An Epidemiological Correlation of Oral Candidiasis Mice Model Study of an Isolate from Mollugo pentaphylla Linn. and In silico Docking Approach

Abstract This study aims to identify anthocyanin pigments in Sudanese roselle and examine their inhibitory activity toward xanthine oxidase (XO) enzyme via in silico docking approach. A number of four samples of Sudanese roselle (red and white) from different regions of Sudan were investigated by high sensitive technique, i.e. LC-MS to identify anthocyanins. Four anthocyanins were identified in all samples; delphinidin-3-glucoside (Dp-3-glu), cyanidin-3-sambubioside (Cy-3-sam), pelargonidin chloride (Pg Chloride), and petuinidin-3-glucoside (Pt-3-glu); in addition to one flavanol; gossypetin (Goss). The anthocyanins of the white samples are suggested to be presented in the yellowish or colorless pseudo base structures. The identified anthocyanins were tested against the inhibition toward xanthine oxidase via molecular docking. All anthocyanins were found to be excellent XO inhibitors superior to the most recent commercially used hyperuricemia drug; i.e. topiroxostat. The binding energies of the complexes (ligand-XO) are lower than the energy of the topiroxostat-XO complex. The binding energies order is: pt-3- dp-3-glu > cy-3-sam > goss > pg chloride. According to our investigation, roselle anthocyanins are considered as good potential future XO-inhibitors drugs; and promising candidates to treat several related diseases.

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β-amyrin as an analgesic component of the leaves of Callistemon citrinus (Curtis) Skeels: Chemical, biological and in silico studies

Bangladesh Journal of Botany ◽

10.3329/bjb.v48i2.47685 ◽

2019 ◽

Vol 48 (2) ◽

pp. 379-385

Author(s):

Farhana Ahmed ◽

Mohammed Zakiur Rahman ◽

Mohammad Firoz Khan ◽

Mohammad Abdur Rashid ◽

Mohammad Sharifur Rahman

Keyword(s):

Carbon Tetrachloride ◽

In Silico ◽

Gel Permeation Chromatography ◽

Docking Study ◽

Active Principle ◽

Mice Model ◽

In Silico Docking ◽

Peripheral Analgesia ◽

In Silico Studies ◽

Layer Chromatography

The analgesic potential of the leaves of Callistemon citrinus was reported earlier but no active principle for this analgesia was explored. To identify the major analgesic metabolite(s), the leaves were extracted with methanol and fractionated into petroleum ether, carbon tetrachloride, chloroform and aqueous soluble fractions. Based on the thin layer chromatography, the carbon tetrachloride fraction was subjected to gel permeation chromatography and a compound (1) was isolated, which was characterized as β-amyrin. Compound (1) displayed significant peripheral analgesia (p < 0.05) on mice model at an oral dose 200 mg/kg body weight. It also showed noticeable anti-inflammatory membrane stabilizing activity. In silico docking study of β-amyrin with cyclooxygenase (COX)-2 showed a good binding affinity (–9.1 Kcal/mol). Virtual pharmacokinetics and toxicity studies explore its potentials as a lead molecule having no extreme lethality.

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IN SILICO DOCKING APPROACH FOR ANTIATHEROSCLEROTIC ACTIVITY OF PHYTOCONSTITUENTS OF METHANOLIC EXTRACT OF SOLANUM MELANOGENA

International Journal of Research in Pharmacy and Chemistry ◽

10.33289/ijrpc.11.1.2021.11(11) ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

G. Suresh Kumar ◽

B. Nivetha

Keyword(s):

In Silico ◽

Methanolic Extract ◽

In Silico Docking ◽

Docking Approach

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Pass and Swiss ADME collaborated in silico docking approach to the synthesis of certain pyrazoline spacer compounds for dihydrofolate reductase inhibition and antimalarial activity

Bangladesh Journal of Pharmacology ◽

10.3329/bjp.v13i1.33625 ◽

2018 ◽

Vol 13 (1) ◽

pp. 23 ◽

Cited By ~ 6

Author(s):

Krishnakumar Lohidakshan ◽

Manju Rajan ◽

Andhale Ganesh ◽

Mathew Paul ◽

Jithu Jerin

Keyword(s):

In Silico ◽

Antimalarial Activity ◽

Video Clip ◽

Acid Hydrazide ◽

Building Blocks ◽

Docking Study ◽

Discovery Studio ◽

In Silico Docking ◽

Docking Approach

New series of pyrazoline spacer compounds were prepared by the reaction between benzimidazole chalcones and (2-methyl-5-nitro-imidazole-1-yl)-acetic acid hydrazide by the sensible use of Michael addition. The building blocks used for the synthesis of pyrazoline derivatives were opted by using virtual screening by molinspiration search engine. The hypothetically resulted pyrazoline spacer compounds from this list are checked for their reliability on other in silico drug designing online web services like PASS online bioactivity, Swiss ADME predictor. The docking study on final four pyrazoline compounds was carried out using Accelrys Discovery Studio 3.5. These synthesized compounds were, later, characterized with the help of UV, IR, mass and 1H NMR techniques. These compounds were further screened for their in vitro antimalarial effect. The PASS, Swiss ADME assisted docking approach and the use of combo heterocyclic ring with pyrazoline scaffold were found to be beneficial to derive and synthesize effective antimalarial agents in the present study.Video Clip of Methodology:6 min 20 sec: <a href="https://www.youtube.com/v/RWwaZuG1j9E">Full Screen</a> <a href="https://www.youtube.com/watch?v=RWwaZuG1j9E">Alternate</a>

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Binding studies of ferrocene‐steroid conjugates with human serum albumin as potential drug carrier using fluorescence spectroscopy and in silico docking approach

Applied Organometallic Chemistry ◽

10.1002/aoc.6344 ◽

2021 ◽

Author(s):

Xiomara Narváez‐Pita ◽

Enrique Meléndez

Keyword(s):

Human Serum Albumin ◽

Fluorescence Spectroscopy ◽

Serum Albumin ◽

In Silico ◽

Drug Carrier ◽

Potential Drug ◽

Binding Studies ◽

In Silico Docking ◽

Docking Approach ◽

Steroid Conjugates

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In Silico Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of 3C-like Main Proteinase (3CLpro) from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Using Selected African Medicinal Plants

10.26434/chemrxiv.12480434.v1 ◽

2020 ◽

Author(s):

Sahar Qazi ◽

Mustafa Alhaji Isa ◽

Adam Mustapha ◽

Khalid Raza ◽

Ibrahim Alkali Allamin ◽

...

Keyword(s):

Molecular Docking ◽

Severe Acute Respiratory Syndrome ◽

In Silico ◽

Md Simulation ◽

Binding Energies ◽

Anacardium Occidentale ◽

Upper Respiratory Tract ◽

Ligand Complex ◽

In Silico Docking ◽

Main Protease

The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of Zingiber offinale and Anacardium occidentale using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of Zingiber offinale and the leaves of Anacardium occidentale. These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), Pan-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907).

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In Silico Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of 3C-like Main Proteinase (3CLpro) from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Using Selected African Medicinal Plants

10.26434/chemrxiv.12480434 ◽

2020 ◽

Author(s):

Sahar Qazi ◽

Mustafa Alhaji Isa ◽

Adam Mustapha ◽

Khalid Raza ◽

Ibrahim Alkali Allamin ◽

...

Keyword(s):

Molecular Docking ◽

Severe Acute Respiratory Syndrome ◽

In Silico ◽

Md Simulation ◽

Binding Energies ◽

Anacardium Occidentale ◽

Upper Respiratory Tract ◽

Ligand Complex ◽

In Silico Docking ◽

Main Protease

The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of Zingiber offinale and Anacardium occidentale using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of Zingiber offinale and the leaves of Anacardium occidentale. These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), Pan-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907).

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