Identify thrombin inhibitor with novel skeleton based on virtual screening study

Discovery of potential scaffolds for glutaminyl cyclase inhibitors: Virtual screening, synthesis, and evaluation

Glutaminyl cyclase (QC) plays a crucial role in the early stages of Alzheimer's disease (AD), thus inhibition of QC may be a promising strategy for the treatment of early AD. Therefore, QC inhibitors with novel chemical scaffolds may contribute to the development of additional anti-AD agents. We conducted a virtual screening of 3 million compounds from the Chemdiv and Enamine databases, to discover potential scaffolds for QC inhibitors. Three scaffolds, 120974, 147706, and 141449, were selected from this structure-based virtual screening through a combination of pharmacophore modeling, a receptor-ligand pharmacophore model, and the GALAHAD model, and furtherly filtered by chelation with zinc ion and docking properties. Consequently, three compounds, 1, 2, and 3, were designed and synthesized based on these three scaffolds, respectively. The IC50 of compounds 1 and 3 against QC were 14.19 ± 4.21 and 4.34 ± 0.35 μM, respectively. Our results indicate that the new scaffolds selected using a virtual screening process exhibit potential as novel QC inhibitors.

(1R,3S)-THCCA-Asn: To show the discovery of selective inhibitor of thrombin by successfully combining virtual screening and biological assay

Thrombin is the most potent platelet aggregator. To discover the selective inhibitor of thrombin that is important to curing platelet aggregation-related diseases, docking experiments were performed to dock (1R,3S)-2,3,4,9-tetrahydro-β-carboline-3- carboxylic acid, [(1R,3S)-THCCA], and (1S,3S)-2,3,4,9-tetrahydro-β-carboline-3- carboxylic acid, [(1S,3S)-THCCA], into the p pocket of bovine thrombin. The ideal match supported that (1R,3S)-THCCA could be used as a potential lead compound. In this case 20 natural amino acids were theoretically introduced into the 3-carboxyl of (1R,3S)-THCCA and 20 derivatives, (1R,3S)-THCCA-amino acids, were docked into p pocket of bovine thrombin to perform virtual screening. The screening revealed that comparing to (1R,3S)-THCCA itself the DockScores of 16 derivatives were higher, and (1R,3S)-THCCA-Asn (4j) got the highest DockScore. Thus, 16 derivatives were synthesized for experimental study. The in vitro anti-platelet aggregation assay showed that at 100 μM of concentration the 16 derivatives failed to inhibit the platelet aggregation induced by both adenosine diphosphate and arachidonic acid. On the other hand, however, the IC₅₀ value of the 16 derivatives inhibiting the platelet aggregation induced by platelet activating factor and thrombin ranged from 9.44 μM to 194.64 μM and from 0.07 μM to 9.56 μM, respectively. The in vitro anti-platelet aggregation assay suggested that the 16 derivatives selectively inhibited the platelet aggregation induced by thrombin. In particular, the IC₅₀ of (1R,3S)-THCCA-Asn (4j) had the lowest value. On rat model at 1 nmol/kg of dosage the 16 derivatives effectively prevented thrombus formation. It is worth pointing out that even at 0.01 nmol/kg of dosage, 4j still effectively prevented thrombus formation. 4j hardly has effects on the proliferation of mammalian cells and rat tail bleeding time. In conclusion, the combination of virtual screening and biological assays successfully lead to the discovery of 4j as a promising candidate of selective inhibitor of thrombin.

Screening and bioavailability evaluation of anti-oxidative selenium-containing peptides from soybeans based on specific structures

Our previous study has evaluated the antioxidant capacity and identified the sequences of soybean selenium-containing peptides. Herein, pharmacophore screening, gastrointestinal simulation and in vivo pharmacokinetics were performed to predict the potentials of selenium-containing peptides in terms of antioxidant activity, safety and bioavailability. A pharmacophore model with 6 structure features was constructed for virtual screening to determine the potential activities of 85 selenium sequences from soybean peptides. Strong reversing effects (p < 0.05) of the targeted sequences were observed in tumor necrosis factor-α (TNF-α)-induced inflammatory cytokines and adhesion factors burst in EA·hy926/Caco-2 co-culture cell models. Ser-Phe-Gln-SeMet (SFQSeM), a promising peptide selected from both virtual screening and cell models, was proved to be stable in the gastrointestinal tract and could be transported across the Caco-2 monolayer via the paracellular pathway. Additionally, SFQSeM showed a long residence time (89.42 ± 1.34 min) and half-life (81.60 ± 11.88 min) after consumption, and it induced lower liver alanine/aspartate transaminase (ALT/AST) and serum nitric oxide (NO) levels compared to Na2SeO3 and SeMet (p < 0.05). The potency of SFQSeM against oxidative stress as well as its oral bioavailability and low risk highlight its potential utility as an effective Se nutritional supplement.