Combined ligand based pharmacophore modeling, virtual screening methods to identify critical chemical features of novel potential inhibitors for phosphodiesterase-5

Discovery of novel and highly potential inhibitors of glycogen synthase kinase 3-beta (GSK-3β) through structure-based pharmacophore modeling, virtual computational screening, docking and in silico ADMET analysis

The protein Glycogen Synthase Kinase 3-Beta (GSK-3β), is a promising therapeutic target for treating various diseases such as neurodegenerative disorders, diabetes, inflammation and cancer. This study aims to investigate the potential of compounds targeting inflammation or carbohydrate metabolism to selectively inhibit GSK3β by binding to its ATP site. To achieve this goal, we filtered a database of 49367 molecules involved in carbohydrate metabolism or targeting inflammation using various computational analyses, including pharmacophore modeling, molecular docking, dynamic simulation, prime MM-GBSA calculation, and in silico ADME studies. We generated a pharmacophore model (hypo S: AADDHRR) using two different crystallographic complexes of GSK3β and evaluated the model's performance in identifying hits using various parameters, including EF, GH, ROC, AUC and BEDROC. Subsequently, we performed various dockings (HTVS, SP, XP and IFD) for the retrieved hits and found that, 5 out of the top 10 ranked compounds had the scaffold of pyrazolidine 3,5-dione, which has never been reported to inhibit kinases. We also conducted ADMET studies to and concluded that compound N6 exhibited the best pharmacokinetic profile passing the blood-brain barrier, possessing high lipophilicity and a high coefficient of skin permeability in the intestines, along with good bioavailability and low toxicity risk assessment. Dynamic simulation were also performed indicating that compounds N6 derived from pyrazolidine 3,5-dione demonstrated better binding potential for GSK3β during the simulation period. Therefore, we propose that compounds derived from pyrazolidine-3,5-dione, which modulate the activity of lysosomal alpha-glucosidase could serve as a novel scaffold for the selective inhibition of GSK-3β.Communicated by Ramaswamy H. Sarma.

Design and development of novel inhibitors of aldo-ketoreductase 1C1 as potential lead molecules in treatment of breast cancer

Aldo-keto reductase 1C1 (AKR1C1) is a hydroxysteroid dehydrogenase, known to inactivate the biologically active progesterone into its corresponding 20 α-hydroxyprogesterone. Increased expression of the AKR1C1 gene in oncogenesis is linked with resistance to various anticancer agents and hence it is considered as an emerging drug target for the design and developing the novel anticancer drugs. We have performed QSAR pharmacophore modeling for AKR1C1 inhibitors followed by a virtual screening of ~ 59,000 compounds present at the Maybridge database. The screened compounds were refined using drug-like filters of Lipinski rule, ADMET plot, molecular docking and scoring and subsequently top 20 hits were selected. Selected compounds were subjected to the in vitro for AKR1C1 inhibition assay and best seven compounds bearing excellent binding affinity to the AKR1C1 were finally selected. The identified compounds may be exploited in hit-to-lead development and may also prove as an interventional strategy in preventing a pre-term birth due to declining levels of progesterone.

Discovery of potent apoptosis signal-regulating kinase 1 inhibitors via integrated computational strategy and biological evaluation

Apoptosis signal-regulating Kinase 1 (ASK1) has been confirmed as a potential therapeutic target for the treatment of non-alcoholic steatohepatitis (NASH) disorder and the discovery of ASK1 inhibitors has attracted increasing attention. In this work, a series of in silico methods including pharmacophore screening, docking binding site analysis, protein-ligand interaction fingerprint (PLIF) similarity investigation and molecular docking were applied to find the potential hits from commercial compound databases. Five compounds with potential inhibitory activity were purchased and submitted to biological activity validation. Thus, one hit compound was discovered with micromolar IC₅₀ value (10.59 μM) against ASK1. Results demonstrated that the integration of computation methods and biological test was quite reliable for the discovery of potent ASK1 inhibitors and the strategy could be extended to other similar targets of interest.

Exploring molecular fingerprints of selective PPARδ agonists through comparative and validated chemometric techniques

Peroxysome proliferator-activated receptors (PPARs) have grown greatly in importance due to their role in the metabolic profile. Among three subtypes (α, γ and δ), we here consider the least investigated δ subtype to explore the molecular fingerprints of selective PPARδ agonists. Validated QSAR models (regression based 2D-QSAR, HQSAR and KPLS) and molecular docking with dynamics analyses support the inference of classification-based Bayesian and recursive models. Chemometric studies indicate that the presence of ether linkages and heterocyclic rings has optimum influence in imparting selective bioactivity. Pharmacophore models and docking with molecular dynamics analyses postulate the occurrence of aromatic rings, HB acceptor and a hydrophobic region as crucial molecular fragments for development of PPARδ modulators. Multi-chemometric studies suggest the essential structural requirements of a molecule for imparting potent and selective PPARδ modulation.

Pharmacophore based virtual screening, molecular docking and biological evaluation to identify novel PDE5 inhibitors with vasodilatory activity

Prompted by the role of PDE5 and its closely associated cAMP and cGMP in hypertension, we have attempted to discover novel PDE5 inhibitors through ligand based virtual screening. Rigorously validated model comprising of one HBA, one HY and one RA was used as a query to search the NCI database leading to retrieval of many compounds which were screened on the basis of estimated activity, fit value and Lipinski's violation. Selected compounds were subjected to docking studies which resulted into visualization of potential interaction capabilities of NCI compounds in line to pharmacophoric features. Finally three compounds were subjected to in vitro evaluation using the isolated rat aortic model. The results showed that all three compounds are potent and novel PDE5 inhibitors with vasodilatory activity range from 10(-2) to 10(-5) M.