Inhibitory Potential of Ferula assafoetida Extract on L-type Calcium Channel
Protein Revealed by Zebrafish Studies and Molecular Docking

Ferula assafoetida is a part of many herbal formulations and hence it is pertinent to check the safety of its components specially to growing embryos. Zebrafish (Danio rerio) is considered to be one of the best models to study human embryonic development and metabolic pathways as its genome is fully sequenced and it possesses easily detectable developmental properties. In present study, the embryos of Danio rerio were treated with different concentrations of methanolic extract of Ferula assafoetida (MEFA) and its effects were checked at different post fertilization periods. Decreased heart beat rates, shrinkage of the chorion wall and other developmental abnormalities leading to the death of the embryos were observed. The methanolic extract of Ferula assafoetida was subjected to GC-MS to determine the different compounds present. Cardiotoxicity of these compounds were studied as it is one of the important factors for the retraction of a drug from the market. Molecular docking studies with L-type calcium channel (LTCC), a protein important for cardiac functioning, showed strong binding to the phytochemicals in the extract, with the maximum binding affinity observed with 26-hydroxycholesterol. The study proves that the methanolic extract of Ferula assafoetida contains phytochemicals which have the potential to cause cardiotoxicity in zebrafish embryos by interfering with the functions of LTCC possibly leading to arrhythmia. Altogether, our data suggest that the usage of these extracts in drug formulations should be done with caution. This is also indicative of the possible cytotoxic effect of the extract which could be tapped in the search for anticancer drugs.

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Computational Analysis for Physicochemical Properties of Compounds in Senna auriculata Leaves Methanolic Extract to have Antidiabetic Potentials and their Molecular Interaction with α-amylase

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2021/v33i54a33716 ◽

2021 ◽

pp. 30-42

Author(s):

Abdulaziz Bin Dukhyil

Keyword(s):

Molecular Docking ◽

Physicochemical Properties ◽

Methanolic Extract ◽

Natural Compounds ◽

Physicochemical Analysis ◽

Dynamics Simulation ◽

Carbohydrate Hydrolysis ◽

Catalytic Active Site ◽

Inhibitory Potential

Aims: Diabetes mellitus (DM) is chronic disorder well known for increased glucose level in blood. This disease can be controlled by inhibiting the enzyme (e.g., α-amylase) involve in carbohydrate hydrolysis. Senna auriculata leaves methanolic extract (SALME) have potential antidiabetic properties and it was also found to be safe in preclinical studies. In this study the aim was to explore the molecular interactions of α-amylase and bioactive compounds in SALME and their physicochemical properties. Methodology: Computational approach such as molecular docking and physicochemical analysis prediction was applied to understand the antidiabetic potential of natural compounds present in SALME. Results: The results showed from physicochemical analysis that out of 11 only 7 compounds are having drug like properties which are orally and intestinally better bioavailable. Furthermore, molecular docking analysis explained that three compounds (C3, C4, and C7) have lower binding energy, ΔG (-8, -9.1, -9.5 kcal/mol) and better binding affinity, Ki (7.31 x 105, 4.68 x 106, and 9.2 x 106 M-1, respectively) than the acarbose ΔG (-7.8 kcal/mol) and Ki (6.18 x 105 M-1), a well-known FDA approved medication for DM. The study also explained the binding pattern that the catalytic residue such as Asp197, Glu233 and Asp300 are involved in stabilizing the natural compounds with in the catalytic active site of target enzyme. Conclusions: From the results it has been concluded that these three compounds found in SALME have better inhibitory potential for α-amylase in comparison with acarbose. Further validation of the findings is required through molecular dynamics simulation, ADME-T study, and in-vitro enzyme inhibition by the purified compounds.

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Garcixanthone D, a New Xanthone, and Other Xanthone Derivatives FromGarcinia mangostanaPericarps: Their α‐Amylase Inhibitory Potential and Molecular Docking Studies

Starch - Stärke ◽

10.1002/star.201800354 ◽

2019 ◽

Vol 71 (7-8) ◽

pp. 1800354 ◽

Cited By ~ 3

Author(s):

Sabrin Ragab Mohamed Ibrahim ◽

Gamal Abdallah Mohamed ◽

Maan Talaat Abdullah Khayat ◽

Sahar Ahmed ◽

Hany Abo‐Haded

Keyword(s):

Molecular Docking ◽

Docking Studies ◽

Molecular Docking Studies ◽

Xanthone Derivatives ◽

Inhibitory Potential

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Quorum sensing inhibitory potential and molecular docking studies of sesquiterpene lactones from Vernonia blumeoides

Phytochemistry ◽

10.1016/j.phytochem.2016.02.012 ◽

2016 ◽

Vol 126 ◽

pp. 23-33 ◽

Cited By ~ 15

Author(s):

Abubakar Babando Aliyu ◽

Neil Anthony Koorbanally ◽

Brenda Moodley ◽

Parvesh Singh ◽

Hafizah Yousuf Chenia

Keyword(s):

Molecular Docking ◽

Quorum Sensing ◽

Sesquiterpene Lactones ◽

Docking Studies ◽

Molecular Docking Studies ◽

Inhibitory Potential

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in silico-Based Virtual Screening and Molecular Docking Analysis of Phytochemicals obtained from Methanolic Extract of Cleome viscosa Linn. by GC-MS Method for its Anticancer Activity

Asian Journal of Chemistry ◽

10.14233/ajchem.2021.23384 ◽

2021 ◽

Vol 33 (12) ◽

pp. 2943-2952

Author(s):

K. Usha S. Pai ◽

Yadav D. Bodke ◽

Suman Manandhar ◽

K. Sreedhara Ranganath Pai

Keyword(s):

Molecular Docking ◽

Anticancer Activity ◽

In Silico ◽

Methanolic Extract ◽

Growth Factor Receptor ◽

Docking Studies ◽

Gas Chromatography Mass Spectrometry ◽

In Silico Docking ◽

Phytochemical Compounds ◽

Cleome Viscosa

Cleome viscosa belonging to the family Capparidaceae, is a weed with ethano-botanical value found in India. In the present investigation, methanolic extract of Cleome viscosa was analyzed by gas chromatography-mass spectrometry (GC-MS) to identify the important phytochemical constituents. The GC-MS analysis of methanol from whole plant of Cleome viscosa detected the presence of 78 phytochemical compounds. Quantitative phytochemical evaluation of the methanolic extract of Cleome viscosa was performed. These identified compounds were analyzed for their anticancer activity through in silico molecular docking studies. Computation based in silico docking studies were done using maestro interface. Three protein, poly (ADP-ribose) polymerase-1 (PARP-1), epidermal growth factor receptor (EGFR), human papilloma virus (HPV) specific to different cancers were selected for screening of these phytochemicals. Phytomolecules with better activity and binding were shortlisted after XP mode of docking. The dock score, glide energy and 2D binding interactions of the top five phytochemicals with three selected proteins have been discussed. The identified hit could be a potent inhibitor these proteins that further requires experimental validation.

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Species of the Genus Salix L.: Biochemical Screening and Molecular Docking Approach to Potential Acetylcholinesterase Inhibitors

Applied Sciences ◽

10.3390/app9091842 ◽

2019 ◽

Vol 9 (9) ◽

pp. 1842 ◽

Cited By ~ 6

Author(s):

Emilia Gligorić ◽

Ružica Igić ◽

Ljiljana Suvajdžić ◽

Nevena Grujić-Letić

Keyword(s):

Antioxidant Activity ◽

Molecular Docking ◽

Total Phenolics ◽

Woody Species ◽

Acetylcholinesterase Inhibitors ◽

Docking Studies ◽

Willow Species ◽

Docking Approach ◽

Willow Bark ◽

Inhibitory Potential

The genus Salix includes about 500 different, mainly woody species with potentially significant medicinal values. The aim of this study was to evaluate the chemical composition and antioxidant activity of little-studied bark and leaves extracts of seven different species of the genus Salix, and to examine the acetylcholinesterase (AChE) inhibitory potential of selected compounds. The extracts were characterized by High Pressure Liquid Chromatography (HPLC). Total phenolics and flavonoids content was determined spectrophotometrically and the antioxidant activity by 2,2-diphenyl-1-picrylhydrazyl (DPPH•) and hydroxyl radical (•OH) scavenging assays. Molecular docking studies were conducted in order to elucidate the interaction and binding affinity between selected compounds of willow bark and leaves against AChE. The major components in bark and leaves of most of the species were rutin (1.26–22.09 mg/g), salicin (1.62–17.33 mg/g), chlorogenic acid (0.74–7.53 mg/g) and epicatechin (0.71–4.83 mg/g). The latter three compounds demonstrated significant inhibitory potential against AChE in docking studies. All extracts exhibited notable antioxidant activity as scavengers of both DPPH• and •OH. The obtained results indicate that willow species other than those in commercial use, and not only bark, but willow leaves as well, could be utilized as sources of valuable phytocompounds with antioxidant and neuroprotective properties.

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Synthesis, in vitro β -glucuronidase inhibitory potential and molecular docking studies of quinolines

European Journal of Medicinal Chemistry ◽

10.1016/j.ejmech.2017.08.052 ◽

2017 ◽

Vol 139 ◽

pp. 849-864 ◽

Cited By ~ 4

Author(s):

Bilquees Bano ◽

Arshia ◽

Khalid Mohammed Khan ◽

Kanwal ◽

Bibi Fatima ◽

...

Keyword(s):

Molecular Docking ◽

Docking Studies ◽

Molecular Docking Studies ◽

Inhibitory Potential

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Naturally Occurring Anthraquinones as Potential Inhibitors of SARS-CoV-2 Main Protease: A Molecular Docking Study

10.26434/chemrxiv.12245270.v1 ◽

2020 ◽

Author(s):

Sourav Das ◽

Atanu Singha Roy

Keyword(s):

Molecular Docking ◽

Drug Targets ◽

Docking Study ◽

Docking Studies ◽

World Health ◽

Molecular Docking Study ◽

Inhibitory Potential ◽

Novel Coronavirus ◽

Health Organization ◽

Potential Inhibitors

Background: The novel coronavirus (COVID-19) has quickly spread throughout the globe, affecting millions of people. The World Health Organization (WHO) has recently declared this infectious disease as a pandemic. At present, several clinical trials are going on to identify possible drugs for treating this infection. SARS-CoV-2 Mpro is one of the most critical drug targets for the blockage of viral replication. Method: The blind molecular docking analyses of natural anthraquinones with SARS-CoV-2 Mpro were carried out in an online server, SWISSDOCK, which is based on EADock DSS docking software. Results: Blind molecular docking studies indicated that several natural antiviral anthraquinones could prove to be effective inhibitors for SARS-CoV-2 Mpro of COVID-19 as they bind near the active site having the catalytic dyad, HIS41 and CYS145 through non-covalent forces. The anthraquinones showed less inhibitory potential as compared to the FDA approved drug, remdesivir. Conclusion: Among the natural anthraquinones, alterporriol Q could be the most potential inhibitor of SARS-CoV-2 Mpro among the natural anthraquinones studied here, as its ∆G value differed from that of remdesivir only by 0.51 kcal/ mol. The uses of these alternate compounds might be favorable for the treatment of the COVID-19.

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Molecular Docking Studies of Bioactive Nicotiflorin against 6W63 Novel Coronavirus 2019 (COVID-19)

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323999200820162551 ◽

2020 ◽

Vol 23 ◽

Author(s):

Raghvendra Dubey ◽

Kushagra Dubey

Keyword(s):

Molecular Docking ◽

Data Bank ◽

Docking Studies ◽

Molecular Docking Studies ◽

Molegro Virtual Docker ◽

Main Protease ◽

Docking Approach ◽

Inhibitory Potential ◽

Efficacy Parameters ◽

Novel Coronavirus

Background: COVID-19 which is known as the novel coronavirus was reported in December 2019 in Wuhan city, China and many of the patients have been contaminated by environmental contamination and transmission from one human to another. Objective: The objective of work is to establish the inhibitory potential of nicotiflorin, a Kaempferol 3-O-rutinoside flavonoid, against the deadly coronavirus (COVID-19) 6W63 (main protease 3Clpro protein) , using molecular docking approach. Method: The Molegro Virtual Docker software (MVD) with a 30 Å grid resolution was used. The structure was drawn by Chem 3D software and energy minimization was done by the MM2 force field. The protein 6W63 was downloaded from the protein data bank. Molegro modeller was used for score calculations. Result: The molecular docking studies were carried out on nicotiflorin and standard inhibitor X77, where standard inhibitor was observed in a co-crystallized state with main protease 3Clpro protein 6W63. The MolDock score, Rerank Sore and H Bond score of nicotiflorin and standard inhibitor X77 was observed as -173.058, -127.302, -21.9398 and -156.913,- 121.296,-5.7369, respectively. Conclusion: Molecular docking studies have confirmed that the affinity of flavonoid nicotiflorin with the amino acids of the viral protein 6W63 was relatively more than the standard X77. For the effective treatment of novel coronavirus COVID-19, the effectiveness of the identified flavonoid nicotiflorin can further be evaluated for safety and efficacy parameters at both preclinical and clinical stages.

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Carbazole‐Linked 1,2,3‐Triazoles: In Vitro β ‐Glucuronidase Inhibitory Potential, Kinetics, and Molecular Docking Studies

ChemistrySelect ◽

10.1002/slct.201900647 ◽

2019 ◽

Vol 4 (20) ◽

pp. 6181-6189 ◽

Cited By ~ 2

Author(s):

Nimra Naveed Shaikh ◽

Shazia Iqbal ◽

Naima Syed ◽

Maria A. Khan ◽

Syed Tarique Moin ◽

...

Keyword(s):

Molecular Docking ◽

Docking Studies ◽

Molecular Docking Studies ◽

Inhibitory Potential

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Peptidyl-tRNA Hydrolase Screening Combined with Molecular Docking Reveals the Antibiotic Potential of Syzygium johnsonii Bark Extract

Natural Product Communications ◽

10.1177/1934578x1100601003 ◽

2011 ◽

Vol 6 (10) ◽

pp. 1934578X1100601 ◽

Cited By ~ 2

Author(s):

Sarah M. Harris ◽

Hana McFeeters ◽

Ifedayo V. Ogungbe ◽

Luis R. Cruz-Vera ◽

William N. Setzer ◽

...

Keyword(s):

Molecular Docking ◽

Pathogenic Bacteria ◽

Antibacterial Agents ◽

Docking Studies ◽

Bark Extract ◽

Tropical Plant ◽

Potential Source ◽

Inhibitory Components ◽

Essential Enzyme ◽

Inhibitory Potential

With the rapid rise of antibiotic resistance in pathogenic bacteria, the need for new antibacterial agents is overwhelming. Herein we report the limited screening of tropical plant extracts for inhibitory activity against the essential enzyme peptidyl-tRNA hydrolase (Pth). Initial screening was conducted through an electrophoretic mobility assay and Northern blot detection. The ability of Pth to cleave the peptide-tRNA ester bond was assessed. The ethanol bark extract of Syzygium johnsonii showed strong inhibitory potential. Molecular docking studies point to Syzygium polyphenolics as the potential source of inhibition. This work is the forerunner of activity-directed isolation, purification, and structure elucidation of the inhibitory components from Syzygium johnsonii extracts and studies of compound interaction with Pth.

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