Structural Changes of Sarco/Endoplasmic Reticulum Ca2+-ATPase Induced by Rutin Arachidonate: A Molecular Dynamics Study

Endoplasmic Reticulum as a Therapeutic Target in Cancer: Is there a Role for Flavonoids?

Flavonoids are classified into subclasses of polyphenols, a multipurpose category of natural compounds which comprises secondary metabolites extracted from vascular plants and are plentiful in the human diet. Although the details of flavonoid mechanisms are still not realized correctly, they are generally regarded as antimicrobial, anti-fungal, anti-inflammatory, anti-oxidative; anti-mutagenic; anti-neoplastic; anti-aging; anti-diabetic, cardio-protective, etc. The anti-cancer properties of flavonoids are evident in functions such as prevention of proliferation, metastasis, invasion, inflammation and activation of cell death. Tumors growth and enlargement expose cells to acidosis, hypoxia, and lack of nutrients which result in endoplasmic reticulum (ER) stress; it triggers the unfolded protein response (UPR), which reclaims homeostasis or activates autophagy. Steady stimulation of ER stress can switch autophagy to apoptosis. The connection between ER stress and cancer, in association with UPR, has been explained. The signals provided by UPR can activate or inhibit anti-apoptotic or apoptotic pathways depending on the period and grade of ER stress. In this review, we will peruse the link between flavonoids and their impact on the endoplasmic reticulum in association with cancer therapy.

Novel scaffolds targeting Mycobacterium tuberculosis plasma membrane Ca2+ transporter CtpF by structure-based strategy

CtpF is a Ca2+ transporter P-type ATPase key to the response to stress conditions and to Mycobacterium tuberculosis virulence, therefore, an interesting target for the design of novel anti-Mtb compounds. In this work, molecular dynamics simulations of four previously identified CtpF inhibitors allowed recognizing the key protein-ligand (P-L) interactions, which were then used to perform a pharmacophore-based virtual screening (PBVS) of 22 million compounds from ZINCPharmer. The top-rated compounds were then subjected to molecular docking, and their scores were refined by MM-GBSA calculations. In vitro assays showed that ZINC04030361 (Compound 7) was the best promising candidate, showing a MIC of 25.0 μg/mL, inhibition of Ca2+-ATPase activity (IC50) of 3.3 μM, cytotoxic activity of 27.2 %, and hemolysis of red blood cells lower than 0.2 %. Interestingly, the ctpF gene is upregulated in the presence of compound 7, compared to other alkali/alkaline P-type ATPases coding genes, strongly suggesting that CtpF is a compound 7-specific target.

Chemistry towards Biology-Instruct: Snapshot

The knowledge of interactions between different molecules is undoubtedly the driving force of all contemporary biomedical and biological sciences. Chemical biology/biological chemistry has become an important multidisciplinary bridge connecting the perspectives of chemistry and biology to the study of small molecules/peptidomimetics and their interactions in biological systems. Advances in structural biology research, in particular linking atomic structure to molecular properties and cellular context, are essential for the sophisticated design of new medicines that exhibit a high degree of druggability and very importantly, druglikeness. The authors of this contribution are outstanding scientists in the field who provided a brief overview of their work, which is arranged from in silico investigation through the characterization of interactions of compounds with biomolecules to bioactive materials.

In Vitro and in Silico Analyses of the Adiponectin Receptor Agonistic Action of Soybean Tripeptides

The Tyr-Pro (YP) dipeptide can serve as an adiponectin receptor 1 (AdipoR1) agonist. We thus investigated the AdipoR1-agonistic potential of YP-related tripeptides in the soybean protein sequence. Among the 17 soybean candidate tripeptides, those elongated at the C-terminus of YP (0.1 μM YPG, 140 ± 16%; 0.1 μM YPE, 141 ± 22%; 0.1 μM YPP, 145 ± 19%; 0.1 μM YPQ, 143 ± 20%; p < 0.05) significantly promoted glucose uptake by L6 muscle myotubes, comparable to the effect of 0.1 μM AdipoRon (163 ± 52%, p < 0.05). The knockdown of AdipoR1 expression in L6 cells abrogated this effect of YPG and YPP, indicating that the two tripeptides had an AdipoR1 agonistic effect. CHARMM-GUI-aided molecular dynamics simulation in a virtual phospholipid membrane revealed that YPG and YPP were stably positioned at the binding pockets of AdipoR1 (binding free energy < -10 kcal/mol). These findings demonstrate that the tripeptides YPG and YPP, with AdipoR1 agonistic YP sequences, have alternative adiponectin-like potential via their preferential binding to AdipoR1.