scholarly journals In Silico Study to Assess Antibacterial Activity from Cladophora Sp. on Peptide Deformylase: Molecular Docking Approach

2019 ◽  
Vol 2 (1) ◽  
pp. 20-23
Author(s):  
Yoni Rina Bintari ◽  
Rio Risandiansyah
Keyword(s):  
Molecular Docking ◽  
Stearic Acid ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
Drug Target ◽  
Pathogenic Bacteria ◽  
Peptide Deformylase ◽  
Severe Problem ◽  
New Drug ◽  
Docking Approach

Increasing antibiotic-resistant pathogenic bacteria is a severe problem in the world. Therefore, there is a need to identify new drugs from natural products and also new drug targets. Cladophora sp. is a marine organism which is known to have bioactive compounds and a potential antibacterial. On the other hand, Peptide Deformylase (PDf) may prove to be a novel drug target since it is crucial for native peptide functioning in most pathogenic bacteria. This study screens for PDf inhibition activity of compounds from Cladophora sp. using molecular docking approach and screening the binding affinity of bioactive compounds against the peptide receptor PDf using Pyrex Autodock Vina software. Docking results were stored and visualized using Biovia Discovery Studio and PyMOL ligand. Ligands were obtained from previous literature in PubChem, and receptor peptide PDf from pathogenic bacteria: Pseudomonas aeruginosa (PDB ID:1N5N), Escherichia coli (PDB ID:1BSK), Enterococcus faecium (PDB ID:3G6N) and Staphylococcus aureus (PDB ID:1LQW), was obtained from the peptide data bank. The results of this screening show with ligand the highest binding affinity against PDf of P. aeruginosa, E. coli, E. faecium, and S. aureus is stearic acid (-5.9 kcal/mol), eicosapentaenoic acid (-6.6 kcal/mol), stearic acid (-5.8 kcal/mol), and stearic acid (-6.2 kcal/mol) respectively. The binding of natural compounds from Cladophora sp. with PDf models may provide a new drug with a different drug target for antibacterial potential.

scholarly journals Hepatoprotective Activity of Pirdot Leaves (Saurauia vulcani Korth) Ethanol Extract in Laboratory Rats (Rattus norvegicus) and Characterization of Bioactive Compounds Using a Molecular Docking Approach

2021 ◽  
Vol 9 (A) ◽  
pp. 1265-1270
Author(s):  
Erlintan Sinaga ◽  
Syafruddin Ilyas ◽  
Salomo Hutahaean ◽  
Panal Sitorus
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
Ethanol Extract ◽  
Treated Group ◽  
Hepatoprotective Activity ◽  
Tnf Α ◽  
Pomolic Acid ◽  
Docking Approach ◽  
Cox 2

AIM: The hepatoprotective activities of  bioactive compounds Pirdot were investigated in vivo and in silico. METHODS: In this study, the completely randomized design non-factorial was experimentally to assess the value of SGPT and SGOT and twenty four adult male rats were divided into four groups : group G0, control group; group G1, a treated group received 0.1 ml sheep red blood cell; group G2, a treated group received 500 mg ethanol extract Pirdot; group G3, a group treated received 500 mg ethanol extract Pirdot and 0,1 ml sheep red blood cell. On thirty one days of treatment, the blood of all rats group were taken to value SGPT and SGOT using DiaLab kit. Furthermore, the molecular docking study was done to analyse molecular interaction that COX-2 and  TNF-α were the primary target protein of bioactive compounds of Pirdot associated with hepatoprotective activities. In addition, it tends to be the target of non-steroidal anti-inflammatory drugs such as Ibuprofen. RESULTS: The results show SGOT and SGPT value significantly [p<0.05] decreased on Group G2 and G3. Moreover, the bioactive compounds of Pirdot, such as Pomolic acid and Ursolic acid tend to be the potential compound on liver protection. Moreover, Pomolic acid has a good binding affinity -14.6 kcal mol-1 with COX-2 Protein and the binding affinity of cis-3-O-p-hydroxycinnamoyl Ursolic acid was -15.1 kcal mol-1 associated with TNF-α Protein. CONLUSION:  Pirdot Leaves (Saurauia vulcani Korth.)  Ethanol Extract showed Hepatoprotective activity in rats (Rattus norvegicus). Molecular docking approach showed that pomolic acid has a good binding affinity with COX-2 Protein and TNF-α Protein.

scholarly journals Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

2021 ◽  
Vol 22 (7) ◽  
pp. 3595
Author(s):  
Md Afjalus Afjalus Siraj ◽  
Md. Sajjadur Rahman ◽  
Ghee T. Tan ◽  
Veronique Seidel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cannabinoid Type 1 Receptor ◽  
Docking Approach

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.

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 TEA BIOACTIVE COMPOUNDS AS INHIBITOR OF MRSA PENICILLIN BINDING PROTEIN 2a (PBP2a): A MOLECULAR DOCKING STUDY

2021 ◽  
Vol 3 (2) ◽  
pp. 70
Author(s):  
Marko Jeremia Kalalo ◽  
Fatimawali Fatimawali ◽  
Tekla Kalalo ◽  
Christani I J Rambi
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Bioactive Compounds ◽  
Docking Study ◽  
Antibacterial Activities ◽  
Multidrug Resistant ◽  
Tea Polyphenols ◽  
Resistant Bacteria ◽  
Molecular Docking Study ◽  
Docking Approach

ABSTRACT Methicillin-Resistant Staphylococcus aureus (MRSA) is a hypervirulent multidrug- resistant bacteria. It is spreading around the globe and starting to be a global health problem. It causes bacteremia, infective endocarditis, and bloodstream infection. PBP2a is a protein responsible for MRSA’s resistance to antibiotics, especially beta-lactams. Tea contains bioactive compounds such as polyphenols. It is known to have great antibacterial activities. Therefore, this study aims to find potentials antibacterial compounds from tea polyphenols that can inhibit PBP2a in MRSA with better binding energy than the currently available drugs using the molecular docking approach. We found that theaflavin (-9,7 kcal/mol), as one of the tea polyphenols compound, has a better binding energy with ceftaroline (9,5 kcal/mol) therefore predicted to have better antibacterial activity. (−)- Epigallocatechingallate (-9,1 kcal/mol), (−)-epicatechingallate (-8,8 kcal/mol), myricetin (- 8,7 kcal/mol), quercetin (-8,5 kcal/mol), (−)-epicatechin (-8,3 kcal/mol), (−)- epigallocatechin (-8,3 kcal/mol), kaempferol (-8,3 kcal/mol), procyanidin B2 (-8,1), and theflavindigallate (-7,6 kcal/mol) also have the potential to inhibit MRSA due to its low binding energy. Key words : Molecular docking, MRSA, PBP2a, Tea polyphenols.

scholarly journals Evaluation of Seaweed Sulfated Polysaccharides As Natural Antagonists Targeting Salmonella typhi OmpF: Molecular Docking and Pharmacokinetic Profiling

2021 ◽  
Author(s):  
ARUN KUMAR MALAISAMY ◽  
Mahalakshmi Murugan ◽  
Ashok Kumar Vairamuthu ◽  
Manikka Kubendran Aravind ◽  
Sathaiah Gunaseelan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Pathogenic Bacteria ◽  
Biological Activities ◽  
Salmonella Typhi ◽  
Sulfated Polysaccharides ◽  
Drug Resistant ◽  
Bacterial Strains ◽  
Microbial Diseases ◽  
Wide Range ◽  
Docking Approach

Abstract Background: Salmonella belongs to the Enterobacteriaceae family, a gram-negative, non-spore-forming, rod-shaped, motile, and pathogenic bacteria that transmit through unhygienic conditions. It is estimated that 21 million new infections arise every year, resulting in approximately 200,000 deaths. It is more prevalent among children, the old aged, and immunocompromised individuals. The frequent usage of classical antimicrobials has begun the increasing emergence of various drug-resistant pathogenic bacterial strains. Hence, this study was intended to evaluate the bioactive seaweed sulfated polysaccharides (SSP) against the ompF (outer membrane porin F) protein target of Salmonella typhi. SSP are sulfated compounds with a wide range of biological activities, such as anti-microbial, anti-allergy, anti-cancer, anti-coagulant, anti-inflammation, anti-oxidant, and anti-viral. Results: In this study, eleven compounds were targeted against S. typhi OmpF by molecular docking approach and were compared with two commercially available typhoid medications. The SSP showed good binding affinity compared to commercial drugs, particularly carrageenan/MIV-150, carrageenan lambda, fucoidan, and 3-Phenyllactate, ranked as top antagonists against OmpF. Further, pharmacokinetics and toxicology (ADMET) studies corroborated that SSP possessed drug-likeness and highly progressed in all parameters.Conclusion: AutoDockTools and Schrodinger's QikProp module results suggest that SSP could be a promising drug for extensively drug-resistant (XDR) S. typhi. To our best of knowledge, this is the first report on in-silico analysis of SSP against S. typhi OmpF. Thus, implying the capabilities of SSP's especially compounds like carrageenans, as a potential anti-microbial agent against Salmonella typhi infections. Eventually, advanced studies could corroborate SSPs to the next level of application in the crisis of XDR microbial diseases.

scholarly journals Molecular docking studies of pancreatic cancer expressed proteins with Psidium guajava (guava) derived bioactive compounds

2020 ◽  
Vol 11 (SPL4) ◽  
pp. 3176-3183
Author(s):  
Tharrun Daniel Paul L ◽  
Roshan Kumar Sah ◽  
Thirunavukkarasu Palaniyandi
Keyword(s):  
Pancreatic Cancer ◽  
Molecular Docking ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
Ethanolic Extract ◽  
Psidium Guajava ◽  
Docking Studies ◽  
Discovery Studio ◽  
Gene And Protein Expression

The current study evaluates the binding affinities (kcal/mol) of different proteins expressed in pancreatic cancer with Psidium guajava derived bioactive compounds by performing molecular docking through auto dock vina. Auto dock vina was used to perform molecular docking between the proteins expressed in pancreatic cancer and P. guajava derived bioactive compounds. Nine proteins and nine ligands were chosen for molecular docking. Among the nine ligands, gemcitabine which is a commercial first-line drug used to treat pancreatic cancer, was selected. The docking output was visualized using the Biovia Discovery Studio visualizer. From the docking results, we found that, out of the nine ligands, quercetin had a better binding affinity than the other ligands and the commercial drug (gemcitabine). SNAI1 docked with quercetin had a binding affinity of -9.6 kcal/mol, which was found to be the highest. In conclusion, it can be said that the compound quercetin derived from the ethanolic extract of the P. guajava has the highest binding affinity, so it can be used for the treatment of pancreatic cancer after modification to its properties so that it has good efficacy and pharmacokinetic properties. Further studies will be based on the in-vitro testing of the extract and gene and protein expression analysis using RT-PCR and MALDI-TOF, respectively.

scholarly journals Molecular docking and dynamics simulation study of bioactive compounds from Ficus carica L. with important anticancer drug targets

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254035
Author(s):  
Arun Bahadur Gurung ◽  
Mohammad Ajmal Ali ◽  
Joongku Lee ◽  
Mohammad Abul Farah ◽  
Khalid Mashay Al-Anazi
Keyword(s):  
Molecular Docking ◽  
Molecular Mechanics ◽  
Surface Area ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
Anticancer Drug ◽  
Drug Targets ◽  
Ficus Carica ◽  
Dynamics Simulation ◽  
Cyclin Dependent Kinase

Ficus carica L., commonly known as fig, has been used in traditional medicine for metabolic disorders, cardiovascular diseases, respiratory diseases and cancer. Various bioactive compounds have been previously isolated from the leaves, fruit, and bark, which have different pharmacological properties, but the anticancer mechanisms of this plant are not known. In the current study we focused on understanding the probable mechanisms underlying the anticancer activity of F. carica plant extracts by molecular docking and dynamic simulation approaches. We evaluated the drug-likeness of the active constituents of the plant and explored its binding affinity with selected anticancer drug target receptors such as cyclin-dependent kinase 2 (CDK-2), cyclin-dependent kinase 6 (CDK-6), topoisomerase-I (Topo I), topoisomerase-II (Topo II), B-cell lymphoma 2 (Bcl-2), and vascular endothelial growth factor receptor 2 (VEGFR-2). In silico toxicity studies revealed that thirteen molecules out of sixty-eight major active compounds in the plant extract have acceptable drug-like properties. Compound 37 (β-bourbonene) has a good binding affinity with the majority of drug targets, as revealed by molecular docking studies. The complexes of the lead molecules with the drug receptors were stable in terms of molecular dynamics simulation derived parameters such as root mean square deviation and radius of gyration. The top ten residues contributing significantly to the binding free energies were deciphered through analysis of molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA). Thus, the results of our studies unravel the potential of F. carica bioactive compounds as anticancer candidate molecules against selected macromolecular receptors.

scholarly journals Evaluation of seaweed sulfated polysaccharides as natural antagonists targeting Salmonella typhi OmpF: molecular docking and pharmacokinetic profiling

2022 ◽  
Vol 11 (1) ◽  
Author(s):  
Malaisamy Arunkumar ◽  
Murugan Mahalakshmi ◽  
Vairamuthu Ashokkumar ◽  
Manikka Kubendran Aravind ◽  
Sathaiah Gunaseelan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Pathogenic Bacteria ◽  
Biological Activities ◽  
Salmonella Typhi ◽  
Sulfated Polysaccharides ◽  
Drug Resistant ◽  
Bacterial Strains ◽  
Microbial Diseases ◽  
Wide Range ◽  
Docking Approach

Abstract Background Salmonella belongs to the Enterobacteriaceae family, a gram-negative, non-spore-forming, rod-shaped, motile, and pathogenic bacteria that transmit through unhygienic conditions. It is estimated that 21 million new infections arise every year, resulting in approximately 200,000 deaths. It is more prevalent among children, the old aged, and immunocompromised individuals. The frequent usage of classical antimicrobials has begun the increasing emergence of various drug-resistant pathogenic bacterial strains. Hence, this study was intended to evaluate the bioactive seaweed sulfated polysaccharides (SSPs) against the ompF (outer membrane porin F) protein target of Salmonella typhi. SSP is the sulfated compound with a wide range of biological activities, such as anti-microbial, anti-allergy, anti-cancer, anti-coagulant, anti-inflammation, anti-oxidant, and anti-viral. Results In this study, eleven compounds were targeted against S. typhi OmpF by the molecular docking approach and were compared with two commercially available typhoid medications. The SSP showed good binding affinity compared to commercial drugs, particularly carrageenan/MIV-150, carrageenan lambda, fucoidan, and 3-phenyllactate, ranked as top antagonists against OmpF. Further, pharmacokinetics and toxicology (ADMET) studies corroborated that SSP possessed drug-likeness and highly progressed in all parameters. Conclusions AutoDockTools and Schrodinger's QikProp module results suggest that SSP could be a promising drug for extensively drug-resistant (XDR) S. typhi. To the best of our knowledge, this is the first report on in silico analysis of SSP against S. typhi OmpF, thus implying the capabilities of SSPs especially compounds like carrageenans, as a potential anti-microbial agent against Salmonella typhi infections. Eventually, advanced studies could corroborate SSPs to the next level of application in the crisis of XDR microbial diseases. Graphical Abstract

scholarly journals IDENTIFYING PROPOLIS COMPOUNDS POTENTIAL TO BE COVID-19 THERAPIES BY TARGETING SARS-COV-2 MAIN PROTEASE

2021 ◽  
pp. 103-110
Author(s):  
LIA KUSUMA DEWI ◽  
MUHAMAD SAHLAN ◽  
DIAH KARTIKA PRATAMI ◽  
ALI AGUS ◽  
AGUSSALIM ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Docking ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
Protease Activity ◽  
Protein Target ◽  
Main Protease

Objective: The study aims to perform molecular docking to examine the interaction between propolis compound and SARS-CoV-2 main protease. Methods: The protein target of this research was the crystal structure of SARS-CoV-2 main protease in complex with an inhibitor N3 (PDB ID: 6LU7). The ligand of this research was the bioactive compounds from Propolis of Tetragonula aff. biroi. Results: The results showed that propolis compound which has the potential to inhibit SARS-CoV-2 protease activity was Sulabiroins A (binding affinity-8.1 kcal/mol), following by (2S)-5,7-dihydroxy-4'-methoxy-8-prenylflavanone acid and broussoflavonol F (binding affinity-7.9 kcal/mol) with binding similarity more than 50% compared to N3-main protease interaction. Conclusion: Molecular docking showed propolis compounds of Tetragonula aff. biroi potential to inhibit SARS-CoV-2 main protease activity. The highest binding affinity presented by Sulabiroins A, following by (2S)-5,7-dihydroxy-4'-methoxy-8-prenylflavanone acid and broussoflavonol F, with values of-8.1 kcal/mol,-7.9 kcal/mol, and-7.9 kcal/mol, respectively, with binding similarity more than 50% compared to N3 and SARS-CoV-2 main protease interaction.

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