Investigates interaction between abscisic acid and bovine serum albumin using various spectroscopic and in-silico techniques

Bhimaneni, Sai Priyanka; Bhati, Vipin; Bhosale, Shailesh; Kumar, Anoop

doi:10.1016/j.molstruc.2020.129018

Cited by 16 publications

(5 citation statements)

References 30 publications

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“…Consequently, the interaction force between luteoloside and XO can be determined by thermodynamic parameters 45 . And these parameters of luteoloside and XO were calculated by the following equations 46

\ln K_{b} = - \frac{{ΔH}^{°}}{italicRT} + \frac{{ΔS}^{°}}{R},

{italicΔG}^{°} = - RT \ln K_{b},

where K b is the binding constant, R is the gas constant, whose value is 8.314 J mol −1 K −1 .…”

Section: Resultsmentioning

confidence: 99%

Study on the interaction mechanism between luteoloside and xanthine oxidase by multi‐spectroscopic and molecular docking methods

Chen

Wang

Pan

et al. 2022

J of Molecular Recognition

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Gout is an inflammatory joint disease caused by urate crystal deposition, which is associated with hyperuricemia. Gout will take place when the uric acid accumulates. Xanthine oxidase (XO) is a crucial enzyme in the formation of uric acid. Inhibiting XO is one of the means to ameliorate gout. Luteoloside is a kind of natural flavonoid, which has an excellent prospect for relieving gout. But there are few reports on the interaction mechanism between luteoloside and XO currently. In this study, the interaction mechanism between luteoloside and XO was explored using spectroscopy and molecular docking. The fluorescence spectroscopy results indicated that luteoloside could make the intrinsic fluorescence of XO quenched, and the binding constant between luteoloside and XO was (1.85 ± 0.22) × 103 L mol−1 at 298 K. The synchronous fluorescence spectroscopy results showed that the absorption peaks of Tyr and Trp shifted blue, and the hydrophobicity of the microenvironment increased. Moreover, CD spectra showed that α‐helix of XO decreased, β‐sheet and β‐turn increased after adding luteoloside. The results of molecular docking analysis showed that XO could combine with luteoloside through hydrogen bonds and hydrophobic force. The results indicated that luteoloside could remarkably interact with XO. Insights into the interaction mechanism provide a necessary basis for the search for low‐toxic natural products as targets of XO. Highlights Luteoloside and xanthine oxidase was a strong binding mode and had only one binding site. Luteoloside could cause α‐helix reduced, β‐sheet and β‐turn increased, and change the secondary structure of XO. The binding between luteoloside and xanthine oxidase was a spontaneous process. The main binding force was hydrophobic force between luteoloside and xanthine oxidase.

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\ln K_{b} = - \frac{{ΔH}^{°}}{italicRT} + \frac{{ΔS}^{°}}{R},

{italicΔG}^{°} = - RT \ln K_{b},

where K b is the binding constant, R is the gas constant, whose value is 8.314 J mol −1 K −1 .…”

Section: Resultsmentioning

confidence: 99%

Study on the interaction mechanism between luteoloside and xanthine oxidase by multi‐spectroscopic and molecular docking methods

Chen

Wang

Pan

et al. 2022

J of Molecular Recognition

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“…The molecular docking investigation was conducted using the PyRx-v0.8 virtual screening software, which featured AutoDock Vina with the Lamarckian genetic algorithm [ 86 , 87 , 88 , 89 ]. The active sites for the target proteins, 4CGS (Tyr102, Gly15, Arg140, Lys46, Lys16, Tyr14, Tyr58, Lys89, Asn101, Gly110, Gln60, Ser95, Phe85, Asp97, Asp107, Phe340, Tyr106, Gln339), 4CGP (Tyr294, Arg42, Leu291, Asn316, Tyr32, Arg82, Glu117, Val326, Gly119, Ala123, Arg132, Tyr124, Pro239, Arg167, Ile240, Asp121, Asp113, Val292, Phe118, Gly120, Asn293, Thr241, Ile318, Gly327), and 4CGQ (Leu115, Leu83, Tyr106, Asp107, Gly110, Tyr111, Met114, Arg140, Asn152, Ser177, Ser179, Glu181, Lys16, Val188, Lys219, Gln262, Asp113, Tyr102, Pro116, Arg270, Arg82, Thr300, Glu62, Tyr302) were identified through an extensive literature review [ 84 , 90 ] and were used in the docking approach.…”

Section: Methodsmentioning

confidence: 99%

Isolation, Identification, and Antibacterial Properties of Prodigiosin, a Bioactive Product Produced by a New Serratia marcescens JSSCPM1 Strain: Exploring the Biosynthetic Gene Clusters of Serratia Species for Biological Applications

Arivuselvam,

Dera,

Parween Ali

et al. 2023

Antibiotics

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Prodigiosin pigment has high medicinal value, so exploring this compound is a top priority. This report presents a prodigiosin bioactive compound isolated from Serratia marcescens JSSCPM1, a new strain. The purification process of this compound involves the application of different chromatographic methods, including UV-visible spectroscopy, high-performance liquid chromatography (HPLC), and liquid chromatography–mass spectrometry (LC/MS). Subsequent analysis was performed using nuclear magnetic resonance (NMR) to achieve a deeper understanding of the compound’s structure. Finally, through a comprehensive review of the existing literature, the structural composition of the isolated bioactive compound was found to correspond to that of the well-known compound prodigiosin. The isolated prodigiosin compound was screened for antibacterial activity against both Gram-positive and Gram-negative bacteria. The compound inhibited the growth of Gram-negative bacterial strains compared with Gram-positive bacterial strains. It showed a maximum minimum inhibitory concentration against Escherichia coli NCIM 2065 at a 15.9 ± 0.31 μg/mL concentration. The potential binding capabilities between prodigiosin and the OmpF porin proteins (4GCS, 4GCP, and 4GCQ) were determined using in silico studies, which are generally the primary targets of different antibiotics. Comparative molecular docking analysis indicated that prodigiosin exhibits a good binding affinity toward these selected drug targets.

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“…The molecular docking analysis was performed using the PyRx-v0.8 virtual screening tool coupled with AutoDock-Vina, employing the Lamarckian genetic algorithm [ 27–30 ]. All the 13 ligands were individually docked with the selected target enzymes as separate docking runs.…”

Section: Methodsmentioning

confidence: 99%

Concatenation of molecular docking and molecular simulation of BACE-1, γ-secretase targeted ligands: in pursuit of Alzheimer’s treatment

et al. 2021

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Introduction Alzheimer's disease (AD), the most predominant cause of dementia, has evolved tremendously with an escalating frequency, mainly affecting the elderly population. An effective means of delaying, preventing, or treating AD is yet to be achieved. The failure rate of dementia drug trials has been relatively higher than in other disease-related clinical trials. Hence, multi-targeted therapeutic approaches are gaining attention in pharmacological developments. Aims As an extension of our earlier reports, we have performed docking and molecular dynamic (MD) simulation studies for the same 13 potential ligands against beta-site APP cleaving enzyme 1 (BACE-1) and γ-secretase as a therapeutic target for AD. The In-silico screening of these ligands as potential inhibitors of BACE-1 and γ- secretase was performed using AutoDock enabled PyRx v-0.8. The protein-ligand interactions were analyzed in Discovery Studio 2020 (BIOVIA). The stability of the most promising ligand against BACE-1 and γ- secretase was evaluated by MD simulation using Desmond-2018 (Schrodinger, LLC, NY, USA). Results The computational screening revealed that the docking energy values for each of the ligands against both the target enzymes were in the range of −7.0 to −10.1 kcal/mol. Among the 13 ligands, 8 (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed binding energies of ≤−8 kcal/mol against BACE-1 and γ-secretase. For the selected enzyme targets, BACE-1 and γ-secretase, 6Z5 displayed the lowest binding energy of −10.1 and −9.8 kcal/mol, respectively. The MD simulation study confirmed the stability of BACE-6Z5 and γ-secretase-6Z5 complexes and highlighted the formation of a stable complex between 6Z5 and target enzymes. Conclusion The virtual screening, molecular docking, and molecular dynamics simulation studies revealed the potential of these multi-enzyme targeted ligands. Among the studied ligands, 6Z5 seems to have the best binding potential and forms a stable complex with BACE-1 and γ-secretase. We recommend the synthesis of 6Z5 for future in-vitro and in-vivo studies.

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Investigates interaction between abscisic acid and bovine serum albumin using various spectroscopic and in-silico techniques

Cited by 16 publications

References 30 publications

Study on the interaction mechanism between luteoloside and xanthine oxidase by multi‐spectroscopic and molecular docking methods

Study on the interaction mechanism between luteoloside and xanthine oxidase by multi‐spectroscopic and molecular docking methods

Isolation, Identification, and Antibacterial Properties of Prodigiosin, a Bioactive Product Produced by a New Serratia marcescens JSSCPM1 Strain: Exploring the Biosynthetic Gene Clusters of Serratia Species for Biological Applications

Concatenation of molecular docking and molecular simulation of BACE-1, γ-secretase targeted ligands: in pursuit of Alzheimer’s treatment

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