scholarly journals Combination of Curcumin from Curcuma longa and Procyanidin from Tamarindus indica in Inhibiting Cyclooxygenases for Primary Dysmenorrhea Therapy: In silico study

2020 ◽  
Vol 11 (1) ◽  
pp. 7460-7467
Keyword(s):  
Binding Affinity ◽  
Bioactive Compounds ◽  
In Silico ◽  
Curcuma Longa ◽  
Complex Form ◽  
Bioactive Compound ◽  
Primary Dysmenorrhea ◽  
Tamarindus Indica ◽  
Ligand Interaction ◽  
Discovery Studio

Turmeric (Curcuma longa) and Tamarind (Tamarindus indica) are known for the anti-inflammatory and antioxidant activity. The major bioactive compound found in turmeric is curcumin, and tamarind is procyanidin. Both compounds could reduce prostaglandin concentration, leading to the reduction of primary dysmenorrhea by inhibiting COXs. This study aims to identify the interaction of tamarind and turmeric bioactive compounds as single isolated compound and complex compounds to COXs using in silico as a model study. Proteins and bioactive compounds were obtained from PDB database and Pubchem, respectively. Both proteins and ligands will be prepared using Discovery Studio Client 3.5 and PyRx 0.8. The interaction will be performed by docking using Autodock Vina in PyRx 0.8. It showed that turmeric and tamarind bioactive compounds in single isolated form have potency in inhibiting COX-1/COX-2, and both ligands bind to the catalytic site of proteins. Binding sites are surrounding the binding site of the natural substrate with an efficient binding affinity. In the complex form of turmeric-tamarind, the binding affinity is not as efficient as single compounds. However, its complex form of both compounds provides strong inhibition. This study suggested that complex forms of curcumin and procyanidin can reduce prostaglandin concentration and stabilize protein-ligand interaction lead to healing dysmenorrhea.

scholarly journals Phytocompounds of Curcuma longa extract are more effective against bacterial biofilm than pure curcumin only: An in-vitro and in-silico analysis

2021 ◽  
Vol 48 (2) ◽  
Author(s):  
Dibyajit Lahiri ◽  
◽  
Moupriya Nag ◽  
Soumik Dey ◽  
Bandita Dutta ◽  
...  
Keyword(s):  
Bioactive Compounds ◽  
In Silico ◽  
Methyl Palmitate ◽  
Curcuma Longa ◽  
Research Work ◽  
Bioactive Compound ◽  
Bacterial Biofilm ◽  
Antibiofilm Activity ◽  
Electron Microscopic ◽  
In Silico Studies

Bioactive compounds are the group of secondary metabolites of plants that have a potent impact on antimicrobial and antibiofilm agents. Although Curcuma longa (turmeric) is well known for its antimicrobial activity, the question arises if curcumin, the primary bioactive compound is only responsible for it or the synergistic and simultaneous contribution of more than one bioactive compound are responsible for this antibiofilm efficacy. The research work aims to determine the efficacy of the extract Curcuma longa has a higher potential of antimicrobial and antibiofilm activity than the purchased curcumin and standard antibiotic. Present work was initiated with GC-MS analysis of the ethanolic extract of Curcuma longa (turmeric) and showed that in addition to curcumin, methyl palmitate de-hydro zingerone had a higher percent of availability within the extract. The in-silico studies also showed that when targeted upon Gram-positive biofilm-forming protein of Staphylococcus aureus (3TIP), curcumin alone had a binding constant value of -6.33 Kcal/mol but showed a value of -17.811 Kcal/mol when acted in association with Dehydrozingerone. Similarly, the binding constant's value changed from -6.07 Kcal/mol to - 23.844 Kcal/mol, when Gram-negative biofilm-forming protein (3ZYB) of Pseudomonas aeruginosa was acted upon by curcumin only and in association with methyl palmitate, respectively. Lower minimum inhibitory concentration (MIC) and higher effectivity in reducing the bacterial quorum sensing (QS) activity of the turmeric extract than pure Curcumin indicated the higher antimicrobial and antibiofilm efficiency of the extract, respectively. This indicated clearly that the synergistic action of all the bioactive compounds imparts the antibiofilm activity of turmeric. The result was further confirmed by the scanning electron microscopic (SEM) studies, fluorescent microscopic studies, and FTIR analysis of EPS as well.

scholarly journals Characterization of α-Glucosidase Inhibitors from Psychotria malayana Jack Leaves Extract Using LC-MS-Based Multivariate Data Analysis and In-Silico Molecular Docking

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5885
Author(s):  
Tanzina Sharmin Nipun ◽  
Alfi Khatib ◽  
Zalikha Ibrahim ◽  
Qamar Uddin Ahmed ◽  
Irna Elina Redzwan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Data Analysis ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
In Silico ◽  
Multivariate Data Analysis ◽  
Multivariate Data ◽  
Partial Least Square ◽  
Protein Data Bank Code ◽  
Glucosidase Inhibitors

Psychotria malayana Jack has traditionally been used to treat diabetes. Despite its potential, the scientific proof in relation to this plant is still lacking. Thus, the present study aimed to investigate the α-glucosidase inhibitors in P.malayana leaf extracts using a metabolomics approach and to elucidate the ligand–protein interactions through in silico techniques. The plant leaves were extracted with methanol and water at five various ratios (100, 75, 50, 25 and 0% v/v; water–methanol). Each extract was tested for α-glucosidase inhibition, followed by analysis using liquid chromatography tandem to mass spectrometry. The data were further subjected to multivariate data analysis by means of an orthogonal partial least square in order to correlate the chemical profile and the bioactivity. The loading plots revealed that the m/z signals correspond to the activity of α-glucosidase inhibitors, which led to the identification of three putative bioactive compounds, namely 5′-hydroxymethyl-1′-(1, 2, 3, 9-tetrahydro-pyrrolo (2, 1-b) quinazolin-1-yl)-heptan-1′-one (1), α-terpinyl-β-glucoside (2), and machaeridiol-A (3). Molecular docking of the identified inhibitors was performed using Auto Dock Vina software against the crystal structure of Saccharomyces cerevisiae isomaltase (Protein Data Bank code: 3A4A). Four hydrogen bonds were detected in the docked complex, involving several residues, namely ASP352, ARG213, ARG442, GLU277, GLN279, HIE280, and GLU411. Compound 1, 2, and 3 showed binding affinity values of −8.3, −7.6, and −10.0 kcal/mol, respectively, which indicate the good binding ability of the compounds towards the enzyme when compared to that of quercetin, a known α-glucosidase inhibitor. The three identified compounds that showed potential binding affinity towards the enzymatic protein in molecular docking interactions could be the bioactive compounds associated with the traditional use of this plant.

scholarly journals STUDI MOLECULAR DOCKING SENYAWA GOLONGAN FLAVONOL SEBAGAI ANTIBAKTERI

2018 ◽  
Vol 1 (2) ◽  
pp. 20-27
Author(s):  
Isna Wardaniati ◽  
Muhammad Azhari Herli
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
In Silico ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Receptor Interactions

In this paper we studied the bioactive compounds of Flavonol-D-alanil D-alanin dekarboksipeptidase receptor interactions In silico. First, prepared three dimensional structure of D-alanil D-alanin dekarboksipeptidase as receptor. Preparation of fourth bioactive compounds of flavonol which will be as ligands, klokasilin and D-alanil D-alanin as a comparison. The fourth bioactive compounds of flavonol, klokasilin and D-alanil D-alanin were docked with D-alanil D-alanin dekarboksipeptidase until energy values were obtained. The fourth bioactive compounds of flavonol had lesser binding energy values than D-alanil D-alanin, Quercitrine and rutin also predicted to have greater binding energy and binding affinity than klokasilin (antibiotic) and D-alanil D-alanin (nature ligand).

scholarly journals Molecular Docking Terhadap Senyawa Kurkumin dan Arturmeron pada Tumbuhan Kunyit (Curcuma Longa Linn.) yang Berpotensi Menghambat Virus Corona

2021 ◽  
Vol 9 (2) ◽  
Author(s):  
Tiara C. Pradani ◽  
. Fatimawali ◽  
Aaltje E. Manampiring ◽  
Billy J. Kepel ◽  
Fona D. Budiarso ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
In Silico ◽  
Virus Disease ◽  
Curcuma Longa ◽  
Positive Control ◽  
Tropical Plant ◽  
Corona Virus ◽  
Main Protease ◽  
Close Relationship

Abstract: At the end of 2019 the world was shocked by the emergence of a new virus, namely the corona virus (SARS-CoV 2) which is called Corona Virus Disease 2019 or COVID-19. The origin of the emergence of this virus is known to have originated in the city of Wuhan, Hubei Province, China in December 2019.1 Research shows a close relationship with the corona virus that causes Severe Acute Respitatory Syndrome (SARS) which broke out in Hong Kong in 2003, until WHO named it the novel corona virus ( nCoV19). Turmeric (Curcuma longa L.) is a tropical plant that has many benefits and is found in many parts of Indonesia. Turmeric is widely used by the community as a traditional medicine to treat several diseases, such as: anti-inflammatory, antioxidant, hepatoprotective, and others. This study aims to determine the content in several compounds in the turmeric plant that have the potential to inhibit COVID-19 by using the molecular docking method. Using the In Silico method, namely molecular docking with the compounds taken were curcumin and ar-turmerone and the main protease COVID-19 (6LU7). This study obtained the binding affinity of curcumin compounds, namely -7.2 and Ar-turmerone -5.8 compounds against Mpro COVID-19. Remdesivir, which was used as a positive control, had a binding affinity of -7.7. In conclusion, remdesivir got better results compared to curcumin and Ar-turmerone compounds.Keywords: Molecular Docking, Turmeric, COVID-19.  Abstrak: Pada akhir tahun 2019 dunia digemparkan dengan munculnya virus baru yaitu corona virus (SARS-CoV 2) yang disebut dengan Corona Virus Disease 2019 atau COVID-19. Awal mula munculnya virus ini diketahui berasal dari Kota Wuhan, Provinsi Hubei, China pada Desember 2019.1  Penelitian menunjukkan hubungan yang dekat dengan virus corona penyebab Severe Acute Respitatory Syndrome (SARS) yang mewabah di Hongkong pada tahun 2003, hingga WHO menamakannya sebagai novel corona virus (nCoV19). Kunyit (Curcuma longa L.) merupakan salah satu jenis tanaman tropis yang banyak memiliki manfaat dan banyak ditemukan di wilayah Indonesia. Kunyit banyak dimanfaatkan masyarakat sebagai obat tradisional untuk mengobati beberapa penyakit seperti: antiinflamasi, antioksidan, hepatoprotektor, dan lain-lain. Penelitian ini bertujuan untuk mengetahui kandungan dalam beberapa senyawa pada tumbuhan kunyit yang berpotensi menghambat COVID-19 dengan metode molecular docking. Menggunakan metode In Silico yaitu molecular docking dengan senyawa yang diambil adalah kurkumin dan ar-Turmerone dan main protease COVID-19 (6LU7). Penelitian ini didapatkan hasil binding affinity senyawa kurkumin yaitu -7.2 dan senyawa ar-turmeron -5.8 terhadap Mpro COVID-19. Remdesivir yang digunakan sebagai control positif mendapatkan hasil binding affinity yaitu -7.7. Sebagai simpulan, remdesivir mendapat hasil yang lebih baik dibandingkan dengan senyawa kurkumin dan ar-turmeron.Kata Kunci: Molecular Docking, Kunyit, COVID-19.

scholarly journals Homology modeling of actin protein in Leishmania donovani and in silico prediction of active drugs

2020 ◽  
Vol 2 ◽  
pp. 52-57
Author(s):  
Dimpal Rani Bansal ◽  
Hanumanthrao Chandershekar Patil ◽  
Rajesh Kumari Patil
Keyword(s):  
Homology Modeling ◽  
Binding Affinity ◽  
In Silico ◽  
Structure Prediction ◽  
Leishmania Donovani ◽  
Secondary Structure Prediction ◽  
3D Structure ◽  
Data Bank ◽  
Discovery Studio ◽  
Actin Protein

Objectives: Leishmaniasis is a disease caused by leishmania parasite which is genus of trypanosome protozoa. Leishmania donovani promastigote inhibits biogenesis of phagolysosome due to the accumulation of periphagosomal F-actin. This inhibition of phagosome maturation gives favorable environment for differentiation of promastigote-to-amastigote and causes disease progression. L. donovani actin (LdACT) has been found to have unconventional biochemical behavior due to the different amino acid region in its sequence suggesting that it must have a three-dimensional (3D) structure different from eukaryotic actins making it a more specific for predication of antileishmanial drugs which is main objective of this study. Material and Methods: For carrying out this study, protein sequence was retrieved from the database SWISSPROT, analyzed by BIOEDIT software followed by primary and secondary structure prediction by PROTPARAM and SOPMA. A 3D structure of same was constructed by homology modeling using the yeast actin-human gelsolin segment 1 complex (protein data bank [PDB] ID:1yag) as a template with the help of Swiss model. The final model obtained was further accessed by PROCHECK and VERIFY 3D software which ensured the reliability of the model. This model of actin protein was further used for screening different chemical compounds with high binding affinity by GOLD and DISCOVERY STUDIO. Results: The results give information about the some inhibitors having highest binding affinity to the actin protein. Conclusion: This study will be useful for the development of pharmacophore models for in silico predication of active drugs as a part of antileishmanial drug therapy.

scholarly journals Antimalarial Flavonoid-Glycoside from Acacia pennata with Inhibitory Potential Against PfDHFR-TS: An In-silico Study

2021 ◽  
Vol 12 (4) ◽  
pp. 4871-4887
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Enzyme Inhibitor ◽  
Docking Simulation ◽  
Flavonoid Glycoside ◽  
Flavonoid Glycosides ◽  
Discovery Studio ◽  
Antimalarial Agents ◽  
In Silico Studies ◽  
Inhibitory Potential

Drug resistance, toxicity, and adverse effects of current antimalarial drugs have mandated the need to search for newer antimalarial agents. The present study aims to identify promising flavonoid-glycosides (FGs) from Acacia pennata as possible antimalarial agents effective against PfDHFR-TS (PDB ID: 3DGA) by in-silico studies. The co-crystal inhibitor (RJ1) of PfDHFR-TS was used as the reference standard compound. A compound library of 17 FGs reported to be isolated from A. pennata was prepared and subjected to molecular docking simulation studies. PyRx 0.8 and AutoDock Vina revealed Pinocembrin-7-O-β-D-glucopyranoside (FG17) as the best PfDHFR-TS inhibitor with a binding affinity of -10.4 kcal/mol and -10.8 kcal/mol, respectively. In both methods, FG17 has a better binding affinity than the co-crystal inhibitor, RJ1 (-7.9 kcal/mol). The docking protocols were validated by RMSD calculation with Discovery Studio Visualizer software (2020). FG17 interacted with amino acids ALA16, LEU40, SER167, GLY41, GLY44, MET55, PHE58, ILE112, LEU119, GLY166, and TYR170 at the active binding site of PfDHFR-TS. Further, FG17 was computed as a non-toxic, bioavailable, synthetically accessible compound and a better enzyme inhibitor than RJ1. Hence, we conclude that FG17 may be used as a lead scaffold to design antimalarial agents against PfDHFR-TS in the future.

scholarly journals IN SILICO DOCKING ANALYSIS OF BIOACTIVE COMPOUNDS FROM CALOPHYLLUM INOPHYLLUM L. ETHANOL LEAF EXTRACT AGAINST EGFR PROTEIN

2017 ◽  
Vol 10 (8) ◽  
pp. 214 ◽  
Author(s):  
Jaikumar K ◽  
Sheik Noor Mohamed ◽  
John Wyson W ◽  
Deventhiran M ◽  
Babu A ◽  
...  
Keyword(s):  
Bioactive Compounds ◽  
In Silico ◽  
Leaf Extract ◽  
Growth Factor Receptor ◽  
Docking Studies ◽  
Docking Analysis ◽  
Calophyllum Inophyllum ◽  
Discovery Studio ◽  
In Silico Docking ◽  
Ms Analysis

Objective: The objective of this study was to evaluate the effective new phytocomponents from Calophyllum inophyllum ethanol leaf extract against breast cancer target protein of Epidermal Growth Factor Receptor (EGFR) using in silico docking studies.Materials and Methods: The identification of compounds was done by GC-MS analysis. The in silico docking studies were carried out using Discovery Studio 4.0 software.Results: The GC-MS analysis of ethanol leaf extract revealed the presence of eleven compounds. The docking analysis have exhibited moderate to potent inhibition with a range of dock score 3 to 55. 2H-Benzo(cd) pyrene-2,6(1,H)-dione, 3,5,7,10-tetrahydroxy-compound showed the dock score of 55.427.Conclusion: The results revealed out that the compounds present in Calophyllum inophyllum can inhibit the EGFR protein. The plant possesses anticancer potential because of the various bioactive compounds presence which is mainly responsible for anticancer activity. 

scholarly journals APPLICATION OF IN SILICO STUDIES TARGETING TELOMERIC G-QUADRUPLEX COMPLEX BY PERYLENE DIIMIDES FOR ANTICANCER THERAPY

2018 ◽  
Vol 11 ◽  
Author(s):  
Hemalatha Cn, ◽  
Vijey Aanandhi M
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Data Bank ◽  
Anticancer Therapy ◽  
Standard Drug ◽  
Perylene Diimides ◽  
Discovery Studio ◽  
In Silico Studies ◽  
G Quadruplex ◽  
Ic50 Values

Objective: Telomerase enzyme which is expressed in detectable levels and its mechanism was that it increases the length when it binds to telomeres. This eventually leads to extension of lifespan of cells and also makes an attractive target for cancer therapy. Perylene diimides bind to telomerase with duplex genomic DNA, and these G-quadruplex ligands are of responsible for binding affinity with respective proteins. Based on the IC50 values of perylene diimides, QSAR has been studied out and the results are elaborated in preliminary research works. From the results of QSAR, the selected perylene ligands are selected for docking choosing telomerase as a target/protein. From the results of in silico studies, new compounds are designed and synthesized accordingly. Now, the objective of the study was to dock the final synthesized compounds with the telomerase protein to study regarding the pKi value using G-quadruplex ligand database (G4LDB). The docked results are visualized using Discovery Studio Visualizer 4.1. The results are compared with the standard N,N’-bis-(2-(1-piperidino)ethyl)-3,4,9,10-perylene tetracarboxylic acid diimide (PIPER) drug and these compounds will be effective for anticancer therapy.Methods: The study was to investigate the docking results of synthesized perylene compounds with the results from G4LDB and visualized by Discovery Studio 4.1 Visualizer. The telomerase proteins selected for the study were extracted from Protein Data Bank, and the proteins selected for the study are 3SC8 and 3CE5. Among the compounds (R1, R2, R3, and R4) screened in G-Quadruplex Ligand Database, compound R3 shows better binding affinity with good pKi value as well the interactions with the protein and ligand show better affinity with the targets and these are compared with the standard drug PIPER drug.Results: Compound R3 possesses the best binding affinity with the target 3CE5 and 3SC8 which shows that the compound will be effective for anticancer therapy.

scholarly journals Interaction of Selected Terpenoids From Dalbergia sissoo With Catalytic Domain of Matrix Metalloproteinase-1: An In Silico Assessment of Their Anti-wrinkling Potential

2019 ◽  
Vol 13 ◽  
pp. 117793221989653 ◽  
Author(s):  
Shagufta Yasmeen ◽  
Promila Gupta
Keyword(s):  
Matrix Metalloproteinase ◽  
Binding Affinity ◽  
In Silico ◽  
Catalytic Domain ◽  
Hydroxyl Groups ◽  
Dalbergia Sissoo ◽  
Ligand Interaction ◽  
Reference Drug ◽  
Matrix Metalloproteinase 1 ◽  
Lupeol Acetate

Matrix metalloproteinase-1 (MMP-1) is a predominant collagenase enzyme that cleaves collagen fibers, contributing to skin wrinkling. Matrix metalloproteinase-1 inhibitors of herbal origin may provide an earnest probability to offer a novel curative approach against MMP-1-mediated collagenolysis, prompted by ultraviolet (UV)-induced overexpression of MMP-1. In this in silico study, we have explored the MMP-1 inhibitory potential of selected terpenoids from Dalbergia sissoo extracts. Two triterpenoids (lupeol and betulin), 1 diterpenoid (phytol), and 1 ester derivative of lupeol (lupeol acetate) were studied along with a reference inhibitor (doxycycline) using molecular docking approach. Non covalent interaction between the target ligands was found. Lupeol was found interacting with amino acid (AA) residues in the catalytic domain of MMP-1 with 3 hydrogen bonds (H-bond) formation, phytol with 1 and doxycycline with 2 H-bonds, whereas betulin and lupeol acetate were not able to form any H-bond with the AA residues in the catalytic site of the target protein. However, hydrophobic interaction between these ligands and protein was evident with select residues. The binding affinity of lupeol was highest (binding free energy, Δ G = −8.24 kcal/mol), which was greater than reference drug, doxycycline (Δ G = −8.05 kcal/mol). Lupeol acetate and phytol displayed a Δ G value of −7.12 and −7.06 kcal/mol, respectively, whereas betulin holds less binding affinity for the target receptor (Δ G = −4.66 kcal/mol). In silico pharmacokinetic studies demonstrated drug-like properties of the ligand compounds. This study shows that hydroxyl groups present in the ligands play a substantial role in establishing protein ligand interaction via hydrogen bonding.

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