The inhibition of the soluble epoxide hydrolase (sEH) is a promising new therapy in the treatment of cardiovascular, inflammation and other disorders. A piperazino functionality as the tertiary pharmacophore remarkably improved the drug-like profile of the 1,3-disubstituted urea sEH inhibitors. However, the potency was more dependent on the overall best balance of the hydrophilicity and lipophi...

Chemical-feature based pharmacophore models have been established as state-of-the-art technique for bioactivity prediction. While in ligand-based drug design, chemical feature-based pharmacophore creation from a set of bio-active molecules is a frequently chosen approach, structure-based pharmacophores are still lacking the reputation to be an alternative or at least a supplement to docking tec...

Stimulation of the PI3K/Akt/mTOR pathway, which controls cell proliferation and growth, is often observed in cancer cell. Inhibiting both PI3K and mTOR in this pathway can switch off Akt activation and hence, plays a powerful role for modulating this pathway. PKI-587, a drug containing the structure of morpholino-triazines, shows a dual and nano-molar inhibition activity and is currently in cli...

B-Raf kinase is an important target in treatment of cancers. In order to design and find potent B-Raf inhibitors (BRIs), 3D pharmacophore models were created using the Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database (GALAHAD). The best pharmacophore model obtained which was used in effective alignment of the data set contains two acceptor atoms, three donor atom...

In order to elucidate the essential structural features for Epidermal Growth Factor Receptor (EGFR) inhibitors, a ligand-based pharmacophore hypothesis was built on the basis of a set of twelve known EGFR inhibitors belonging to three different classes using Molecular Operating Environment (MOE) software. In a first step, three alignments, one for each group of compounds were generated. All of ...

Histone deacetylase 8 (HDAC8) is an enzyme involved in deacetylating the amino groups of terminal lysine residues, thereby repressing the transcription of various genes including tumor suppressor gene. The over expression of HDAC8 was observed in many cancers and thus inhibition of this enzyme has emerged as an efficient cancer therapeutic strategy. In an effort to facilitate the future discove...

Classification is supervised machine learning applicable to predict chemicals based on their properties. The chemical properties are derived from its structural and functional groups. Many molecular descriptors have been developed, one of which, was pharmacophore. Pharmacophore a quantitative measure molecules in application as pharmaceutical ingredient. training datasets were 59 categorized ad...

A group of 1,3-biarylhydrazide derivatives possessing a COX-2 azido pharmacophore at the Para- position of the C-1 phenyl ring in conjunction with a N-3 phenyl or substituted-phenyl ring (4-F,4-Cl,4-OMe) were designed and synthesized based on nucleophilic substitution reaction. A molecular modelling study of these compounds showed that the designed molecules were well bound with the active site...

Farnesyltransferase enzyme (FTase) is considered an essential enzyme in the Ras signaling pathway associated with cancer. Thus, designing inhibitors for this enzyme might lead to the discovery of compounds with effective anticancer activity. In an attempt to obtain effective FTase inhibitors, pharmacophore hypotheses were generated using structure-based and ligand-based approaches built in Disc...

BACKGROUND Protein-based pharmacophore models are enriched with the information of potential interactions between ligands and the protein target. We have shown in a previous study that protein-based pharmacophore models can be applied for ligand pose prediction and pose ranking. In this publication, we present a new pharmacophore-based docking program PharmDock that combines pose sampling and r...