Golgi α-mannosidase: opposing structures of Drosophila melanogaster and novel human model using molecular dynamics simulations and docking at different pHs

• Published in: Journal of biomolecular structure & dynamics Vol. 42; no. 5; pp. 2714 - 2725
• Main Authors: Drogalin, Artem, Monteiro, Luís S., Alves, Maria José, Castro, Tarsila G.
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis 23-03-2024
• Subjects: alpha-Mannosidase - chemistry; Animals; Ciências Naturais; Ciências Químicas; Drosophila melanogaster - metabolism; Golgi Apparatus - metabolism; Golgi α-mannosidase II; Humans; Iminosugars; Inhibitors; Mammals - metabolism; Mannosidases - chemistry; Mannosidases - metabolism; Molecular docking; Molecular Dynamics Simulation; Molecular dynamics simulations; Saúde de qualidade; Structural assessment; molecular dynamics simulations; inhibitors; molecular docking; iminosugars; pH; structural assessment; Golgi α-mannosidase II
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2023.2209184

The search for Golgi α-mannosidase II (GMII) potent and specific inhibitors has been a focus of many studies for the past three decades since this enzyme is a key target for cancer treatment. α-Mannosidases, such as those from Drosophila melanogaster or Jack bean, have been used as functional models of the human Golgi α-mannosidase II (hGMII) because mammalian mannosidases are difficult to purify and characterize experimentally. Meanwhile, computational studies have been seen as privileged tools able to explore assertive solutions to specific enzymes, providing molecular details of these macromolecules, their protonation states and their interactions. Thus, modelling techniques can successfully predict hGMII 3D structure with high confidence, speeding up the development of new hits. In this study, Drosophila melanogaster Golgi mannosidase II (dGMII) and a novel human model, developed in silico and equilibrated via molecular dynamics simulations, were both opposed for docking. Our findings highlight that the design of novel inhibitors should be carried out considering the human model's characteristics and the enzyme operating pH. A reliable model is evidenced, showing a good correlation between K
i
/IC
50
experimental data and theoretical ΔG
binding
estimations in GMII, opening the possibility of optimizing the rational drug design of new derivatives.
Communicated by Ramaswamy H. Sarma