Benzimidazole inhibitors of the protein kinase CHK2: clarification of the binding mode by flexible side chain docking and protein-ligand crystallography.

Two closely related binding modes have previously been proposed for the ATP-competitive benzimidazole class of checkpoint kinase 2 (CHK2) inhibitors; however, neither binding mode is entirely consistent with the reported SAR. Unconstrained rigid docking of benzimidazole ligands into representative CHK2 protein crystal structures reveals an alternative binding mode involving a water-mediated interaction with the hinge region; docking which incorporates protein side chain flexibility for selected residues in the ATP binding site resulted in a refinement of the water-mediated hinge binding mode that is consistent with observed SAR. The flexible docking results are in good agreement with the crystal structures of four exemplar benzimidazole ligands bound to CHK2 which unambiguously confirmed the binding mode of these inhibitors, including the water-mediated interaction with the hinge region, and which is significantly different from binding modes previously postulated in the literature.

Exploration of potential ligands against cancer-causing transcription factor E2F3.

The transcription factor-based therapeutic approaches are the mainstay of current anticancer drug design options to develop highly selective agents with novel modes of action. In this paper, a homology model of DNA-binding domain of transcription factor E2F3 was generated according to X-ray structure of E2F4. As a first step of our proposed project aspired towards exploration of highly selective potential E2F3 ligands, we performed structure-based virtual screening of ZINC 3D chemical database by using Dock Blaster server.

Comparative sequence, antigenic and phylogenetic analysis of avian influenza (H9N2) surface proteins isolated in Pakistan between 1999 and 2008.

Introduction: Influenza A viruses possess a unique genomic structure which leads to genetic instability, especially in products of neuraminidase and hemagglutinin genes. These surface proteins play major roles in viral entry and release, and in the activation of the host immune system.

Methodology: This study involved an in silico sequence, phylogenetic and antigenic analyses of hemagglutinin and neuraminidase proteins of avian influenza A (H9N2) strains that circulated in Pakistan's poultry flocks from 1999 to 2008 and determined variations among these sequences at different levels.

Avian influenza A (H9N2): computational molecular analysis and phylogenetic characterization of viral surface proteins isolated between 1997 and 2009 from the human population.

Background: H9N2 avian influenza A viruses have become panzootic in Eurasia over the last decade and have caused several human infections in Asia since 1998. To study their evolution and zoonotic potential, we conducted an in silico analysis of H9N2 viruses that have infected humans between 1997 and 2009 and identified potential novel reassortments.

Results: A total of 22 hemagglutinin (HA) and neuraminidase (NA) nucleotide and deduced amino acid sequences were retrieved from the NCBI flu database.