Anopheles gambiae Trehalase Inhibitors for Malaria Vector Control: A Molecular Docking and Molecular Dynamics Study

Abstract

Trehalase inhibitors are considered safe alternatives for insecticides and fungicides. However, there are no studies testing these compounds on Anopheles gambiae, a major vector of human malaria. This study predicted the three-dimensional structure of Anopheles gambiae trehalase (AgTre) and identified potential inhibitors using molecular docking and molecular dynamics methods. Robetta server, C-I-TASSER, and I-TASSER were used to predict the protein structure, while the structural assessment was carried out using SWISS-MODEL, ERRAT, and VERIFY3D. Molecular docking and screening of 3022 compounds was carried out using AutoDock Vina in PyRx, and MD simulation was carried out using NAMD. The Robetta model outperformed all other models and was used for docking and simulation studies. After a post-screening analysis and ADMET studies, uniflorine, 67837201, 10406567, and Compound 2 were considered the best hits with binding energies of -6.9, -8.9, -9, and -8.4 kcal/mol, respectively, better than validamycin A standard (-5.4 kcal/mol). These four compounds were predicted to have no eco-toxicity, Brenk, or PAINS alerts. Similarly, they were predicted to be non-mutagenic, carcinogenic, or hepatoxic. 67837201, 10406567, and Compound 2 showed excellent stability during simulation. The study highlights uniflorine, 67837201, 10406567, and Compound 2 as good inhibitors of AgTre and possible compounds for malaria vector control.

Keywords: casuarine; mosquito; trehalase; trehazolin; uniflorine; validamycin; validoxylamine; vector control.

Figure 1

(A) Normalised QMEAN score of AgTre structure predicted from RoseTTAFold; (B) normalised QMEAN score of AgTre structure predicted by AlphaFold; (C) predicted 3D structure of AgTre. Green: predicted structure from AlphaFold. Purple: predicted structure using RoseTTAFold. RMSD of 0.896 Å considering 476/570 residues; (D) Ramachandran plot of the AgTre structure predicted using RoseTTAFold showing 98.06% of residues in Ramachandran favoured region. AgTre: trehalase of An. gambiae.

Figure 2

Conformational changes, residue flexibilities of the protein, and conformational changes of the ligand. (A) Protein Cα-RMSDs during MD simulation with ligand; (B) protein Cα-RMSFs; (C) ligand RMSDs; (D) RMSD of Compound 1.

Figure 3

PCA plots of the protein backbone in the complex, comprising graphs of PC2 vs PC1, PC2 vs PC3, PC3 vs PC1, and an eigenvalue rank plot with the cumulative variance annotated for each data point. (A) Validoxylamine A; (B) validamycin A; (C) 67837201; (D) 10406567; (E) Compound 2; (F) Compound 1.