Molecular Docking in Formulation and Development

Kaur, Tejinder; Madgulkar, Ashwini; Bhalekar, Mangesh R.; Asgaonkar, Kalyani

doi:10.2174/1570163815666180219112421

Cited by 78 publications

(48 citation statements)

References 16 publications

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“…We also exploit a docking assay to reveal more details about the apoptotic activity of C. albicans. Docking assay has recently been considered as a valuable technique to elucidate the interaction between receptor and ligand [36][37][38] . It is well known that the Bcl-2 family members are critical targets for apoptotic and anti-apoptotic agents 39,40 .…”

Section: Discussionmentioning

confidence: 99%

Partridge and embryonated partridge egg as new preclinical models for candidiasis

Tavakkoli

Khosravi

Sharifi

et al. 2021

Sci Rep

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Candida albicans (C. albicans) is the most common cause of candidiasis in humans and animals. This study was established to a new experimental infection model for systemic candidiasis using partridge and embryonated partridge egg. First, we tested the induction of systemic candidiasis in partridge and embryonated partridge egg. Finally, interaction between virulence factors of C. albicans and Bcl-2 family members was predicted. We observed that embryonic infection causes a decrease in survival time and at later embryonic days (11–12th), embryos showed lesions. Morphometric analysis of the extra-embryonic membrane (EEM) vasculature showed that vascular apoptotic effect of C. albicans was revealed by a significant reduction in capillary area. In immunohistochemistry assay, low expression of Bcl-2 and increased expression of Bax confirmed apoptosis. The gene expression of Bax and Bcl-2 was also altered in fungi-exposed EEM. Ourin silico simulation has shown an accurate interaction between aspartic proteinase, polyamine oxidase, Bcl-2 and BAX. We observed that the disease was associated with adverse consequences, which were similar to human candidiasis. Acquired results support the idea that partridge and embryonated partridge egg can be utilized as appropriate preclinical models to investigate the pathological effects of candidiasis.

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Section: Discussionmentioning

confidence: 99%

Partridge and embryonated partridge egg as new preclinical models for candidiasis

Tavakkoli

Khosravi

Sharifi

et al. 2021

Sci Rep

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show abstract

“…These information were used to generate the grid boxes during molecular docking. Molecular docking is a method that foretells preferred placement of a compound bound to another one (like protein) during the formation of a stable complex and finds its frequent application in in silico pharmaceutical drug design [19]. Current approaches of docking involve pose prediction, employing docking algorithms and energy-based scoring that identify the best binding mode of a drug to the active site of a desired protein, i.e.…”

Section: Binding Site and Molecular Dockingmentioning

confidence: 99%

DFT Study of Efinaconazole, an Antifungal Drug and Its Molecular Docking against a Holoenzyme (pdb id: 3IDB)

Hossen

Pal

2021

J. Sci. Res.

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Efinaconazole (ECZ) is an antifungal drug. Various non-covalent interactions between ECZ and a holoenzyme (protein id: 3idb) has been investigated through computational study. The structure of ECZ was optimized using density functional theory (DFT) applying B3LYP/6-311G+(d,p) method. HOMO, LUMO, chemical hardness and softness, several thermochemical parameters, electrostatic potential surface, vibrational spectrum, total energy, and maximum internal force and maximum internal displacement with respect to optimization step number have been determined. The optimized ECZ ligand was subjected to molecular docking against the protein 3idb in Autodock Vina program. The different non-covalent interactions in the ligand-protein complex were visualized in BIOVIA Discovery Studio Visualizer. Various surface plots such as hydrogen bonds, ionizability, SAS, hydrophobicity, aromatic and charge surfaces were excerpted. ECZ molecule forms three strong hydrogen bonds with amino acid residues of the holoenzyme. In addition to this, it is significantly capable to form several other bonds which strengthen the ligand-protein interaction. The result showed that the ECZ molecule posed considerable binding affinity against the macromolecule.

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“…In many previous studies, network pharmacology has successfully unveiled potential targets and pathways of TCM [18][19][20] . Meanwhile, molecular docking simulation is frequently employed to further validate the potential bioactive components and core targets [21][22][23] .…”

Section: Introductionmentioning

confidence: 99%

Anti-inflammatory Properties of Fangji Huangqi Tang: Discovery Based on Network Pharmacology, Molecular Docking and Arrowsmith Tools

Jiang¹,

Han²,

Liu³

et al. 2021

Preprint

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Fangji Huangqi Tang (FHT) is a classical formula widely used in Chinese clinical practice. In this study, a creative application of FHT for inflammation has been identified by network pharmacology-based framework. Specifically, a total of 17 bioactive compounds including 42 potential targets of FHT, and 205 related targets involved in inflammation were retrieved from mainstream databases and subjected to network analysis. 13 intersection targets indicated the principal elements linked to inflammation therapy. Top terms of Gene Ontology (GO) analysis were identified, while 7 related signaling pathways were revealed by Kyoto Encyclopedia of Genes and Genomes (KEGG) results. Subsequently, Calycosin-PTGS2 with tight binding affinity (BA) was manifested by molecular docking as the critical compound-target couple. Meaningful links between Calycosin and inflammation were implied through Arrowsmith, which overlapped with the findings in enrichment analysis, such as MAPK, NF-κB that could be regulators of PTGS2. In summary, the present study explored the potential targets and signaling pathways of FHT against inflammation, which may help to illustrate the mechanisms responsible for the action of FHT and provide a better understanding of its anti-inflammatory effects.

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Molecular Docking in Formulation and Development

Cited by 78 publications

References 16 publications

Partridge and embryonated partridge egg as new preclinical models for candidiasis

Partridge and embryonated partridge egg as new preclinical models for candidiasis

DFT Study of Efinaconazole, an Antifungal Drug and Its Molecular Docking against a Holoenzyme (pdb id: 3IDB)

Anti-inflammatory Properties of Fangji Huangqi Tang: Discovery Based on Network Pharmacology, Molecular Docking and Arrowsmith Tools

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