A computational study of the stem cell factor (SCF) and potential ligands was carried out starting with a crystallographic model deposited in the protein data bank. The inhibition of the SCF dimerization equilibrium was considered as the rationale for the lead identification of specific ligands. A preliminary molecular dynamics characterization of the SCF dimer allowed to verify the most flexible loop involved in the dimeric area. Then a virtual screening, coupled with energy minimization in GB/SA water, scored the compounds implemented in the NCI diversity molecular database. Ten top ranked ligands were analyzed considering both the SCF loop perturbation in the dimerization area and the network of intermolecular hydrogen bonds. Among these ten compounds two natural agents were identified. The computational work revealed useful new insights for rational design of novel SCF dimerization inhibitors.

Alcaro, S., Gontrani, L., Incani, O., Ortuso, F. (2008). Computational methods applied to the discovery of stem cell factor ligands. THEORETICAL CHEMISTRY ACCOUNTS, 120(4-6), 523-531 [10.1007/s00214-008-0431-x].

Computational methods applied to the discovery of stem cell factor ligands

Gontrani, Lorenzo
Investigation
;
2008-01-01

Abstract

A computational study of the stem cell factor (SCF) and potential ligands was carried out starting with a crystallographic model deposited in the protein data bank. The inhibition of the SCF dimerization equilibrium was considered as the rationale for the lead identification of specific ligands. A preliminary molecular dynamics characterization of the SCF dimer allowed to verify the most flexible loop involved in the dimeric area. Then a virtual screening, coupled with energy minimization in GB/SA water, scored the compounds implemented in the NCI diversity molecular database. Ten top ranked ligands were analyzed considering both the SCF loop perturbation in the dimerization area and the network of intermolecular hydrogen bonds. Among these ten compounds two natural agents were identified. The computational work revealed useful new insights for rational design of novel SCF dimerization inhibitors.
2008
Pubblicato
Rilevanza internazionale
Articolo
Esperti anonimi
Settore CHIM/09 - FARMACEUTICO TECNOLOGICO APPLICATIVO
Settore CHIM/02 - CHIMICA FISICA
English
Con Impact Factor ISI
SCF; c-kit; virtual screening; molecular dynamics; NCI-diversity database; protein-protein interface
Alcaro, S., Gontrani, L., Incani, O., Ortuso, F. (2008). Computational methods applied to the discovery of stem cell factor ligands. THEORETICAL CHEMISTRY ACCOUNTS, 120(4-6), 523-531 [10.1007/s00214-008-0431-x].
Alcaro, S; Gontrani, L; Incani, O; Ortuso, F
Articolo su rivista
File in questo prodotto:
File Dimensione Formato  
appo.pdf

solo utenti autorizzati

Tipologia: Versione Editoriale (PDF)
Licenza: Copyright dell'editore
Dimensione 825.09 kB
Formato Adobe PDF
825.09 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

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: https://hdl.handle.net/2108/294070
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 1
  • ???jsp.display-item.citation.isi??? 0
social impact