Identification of phytochemicals from Eclipta alba and assess their potentiality against Hepatitis C virus envelope glycoprotein: virtual screening, docking, and molecular dynamics simulation study

Unveiling critical structural features for effective HDAC8 inhibition: a comprehensive study using quantitative read-across structure-activity relationship (q-RASAR) and pharmacophore modeling

Histone deacetylases constitute a group of enzymes that participate in several biological processes. Notably, inhibiting HDAC8 has become a therapeutic strategy for various diseases. The current inhibitors for HDAC8 lack selectivity and target multiple HDACs. Consequently, there is a growing recognition of the need for selective HDAC8 inhibitors to enhance the effectiveness of therapeutic interventions. In our current study, we have utilized a multi-faceted approach, including Quantitative Structure-Activity Relationship (QSAR) combined with Quantitative Read-Across Structure-Activity Relationship (q-RASAR) modeling, pharmacophore mapping, molecular docking, and molecular dynamics (MD) simulations. The developed q-RASAR model has a high statistical significance and predictive ability (Q2F1:0.778, Q2F2:0.775). The contributions of important descriptors are discussed in detail to gain insight into the crucial structural features in HDAC8 inhibition. The best pharmacophore hypothesis exhibits a high regression coefficient (0.969) and a low root mean square deviation (0.944), highlighting the importance of correctly orienting hydrogen bond acceptor (HBA), ring aromatic (RA), and zinc-binding group (ZBG) features in designing potent HDAC8 inhibitors. To confirm the results of q-RASAR and pharmacophore mapping, molecular docking analysis of the five potent compounds (44, 54, 82, 102, and 118) was performed to gain further insights into these structural features crucial for interaction with the HDAC8 enzyme. Lastly, MD simulation studies of the most active compound (54, mapped correctly with the pharmacophore hypothesis) and the least active compound (34, mapped poorly with the pharmacophore hypothesis) were carried out to validate the observations of the studies above. This study not only refines our understanding of essential structural features for HDAC8 inhibition but also provides a robust framework for the rational design of novel selective HDAC8 inhibitors which may offer insights to medicinal chemists and researchers engaged in the development of HDAC8-targeted therapeutics.

An investigation into the usage of black cumin derivatives against cancer and COVID-19 as the nature medicine

Black cumin has been used as a spice and food preservative for years. Thymol, thymoquinone, thymohydroquinone and dihydrothymoquinone are the most important natural agents in black cumin. In order to determine the most active compound in black cumin the theoretical calculations have been carried out in different phases by using the density functional theory (DFT). The inhibition effect of black cumin derivatives on Histone deacetylase 2 (HDAC2) has been determined and supported the experimental studies without losing time and matter. The chemical activity, stability and solubility of the active substances in black cumin have been theoretically calculated. The chemical active compounds had been investigated in the black seeds when extracted with water. Their stability and polarity in blood and water are important parameters. HDAC2- dihydrothymoquinone interaction has been investigated. It has been determined that the active substances found in black cumin are very effective in protecting ACE2 against COVID-19 and by comparing the docking results of important receptors and selected ligands on COVID-19.Communicated by Ramaswamy H. Sarma.

Molecular recognition of bio-active triterpenoids from Swertia chirayita towards hepatitis Delta antigen: a mechanism through docking, dynamics simulation, Gibbs free energy landscape

Medicinal plants the underpinning of indigenous herbal serve, are the possible source of key compounds for the development of new drugs. Hepatitis D, one of the most widespread infectious diseases associated with global public health issues. Therefore, we aim to screen natural compounds to find out potent inhibitor towards hepatitis delta antigen. Through ADMET investigation, we have screened twenty phytochemicals for this study. Additionally, using molecular docking, these phytochemicals were docked with the HDV protease which signifies the phytochemicals beta-amyrin, chiratenol, episwertenol and swertanone have a significant capability to bind with hepatitis D virus protein. The docking study was further accompanied by analyzes RMSD, RMSF, Rg, SASA, Hbond number, and principal component analysis through 100 ns MD simulations. Based on our principal component analysis, beta-amyrin, chiratenol, episwertenol and swertanone phytochemicals can be a potential drug candidates for inhibition of hepatitis D. The above observation is also supported by our Gibbs free energy landscape study. The potential therapeutic characteristics of the phytochemicals against hepatitis D inhibition offer additional support for the in vitro and in vivo studies in future.

Effect of carbon quantum dots derived from extracts of UV-B-exposed Eclipta alba on alcohol-induced liver cirrhosis in Golden Hamster

The Eclipta alba plant is considered hepatoprotective, owing to its phytoconstituents wedelolactone. In the current study, effect of elevated ultraviolet-B (eUV-B) radiation was investigated on biochemical, phytochemical, and antioxidative enzymatic activities of E. alba (Bhringraj) plant. The UV-B exposure resulted in an increase in oxidative stress, which has caused an imbalance in phytochemical, biochemical constituents, and induced antioxidative enzymatic activities. It was observed that the UV-B exposure promoted wedelolactone yield by 23.64%. Further, the leaf extract of UV-B-exposed plants was used for the synthesis of carbon quantum dots (CQDs) using low cost, one-step hydrothermal technique and its biocompatibility was studied using in vitro MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay on HepG2 liver cell line. It revealed no toxicity in any treatment groups in comparison to the control. Both CQDs and leaf extract were orally administered to the golden hamster suffering from alcohol-induced liver cirrhosis. In the morphometric study, it was clearly observed that a combination of UV-B-exposed leaf extract and synthesized CQDs delivered the best result with maximum recovery of liver tissues. The present study reveals the positive impact of UV-B exposure on the medicinally important plant, increased yield of wedelolactone, and its enhanced hepatoprotective efficacy for the treatment of damaged liver tissues.