Background: There is an increasing interest in TRPM8 ligands of medicinal interest, the rational design of which can be nowadays supported by structure-based in silico studies based on the recently resolved TRPM8 structures. Methods: The study involves the generation of a reliable hTRPM8 homology model, the reliability of which was assessed by a 1.0 μs MD simulation which was also used to generate multiple receptor conformations for the following structure-based virtual screening (VS) campaigns; docking simulations utilized different programs and involved all monomers of the selected frames; the so computed docking scores were combined by consensus approaches based on the EFO algorithm. Results: The obtained models revealed very satisfactory performances; LiGen™ provided the best results among the tested docking programs; the combination of docking results from the four monomers elicited a markedly beneficial effect on the computed consensus models. Conclusions: The generated hTRPM8 model appears to be amenable for successful structure-based VS studies; cross-talk modulating effects between interacting monomers on the binding sites can be accounted for by combining docking simulations as performed on all the monomers; this strategy can have general applicability for docking simulations involving quaternary protein structures with multiple identical binding pockets.

Combining molecular dynamics and docking simulations to develop targeted protocols for performing optimized virtual screening campaigns on the HTRPM8 channel / C. Talarico, S. Gervasoni, C. Manelfi, A. Pedretti, G. Vistoli, A.R. Beccari. - In: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. - ISSN 1661-6596. - 21:7(2020 Apr).

Combining molecular dynamics and docking simulations to develop targeted protocols for performing optimized virtual screening campaigns on the HTRPM8 channel

S. Gervasoni;A. Pedretti;G. Vistoli;
2020-04

Abstract

Background: There is an increasing interest in TRPM8 ligands of medicinal interest, the rational design of which can be nowadays supported by structure-based in silico studies based on the recently resolved TRPM8 structures. Methods: The study involves the generation of a reliable hTRPM8 homology model, the reliability of which was assessed by a 1.0 μs MD simulation which was also used to generate multiple receptor conformations for the following structure-based virtual screening (VS) campaigns; docking simulations utilized different programs and involved all monomers of the selected frames; the so computed docking scores were combined by consensus approaches based on the EFO algorithm. Results: The obtained models revealed very satisfactory performances; LiGen™ provided the best results among the tested docking programs; the combination of docking results from the four monomers elicited a markedly beneficial effect on the computed consensus models. Conclusions: The generated hTRPM8 model appears to be amenable for successful structure-based VS studies; cross-talk modulating effects between interacting monomers on the binding sites can be accounted for by combining docking simulations as performed on all the monomers; this strategy can have general applicability for docking simulations involving quaternary protein structures with multiple identical binding pockets.
Consensus approaches; Docking simulations; EFO; LiGen™; Multiple receptor conformations; PLANTS; Structure-based virtual screening; TRPM8; Humans; Models, Molecular; Molecular Dynamics Simulation; Protein Binding; Protein Structure, Quaternary; Protein Structure, Tertiary; TRPM Cation Channels
Settore CHIM/08 - Chimica Farmaceutica
Article (author)
File in questo prodotto:
File Dimensione Formato  
ijms-21-02265-v3.pdf

accesso aperto

Tipologia: Publisher's version/PDF
Dimensione 4.18 MB
Formato Adobe PDF
4.18 MB Adobe PDF Visualizza/Apri
Pubblicazioni consigliate

Caricamento pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/739984
Citazioni
  • ???jsp.display-item.citation.pmc??? 5
  • Scopus 16
  • ???jsp.display-item.citation.isi??? 14
social impact