Combined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing.

Histone deacetylases (HDACs), a critical family of epigenetic enzymes, has emerged as a promising target for antitumor drugs. Here, we describe our protocol of virtual screening in identification of novel potential HDAC inhibitors through pharmacophore modeling, 3D-QSAR, molecular docking and molecular dynamics (MD) simulation. Considering the limitation of current virtual screening works, drug repurposing strategy was applied to discover druggable HDAC inhibitor. The ligand-based pharmacophore and 3D-QSAR models were established, and their reliability was validated by different methods. Then, the DrugBank database was screened, followed by molecular docking. MD simulation (100 ns) was performed to further study the stability of ligand binding modes. Finally, results indicated the hit DB03889 with high in silico inhibitory potency was suitable for further experimental analysis.Communicated by Ramaswamy H. Sarma.

Discovery of novel serine/threonine protein phosphatase 1 inhibitors from traditional Chinese medicine through virtual screening and biological assays.

Protein phosphatase 1 (PP1) is a critical regulator of several processes, such as muscle contraction, neuronal signaling, glycogen synthesis, and cell proliferation. Dysregulation of PP1 has recently been found to be implicated in cardiac dysfunctions, which indicates that PP1 could be an attractive therapeutic target. However, discovery of PP1 inhibitors with satisfied safety and efficiency is still a challenge. Here, in order to discover potential PP1 inhibitors, compounds extracted from traditional Chinese medicine (TCM) were screened by a novel integrated virtual screening protocol including pharmacophore modeling and docking approaches. Combined with protein phosphatase inhibition assay, ZINC43060554 showed strongly inhibitory activity with IC50 values of 26.78 µM. Furthermore, molecular dynamics simulation and Molecular Mechanics/Generalized Born Surface Area binding free-energy analysis were performed to examine the stability of ligand binding modes. These novel scaffolds discovered in the present study can be used for rational design of PP1 inhibitors with high affinity.Communicated by Ramaswamy H. Sarma.

Bio-succinic acid production from coffee husk treated with thermochemical and fungal hydrolysis.

Coffee husk (CH), a waste obtained from processing of coffee cherries via dry method, causes serious environmental problems. In this study, strategies were designed to utilize CH for succinic acid (SA) production. Three different CH hydrolysis methods: thermal, thermochemical and crude enzymes obtained by solid state fermentation of Aspergillus niger and Trichoderma reesei, were evaluated to generate fermentable feedstock for SA production using Actinobacillus succinogenes. The feasibility of these pretreatment methods was investigated. Accordingly, thermochemical hydrolysis using H2SO4 at 121 °C for 30 min, appeared the most effective method for CH hydrolysis, producing 24.4 g/L of reducing sugars (RS). Finally, 19.3 g/L of SA with yield and productivity of 0.95 g SA/g RS and 0.54 g/L/h, respectively, were obtained using CH hydrolysate. The current study revealed an alternative way of utilization coffee waste for value addition while mitigating environmental problems caused by its disposal.

High-yield production of mannitol by Leuconostoc pseudomesenteroides CTCC G123 from chicory-derived inulin hydrolysate.

Chicory is an agricultural plant with considerable potential as a carbohydrate substrate for low-cost production of biochemicals. In this work, the production of mannitol by Leuconostoc pseudomesenteroides CTCC G123 from chicory-derived inulin hydrolysate was investigated. The bioconversion process initially suffered from the leakage of fructose to the phosphoketolase pathway, resulting in a low mannitol yield. When inulin hydrolysate was supplemented with glucose as a substrate for mannitol production in combination with aeration induction and nicotinic acid induced redox modulation strategies, the mannitol yield greatly improved. Under these conditions, significant improvement in the glucose consumption rate, intracellular NADH levels and mannitol dehydrogenase specific activity were observed, with mannitol production increasing from 64.6 to 88.1 g/L and overall yield increase from 0.69 to 0.94 g/g. This work demonstrated an efficient method for the production of mannitol from inulin hydrolysate with a high overall yield.

A new lignan with anti-tumour activity from Polygonum perfoliatum L.

The methanol extract of the tubers of Polygonum perfoliatum L. afforded a new lignan: 8-oxo-pinoresinol (1), and five known compounds 3',5-dihydroxy-3,4',5',7-tetramethoxy-flavone (2), catechin (3), quercetin (4), quercetin-3-O-ß-D-glucuronide (5) and rutin (6). Their structures were established by MS, one- and two-dimensional NMR experiments. Compound 1 showed cytotoxicity against human mammary carcinoma (Bcap-37), human colon carcinoma (RKO), human hepatocellular carcinoma (SMMC-7721), human prostate carcinoma (PC3) and human erythroleukaemia (K562) cells.