Computational approaches to define poncirin from
            <i>Magnolia champaka</i>
            leaves as a novel multi-target inhibitor of SARS-CoV-2

Patil, Shashank M.; Phanindra, Bhaskar; Shirahatti, Prithvi S.; Martiz, Reshma Mary; Sajal, Harshit; Babakr, Abdullatif Taha; Ramu, Ramith

doi:10.1080/07391102.2023.2171137

Cited by 8 publications

(6 citation statements)

References 56 publications

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“…The hydrogen bonds were formed via ASN241, ARG439, ASP408, PRO309, HIS239, and HIS279 forming one hydrophobic bond of pi-sigma and the unfavorable acceptor-acceptor bonds were formed via THR307 and ASP349; see Figure 8. The results obtained in this study are in accordance with the previous studies by Patil et al [49] and Prabhakaran et al [98], with respect to the binding interactions of the ligands with the residues from the inhibitor binding site. Since hydroxycitric acid binds to the same inhibitor binding region reported in these studies and ligands reported in these studies show in vitro effect, hydroxycitric acid from our study is expected to be a potential inhibitor of α-glucosidase protein.…”

Section: Molecular Docking Studiessupporting

confidence: 93%

“…Prediction of the pharmacological activity was done using the PASS online server (http://www.way2drug.com/passonline/ (accessed on 7 January 2023). It evaluates the potential of the input compounds to elicit a specified pharmacological impact [49]. The collected data were computed and classified as "Pa" and "Pi," where "Pa" represents probable pharmacological activity and "Pi" represents probable pharmacological inactivity.…”

Section: Pass Pharmacological Analysismentioning

confidence: 99%

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Antidiabetic Activity of Potential Probiotics Limosilactobacillus spp., Levilactobacillus spp., and Lacticaseibacillus spp. Isolated from Fermented Sugarcane Juice: A Comprehensive In Vitro and In Silico Study

Huligere

Alotaibi

et al. 2023

Nutrients

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Probiotics are regarded as a potential source of functional foods for improving the microbiota in human gut. When consumed, these bacteria can control the metabolism of biomolecules, which has numerous positive effects on health. Our objective was to identify a probiotic putative Lactobacillus spp. from fermented sugarcane juice that can prevent α-glucosidase and α-amylase from hydrolyzing carbohydrates. Isolates from fermented sugarcane juice were subjected to biochemical, molecular characterization (16S rRNA) and assessed for probiotic traits. Cell-free supernatant (CS) and extract (CE) and also intact cells (IC) were examined for the inhibitory effect on α-glucosidase and α-amylase. CS of the strain showed the highest inhibition and was subjected to a liquid chromatography–mass spectrometry (LCMS) analysis to determine the organic acid profile. The in silico approach was employed to assess organic acid stability and comprehend enzyme inhibitors’ impact. Nine isolates were retained for further investigation based on the preliminary biochemical evaluation. Limosilactobacillus spp., Levilactobacillus spp., and Lacticaseibacillus spp. were identified based on similarity > 95% in homology search (NCBI database). The strains had a higher survival rate (>98%) than gastric and intestinal fluids, also a high capacity for adhesion (hydrophobicity > 56%; aggregation > 80%; HT-29 cells > 54%; buccal epithelial cells > 54%). The hemolytic assay indicated that the isolates could be considered safe. The isolates’ derivatives inhibited enzymes to varying degrees, with α-glucosidase inhibition ranging from 21 to 85% and α-amylase inhibition from 18 to 75%, respectively. The CS of RAMULAB54 was profiled for organic acid that showed the abundance of hydroxycitric acid, citric acid, and lactic acid indicating their role in the observed inhibitory effects. The in silico approach has led us to understand that hydroxycitric acid has the ability to inhibit both the enzymes (α-glucosidase and α-amylase) effectively. Inhibiting these enzymes helps moderate postprandial hyperglycemia and regulates blood glucose levels. Due to their promising antidiabetic potential, these isolates can be used to enhance intestinal health.

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Section: Molecular Docking Studiessupporting

confidence: 93%

Section: Pass Pharmacological Analysismentioning

confidence: 99%

Antidiabetic Activity of Potential Probiotics Limosilactobacillus spp., Levilactobacillus spp., and Lacticaseibacillus spp. Isolated from Fermented Sugarcane Juice: A Comprehensive In Vitro and In Silico Study

Huligere

Alotaibi

et al. 2023

Nutrients

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“…Simulation studies analyze the dynamic behavior of protein–ligand complexes in a solvated environment [ 51 , 52 ]. They measure the protein–ligand complex’s root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), ligand RMSD, hydrogen bonds, and variation of the secondary-structure pattern between the protein and their complexes [ 53 ]. The RMSD of the protein–ligand complex reflects its stability and indicates the presence of a ligand in the binding pocket.…”

Section: Resultsmentioning

confidence: 99%

“…G Binding : binding free energy; G Complex : total free energy of the protein–ligand complex; G Protein and G Ligand : total free energies of the isolated protein and ligand in a solvent, respectively; ΔG: standard free energy; ΔE MM : average molecular mechanics potential energy in a vacuum; G Solvation : solvation energy; ΔE: the total energy of bonded as well as nonbonded interactions; ΔS: change in the entropy of the system upon ligand binding; T: temperature in Kelvin [ 53 , 54 , 55 ].…”

Section: Methodsmentioning

confidence: 99%

Quinoline- and Isoindoline-Integrated Polycyclic Compounds as Antioxidant, and Antidiabetic Agents Targeting the Dual Inhibition of α-Glycosidase and α-Amylase Enzymes

Al-Ghorbani,

Alharbi,

Al-Odayni

et al. 2023

Pharmaceuticals

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Novel analogs of quinoline and isoindoline containing various heterocycles, such as tetrazole, triazole, pyrazole, and pyridine, were synthesized and characterized using FT-IR, NMR, and mass spectroscopy, and their antioxidant and antidiabetic activities were investigated. The previously synthesized compound 1 was utilized in conjugation with ketone-bearing tetrazole and isoindoline-1,3-dione to synthesize Schiff’s bases 2 and 3. Furthermore, hydrazide 1 was treated with aryledines to provide pyrazoles 4a–c. Compound 5 was obtained by treating 1 with potassium thiocyanate, which was then cyclized in a basic solution to afford triazole 6. On the other hand, pyridine derivatives 7a–d and 8a–d were synthesized using 2-(4-acetylphenyl)isoindoline-1,3-dione via a one-pot condensation reaction with aryl aldehydes and active methylene compounds. From the antioxidant and antidiabetic studies, compound 7d showed significant antioxidant activity with an EC50 = 0.65, 0.52, and 0.93 mM in the free radical scavenging assays (DPPH, ABTS, and superoxide anion radicals). It also displayed noteworthy inhibitory activity against both enzymes α-glycosidase (IC50: 0.07 mM) and α-amylase (0.21 mM) compared to acarbose (0.09 mM α-glycosidase and 0.25 mM for α-amylase), and higher than in the other compounds. During in silico assays, compound 7d exhibited favorable binding affinities towards both α-glycosidase (−10.9 kcal/mol) and α-amylase (−9.0 kcal/mol) compared to acarbose (−8.6 kcal/mol for α-glycosidase and −6.0 kcal/mol for α-amylase). The stability of 7d was demonstrated by molecular dynamics simulations and estimations of the binding free energy throughout the simulation session (100 ns).

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“…To understand the binding efficiency of hydroxy citric acid with the target protein, RMSF analysis was conducted. Furthermore, to know the possible change in the structure of the protein, during complex formation, Rg plot was analyzed (Maradesha et al, 2023 ; Patil et al, 2023 ). The SASA plot was evaluated to predict the conformational change in the binding region (Pradeep et al, 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Screening for potential novel probiotic Levilactobacillus brevis RAMULAB52 with antihyperglycemic property from fermented Carica papaya L.

Sreepathi,

Kumari,

Huligere

et al. 2023

Front. Microbiol.

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Probiotics are live microorganisms with various health benefits when consumed in appropriate amounts. Fermented foods are a rich source of these beneficial organisms. This study aimed to investigate the probiotic potential of lactic acid bacteria (LAB) isolated from fermented papaya (Carica papaya L.) through in vitro methods. The LAB strains were thoroughly characterized, considering their morphological, physiological, fermentative, biochemical, and molecular properties. The LAB strain's adherence and resistance to gastrointestinal conditions, as well as its antibacterial and antioxidant capabilities, were examined. Moreover, the strains were tested for susceptibility against specific antibiotics, and safety evaluations encompassed the hemolytic assay and DNase activity. The supernatant of the LAB isolate underwent organic acid profiling (LCMS). The primary objective of this study was to assess the inhibitory activity of α-amylase and α-glucosidase enzymes, both in vitro and in silico. Gram-positive strains that were catalase-negative and carbohydrate fermenting were selected for further analysis. The LAB isolate exhibited resistance to acid bile (0.3% and 1%), phenol (0.1% and 0.4%), and simulated gastrointestinal juice (pH 3–8). It demonstrated potent antibacterial and antioxidant abilities and resistance to kanamycin, vancomycin, and methicillin. The LAB strain showed autoaggregation (83%) and adhesion to chicken crop epithelial cells, buccal epithelial cells, and HT-29 cells. Safety assessments indicated no evidence of hemolysis or DNA degradation, confirming the safety of the LAB isolates. The isolate's identity was confirmed using the 16S rRNA sequence. The LAB strain Levilactobacillus brevis RAMULAB52, derived from fermented papaya, exhibited promising probiotic properties. Moreover, the isolate demonstrated significant inhibition of α-amylase (86.97%) and α-glucosidase (75.87%) enzymes. In silico studies uncovered that hydroxycitric acid, one of the organic acids derived from the isolate, interacted with crucial amino acid residues of the target enzymes. Specifically, hydroxycitric acid formed hydrogen bonds with key amino acid residues, such as GLU233 and ASP197 in α-amylase, and ASN241, ARG312, GLU304, SER308, HIS279, PRO309, and PHE311 in α-glucosidase. In conclusion, Levilactobacillus brevis RAMULAB52, isolated from fermented papaya, possesses promising probiotic properties and exhibits potential as an effective remedy for diabetes. Its resistance to gastrointestinal conditions, antibacterial and antioxidant abilities, adhesion to different cell types, and significant inhibition of target enzymes make it a valuable candidate for further research and potential application in the field of probiotics and diabetes management.

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Computational approaches to define poncirin from Magnolia champaka leaves as a novel multi-target inhibitor of SARS-CoV-2

Cited by 8 publications

References 56 publications

Antidiabetic Activity of Potential Probiotics Limosilactobacillus spp., Levilactobacillus spp., and Lacticaseibacillus spp. Isolated from Fermented Sugarcane Juice: A Comprehensive In Vitro and In Silico Study

Antidiabetic Activity of Potential Probiotics Limosilactobacillus spp., Levilactobacillus spp., and Lacticaseibacillus spp. Isolated from Fermented Sugarcane Juice: A Comprehensive In Vitro and In Silico Study

Quinoline- and Isoindoline-Integrated Polycyclic Compounds as Antioxidant, and Antidiabetic Agents Targeting the Dual Inhibition of α-Glycosidase and α-Amylase Enzymes

Screening for potential novel probiotic Levilactobacillus brevis RAMULAB52 with antihyperglycemic property from fermented Carica papaya L.

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