In Silico Anti-Inflammatory Activity Evaluation from Usnea misaminensis through Molecular Docking Approach

Al-Ghani, Ranggaweny; Nirwani, Wita Putri; Novianti, Tria Nurwina; Sari, Adani Ghina Puspita

doi:10.56425/cma.v1i3.40

Cited by 7 publications

(3 citation statements)

References 19 publications

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“…Prior to docking in AutoDock Vina 1.1.2, the ligand and target proteins were prepared using BIOVIA Discovery Studio 2021 molecular visualization software. The grid for each of the target proteins was adjusted separately using AutoDock Tools 1.5.7, and docking was performed using AutoDock Vina 1.1.2 ( Al-Ghani et al, 2022 ). Subsequently, the intermolecular interactions between β-cyclodextrin and amino acid residues in the binding pocket of each of the target protein were visualized using Discovery Studio 2021 molecular visualization software ( Kumar et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Preparation and investigation of a novel combination of Solanum nigrum-loaded, arabinoxylan-cross-linked β-cyclodextrin nanosponges for the treatment of cancer: in vitro, in vivo, and in silico evaluation

Shah,

Zaib,

Khan

et al. 2023

Front. Pharmacol.

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Introduction: Cancer contributes to a high mortality rate worldwide spanning its diversity from genetics to resistant therapeutic response. To date emerging strategies to combat and manage cancer are particularly focused on the development of targeted therapies as conventional treatments account for the destruction of normal cells as well. In this regard, medicinal plant-based therapies are quite promising in imposing minimal side effects; however, limitations like poor bioavailability and stability of bioactive phytochemicals are associated with them. In parallel, nanotechnology provides nominal solution to deliver particular therapeutic agent without compromising its stability.Methods: In this study, Solanum nigrum, an effective medicinal plant, loaded arabinoxylan cross-linked β-cyclodextrin nanosponges (SN-AXCDNS) were designed to evaluate antitumor activity against breast cancer. Therefore, SN-AXCDNS were prepared by using cross-linker melt method and characterized by physicochemical and pharmacological parameters.Results: Hydrodynamic size, zeta potential and entrapment efficiency (EE%) were estimated as 226 ± 4 nm, −29.15 ± 5.71 mV and 93%, respectively. Surface morphology of nanocomposites showed spherical, smooth, and porous form. Antitumor pharmacological characterization showed that SN loaded nanosponge demonstrated higher cytotoxicity (22.67 ± 6.11 μg/mL), by inducing DNA damage as compared to void SN extract. Flow cytometry analysis reported that encapsulated extract promoted cell cycle arrest at sub-G1 (9.51%). Moreover, in vivo analysis demonstrates the reduction in tumor weight and 85% survival chances in nanosponge treated mice featuring its effectiveness. In addition, in silico analysis revealed that β-cyclodextrin potentially inhibits MELK in breast cancer cell lines (B.E = −10.1 Kcal/mol).Conclusion: Therefore, findings of current study elucidated the therapeutic potential of β-cyclodextrin based nanosponges to be an alternative approach regarding the delivery and solubilization of antitumor drugs.

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Section: Methodsmentioning

confidence: 99%

Preparation and investigation of a novel combination of Solanum nigrum-loaded, arabinoxylan-cross-linked β-cyclodextrin nanosponges for the treatment of cancer: in vitro, in vivo, and in silico evaluation

Shah,

Zaib,

Khan

et al. 2023

Front. Pharmacol.

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“…AutoDock Vina (in UCSF [University of California, San Francisco] Chimera) [20] is one of the most right programs used in docking analysis. Molecular docking analysis was realized to estimate the binding locations, using AutoDock Vina in UCSF Chimera software (version 1.16) [21], and the crystal structure of target was provided from the protein data bank (https://www.rcsb.org) in the pdb format. The target protein contains human MATs (PDB ID: 5A19).…”

Section: Methodsmentioning

confidence: 99%

Quantum Chemical Computations, Molecular Docking, and ADMET Predictions of Cynarin

Çağlar Yavuz

2024

Bitlis Eren Üniversitesi Fen Bilimleri Dergisi

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Cynarin (1,3-o-dicaffeoylquinic acid) is one of the biologically active functional food components which is the most well-known caffeoylquinic acid derivative found in artichoke. The structural and electronic features of cynarin compound were investigated theoretically using density functional theory (DFT). The highest occupied molecular orbital (HOMO) and the least occupied molecular orbital (LUMO) are the most significant orbitals in molecules, these orbitals are quite helpful to know several molecular features such as the chemical reactivity, kinetic stability, electronegativity, chemical potential, electrophilicity index, chemical hardness and softness and electronegativity. Molecular orbital analysis HOMO-LUMO was used to explore the stability of the molecule. Moreover, physicochemical properties, drug-likeness, and toxicity estimation of the cynarin compound were appraised owing to ADMET (including absorption, distribution, metabolism, excretion, and toxicology). Molecular docking was carried out to examine the biological activity of the cynarin compound. 5A19, a liver cancer biomarker, is human methionine adenosyl-transferase enzymes. Cynarin-methionine adenosyl-transferase enzyme binding energy value was calculated as -7.9 kcal/mol. As a result, this in silico study confirmed that cynarin has the potential to be a drug by revealing its protective effect against liver diseases.

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“…In addition, the receptor proteins were given polar hydrogen atoms and Kollman charges before being stored in PDBQT format for docking. 35 …”

Section: Methodsmentioning

confidence: 99%

Computational Exploration of Berberis lycium Royle: A Hidden Treasure Trove for Antiviral Development

Mukhtar,

Khan,

Ibisanmi

et al. 2024

Bioinform Biol Insights

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Viral infections and associated illnesses account for approximately 3.5 million global fatalities and public health problems. Medicinal plants, with their wide therapeutic range and minimal side effects, have gained limelight particularly in response to growing concerns about drug resistance and sluggish development of antiviral drugs. This study computationally assessed 11 chemical compounds from Berberis lycium along with two antiviral drugs to inhibit SARS CoV 2 (coronavirus disease 2019 [COVID-19]) RNA-dependent RNA polymerase (RdRP), influenza virus RdRP, and two crucial dengue virus (DENV) enzymes (NS2B/NS3 protease and NS5 polymerase). Berberine and oxyberberine passed all pharmacokinetics analysis filters including Lipinski rule, blood-brain barrier permeant, and cytochrome suppression and demonstrated drug-likeness, bioavailability, and a non-toxic profile. Docking of phytochemicals from B lycium returned promising results with selected viral proteins, ie, DENV NS2BNS3 (punjabine –10.9 kcal/mol), DENV NS5 (punjabine –10.4 kcal/mol), COVID-19 RdRP (oxyacanthine –9.5 kcal/mol), and influenza RdRP (punjabine –10.4 kcal/mol). The optimal pharmacokinetics of berberine exhibited good binding energies with NS2BNS3 (–8.0 kcal/mol), NS5 (–8.3 kcal/mol), COVID RdRP (–7.7 kcal/mol), and influenza RdRP (–8.3 kcal/mol), while molecular dynamics simulation of a 50-ns time scale by GROMACS software package provided insights into the flexibility and stability of the complexes. A hidden treasure trove for antiviral research, berberine, berbamine, berbamunine, oxyberberine, oxyacanthine, baluchistanamine, and sindamine has showed encouraging findings as possible lead compounds. Pharmacological analyses provide credence for the proposed study; nevertheless, as the antiviral mechanisms of action of these phytochemicals are not well understood, additional research and clinical trials are required to demonstrate both their efficacy and toxicity through in vitro and in vivo studies.

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In Silico Anti-Inflammatory Activity Evaluation from Usnea misaminensis through Molecular Docking Approach

Cited by 7 publications

References 19 publications

Preparation and investigation of a novel combination of Solanum nigrum-loaded, arabinoxylan-cross-linked β-cyclodextrin nanosponges for the treatment of cancer: in vitro, in vivo, and in silico evaluation

Preparation and investigation of a novel combination of Solanum nigrum-loaded, arabinoxylan-cross-linked β-cyclodextrin nanosponges for the treatment of cancer: in vitro, in vivo, and in silico evaluation

Quantum Chemical Computations, Molecular Docking, and ADMET Predictions of Cynarin

Computational Exploration of Berberis lycium Royle: A Hidden Treasure Trove for Antiviral Development

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