Drosophila telomere capping protein HOAP interacts with DSB sensor proteins Mre11 and Nbs

In eukaryotes, specific DNA-protein structures called telomeres exist at linear chromosome ends. Telomere stability is maintained by a specific capping protein complex. This capping complex is essential for the inhibition of the DNA damage response (DDR) at telomeres and contributes to genome integrity. In Drosophila, the central factors of telomere capping complex are HOAP and HipHop. Furthermore, a DDR protein complex Mre11-Rad50-Nbs (MRN) is known to be important for the telomere association of HOAP and HipHop. However, whether MRN interacts with HOAP and HipHop, and the telomere recognition mechanisms of HOAP and HipHop are poorly understood. Here, we show that Nbs interacts with Mre11 and transports the Mre11-Rad50 complex from the cytoplasm to the nucleus. In addition, we report that HOAP interacts with both Mre11 and Nbs. The N-terminal region of HOAP is essential for its co-localization with HipHop. Finally, we reveal that Nbs interacts with the N-terminal region of HOAP.

Identification of Novel TRPC5 Inhibitors by Pharmacophore-Based and Structure-Based Approaches

Canonical transient receptor potential-5 (TRPC5), which belongs to the subfamily of transient receptor potential (TRP) channels, is a non-selective cation channel mainly expressed in the central nervous system and shows more restricted expression in the periphery. TRPC5 plays a crucial role in human physiology and pathology, for instance, anxiety, depression, epilepsy, pain, memory and chronic kidney disease (CKD). However, due to lack of the effective and selective inhibitors, its physiological and pathological mechanism remains so far unknown. It is therefore pivotal to identify potential TRPC5 inhibitors. We have applied ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS) methods. The pharmacophore models of TRPC5 antagonists generated by using the HypoGen and HipHop algorithms were used as a query model for the screening of potential inhibitors against the Specs database. The resultant hits from LBVS were further screened by SBVS. SBVS was carried out based on the homology model generation of human TRPC5, binding site identification, molecular dynamics optimization and molecular docking studies. In our systematic screening approaches, we have identified 7 hits compounds with comparable dock score after Lipinski and Veber rules, ADMET, PAINS analysis, cluster analysis, and similarity analysis. In conclusion, the current research provides novel backbones for the new-generation of TRPC5 inhibitors.

In silico identification of T-type calcium channel blockers: A ligand-based pharmacophore mapping approach

Limited progress has been made in the quest to identify both selective and non-toxic T-type calcium channel blocking compounds. The present research work was directed toward slaking the same by identifying the selective three dimensional (3D) pharmacophore map for T-type calcium channel blockers (CCBs). Using HipHop module in the CATALYST 4.10 software, both selective and non-selective HipHop pharmacophore maps for T-type CCBs were developed to identify its important common pharmacophoric features. HipHop pharmacophore map of the selective T-type CCBs contained six different chemical features, namely ring aromatic (R), positive ionizable (P), two hydrophobic aromatic (Y), hydrophobic aliphatic (Z), hydrogen bond acceptor (H) and hydrogen bond donor (D). However, non-selective T-type CCBs contain all the above mentioned features except ring aromatic (R). The present ligand-based pharmacophore mapping approach could thus be utilized in classifying selective vs. non-selective T-type CCBs. Further, the model can be used for virtual screening of several small molecule databases.

Generated 3D-common feature hypotheses using the HipHop method for developing new topoisomerase I inhibitors

The continued interest in designing novel topoisomerase I (Topo I) inhibitors and the lack of adequate ligand-based computer-aided drug discovery efforts combined with the drawbacks of structure-based design prompted us to explore the possibility of developing ligand-based three-dimensional (3D) pharmacophore(s). This approach avoids the pitfalls of structure-based techniques because it only focuses on common features among known ligands; furthermore, the pharmacophore model can be used as 3D search queries to discover new Topo I inhibitory scaffolds. In this article, we employed the HipHop module using Discovery Studio to construct plausible binding hypotheses for clinically used Topo I inhibitors, such as camptothecin, topotecan, belotecan, and SN-38, which is an active metabolite of irinotecan. The docked pose of topotecan was selected as a reference compound. The first hypothesis (Hypo 01) among the obtained 10 hypotheses was chosen for further analysis. Hypo 01 had six features, which were two hydrogen-bond acceptors, one hydrogen-bond donor, one hydrophob aromatic and one hydrophob aliphatic, and one ring aromatic. Our obtained hypothesis was checked by using some of the aromathecin derivatives which were published for their Topo I inhibitory potency. Moreover, five structures were found to be possible anti-Topo I compounds from the DruglikeDiverse database. From this research, it can be suggested that our model could be useful for further studies in order to design new potent Topo I-targeting antitumor drugs.

Pharmacophore generation of 2-substituted benzothiazoles as AdeABC efflux pump inhibitors in A. baumannii

RND family efflux pumps are important for multidrug resistance in Gram-negative bacteria. To date no efflux pump inhibitors for clinical use have been found, so developing the specific inhibitors of this pump system will be beneficial for the treatment of infections caused by these multidrug-resistant pathogens. A set of BSN-coded 2-substituted benzothiazoles were tested alone and in combination with ciprofloxacin (CIP) against the RND family efflux pump AdeABC overexpressor Acinetobacter baumannii SbMox-2 strain. The results indicated that the BSN compounds did not have antimicrobial activity when tested alone. However, if they were applied in combination with CIP, it was observed that the antibiotic had antimicrobial activity against the tested pathogen, possessing a minimum inhibitory concentration value that could be utilized in clinical treatment. A 3D-common features pharmacophore model was applied by using the HipHop method and the generated pharmacophore hypothesis revealed that the hydrogen bond acceptor property of nitrogen in the thiazole ring and the oxygen of the amide substituted at the second position of the benzothiazole ring system were significant for binding to the target protein. Moreover, three hydrophobic aromatic features were found to be essential for inhibitory activity.

Pharmacophore mapping based inhibitor selection and molecular interaction studies for identification of potential drugs on calcium activated potassium channel blockers, tamulotoxin

Background:

Tamulotoxin (TmTx) from Buthus tamulus was found to be a highly venomous toxin which accelerates the neurotransmitter release that directly affects the cardiovascular tissues and the respiratory system leading to death. TmTx from red Indian scorpion is a crucial inhibitor for Ca²⁺ activated K⁺ channel in humans.

Objective:

The study is aimed at the identification of potential inhibitors of TmTx through pharmacophore based inhibitor screening and understanding the molecular level interactions.

Materials and Method:

The potential inhibitors for TmTx were identified using pharmacophore model based descriptor information present in existing drugs with the analysis of pharmacokinetic properties. The compounds with good ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) descriptors were subjected to molecular interaction studies. The stability of bound toxin-inhibitor complex was studied using molecular dynamics simulation over a period of one nanosecond.

Results:

From a dataset of 3406 compounds, few compounds were selected as potential inhibitors based on the generated best pharmacophore models, pharmacokinetic analysis, molecular docking and molecular dynamics studies.

Conclusion:

In conclusion, two compounds containing better inhibition properties against TmTx are suggested to be better lead molecules for drug development in future and this study will help us to explore more inhibitors from natural origin against tamulotoxin.