Molecular dynamics simulations reveal the inhibitory mechanism of Withanolide A against α-glucosidase and α-amylase

Inhibitory mechanisms of galloylated forms of theaflavins on α-glucosidase

Theaflavins, oxidation product of tea polyphenols, have demonstrated significant inhibitory effects on α-glucosidase, which is beneficial in alleviating hyperglycemia. This study found that the inhibition of four monomers of theaflavins on α-glucosidase was related to the presence of the galloyl moiety (GM), with IC50 values ranging from TFDG (0.26 mg/mL) < TF3'G (0.33 mg/mL) < TF3G (0.39 mg/mL) ≪ TF (3.26 mg/mL). The multi-spectroscopic analyses revealed that theaflavin monomers changed the microenvironment around aromatic amino acid residues and conformation of α-glucosidase, with the hierarchy being TFDG > TF3'G > TF3G > TF. The binding of theaflavins with α-glucosidase was confirmed by differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC), molecular docking and molecular dynamics simulations analysis. It was confirmed that theaflavins can form stable complexes with α-glucosidase, and that hydrogen bonding and van der Waals forces play important roles in the binding of theaflavins to α-glucosidase. The strongest binding affinity was observed between TFDG and the enzyme's active site, which corresponded with its enzyme activity inhibition ability. The study suggests that GM substitution plays a crucial role in enhancing the binding of theaflavins to α-glucosidase, thereby inducing greater conformational changes and leading to a stronger inhibitory effect on α-glucosidase.

Ex-vivo antioxidant, enzyme inhibitory properties and computational analysis unveil the molecular mechanism of cardiac and penile phosphodiesterase-5 inhibition by bacterial strain HOKA1 extract as an aphrodisiac's agent

The study uses in-vitro antioxidant, ex-vivo enzyme kinetics and in-silico approach using standard protocols to understand their inhibitory mechanism better. The study revealed that bacterial strain HOKA1 isolated from Oniru beach, grown in nutrient agar supplemented with sodium chloride (30%NaCl). Moreso, the bacterial strain HOKA1 extract showed better antioxidant capability and greatly reduced the penile and cardiac cGMP with the highest penile and cardiac concentration between 0.013 and 0.183 μM/Min as compared to the sildenafil citrate (0.00-0.203 μM/Min). Moreover, the kinetic parameters (Vmax and Km) effects revealed that bacterial strain HOKA1 extract inhibited PDE-5 activities better than sildenafil citrate. The GC-MS analysis revealed twenty-nine bioactive compounds in the extract, and these compounds could provide comprehensible supporting evidence for the antioxidant and inhibitory potential of the strain HOKA1 extract on PDE-5 activity. Molecular docking study revealed majority of the GC-MS-identified bioactive constituents from the HOKA1 extract showed high binding energy or lower bonding affinities (-6.8 to -3.3 kcal/mol) compared to reference drug sildenafil citrate (-9.6 kcal/mol), except campesterol (-10.0 kcal/mol); also, ergostane (-9.9 kcal/mol). The results of 100 ns simulation (RMSF, RMSD, Rg and H-bond) show extraordinary stability of PDE-5 with campesterol and ergostane, so also complimentary binding energy of MM-PBSA (campesterol -65.92±4.09 kcal/mol; ergostane -57.23±4.70 kcal/mol) indicating their probability of acting promising PDE-5 inhibitors. Therefore, the study revealed that bacterial strain HOKA1 extract showed a better aphrodisiac property, and its bioactive compounds (campesterol and ergostane) should be considered in upcoming rational development and design of more active selective PDE-5 inhibitors, making a treatment for erectile dysfunction.

Apigenin analogs as α-glucosidase inhibitors: Molecular docking, biochemical, enzyme kinetic, and an in vivo mouse model study

Due to the high incidence of diabetes and its associated complications, diabetes is widely recognized as a serious global health problem. In diabetes treatment strategies, targeting α-glucosidase, a key carbohydratehydrolyzing enzyme, has emerged as a highly regarded approach. To develop novel α-glucosidase inhibitors, we successfully synthesized a series of apigenin analogs, collectively referred to as H1-H27 compounds and examined their inhibitory effects on α-glucosidase activity. H7 showed a remarkable inhibitory effect, surpassing that of the standard drug acarbose. Further analysis revealed that H7, H10, and H24 act as non-competitive inhibitors of α- glucosidase. In vivo experiments using a type 2 diabetes mouse model demonstrated the diverse therapeutic potential of H7; it effectively lowered blood sugar levels, improved glucose tolerance, and corrected lipid metabolism. In addition, H7 showed hepatoprotective effects, highlighting its ability to improve liver function. H7 also positively influenced the gut microbiota composition in diabetic mice, increasing diversity and richness. These results highlight the promising therapeutic effects of apigenin analogs, such as H7, for treating type 2 diabetes and show how they could provide numerous benefits, including effective inhibition of α-glucosidase, improved glucose control, correction of lipid metabolism, hepatoprotection, and modulation of the intestinal microbiota.

Biological and molecular approaches of the degradation or decolorization potential of the hypersaline Lake Tuz Bacillus megaterium H2 isolate

The presence of synthetic dyes in water bodies and soil is one of the major issues affecting the global ecology, possibly impacting societal well-being adversely due to the colorants' recalcitrance and toxicity. Herein, the study spectrophotometrically monitored the ability of the Bacillus megaterium H2 azoreductase (AzrBmH2) to degrade four synthetic dyes, reactive blue 4, remazol brilliant red, thymol blue, and methyl red, followed by in-silico assessment using GROMACS. We found that the bacterium degraded as much as 60% of all four synthetic dyes at various tested concentrations. The genome analysis revealed five different azoreductase genes, which were then modeled into the AzrBmH21, AzrBmH22/3, and AzrBmH24/5 templates. The AzrBmH2-substrate complexes showed binding energies with all the dyes of between -10.6 to -6.9 kcal/mol and formed 4-6 hydrogen bonds with the predicted catalytic binding residues (His10, Glu 14, Ser 58, Met 99, Val 107, His 183, Asn184 and Gln 191). In contrast, the lowest binding energies were observed for the AzrBmH21-substrates (-10.6 to -7.9). Molecular dynamic simulations revealed that the AzrBmH21-substrate complexes were more stable (RMSD 0.2-0.25 nm, RMSF 0.05 - 0.3 nm) and implied strong bonding with the dyes. The Molecular Mechanics Poisson-Boltzmann Surface Area results also mirrored this outcome, showing the lowest azoreductase-dye binding energy in the order of AzrBmH21-RB4 (-78.18 ± 8.92 kcal/mol), AzrBmH21-RBR (-67.51 ± 7.74 kcal/mol), AzrBmH21-TB (-46.62 ± 5.23 kcal/mol) and AzrBmH21-MR (-40.78 ± 7.87 kcal/mol). In short, the study demonstrated the ability of the B. megaterium H2 to efficiently decolorize the above-said synthetic dyes, conveying the bacterium's promising use for large-scale dye remediation.Communicated by Ramaswamy H. Sarma.

Discovery of Novel and Selective Schiff Base Inhibitors as a Key for Drug Synthesis, Molecular Docking, and Pharmacological Evaluation

Diabetes mellitus (DM) is a chronic disorder and still a challenge throughout the world, and therefore the search for safe and effective inhibitors for α-amylase and α-glucosidase is increasing day by day. In this work, we try to carry out the synthesis, modification, and computer-aided results of and biological research on thiadiazole-based Schiff base derivatives and evaluate their in vitro α-amylase and α-glucosidase inhibitory potential (1-15). In the current series, all of the synthesized analogues were shown to have potential inhibitory effects on targeted enzymes. The IC50 values for α-amylase values ranged from 20.10 ± 0.40 to 0.80 ± 0.05 μM, compared with the standard drug acarbose having an IC50 value of 10.30 ± 0.20 μM, while for α-glucosidase, the IC50 values ranged from 20.10 ± 0.50 to 1.20 ± 0.10 μM, compared to acarbose with an IC50 value of 9.80 ± 0.20 μM. For better understanding, a SAR investigation was undertaken. In this series, nine scaffolds (1, 2, 3, 6, 9, 10, 11, 13, and 15) were more active than the reference drug and the docking parameter RMSD values for α-glucosidase and α-amylase were 1.766, 2.7746, 1.6025, 2.2112, 3.5860, 2.3360, 1.6178, 2.0254, and 2.0797 and 2.6020, 1.9509, 3.1642, 1.7547, 2.2130, 1.4221, and 1.1087, respectively. The toxicity of the selected analogues was calculated by using the OSIRIS tool, and the TPSA values were found to be lower than 140 to represent the drug-like properties; those from Molinspiration were studied as well. The following properties were studied and found to have better biological properties. The remaining analogues (4, 5, 7, 8, 12, and 14) were also identified as potential inhibitors of both enzymes, but they were less active than the reference due to the substituents attached to the aromatic parts. The structures of synthesized compounds were confirmed through different spectroscopic analyses.

Phyto-therapeutic potential of Withania somnifera: Molecular mechanism and health implications

Withania somnifera, the plant named Indian ginseng, Ashwagandha, or winter cherry, has been used since ancient times to cure various health ailments. Withania somnifera is rich in constituents belonging to chemical classes like alkaloids, saponins, flavonoids, phenolic acids, and withanolides. Several chemotypes were identified based on their phytochemical composition and credited for their multiple bioactivities. Besides, exhibiting neuroprotective, immunomodulatory, adaptogenic, anti-stress, bone health, plant has shown promising anti-cancer properties. Several withanolides have been reported to play a crucial role in cancer; they target cancer cells by different mechanisms such as modulating the expression of tumor suppressor genes, apoptosis, telomerase expression, and regulating cell signaling pathway. Though, many treatments are available for cancer; however, to date, no assured reliable cure for cancer is made available. Additionally, synthetic drugs may lead to development of resistance in time; therefore, focus on new and natural drugs for cancer therapeutics may prove a longtime effective alternative. This current report is a comprehensive combined analysis upto 2023 with articles focused on bio-activities of plant Withania somnifera from various sources, including national and international government sources. This review focuses on understanding of various mechanisms and pathways to inhibit uncontrolled cell growth by W. somnifera bioactives, as reported in literature. This review provides a recent updated status of the W. somnifera on pharmacological properties in general and anti-cancer in particular and may provide a guiding resource for researchers associated with natural product-based cancer research and healthcare management.

Withaferin A suppressed hepatocellular carcinoma progression through inducing IGF2BP3/FOXO1/JAK2/STAT3 pathway-mediated ROS production

OBJECTIVE

This study aimed to investigate the underlying molecular mechanisms of Withaferin A (WA) in hepatocellular carcinoma (HCC).

MATERIALS AND METHODS

The gene and protein expression were analyzed using RT-qPCR and western blot, respectively. The proliferation of HCC cells was evaluated by CCK-8 assays. The migrative ability of HCC cells was measured by transwell assays.

RESULTS

We revealed that WA suppressed the proliferation and migration of HCC cells and inhibited IGF2BP3 (insulin like growth factor 2 mRNA binding protein 3) expression. IGF2BP3 abundance reversed the reactive oxygen species (ROS) accumulation and suppression of HCC cell proliferation and migration induced by WA. Besides, IGF2BP3 suppressed ROS production to promote the growth and migration of HCC cells. Furthermore, we found that IGF2BP3 exerted its tumor-promotive and ROS-suppressive effect on HCC cells by regulating the expression of FOXO1 (forkhead box O1). In addition, IGF2BP3-stimulated activation of JAK2 (Janus kinase 2)/STAT3 (signal transducer and activator of transcription 3) phosphorylation effectively decreased the transcription of FOXO1. FOXO1 abundance decreased the phosphorylation of JAK2 and STAT3 by increasing ROS level, forming a feedback loop for the inhibition of JAK2/STAT3 signaling activated by IGF2BP3.

CONCLUSIONS

WA-induced ROS inhibited HCC cell growth and migration through the inhibition of IGF2BP3 to deactivate JAK2/STAT3 signaling, resulting in increased FOXO1 expression to further stimulate ROS production and inhibit JAK2/STAT3 signaling.

Apigenin analogs as α-glucosidase inhibitors with antidiabetic activity

This study investigated the inhibitory potential of a series of synthesized compounds (L1-L27) on α-glucosidase. Among them, compound L22 showed significant inhibitory effect. Through enzymatic kinetics studies, we demonstrated that L22 acts via a non-competitive inhibition mode with a Ki value of 2.61 μM, highlighting its high affinity for the enzyme. Molecular docking studies revealed the formation of hydrogen bonds between L22 and α-glucosidase and diverse interactions with neighboring amino acid residues. Furthermore, molecular dynamics simulations confirmed the stability of the L22-α-glucosidase complex. In a mouse model of type 2 diabetes, treatment with L22 significantly lowered fasting blood glucose levels, and reduced insulin resistance, suggesting its potential as a therapeutic agent for type 2 diabetes. Furthermore, L22 showed a protective effect against oxidative stress in the liver and alleviated liver and pancreatic abnormalities. These results provide valuable insights into the mechanism of action of L22 and its potential applications to treat type 2 diabetes, and improve liver health.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Design of a dual-function agent by fusing a designed anti-VEGF-A binder and CPG-2 enzyme

Anti-VEGF therapies are common for the treatment of cancer. Carboxypeptidase G (CPG-2) enzyme is a zinc-dependent metalloenzyme that metabolizes non-toxic synthetic 'benzoic mustard prodrugs' to cytotoxic moieties in tumor cells. In this study, we designed a dual-activity agent by combining a designed anti-VEGF- and CPG-2 enzyme to convert methotrexate (MTX). VEGF-A was docked against a set of scaffolds, and suitable inverse rotamers were made. Rosetta design was used for the interface design. The top 1200 binders were chosen by flow cytometry and displayed in yeast. The activity of CPG-2 enzyme was analyzed at different temperature conditions and in the presence of the substrate, MTX. Optimal binders were selected and protein was eluted using immobilized metal affinity chromatography and size-exclusion chromatography. Both, native PAGE and on-yeast flow cytometry confirmed the binding of the binder to VEGF-A. The activity of truncated enzymes was slightly lower than that of full-length enzymes linked to VEGF-A. The method should be generally useful as a dual-activity agent for targeting VEGF-A and combination therapy with the enzyme CPG-2 for metabolizing non-toxic prodrugs to cytotoxic moieties.Communicated by Ramaswamy H. Sarma.