Discovery and evaluation of potential sonic hedgehog signaling pathway inhibitors using pharmacophore modeling and molecular dynamics simulations

• Published in: Journal of bioinformatics and computational biology Vol. 9 Suppl 1; p. 15
• Main Authors: Hwang, Swan, Thangapandian, Sundarapandian, Lee, Yuno, Sakkiah, Sugunadevi, John, Shalini, Lee, Keun Woo
• Format: Journal Article
• Language: English
• Published: Singapore 01.12.2011
• Subjects: Amino Acid Sequence; Binding Sites; Catalytic Domain; Hedgehog Proteins - antagonists & inhibitors; Hedgehog Proteins - chemistry; Hedgehog Proteins - metabolism; Lactams - chemistry; Lactams - metabolism; Lactones - chemistry; Lactones - metabolism; Models, Molecular; Molecular Dynamics Simulation; Molecular Sequence Data; Protein Conformation; Signal Transduction
• ISSN: 1757-6334
• DOI: 10.1142/S0219720011005732

Sonic hedgehog (Shh) plays an important role in the activation of Shh signaling pathway that regulates preservation and rebirth of adult tissues. An abnormal activation of this pathway has been identified in hyperplasia and various tumorigenesis. Hence the inhibition of this pathway using a Shh inhibitor might be an efficient way to treat a wide range of malignancies. This study was done in order to develop a lead chemical candidate that has an inhibitory function in the Shh signaling pathway. We have generated common feature pharmacophore models using three-dimensional (3D) structural information of robotnikinin, an inhibitor of the Shh signaling pathway, and its analogs. These models have been validated with fit values of robotnikinin and its analogs, and the best model was used as a 3D structural query to screen chemical databases. The hit compounds resulted from the screening docked into a proposed binding site of the Shh named pseudo-active site. Molecular dynamics (MD) simulations were performed to investigate detailed binding modes and molecular interactions between the hit compounds and functional residues of the pseudo-active site. The results of the MD simulation analyses revealed that the hit compounds can bind the pseudo-active site with high affinity than robotnikinin. As a result of this study, a candidate inhibitor (GK 03795) was selected as a potential lead to be employed in future Shh inhibitor design.