Construction of a three-dimensional pharmacophore for Bcl-2 inhibitors by flexible docking and the multiple copy simultaneous search method.

B-Cell lymphoma-2 (Bcl-2) protein is a new promising target for anticancer drugs. A number of anticancer Bcl-2 inhibitors with diverse chemical structures have been discovered in recent years. In this paper, the flexible docking was performed to determine the binding modes of the representative inhibitors from different structural types. Subsequently, the binding modes of inhibitor were used to construct a primary three- dimensional (3D) pharmacophore model. It proved that this model can effectively disrupt the binding of the BH3 domain of proapoptotic Bcl-2 family members to Bcl-2, and match the structural requirement of a new type of Bcl-2 inhibitors. However, these distances between pharmacophoric points are not optimal due to the fact that not all of individual functional groups are located in the ideal position when inhibitors bind to its receptor. In this paper, we proposed a new idea to improve the quality of the pharmacophore model: the multiple copy simultaneous search (MCSS) method was performed to determine the energetically favorable distribution of functional groups with similar features to these pharmacophoric points in the active site of Bcl-2 first. Then their most energetically favorable minima in the positions near the pharmacophoric points were used to optimize the distances between pharmacophoric points. By examining the binding modes of several inhibitors from the same structural type, it was found that the more potent the inhibitor was, the closer it was to the optimized distances between pharmacophoric points. The optimized 3D pharmacophore model obtained in this paper may provide a good starting point for further rational design of Bcl-2 inhibitors.

[Synthesis and antifungal activity of novel triazole antifungal agents].

AIM: A series of triazole antifungal agents were synthesized to search for novel triazole antifungal agents with more potent activity, less toxicity and broader spectrum. METHODS: Twenty-one 1-(1H-1, 2, 4-triazolyl)-2-(2, 4-diflurophenyl)-3-(4-substituted-1-piperazinyl)-2-propanols were synthesized, on the basis of the three dimensional structure of P450 cytochrome 14alpha-sterol demethylase (CYP51) and their antifungal activities were also evaluated. RESULTS: Results of preliminary biological tests showed that most of title compounds exhibited activity against the eight common pathogenic fungi to some extent and the activities against deep fungi were higher than that against shallow fungi. In general, phenyl and pyridinyl analogues showed higher antifungal activity than that of the phenylacyl analogues. CONCLUSION: Several title compounds showed higher antifungal activities than fluconazole and terbinafine. Compound VIII-1, 4, 5 and IX-3 showed the best antifungal activity with broad antifungal spectrum and were chosen for further study.

[Synthesis and antifungal activity of 1-(1,2,4-triazolyl-1H-1-yl)-2-(2,4-diflurophenyl)-3-(4-substituted benzyl-1-piperazinyl)-2-propanols].

AIM: A series of triazole antifungals were synthesized to search for novel triazole antifungals with more potent activity, less toxicity and broader spectrum. METHODS: Nineteen 1-(1,2,4-triazolyl-1H-1-yl)-2-(2,4-diflurophenyl)-3-(4-substituted benzyl-1-piperazinyl)-2-propanols were designed and synthesized, on basis of the three dimensional structure of P450 cytochrome 14 alpha-sterol demethylase (CYP51) and their antifungal activities were also evaluated. RESULTS: All the title compounds were first reported. Results of preliminary biological tests showed that most of the title compounds exhibited high activity against the eight common pathogenic fungi and the activities against deep fungi were higher than that against shallow fungi. CONCLUSION: Most of the title compounds showed higher antifungal activities than Fluconazole and Terbinafine. Compound VIII-1, 10, 12, 17 showed best antifungal activity with broad antifungal spectrum and were chosen for further development.

A Three-dimensional Model of Lanosterol 14alpha-demethylase of Candida albicans.

The three-dimensional structure of lanosterol 14alpha demethylase (P450(14DM), P450(51() of Candida albicans was modeled based on crystallographic coordinates of four prokaryotic cytochrome P450(S): P450BM3, P450cam, P450terp and P450eryF. The sequence of P450(51) was aligned to those of known proteins using a knowledge-based alignment method. The main chain coordinates of the structurally conserved regions (SCRs)) were transferred directly from the corresponding coordinates of P450BM3. The side chain conformations of SCRs) were determined based on the equivalent residues of four crystal structures which had the highest homologous scores. The model was then refined using molecular mechanics and molecular dynamics.The rationale of the resulting model were validated by Ramachandran plot,Profile-3K and hydropathy plot analysis. The structure-functionally important residues, such as the heme binding residues, the residues interacting with redox-partner protein and/or involved in electron transfer, the residues lining substrate access channel and the substrate binding residues, were identified from the model. These residues are candidates for further site-directed mutagensis and site-specific antipeptide antibody binding experiments.

Comparative Studies on Crystal Structures of Four Members of Cytochrome P450 Superfamily.

Secondary and steric structures and hydropathy plots of the 4 crystals of P450cam, P450terp, P450eryF and P450BM3 were compared to illustrate the structural conservation of cytochrome P450 superfamily proteins. Although sequence identities of four P450s are generally low (19%-26%), their topology is quite similar. All four structures have 13 alpha-helices and beta1-beta4 sheets in common. Four crystal structures were superimpossed by root-mean-square (RMS) fit of the prophyrin ring carbon atoms of prosthetic group heme to obtain the structure-based sequence alignment of four proteins. The RMS deviations of Calpha distance of each motifs were analyzed by hierarchical cluster analysis. The structural subsets were divided into four categories of structural conservation: the most conserved region, the less conserved region, the less variable region and the variable region. The first two groups (56.9 percentage of the aligned positions that have no gaps) include all the interior structures and active site residues. All four P450 proteins have the common hydrophobic and hydrophilic segments by hydropathy plots analyses. All the comparison results of P450 protein crystal structures provided the basis for structure-based sequence alignment of cytochrome P450 proteins.