the benzene ring may enhance their affinity scoring.
A pharmacophore against the ROP18 ATP-binding pocket was successfully constructed, and 25 representative inhibitors from 15 scaffold clusters were screened using the Specs database. Our results provide useful scaffold types for the chemical inhibition of ROP18 or alternative conformations to develop new anti-toxoplasmosis drug leads.