IN SILICO AND IN VITRO ANTIDIABETIC ACTIVITY STUDIES ON THE ETHANOL EXTRACT OF DESMANTHUS VIRGATUS (L.) LEAVES

Increasing levels of angiogenic factors such as gamma interferon (Y-IF), tumor necrosis factor-beta (TNF-β), and transforming growth factor-beta (TGF-β) are thought to be the cause of the angiogenesis process in hemangiomas. Endophytic fungi are potential in searching for new drug sources due to their antimicrobial, antifungal, and anticancer compounds. This study aimed to determine the potential and interactions of endophytic fungi as candidates for vascular endothelial growth factor receptor-2 (VEGFR-2) angiogenesis hemangiomas and apply Lipinski's rule of five to differentiate drug-like and non-drug-like molecules and in-line toxicity using in silico test. The research method was molecular docking using several programs, namely Autodock Vina (PyRx), PyMol, and Discovery Studio 2019, and tethering five ligands from the endophytic fungus Trichoderma sp. and Aspergillus sp. with 2 VEGFR-2 target proteins (protein codes were 3VHE and 1Y6A). The best binding affinity of the ligands was tested by Lipinski's rule of five and toxicity test using Toxtree. The results showed that benzyl benzoate is potentially an antiangiogenesis inhibitor for VEGFR-2 protein based on its binding affinity value, which is close to the control ligand value of -8.7 kcal/mol (3VHE) and -7.4 kcal/mol (1Y6A). Therefore, benzyl benzoate, chloromycetin, and 1-hexyl-3-nitrobenzene compounds comply with Lipinski's rule of five. Based on the results of the toxicity test and the parameters of the Kroes TTC decision tree, benzyl benzoate and chloromycetin are categorized as safe compounds for consumption.
 
 Keywords: angiogenesis, benzyl benzoate, endophytic fungi, molecular docking, VEGFR-2

Diabetes is a metabolic syndrome disease characterized by hyperglycemia in patients. The use of medicinal plants for the treatment of diabetes can control blood levels because it contains anti-diabetic active substances. The medicinal plant as an anti-diabetic through inhibition of the α-glucosidase enzyme thereby reducing the absorption of glucose in the small intestine. Lunacridine, skimmianine and scopoletin are found in the Rutaceae family but there is no information about them as α-glucosidase inhibitors. The purpose of the study to determine the ability of lunacridine, skimmianine and scopoletin as inhibitors of α-glucosidase enzymes based on docking molecular studies. The research method is ligand and receptor preparation using Pymol and docking. The docking process uses Autodoct vina in Pyrx and using acarbose as controls. The docking results are visualized using Ligplot and Discovery studio software. The results showed that lunacridine, skimmianine, scopoletin interacted with α-glucosidase and various binding affinity value. The lunacridine binding affinity is close to the acarbose control and can cross cell membranes based on Lipinski rules. Lunacridine has an anti-diabetic ability through inhibition of α-glucosidase enzyme with the inhibitory value close to acarbose control.

This study aims to evaluate the potential of Moringa oleifera secondary metabolites as inhibitors of the α-glucosidase enzyme using an in silico approach. The study employed molecular docking methods. The structure of the α-glucosidase enzyme was obtained from the Protein Data Bank (PDB ID: 3TOP), while the structures of Moringa oleifera secondary metabolites were sourced from the literature. Docking simulations were conducted using AutoDock Vina, and interaction results were analyzed using Discovery Studio. The analyzed parameters included binding affinity values and the interactions between ligands and active site residues of the enzyme. The results showed that several secondary metabolites of Moringa oleifera, such as lutein and 4-(α-L-rhamnopyranosyloxy)benzyl glucosinolate, exhibited strong binding affinity values: -10.93 kcal/mol for lutein and -10.27 kcal/mol for 4-(α-L-rhamnopyranosyloxy)benzyl glucosinolate. Benzyl glucosinolate enhanced the stability of the ligand-protein complex, demonstrating its potential as a more effective α-glucosidase inhibitor compared to acarbose, the currently used antidiabetic drug. Based on molecular docking analysis, the secondary metabolites of Moringa oleifera indicate great potential for further development as antidiabetic agents.

Rabies is a deadly viral disease that has no effective therapy after clinical symptoms appear. This study aims to evaluate the antirabies potential of the dominant compounds in the ethyl acetate extract of Desmanthus virgatus leaves, as well as several antiviral drugs, through an in silico approach. The extract was obtained through maceration and partitioning methods using ethyl acetate solvent, then analyzed using LC-MS, which identified 182 secondary metabolite compounds, and ten dominant compounds were selected for further analysis. These compounds, along with seven antiviral drugs, were docked against the rabies virus glycoprotein (PDB ID: 6LGX) using AutoDockTools 4.2.6 software. The docking results were analyzed based on the values of binding affinity, inhibition constant (Ki), and interaction with active amino acid residues. Quercitrin and quercimeritrin were the dominant flavonoid glycosides in the ethyl acetate extract of D. virgatus leaves that showed binding affinity values of -8.45 kcal/mol and -8.10 kcal/mol, respectively. In addition, bictegravir and tegobuvir showed binding affinity values of -9.17 kcal/mol and -9.05 kcal/mol, respectively. Four compounds indicated potential as antirabies drugs. Pharmacokinetic feasibility tests using Lipinski parameters showed that most of the dominant compounds violated one or more parameters, especially the number of hydrogen bond donors/acceptors and molecular weight. However, such violations were also found in some antiviral drugs that have been used, such as remdesivir and darunavir. These results suggest that D. virgatus leaf extracts contain compounds with promising potential antirabies activity and deserve further investigation through in vitro and in vivo tests.

This research explores the multifaceted pharmacological actions of essential oils and its constituents, derived as secondary metabolites from aromatic plants, with a particular focus on their potent wound healing and antibacterial activities, elucidating their significance in therapeutic approach towards infected wounds. An in silico screening was carried out to identify the interaction between the bioactive essential oil contituents (EOC) such as cinnamaldehyde, citral, geraniol, linalool, and p-cymene, docked against various target proteins associated with antibiotic resistance and wound healing, including mec A (PDB ID- 4DK1), nor A (PDB ID- 7LO8), TGF- β1 (PDB ID- 1PY5), TGF- β2 (PDB ID- 1M9Z), VEGF (PDB ID-3QTK), GSK-3β (PDB ID-1Q5K) and MMP-9 (PDB ID-5UE4). The docking was done with AutoDock V 4.0 using five EOCs against seven receptors and the binding energy was gaged. The binding energy of EOCs were observed to be ranging from -5.3 kcal/mol to -2.55 kcal/mol. Notably, all the screened EOCs exhibited favourable binding affinity with GSK-3β, indicating their potential role in the inflammatory phase of wound healing. Additionally, towards antibiotic resistance, all EOC displayed adequate binding affinity with norA, suggesting their potential in modulating multidrug resistant efflux pumps. Compliance with Lipinski's rule, positions these EOC as promising candidates for drug development, particularly in the context of wound healing and antibiotic resistance. This study holds the promise of contributing novel insights to the field of wound care and combating antibiotic resistance, paving the way for innovative approaches in addressing the challenges posed by multi-drug resistant Staphylococcus aureus (MDRSA) infected wounds.

Nyale (Annelida, Eunicida, Eunicidae) is a typical sea worm of Kuta-Mandalika beach, Central Lombok, Indonesia. Diabetes mellitus is a chronic disease characterized by high blood sugar levels (glucose). Diabetes occurs because the body cannot produce enough insulin or cannot use insulin effectively. The α-glucosidase enzyme is a potential target in managing diabetes mellitus, particularly type 2 diabetes. This enzyme plays a role in the breakdown of complex carbohydrates into simple sugars in the small intestine. These sugars are then absorbed into the bloodstream and then blood sugar levels are raised. By targeting the α-glucosidase enzyme through the use of α-glucosidase inhibitors, the rate of carbohydrate breakdown and absorption can be slowed down. This mechanism needs to be explored using an in silico approach with the molecular docking method to see the potential of compounds contained in Nyale to inhibit the α-glucosidase enzyme. Compounds contained in Nyale were determined using the gas chromatography-mass spectrometry (GC-MS) method. Molecular docking in this study used Pyrx 0.8 software. Three compounds have the potential to be α-glucosidase enzyme inhibitors, namely tricyclo[10.2.1.02,11] pentadic-4,8-diene, myristic acid, tricyclo[8.6.0.02,9] hexadecane-3,15-diene where the binding affinity value of the three compounds is lower than the innate ligand of α-glucosidase enzyme α-D-glucopyranose. Lower binding affinity values indicate relatively greater stability and mechanism of α-glucosidase enzyme inhibition.

Abstract. Puspa VR, Zumaidar, Nurdin, Fitmawati. 2024. Phytochemical, antioxidant, and in-silico studies of Erigeron sumatrensis from Gayo Highlands as a potential inhibitor of type-2 diabetes mellitus. Biodiversitas 25: 3179-3192. Erigeron sumatrensis Retz., a wild medicinal herb, was determined qualitatively and quantitatively for its leaf extract's phytochemical constituents and antioxidant capacity and to conduct computational studies. Secondary metabolites identified included flavonoids, phenolics, terpenoids, steroids, and alkaloids. The methanol fraction exhibited the greatest TPC (5945.45 mg GAE/g). Antioxidant activity, as determined by the ABTS assay, indicated a significant radical scavenging activity in the methanol fraction of E. sumatrensis leaves, with an IC50 value of 57.67 ?g/mL. In silico molecular docking revealed that cucurbitacin b, 25-desacetoxy-?-sitosterol, and ?-amyrin exhibited potential as ?-glucosidase inhibitors (PDB ID: 2QMJ). The same compounds demonstrated inhibitory properties against ?-amylase (PDB ID: 2QV4), with acarbose as a positive control with a binding energy of -7.8 kcal/mol. The ADMET profiles indicated compliance with Lipinski's rule of five for all compounds, suggesting their suitability as an orally administered drug. Based on these findings, E. sumatrensis has excellent potential as a source of raw materials for antidiabetic drug formulation, so it needs to be further investigated for pharmaceutical applications.

Breast cancer is among the diseases with the highest mortality rate in women in the world. The triple negative cancer subtype with aggressiveness and metastatic ability causes the sufferer to be difficult to treat. Targeted treatment efforts of natural ingredients such as limonene and its derivatives are more profitable due to their easy excretion process. Screening the activity of compounds through docking specifically provides convenience in the synthesis process in the laboratory. Limonene compounds and their derivatives will be interpreted against the enzymes MMP-2 (PDB ID: 3AYU), MMP-9 (PDB ID: 4H1Q) and Cyclin A2 (PDB ID: 2V22) involved in the cellular function of triple-negative breast cancer using PyRx 9.0 software. The docking results showed that the limonelyl salicylate compound provided the best binding affinity value against the enzymes MMP-2, MMP-9, and Cyclin A2 with successive values of -7.7, -8.8, and -6.7 kcal/mol.

Antioxidant activity and in-silico evaluation of natural compounds of Carissa carandas as potential inhibitors of Gamma-Glutamyl Transpeptidase to enhance the efficacy of chemotherapy drugs against prostate cancer.

Polyoxins A-M, which belong to the class of peptidyl-pyrimidine nucleoside antibiotics, are produced by Streptomyces cacaoi var. asoensis. Polyoxins, except C and I, are active against various phytopathogenic fungi. Polyoxins A, B and D are shown to inhibit selectively the incorporation of 14C-glucosamine into cell wall chitin by washed mycelia of Alternaria kikuchiana, Cochliobolus miyabeanus and Pyricularia oryzae at levels which are comparable to their minimal inhibitory concentrations for the fungal frowth. At the same time, each active polyoxin causes an unusually increased accumulation of UDP-14C-N-acetylglucosamine (UDP-GlcNAc). Polyoxins A-M, except C and I, markedly inhibit chitin synthetase preparation from P. oryzae in competition with the substrate, UDP-GlcNAc. Michaelis constant, Km, for UDP-GlcNAc is 3.3×10-3M and inhibitor constant, Ki, for the active polyoxins is found to be in the range of 3.3×10-5-3.4×10-6M. At higher concentrations such as 3mM, polyoxin C also competitively inhibits the enzyme, and the Ki is close to the Km. It is concluded that polyoxins selectively inhibit the synthesis of cell wall chitin and that the primary effect is the competitive inhibition of chitin synthetase. To correlate the polyoxin structure to the enzyme inhibition, the values of binding affinity, -ΔGbind*, for polyoxins and various N-aminoacyl derivatives of polyoxin C are calculated from the Ki values, and the values of partial binding affinity, -Δg*, for structural moieties which constitute the polyoxin J molecule are estimated from the -ΔGbind values. The results indicate that the carbamoylpolyoxamic acid moiety of polyoxins serves to stabilize the complexing of polyoxin with the enzyme. The same kinetic study using nucleosides, nucleotides and nucleotide sugars suggests the presence of a specific binding site on the enzyme for the uridine moiety of UDP-GlcNAc, where the pyrimidine nucleoside moiety of polyoxins also binds. From the pKi-pH plots for the derivatives of polyoxin C and other polyoxins, it is found that the ionized amino group at C-2″ position plays a very important role for the binding of polyoxins to chitin synthetase.* -ΔG=-RTlnKi-ΔGbind=-ΔG+2.4-ΔGbind=-(Δg′+Δg″+Δg′′′+…+Δgn) (kcal/mol, 25°C)

As a part of studies on the mechanism of action of antibiotics polyoxins, effects of various N-aminoacyl derivatives of polyoxin C and other polyoxins on chitin-UDP acetylglucosaminyl-transferase (EC 2.4.1.16, chitin synthetase) prepared from phytopathogenic fungus Piricularia oryzae were investigated. It was found that they inhibited the enzyme in competition with the substrate UDP-N-acetylglucosamine, Inhibitor constants, Ki, for these polyoxins were determined and the values of binding affinity, −ΔGbind of the inhibitors to the enzyme were calculated from the Ki values. In addition, by using these −ΔGbind values the values of partial binding affinity, −Δg for the several atoms and atomic groups or the several moieties contained in the polyoxin J molecule were estimated. From the results obtained, it was concluded that the carbamoylpolyoxamic acid moiety of polyoxins helps to stabilize the polyoxin-enzyme complex through the contributions of its oxygen atom at C−1″, amino group at C−2″, hydroxyl groups at C−3″ and C−4″, aliphatic carbon chain and terminal carbamoyloxy group. The results obtained by the kinetic investigation using various nucleotides and nucleotide sugars suggested that there was a specific binding site on the enzyme corresponding to the uridine moiety of UDP-N-acetylglucosamine, and that the pyrimidine nucleoside moiety of polyoxins was also bound to this site.

As a part of studies on the mechanism of action of antibiotics polyoxins, effects of various N-aminoacyl derivatives of polyoxin C and other polyoxins on chitin-UDP acetylglucosaminyl-transferase (EC 2.4.1.16, chitin synthetase) prepared from phytopathogenic fungus Piricularia oryzae were investigated. It was found that they inhibited the enzyme in competition with the substrate UDP-N-acetylglucosamine, Inhibitor constants, Ki, for these polyoxins were determined and the values of binding affinity, −ΔGbind of the inhibitors to the enzyme were calculated from the Ki values. In addition, by using these −ΔGbind values the values of partial binding affinity, −Δg for the several atoms and atomic groups or the several moieties contained in the polyoxin J molecule were estimated. From the results obtained, it was concluded that the carbamoylpolyoxamic acid moiety of polyoxins helps to stabilize the polyoxin-enzyme complex through the contributions of its oxygen atom at C−1″, amino group at C−2″, hydroxyl groups at C−3″ and C−4″, aliphatic carbon chain and terminal carbamoyloxy group. The results obtained by the kinetic investigation using various nucleotides and nucleotide sugars suggested that there was a specific binding site on the enzyme corresponding to the uridine moiety of UDP-N-acetylglucosamine, and that the pyrimidine nucleoside moiety of polyoxins was also bound to this site.

Objective: This study was designed to search for candidate drugs that act on IL-33 and ST2, which was carried out using a bioinformatics approach. Methods: We first analyzed Network Electronic Cigarette Smokes Predictions of therapeutic targets by Cytoscape. We collected from the Swiss TargetPrediction database [http://www. swisstargetprediction. ch/] by inputting each compound structure of the electronic cigarette smoke in SDF format. The target protein data is then supplemented with UniProt ID data to uniform protein identity. We then identified COPD Related Targets in Humans by Cytoscape. Subsequently, we identified key receptors in the pathogenesis of COPD. All target proteins that have a significant role in the pathogenesis of COPD exposed to cigarette smoke will be known from the combination of this network. Results: Based on the validation results of the protein receptor for ST2, a protein is used as a receptor with PDB ID: 1IRA. After analyzed by PyMol software, a protein with PDB ID 1IRA it has no missing residue in its sequenceDrug candidates analyzed by the structural similarity with the native ligand using PubChem and DRUGBANK analysis are follow: N-acetylmannosamine, Aceneuramic acid, Ceramide AP, Ceramide NP, Hg9a-9, Nonanoyl-N-hydroxyethylglucamide, N-Acetyl-2-deoxy-2-amino-galactose, N-Acetyllactosamine, MLi/2,6-dimethyl-4-[6-[5-[1-methylcyclopropyl] oxy-1H-indazol-3-yl] pyrimidin-4-yl] morpholine, Terazosin, BMS-911543, NAG Inhibitor, FGFR Inhibitor/sodium; 2-amino-5-[1-methoxy-2-methylindolizine-3-carbonyl] benzoate. After docking, the smallest or more negative binding affinity values are obtained. The stronger the FGFR Inhibitor ligand showed the interaction with the Receptor with a binding affinity value of-9.0 kcal/mol with mode/position 0, and RMSD 0.0. The second smallest binding affinity value is the NAG ligand with a-8.5 kcal/mol with mode/position 0 and RMSD 0.0. Conclusion: The findings revealed that FGFR Inhibitor was a suitable repurposing medication for anti-COPD development via the IL-33/ST-2 signaling pathway.

Introduction: In most ancient cultures, honey has been used for both nutritional and medical purposes. Objectives: In this research, phenolic extracts of four Iranian honeys were evaluated to determine the antioxidant potentials using DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging, nitric oxide (NO) radical scavenging and reducing power by ferric reducing activity of plasma (FRAP) method. Additionally, anti-diabetic properties of honey and phenolic extracts were evaluated by determination of α-amylase and α-glucosidase inhibition. Patients and Methods: Besides, reducing potential was evaluated by ferric-reducing antioxidant power method. Moreover, determination of phenolic and flavonoid contents was performed. Moreover, inhibition of α-amylase and α-glucosidase of honey and phenolic extracts were evaluated. Results: With considering to antioxidant potentials, Gavan (Astragalus) sample showed the greatest phenolic (3817±1.52 mg GAE/100 g), flavonoid contents (3.1±0.005 mg QE/100 g), and DPPH radical scavenging (IC50 = 2±0.003 mg/mL). Bahareh honey had the highest NO radical scavenging (IC50=0.0403±0.0009 mg/mL) and Meymand honey possessed the highest reducing potential by FRAP method (IC50=0.0018±0.000003 mg/mL). The maximum inhibition of α-glucosidase was shown in Meymand honey extract (46±0.1%). After sugar isolation, Zataria honey had the highest inhibition of α-glucosidase (54±0.6%) and the mode of α-amylase inhibition was noncompetitive by this honey. Whole extract (23±0.1%) and phenolic extract of Gavan honey presented the maximum inhibition of α-amylase (31.2±0.1%). Conclusion: Honey samples showed antioxidant potentials and anti-diabetic properties by retardation of α-amylase and α-glucosidase.

Pneumonia is one of the respiratory infections caused by Streptococcus pneumoniae. Bacterial resistance problems regarding the treatment of pneumonia can be overcome by exploring active compounds in plants that have potential as antibacterials, one of which is water guava (Syzygium samarangense). This study aims to discover active compounds with the antibacterial potential of S. pneumoniae from water guava leaves (S. samarangense). This study was conducted in September 2022 at Universitas Negeri Surabaya with in silico method (blind molecular docking). The method used in this study was in silico approach, including the collection of proteins and compounds, preparation of proteins and ligands, minimization of compounds, blind molecular docking, and visualization of the results of molecular docking. The results showed that the value of binding affinity and RMSD of PBP-2X protein (PDB ID: 1QME) which binds to 1-methyl ethyl acetate, valeraldehyde, and dibutyl phthalate was -5.6 KJ/mol and 2.575 Å, -5 KJ/mol and 1.373 Å, and -6.7 KJ/mol and 1.637 Å, respectively. The result indicates that the selected compounds have the potential as antibacterial to S. pneumoniae. In the near future, this study requires further in vitro and in vivo testing as a step to validate the activity of the active compound of guava leaves as an antibacterial of S. pneumoniae.