Docking study, molecular dynamic, synthesis, anti-α-glucosidase assessment, and ADMET prediction of new benzimidazole-Schiff base derivatives

Enzymolysis Modes Trigger Diversity in Inhibitor-α-Amylase Aggregating Behaviors and Activity Inhibition: A New Insight Into Enzyme Inhibition

Inhibitors of α-amylase have been developed to regulate postprandial blood glucose fluctuation. The enzyme inhibition arises from direct or indirect inhibitor-enzyme interactions, depending on inhibitor structures. However, an ignored factor, substrate, may also influence or even decide the enzyme inhibition. In this work, it is innovatively found that the difference in substrate enzymolysis modes, i.e., structural composition and concentration of α-1,4-glucosidic bonds, triggers the diversity in inhibitor-enzyme aggregating behaviors and α-amylase inhibition. For competitive inhibition, there exists an equilibrium between α-amylase-substrate catalytic affinity and inhibitor-α-amylase binding affinity; therefore, a higher enzymolysis affinity and concentration of α-1,4-glucosidic structures interferes the balance, unfavoring inhibitor-enzyme aggregate formation and thus weakening α-amylase inhibition. For uncompetitive inhibition, the presence of macromolecular starch is necessary instead of micromolecular GalG2CNP, which not only binds with active site but with an assistant flexible loop (involving Gly304-Gly309) near the site. Hence, the refined enzyme structure due to the molecular flexibility more likely favors the inhibitor binding with the non-active loop, forming an inhibitor-enzyme-starch ternary aggregate. Conclusively, this study provides a novel insight into the evaluation of α-amylase inhibition regarding the participating role of substrate in inhibitor-enzyme aggregating interactions, emphasizing the selection of appropriate substrates in the development and screening of α-amylase inhibitors.

Identification of Antioxidant Methyl Derivatives of Ortho-Carbonyl Hydroquinones That Reduce Caco-2 Cell Energetic Metabolism and Alpha-Glucosidase Activity

α-glucosidase, a pharmacological target for type 2 diabetes mellitus (T2DM), is present in the intestinal brush border membrane and catalyzes the hydrolysis of sugar linkages during carbohydrate digestion. Since α-glucosidase inhibitors (AGIs) modulate intestinal metabolism, they may influence oxidative stress and glycolysis inhibition, potentially addressing intestinal dysfunction associated with T2DM. Herein, we report on a study of an ortho-carbonyl substituted hydroquinone series, whose members differ only in the number and position of methyl groups on a common scaffold, on radical-scavenging activities (ORAC assay) and correlate them with some parameters obtained by density functional theory (DFT) analysis. These compounds' effect on enzymatic activity, their molecular modeling on α-glucosidase, and their impact on the mitochondrial respiration and glycolysis of the intestinal Caco-2 cell line were evaluated. Three groups of compounds, according their effects on the Caco-2 cells metabolism, were characterized: group A (compounds 2, 3, 5, 8, 9, and 10) reduces the glycolysis, group B (compounds 1 and 6) reduces the basal mitochondrial oxygen consumption rate (OCR) and increases the extracellular acidification rate (ECAR), suggesting that it induces a metabolic remodeling toward glycolysis, and group C (compounds 4 and 7) increases the glycolysis lacking effect on OCR. Compounds 5 and 10 were more potent as α-glucosidase inhibitors (AGIs) than acarbose, a well-known AGI with clinical use. Moreover, compound 5 was an OCR/ECAR inhibitor, and compound 10 was a dual agent, increasing the proton leak-driven OCR and inhibiting the maximal electron transport flux. Additionally, menadione-induced ROS production was prevented by compound 5 in Caco-2 cells. These results reveal that slight structural variations in a hydroquinone scaffold led to diverse antioxidant capability, α-glucosidase inhibition, and the regulation of mitochondrial bioenergetics in Caco-2 cells, which may be useful in the design of new drugs for T2DM and metabolic syndrome.

Phytochemical Profile, Antioxidant, Enzyme Inhibition, Acute Toxicity, In Silico Molecular Docking and Dynamic Analysis of Apis Mellifera Propolis as Antidiabetic Supplement

This study aims to identify the phytochemical profile of Apis mellifera propolis and explore the potential of its anti-diabetic activity through inhibition of α-amylase (α-AE), α-glucosidase(α-GE), as well as novel antidiabetic compounds of propolis. Apis mellifera propolis extract (AMPE) exhibited elevated polyphenol 33.26±0.17 (mg GAE/g) and flavonoid (15.45±0.13 mg RE/g). It also indicated moderate strong antioxidant activity (IC50 793.09±1.94 μg/ml). This study found that AMPE displayed promising α-AE and α-GE inhibition through in vitro study. Based on LC-MS/MS screening, 18 unique AMPE compounds were identified, with majorly belonging to anthraquinone and flavonoid compounds. Furthermore, in silico study determined that 8 compounds of AMPE exhibited strong binding to α-AE that specifically interacted with its catalytic residue of ASP197. Moreover, 2 compounds exhibit potential inhibition of α-GE, by interacting with crucial amino acids of ARG315, ASP352, and ASP69. Finally, we suggested that 2,7-Dihydroxy-1-(p-hydroxybenzyl)-4-methoxy-9,10-dihydrophenanthrene and 3(3-(3,4-Dihydroxybenzyl)-7-hydroxychroman-4-one as novel inhibitors of α-AE and α-GE. Notably, these compounds were initially discovered from Apis mellifera propolis in this study. The molecular dynamic analysis confirmed their stable binding with both enzymes over 100 ns simulations. The in vivo acute toxicity assay reveals AMPE as a practically non-toxic product with an LD50 value of 16,050 mg/kg. Therefore, this propolis may serve as a promising natural product for diabetes mellitus treatment.

Rapid screening of the novel bioactive peptides with notable α-glucosidase inhibitory activity by UF-LC-MS/MS combined with three-AI-tool from black beans

This work aimed to propose a rapid method to screen the bioactive peptides with anti-α-glucosidase activity instead of traditional multiple laborious purification and identification procedures. 242 peptides binding to α-glycosidase were quickly screened and identified by bio-affinity ultrafiltration combined with LC-MS/MS from the double enzymatic hydrolysate of black beans. Top three peptides with notable anti-α-glucosidase activity, NNNPFKF, RADLPGVK and FLKEAFGV were further rapidly screened and ranked by the three artificial intelligence tools (three-AI-tool) BIOPEP database, PeptideRanker and molecular docking from the 242 peptides. Their IC50 values were in order as 4.20 ± 0.11 mg/mL, 2.83 ± 0.03 mg/mL, 1.32 ± 0.09 mg/mL, which was opposite to AI ranking, for the hydrophobicity index of the peptides was not included in the screening criteria. According to the kinetics, FT-IR, CD and ITC analyses, the binding of the three peptides to α-glucosidase is a spontaneous and irreversible endothermic reaction that results from hydrogen bonds and hydrophobic interactions, which mainly changes the α-helix structure of α-glucosidase. The peptide-activity can be evaluated vividly by AFM in vitro. In vivo, the screened FLKEAFGV and RADLPGVK can lower blood sugar levels as effectively as acarbose, they are expected to be an alternative to synthetic drugs for the treatment of Type 2 diabetes.

Coumarin linked to 2-phenylbenzimidazole derivatives as potent α-glucosidase inhibitors

α-Glucosidase inhibitors have emerged as crucial agents in the management of type 2 diabetes mellitus. In the present study, a new series of coumarin-linked 2-phenylbenzimidazole derivatives 5a-m was designed, synthesized, and evaluated as anti-α-glucosidase agents. Among these derivatives, compound 5k (IC50 = 10.8 µM) exhibited a significant inhibitory activity in comparison to the positive control acarbose (IC50 = 750.0 µM). Through kinetic analysis, it was revealed that compound 5k exhibited a competitive inhibition pattern against α-glucosidase. To gain insights into the interactions between the title compounds and α-glucosidase molecular docking was employed. The obtained results highlighted crucial interactions that contribute to the inhibitory activities of the compounds against α-glucosidase. These derivatives show immense potential as promising starting points for developing novel α-glucosidase inhibitors.

Receptor-based pharmacophore modeling, molecular docking, synthesis and biological evaluation of novel VEGFR-2, FGFR-1, and BRAF multi-kinase inhibitors

A receptor-based pharmacophore model describing the binding features required for the multi-kinase inhibition of the target kinases (VEGFR-2, FGFR-1, and BRAF) were constructed and validated. It showed a good overall quality in discriminating between the active and the inactive in a compiled test set compounds with F1 score of 0.502 and Mathew's correlation coefficient of 0.513. It described the ligand binding to the hinge region Cys or Ala, the glutamate residue of the Glu-Lys αC helix conserved pair, the DFG motif Asp at the activation loop, and the allosteric back pocket next to the ATP binding site. Moreover, excluded volumes were used to define the steric extent of the binding sites. The application of the developed pharmacophore model in virtual screening of an in-house scaffold dataset resulted in the identification of a benzimidazole-based scaffold as a promising hit within the dataset. Compounds 8a-u were designed through structural optimization of the hit benzimidazole-based scaffold through (un)substituted aryl substitution on 2 and 5 positions of the benzimidazole ring. Molecular docking simulations and ADME properties predictions confirmed the promising characteristics of the designed compounds in terms of binding affinity and pharmacokinetic properties, respectively. The designed compounds 8a-u were synthesized, and they demonstrated moderate to potent VEGFR-2 inhibitory activity at 10 µM. Compound 8u exhibited a potent inhibitory activity against the target kinases (VEGFR-2, FGFR-1, and BRAF) with IC50 values of 0.93, 3.74, 0.25 µM, respectively. The benzimidazole derivatives 8a-u were all selected by the NCI (USA) to conduct their anti-proliferation screening. Compounds 8a and 8d resulted in a potent mean growth inhibition % (GI%) of 97.73% and 92.51%, respectively. Whereas compounds 8h, 8j, 8k, 8o, 8q, 8r, and 8u showed a mean GI% > 100% (lethal effect). The most potent compounds on the NCI panel of 60 different cancer cell lines were progressed further to NCI five-dose testing. The benzimidazole derivatives 8a, 8d, 8h, 8j, 8k, 8o, 8q, 8r and 8u exhibited potent anticancer activity on the tested cell lines reaching sub-micromolar range. Moreover, 8u was found to induce cell cycle arrest of MCF-7 cell line at the G2/M phase and accumulating cells at the sub-G1 phase as a result of cell apoptosis.

New 1,3,4-Thiadiazole Derivatives as α-Glucosidase Inhibitors: Design, Synthesis, DFT, ADME, and In Vitro Enzymatic Studies

Diabetes is an emerging disorder in the world and is caused due to the imbalance of insulin production as well as serious effects on the body. In search of a better treatment for diabetes, we designed a novel class of 1,3,4-thiadiazole-bearing Schiff base analogues and assessed them for the α-glucosidase enzyme. In the series (1-12), compounds are synthesized and 3 analogues showed excellent inhibitory activity against α-glucosidase enzymes in the range of IC50 values of 18.10 ± 0.20 to 1.10 ± 0.10 μM. In this series, analogues 4, 8, and 9 show remarkable inhibition profile IC50 2.20 ± 0.10, 1.10 ± 0.10, and 1.30 ± 0.10 μM by using acarbose as a standard, whose IC50 is 11.50 ± 0.30 μM. The structure of the synthesized compounds was confirmed through various spectroscopic techniques, such as NMR and HREI-MS. Additionally, molecular docking, pharmacokinetics, cytotoxic evaluation, and density functional theory study were performed to investigate their behavior.

Structure-based development of 3,5-dihydroxybenzoyl-hydrazineylidene as tyrosinase inhibitor; in vitro and in silico study

A series of new analogs of 3,5-dihydroxybenzoyl-hydrazineylidene conjugated to different methoxyphenyl triazole (11a-n) synthesized using click reaction. The structures of all synthesized compounds were characterized by FTIR, 1H, 13C-NMR spectroscopy, and CHO analysis. The tyrosinase inhibitory potential of the synthesized compounds was studied. The newly synthesized scaffolds were found to illustrate the variable degree of the inhibitory profile, and the most potent analog of this series was that one bearing 4-methoxyphenyl moiety, and exhibited an IC50 value of 55.39 ± 4.93 µM. The kinetic study of the most potent derivative reveals a competitive mode of inhibition. Next, molecular docking studies were performed to understand the potent inhibitor's binding mode within the enzyme's binding site. Molecular dynamics simulations were accomplished to further investigate the orientation and binding interaction over time and the stability of the 11m-tyrosinase complex.

Aryl-quinoline-4-carbonyl hydrazone bearing different 2-methoxyphenoxyacetamides as potent α-glucosidase inhibitors; molecular dynamics, kinetic and structure-activity relationship studies

Regarding the important role of α-glucosidase enzyme in the management of type 2 diabetes mellitus, the current study was established to design and synthesize aryl-quinoline-4-carbonyl hydrazone bearing different 2-methoxyphenoxyacetamide (11a-o) and the structure of all derivatives was confirmed through various techniques including IR, 1H-NMR, 13C-NMR and elemental analysis. Next, the α-glucosidase inhibitory potentials of all derivatives were evaluated, and all compounds displayed potent inhibition with IC50 values in the range of 26.0 ± 0.8-459.8 ± 1.5 µM as compared to acarbose used as control, except 11f and 11l. Additionally, in silico-induced fit docking and molecular dynamics studies were performed to further investigate the interaction, orientation, and conformation of the newly synthesized compounds over the active site of α-glucosidase.

Rapid identification of α-glucosidase inhibitors from Poria using spectrum-effect, component knock-out, and molecular docking technique

Instruction

Poria (Poria cocos) is known for its health-promoting effects and is consumed as a food due to its potential hypoglycemic activity. However, the composition of Poria is complex, and the bioactive compounds that inhibit α-glucosidase are not clear.

Methods

In this study, the fingerprint of the Poria methanol extract characterized by high-performance liquid chromatography (HPLC) and the model of the corresponding spectrum-effect relationship for α-glucosidase was first established to screen the active compounds from Poria. Then, the predicted bioactive compounds were knocked out and identified using mass spectrometry. Finally, the potential binding sites and main bonds of each compound with α-glucosidase were studied using molecular docking.

Results

The results have shown that at least 11 compounds from Poria could inhibit α-glucosidase effectively. Moreover, eight individual compounds, i.e., poricoic acid B (P8), dehydrotumulosic acid (P9), poricoic acid A (P10), polyporenic acid C (P12), 3- epidehydrotumulosic acid (P13), dehydropachymic acid (P14), 3-O-acetyl-16α-hydroxytrametenolic acid (P21), and pachymic acid (P22), were identified, and they exhibited effective inhibitory activity against α-glucosidase.

Discussion

The possible inhibitory mechanism of them based on molecular docking showed that the binding sites are mainly found in the rings A, B, and C of these compounds, and C-3 C-16 and side chains of C-17, with the phenylalanine, arginine, tyrosine, histidine, and valine of α-glucosidase. The main interactions among them might be alkyl and hydrogen bonds, which theoretically verified the inhibitory activity of these compounds on α-glucosidase. The achievements of this study provided useful references for discovering bioactive compounds with hypoglycemic effects from Poria.

Design, synthesis, biological evaluation, and docking study of chromone-based phenylhydrazone and benzoylhydrazone derivatives as antidiabetic agents targeting α-glucosidase

To develop novel α-glucosidase inhibitors, a series of chromone-based phenylhydrazone and benzoylhydrazone derivatives were designed, synthesized, and evaluated their inhibitory effects on α-glucosidase. The target compounds were characterized using ¹H NMR, ¹³C NMR, and high-resolution mass spectra. Some of the compounds showed a varying degree of α-glucosidase inhibitory activity with IC₅₀ values ranging from 6.59 ± 0.09 to 158.55 ± 0.87 μM. Among them, compound 5c (IC₅₀ = 6.59 ± 0.09 μM) was the most potent inhibitor by comparison with positive control acarbose (IC₅₀ = 685.11 ± 7.46 μM). Enzyme kinetic, fluorescence analysis, circular dichroism spectra, and molecular docking techniques were employed to explain the underlying molecular mechanisms of 5c inhibition on α-glucosidase. In vivo sucrose-loading test showed that 5c could suppress the rise of blood glucose levels after loading sucrose in normal Kunming mice. The cytotoxicity assay indicated that 5c exhibited low cytotoxicity.

Chromone-based benzohydrazide derivatives as potential α-glucosidase inhibitor: Synthesis, biological evaluation and molecular docking study

In order to find new α-glucosidase inhibitors with high efficiency and low toxicity, novel chromone-based benzohydrazide derivatives 6a-6s were synthesized and characterized through ¹H NMR, ¹³C NMR, and HRMS. All the new synthesized compounds were tested for inhibitory activities against α-glucosidase. Compounds 6a-6s with IC₅₀ values ranging from 4.51 ± 0.09 to 27.21 ± 0.83 μM, showed a potential α-glucosidase inhibitory activity as compared to the positive control (acarbose: IC₅₀ = 790.40 ± 0.91 μM). Compound 6i exhibited the highest α-glucosidase inhibitory activity with an IC₅₀ value of 4.51 ± 0.09 μM. Theinteractionbetween α-glucosidase and 6i was further confirmed by enzyme kinetic, fluorescence quenching, circular dichroism, and molecular docking study. In vivo experiment showed that 6i could suppress the rise of blood glucose levels after sucrose loading. The cytotoxicity result indicated that 6i exhibited low cytotoxicity in vitro.