scholarly journals Phytochemicals Target Growth Factor Receptors to Control Cancer: An In Silico Study

2021 ◽  
Author(s):  
Love Edet Mendie ◽  
S Hemalatha
Keyword(s):  
Growth Factor ◽  
Binding Energy ◽  
Bioactive Compounds ◽  
Anticancer Agents ◽  
In Silico ◽  
Growth Factor Receptors ◽  
Lipinski’S Rule ◽  
In Silico Study ◽  
Lipinski’S Rule Of Five ◽  
Cancerous Cells

Abstract Drug delivery in a safe manner is a major challenge in the drug development process. Growth factor receptors (GFRs) are known to have profound roles in the growth and progression of cancerous cells making these receptors a therapeutic target in the effective treatment of cancer. This work focused on exploring bioactive compounds that can target GFRs usingin-silico method. In this study, 50 bioactive compounds from different plant sources were screened as anticancer agent against GFRs using drug likeness parameters of Lipinski’s rule of five. The molecular docking was performed between phytochemicals and GFRs. Ligands with acceptable drug likeness and binding energy comparable to the standard drugs were further screened to determine their pharmacokinetic activities. This study showed phytochemicals with the binding energy comparable with the standard drugs (Dovitinb and Geftinib), while ADME, bioactivity score and bioavailability radar analysis gave further insight on these compounds as potent anticancer agents.

scholarly journals A Possible Role of Pulegone against Glypican-1 for the Treatment of Alzheimer’s Disease through In-Silico Approach

2021 ◽  
Vol 9 (VI) ◽  
pp. 4000-4007
Author(s):  
Nikita Kaushik
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Target Protein ◽  
Receptor Protein ◽  
Lipinski’S Rule ◽  
Lipinski’S Rule Of Five

Alzheimer’s disease (AD) dementia is a type of neurodegenerative disease, refers to a distinct arrival and certainly functional and mental decline which is linked with age which eventually leads to death. This current study was to demonstrate the role of pulegone against Glypican-1 for the treatment of Alzheimer’s disease through an in-silico approach. Methods: All the information and studies were gleaned from molecular docking. With the use of docking software, Docking was implemented between the target protein GPC1 (PDB ID: 4YWT) and the entire ligands. We preferred GPC1 (PDB ID: 4YWT) as a target protein and several natural compounds such as Rosmarinic acid, Allo ocimene, and Pulegone as ligands. When the preparation of protein is done, in PyRx software we introduced the entire ligand for the process of virtual screening. As reported by the result of PyRx and Lipinski’s Rule of Five, the finest compound against GPC1 with its smallest amount of binding energy was Pulegone. Results: For the procedure of molecular docking between the receptor protein GPC1 (PDB ID: 4YWT) and Pulegone a software called AutoDock Vina was used. The outcome showed 9 poses with distinct binding energy, RMSD LB (Root means square deviation Lower Bound), RMSD UB (Root mean square deviation Upper Bound). Through PyMol (an open-access tool for the visualization of the molecule), the interaction amidst Pulegone and GPC1 can be visualized. Conclusion: The merely compound which can restrain the activity of GPC1 (PDB ID: 4YWT) was Pulegone, based on the in-silico approach. Therefore in the advanced studies, Pulegone can be a capable medicine acquired from natural sources for dealing with Alzheimer’s disease.

Design, Synthesis, In vitro and In silico Evaluation of New Hydrazonebased Antitumor Agents as Potent Akt Inhibitors

2020 ◽  
Vol 17 (11) ◽  
pp. 1380-1392
Author(s):  
Emine Merve Güngör ◽  
Mehlika Dilek Altıntop ◽  
Belgin Sever ◽  
Gülşen Akalın Çiftçi
Keyword(s):  
Cell Line ◽  
Anticancer Agents ◽  
In Silico ◽  
Antitumor Agents ◽  
Colorimetric Assay ◽  
Fibroblast Cell ◽  
Lipinski’S Rule ◽  
In Silico Docking ◽  
Embryonic Fibroblast

Background: Akt is overexpressed or activated in a variety of human cancers, including gliomas, lung, breast, ovarian, gastric and pancreatic carcinomas. Akt inhibition leads to the induction of apoptosis and inhibition of tumor growth and therefore extensive efforts have been devoted to the discovery of potent antitumor drugs targeting Akt. Objectives: The objective of this work was to identify potent anticancer agents targeting Akt. Methods: New hydrazone derivatives were synthesized and investigated for their cytotoxic effects on 5RP7 H-ras oncogene transformed rat embryonic fibroblast and L929 mouse embryonic fibroblast cell lines. Besides, the apoptotic effects of the most active compounds on 5RP7 cell line were evaluated using flow cytometry. Their Akt inhibitory effects were also investigated using a colorimetric assay. In silico docking and Absorption, Distribution, Metabolism and Excretion (ADME) studies were also performed using Schrödinger’s Maestro molecular modeling package. Results and Discussion: Compounds 3a, 3d, 3g and 3j were found to be effective on 5RP7 cells (with IC50 values of <0.97, <0.97, 1.13±0.06 and <0.97 μg/mL, respectively) when compared with cisplatin (IC50= 1.87±0.15 μg/mL). It was determined that these four compounds significantly induced apoptosis in 5RP7 cell line. Among them, N'-benzylidene-2-[(4-(4-methoxyphenyl)pyrimidin- 2-yl)thio]acetohydrazide (3g) significantly inhibited Akt (IC50= 0.5±0.08 μg/mL) when compared with GSK690693 (IC50= 0.6±0.05 μg/mL). Docking studies suggested that compound 3g showed good affinity to the active site of Akt (PDB code: 2JDO). According to in silico ADME studies, the compound also complies with Lipinski's rule of five and Jorgensen's rule of three. Conclusion: Compound 3g stands out as a potential orally bioavailable cytotoxic agent and apoptosis inducer targeting Akt.

scholarly journals IN SILICO STUDY OF ARYL EUGENOL DERIVATIVES AS ANTI-COLORECTAL CANCER BY INDUCING OF APOPTOSIS

2017 ◽  
Vol 10 (12) ◽  
pp. 345
Author(s):  
Fadilah Fadilah ◽  
Arry Yanuar ◽  
Ade Arsianti ◽  
Retnosari Andrajati ◽  
Erni Hernawati Purwaningsih
Keyword(s):  
Binding Energy ◽  
In Silico ◽  
Computer Software ◽  
Data Bank ◽  
The Body ◽  
Software Applications ◽  
In Silico Admet ◽  
In Silico Study ◽  
Abnormal Cells ◽  
Cancer Tissues

Objective: Apoptosis is one method the body uses to get rid of unneeded or abnormal cells, but cancer cells have strategies to avoid apoptosis. Apoptosis inducers can get around these strategies to cause the death of cancer cells.Methods: We screened some derivatives aryl eugenol based on their interactions with Bcl-2 in many cancer tissues, using computer software applications (in silico method) to determine the best compounds. The docking experiment on Bcl-2 (Protein Data Bank ID 4LXD) was carried out by suitably positioning the energy-minimized ligand in the active site while carefully monitoring non-bonded interactions of the ligand enzyme.Results: The resulting ligand-receptor complex was docked using the Autodock Vina software. Docking results based free binding energy, EUGACl (21), EUASABr (17), EUGEABr (19), and EUASACL (17), has the lowest binding energy than navitoclax and binds significantly to BCL 2. In silico ADMET predictions revealed that except SA, ASA, and GEA, all other compounds had minimal toxic effects and had good absorption as well as solubility characteristics.Conclusion: These compounds of aryl eugenol (17, 19, and 21) may serve as a potential lead compound for developing new anticancer as apoptosis inducers.

scholarly journals Design of Chalcones of 7-Azaindole as Raf-B Inhibitors

2019 ◽  
Vol 4 (4) ◽  
pp. 606-608 ◽  
Author(s):  
D. Giles ◽  
V.N. Saiprabha ◽  
G. Yeshna
Keyword(s):  
Binding Affinity ◽  
Active Site ◽  
In Silico ◽  
Significant Interaction ◽  
Docking Score ◽  
Lipinski’S Rule ◽  
Lipinski’S Rule Of Five

The present work deals with the design of 7-azaindole derivatives for its Raf-B inhibition. All the designed compounds follows Lipinski’s rule of five. In silico ADME predictions of all the designed compounds suggests that none of the compounds have problem with bioavailability. The compounds were designed on the binding affinity towards the Raf-B inhibition. It was observed that few of the designed compounds were found to have significant interaction with the active site of the receptor. The compounds possessing 3-hydroxyl-2-methyl as substitution in chalcone was found to possess maximum docking score than other designed compounds.

scholarly journals Mengidentifikasi Peptida Bioaktif Angiotensin Converting Enzyme-inhibitor (ACEi) dari Kasein β Susu Kambing dengan Polimorfismenya Melalui Teknik In Silico

2019 ◽  
Vol 7 (4) ◽  
Author(s):  
Hermawan Setyo Widodo ◽  
Tridjoko Wisnu Murti ◽  
Ali Agus ◽  
Widodo Widodo
Keyword(s):  
Angiotensin Converting Enzyme ◽  
In Silico ◽  
Digestive Enzymes ◽  
Bioactive Peptides ◽  
Enzyme Inhibitor ◽  
Goat Milk ◽  
Bioactive Peptide ◽  
Converting Enzyme ◽  
Lipinski’S Rule ◽  
Lipinski’S Rule Of Five

Susu kambing memiliki komponen protein salah satunya protein β dan secara umum terjadi polimorfisme pada level protein. Perubahan urutan asam amino akibat polimorfisme memungkinkan adanya potensi dihasilkannya peptida bioaktif penghambat enzim pengubah angiotensin (ACEi). Penelitian ini bertujuan untuk menyaring peptida bioaktif yang berpotensi sebagai ACEi dari kasein β kambing beserta polimorfismenya. Penelitian ini dilakukan dengan teknik in silico terhadap sekuen kasein β kambing serta struktur tiga dimensi human testicular ACE. Langkah yang dilakukan dalam penelitian ini meliputi simulasi pemotongan peptida dengan enzim pencernaan (pepsin, tripsin dan kimotripsin), peninjauan karakteristik peptida lalu simulasi docking ligan-reseptor. Tampilan parameter Lipinski’s Rule of Five (Ro5), bioaktivitas dan energi afinitas dipertimbangkan untuk memilih peptida bioaktif. Hasil yang didapat menunjukkan bahwa ditemukan peptida bioaktif yakni INK (Ile-Asp-Lys) yang memiliki kemampuan hampir setara dengan lisinopril (afinitas energi -8,2kkal/mol vs. -8,3kkal/mol). Peptida INK dapat ditemukan dari hasil hidrolisis dari alel A, C, D dan E, sehingga polimorfisme tidak menyebabkan perbedaan produksi peptida bioaktif. Kesimpulan yang dapat diambil yakni kasein β susu kambing jika dicerna dengan enzim pencernaan dapat menghasilkan peptida bioaktif ACEi yakni INK.Identification of Angiotensin Converting Enzyme-inhibitor (ACEi) Bioactive Peptide from Goat Milk β-Casein with It's Polymorphism by In Silico TechniqueAbstractPolymorphism eventually may be occurred at the protein level. Changes in the amino acid sequence due to polymorphism may exhibit a potential action to generate of the angiotensin-converting enzyme inhibitors (ACEi) bioactive peptide. This study is aimed to assess bioactive peptides that have a great potent value as ACEi from goat β casein along with its polymorphism. The research was done by in silico technique on goat β-casein sequence and three-dimensional structure human testicular ACE. Peptide-cutting simulations with digestive enzymes (pepsin, trypsin and chymotrypsin), peptide properties review, then ligand-receptor docking simulations was applied in this research. Appearance of Lipinski's Rule of Five (Ro5), bioactivity and affinity energy were considered for selecting bioactive peptides. The results show that bioactive peptide found as INK (Ile-Asp-Lys) which had similar ability as lisinopril (energy affinity –8.2kcal/mol vs. –8.3kcal/mol). The INK peptides could be found from the hydrolysis resulted in alleles A, C, D and E, therefore polymorphism did not affect the differences of production of bioactive peptides. A conclusion, processed goat milk β casein with digestive enzymes could produce ACEi of INK as bioactive peptide.

scholarly journals Docking against Lung cancer protein and Drug-likeliness of Bioactive Compounds from Phymatosorus scolopendria (Burm.F.) Pic. Serm.

2020 ◽  
pp. 437-441
Author(s):  
Sujatha Srinivasan ◽  
Catharin S. Sivaraman ◽  
Ramya R. Issac ◽  
Gayathiri Mahalingam ◽  
Gnana D. R. Roke
Keyword(s):  
Lung Cancer ◽  
Bioactive Compounds ◽  
Vinyl Ester ◽  
In Vivo Studies ◽  
Lipinski’S Rule ◽  
Lipinski’S Rule Of Five ◽  
Gas Chromatography Mass Spectroscopy ◽  
Nitrophenyl Ester

Phymatosorus scolopendria (Burm.F.) Pic. Serm. is a medicinally important fern which is used traditionally by various people all over the World. The aim of this research focuses on the docking against lung cancer protein (2ITO) with bioactive compounds of Phymatosorus scolopendria (Burm.F.) Pic. Serm. which is obtained by using Gas Chromatography Mass Spectroscopy.  The same compounds were analysed using Lipinski’s rule of five for its pharmacological prediction. The bioactive compounds were further referred for ADMET property to find its pharmacokinetic potency and prediction towards its potential as drug in future.   Among the four compounds docked with the Lung cancer protein (2ITO) 4-Nitrophenyl laurate shows high docking score followed by Hexadecanoic acid, 4 Nitrophenyl ester and Myristic acid Vinyl ester. Out of four compounds studied three compounds satisfied the  drug-likeliness based on Lipinski’s rule of five. The present work suggests the bioactive compounds of Phymatosorus scolopendria (Burm.F.) Pic. Serm.  for further in vitro and in vivo studies for its anticancer benefits especially related to lung cancer.

scholarly journals In silico Study of the Interactions between Schiff Base Polyphenols and HPV 16 E6/E6AP/p53 complex

2021 ◽  
pp. 3973-3980
Author(s):  
Jeremiah I. Ogah ◽  
Olatunji M. Kolawole ◽  
Steven O. Oguntoye ◽  
Muhammed Mustapha Suleiman
Keyword(s):  
Molecular Docking ◽  
Anticancer Agents ◽  
In Silico ◽  
In Silico Analysis ◽  
Docking Study ◽  
Hydrogen Atoms ◽  
Molecular Docking Study ◽  
Hpv 16 ◽  
In Silico Study

The rise in the incidence of cervical cancer globally has accentuate attention to the potential role of polyphenols as anticancer agents. Different studies have demonstrated the role of some polyphenols in altering Human Papillomavirus (HPV) carcinogenesis. Thus, this study was aimed at establishing the potentials of Schiff-based polyphenols from imesatin and satin as anticancer agents through in silico analysis. The polyphenols were synthesized and characterized using elemental analyses, spectroscopic analyses, UV-visible, Infrared, and Nuclear Magnetic Resonance (1H NMR and 13C, NMR). Molecular docking study of the polyphenols was carried out using Auto Dock Vina. The oncogenic E6 protein structure of HPV 16 was obtained from the protein bank (ID: 4XR8). The E6 proteins were prepared using AutoDock tools. Water molecules were removed from the protein molecules while hydrogen atoms were added. Also, the structures of Curcumin and Isomericitrin were obtained from PubChem. Results showed that three different Schiff based polyphenols were obtained from the synthesis; 3-(2’,4’-dimethoxy benzylidene hydrazono) indoline-2-one (DMBH), 3-(2’-hydroxy-4’-methoxy benzylidene hydrazono) indoline-2-one (HMBD), and 3-((4-4’-((2’’, 4’’-dimethoxy benzylidene amino) benzyl)phenyl)imino) indoline-2-one (DMBP). Higher ability of the docked polyphenols to bind to the E6/E6AP/p53 complex when compared to Curcumin was revealed. Also, results showed that the binding energy of Curcumin and Isomericitrin were -7.1kcal/mol and -8.4kcal/mol respectively while that of the polyphenols ranged from -7.4kcal/mol to -7.9kcal/mol. The molecular docking results of the polyphenols used in this study further confirm their potentials as strong anti-cancer agents.

scholarly journals In silico docking analysis of selective bioactive compounds of Phyllanthus acidusaqueousfruit extractagainst MAPK1

Biomedicine ◽  
2021 ◽  
Vol 41 (2) ◽  
pp. 349-357
Author(s):  
E. Padmini ◽  
M. Kavitha
Keyword(s):  
Binding Energy ◽  
Cell Survival ◽  
Bioactive Compounds ◽  
In Silico ◽  
Docking Study ◽  
Mitogen Activated Protein Kinase ◽  
Molecular Docking Study ◽  
Ligand Complex ◽  
In Silico Docking ◽  
Methyl Prednisolone

Introduction and Aim: Phyllanthus acidus L.Skeels (Family: Phyllanthaceae) or Star Gooseberry which bears small, edible, juicy, sour, yellow berries fruit is known as a “liver tonic” in ayurvedic medicine. However, the behavior of the plant fruit or its constituents in cell apoptosis/cell survival is unknown. Hence, the purpose of thepresent study was to perform an in silico docking of selective bioactive compounds of aqueous extract of fruit of P.acidus (PAFAE) against MAPK1. Mitogen activated protein kinase is a family of serine threonine specific protein kinases- MAPK1/ERK1/2, JNK1-3, p38MAPK and ERK5.Activation ofMAPK1 promotes cell survival in certain tissues by inhibiting proapoptotic proteins and by stimulating anti apoptotic factors.   Methodology: In silico docking studies was carried out using bioinformatics tools.The active compounds (Trihomovitamin D3; 2Z,6Z,8Z,12E Hexadecatetraenoic acid, Methyl prednisolone, Hydroxysalmeterol and Tridesacetoxykhivorin) ofP.acidus aqueous fruit extract were docked against MAPK1 resulting in receptor-ligand complex.   Results: The binding energy is correlated with the probability of affinity and stable bound between ligand and its receptor.   Conclusion: The molecular docking study of selective bioactive compounds of PAFAE with MAPK1 protein revealed that Tridesacetoxykhivorinand Methyl Prednisolone, is having good interaction in favorable pose with MAPK1 as shownfrom theireffective binding energy(-7.79kcal/mol and -7.19 kcal/mol), strong bond length and interactions with active site of MAPK1.

scholarly journals Promising inhibitors against main protease of SARS CoV-2 from medicinal plants: In silico identification

2021 ◽  
Vol 72 (2) ◽  
pp. 159-169
Author(s):  
OLUWAKEMI EBENEZER ◽  
MICHAEL SHAPI
Keyword(s):  
Medicinal Plants ◽  
Binding Affinity ◽  
In Silico ◽  
Complex Analysis ◽  
Docking Studies ◽  
Lipinski’S Rule ◽  
Main Protease ◽  
Pharmacokinetic Properties ◽  
Lipinski’S Rule Of Five ◽  
In Silico Identification

Abstract Some compounds reported as active against SARS CoV were selected, and docking studies were performed using the main protease of SARS CoV-2 as the receptor. The docked complex analysis shows that the ligands selectively bind with the target residues and binding affinity of amentoflavone (–10.1 kcal mol–1), isotheaflavin-3’-gallate (–9.8 kcal mol–1), tomentin A and D (–8.0 and –8.8 kcal mol–1), theaflavin-3,3’-digallate (–8.6 kcal mol–1), papyriflavonol A (–8.4 kcal mol–1), iguesterin (–8.0 kcal mol–1) and savinin (–8.3 kcal mol–1) were ranked above the binding affinity of the reference, co-crystal ligand, ML188, a furan-2-carboxamide-based compound. To pinpoint the drug-like compound among the top-ranked compounds, the Lipinski’s rule of five and pharmacokinetic properties of all the selected compounds were evaluated. The results detailed that savinin exhibits high gastrointestinal absorption and can penetrate through the blood-brain barrier. Also, modifying these natural scaffolds with excellent binding affinity may lead to discovering of anti-SARS CoV agents with promising safety profiles.

In silico insight into the inhibitory effects of active antidiabetic compounds from medicinal plants against SARS-CoV-2 replication and posttranslational modification

Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Habibu Tijjani ◽  
Adamu Idris Matinja ◽  
Ahmed Olatunde ◽  
Maryam Haladu Zangoma ◽  
Abubakar Mohammed ◽  
...  
Keyword(s):  
Medicinal Plants ◽  
In Silico ◽  
Experimental Studies ◽  
Inhibitory Effects ◽  
Post Translational Modifications ◽  
Lipinski’S Rule ◽  
In Silico Studies ◽  
Lipinski’S Rule Of Five ◽  
Mutation Assay ◽  
Insight Into

Background: The recent reemergence of the coronavirus (COVID-19) caused by the virus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has prompted for the search of effective treatments in forms of drugs and vaccines. Aim: In this regards, we performed an in silico studies of 39 active antidiabetic compounds from medicinal plants to provide insight into their possible inhibitory potentials against SARS-CoV-2 replications and post-translational modifications. Top 12 active antidiabetic compounds with potential for dual inhibition of the replications and post-translational modifications of SARS-CoV-2 were analyzed. Results: Boswellic acids, celastrol, rutin, sanguinarine, silymarin and withanolides expressed binding energy for 3- chymotrypsin-like protease (3CLpro) (-8.0 to -8.9 Kcal/mol), papain-like protease (PLpro) (-9.1 to -10.2 Kcal/mol) and RNA-dependent RNA polymerase (RdRp) (-8.5 to -9.1 Kcal/mol) which were higher than that of the reference drugs (Lopinavir and Remdesivir) used in this study. Sanguinarine, silymarin and withanolides are most drugable phytochemicals among the other following phytochemicals as they obey the Lipinski’s rule of five analyses. Sanguinarine, silymarin and withanolides express moderately soluble with no hepatotoxicity, while silymarin and withanolides cannot permeate the blood-brain barrier and showed no Salmonella typhimurium reverse mutation assay (AMES) toxicity, unlike sanguinarine from the predictive absorption, distribution, metabolism, elimination, and toxicity (ADMET) studies. Conclusion: Sanguinarine, silymarin and withanolides could be proposed for further experimental studies for their development as possible phytotherapy for the COVID-19 pandemic.

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