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1
Kumar, Harsh, Aastha Sharma, Davinder Kumar, Minakshi Gupta Marwaha, and Rakesh Kumar Marwaha. "3-(Substituted Aryl/alkyl)-5-((E)-4-((E)-(Substituted Aryl/alkyl)methyl)benzylidene) thiazolidin-2,4-dione Molecules: Design, ADME Studies and Molecular Docking Analysis as Potential Antimicrobial and Antiproliferative Agents." Asian Journal of Chemistry 34, no. 9 (2022): 2393–405. http://dx.doi.org/10.14233/ajchem.2022.23927.
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A library comprising of 60 synthesizable compounds from three different series having 20 compounds in each series of 3-(furan-2-carbonyl)-5-((E)-4-((E)-(substituted aryl/ alkyl)methyl)benzylidene)thiazolidine-2,4-dione (FC-1 to FC-20), 3-(butyl)-5-((E)-4-((E)-(substituted aryl/alkyl)methyl)benzylidene)thiazolidine-2,4-dione (NB-1 to NB-20) and 3-(allyl)-5-((E)-4-((E)- (substituted aryl/alkyl)methyl)benzylidene)thiazolidine-2,4-dione (NA-1 to NA-20) was designed and screened for antimicrobial and anticancer potential by molecular docking studies using S. aureus GyrB ATPase (PDB code: 3U2D) and CDK-8 (PDB code: 5FGK) proteins as possible drug targets, respectively by Schrödinger-Maestro v13.2. Molecular docking studies revealed, analogues NB-3 (docking score = -6.626), NA-3 (docking score = -6.315) and FC-20 (docking score = -5.552) displayed best docking score in each series, respectively against 3U2D and molecules NB-2 (docking score = -6.517), NA-20 (docking score = -7.668) and FC-12 (docking score = -4.931) exhibited best docking score in each series, respectively against 5FGK having better interaction with crucial amino acid. ADME results revealed all the analogues have significant scores within Qikprop range and also in close agreement with the Pfizer’s rule of five. These analogues can be used as lead structures for the development/ discovery of new anticancer and antimicrobial agents.
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Choi, Jieun, and Juyong Lee. "V-Dock: Fast Generation of Novel Drug-like Molecules Using Machine-Learning-Based Docking Score and Molecular Optimization." International Journal of Molecular Sciences 22, no. 21 (October 27, 2021): 11635. http://dx.doi.org/10.3390/ijms222111635.
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We propose a computational workflow to design novel drug-like molecules by combining the global optimization of molecular properties and protein-ligand docking with machine learning. However, most existing methods depend heavily on experimental data, and many targets do not have sufficient data to train reliable activity prediction models. To overcome this limitation, protein-ligand docking calculations must be performed using the limited data available. Such docking calculations during molecular generation require considerable computational time, preventing extensive exploration of the chemical space. To address this problem, we trained a machine-learning-based model that predicted the docking energy using SMILES to accelerate the molecular generation process. Docking scores could be accurately predicted using only a SMILES string. We combined this docking score prediction model with the global molecular property optimization approach, MolFinder, to find novel molecules exhibiting the desired properties with high values of predicted docking scores. We named this design approach V-dock. Using V-dock, we efficiently generated many novel molecules with high docking scores for a target protein, a similarity to the reference molecule, and desirable drug-like and bespoke properties, such as QED. The predicted docking scores of the generated molecules were verified by correlating them with the actual docking scores.
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Pamungkas, Tri Setyo, and Rosario Trijuliamos Manalu. "STUDI IN SILICO SENYAWA AKTIF ASAM JAWA (Tamarindus indica L.) SEBAGAI ANTIDIABETES MELALUI INHIBISI PROTEIN TYROSINE PHOSPHATASE." Jurnal Ilmiah Ibnu Sina (JIIS): Ilmu Farmasi dan Kesehatan 8, no. 1 (March 31, 2023): 134–44. http://dx.doi.org/10.36387/jiis.v8i1.1282.
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Tamarind leaves (Tamarindus indica L.) are widely cultivated in tropical countries, including Indonesia. Empirically, tamarind leaves are known to have anti-diabetic properties. In this study, an in-silico method was used to test the active compounds found in tamarind leaves (Tamarindus indica L.) as anti-diabetic agents through docking score analysis. The target protein used was Protein Tyrosine Phosphatase (5JNT) which is related to insulin resistance. Glimepiride and native ligand 5JNT were used as reference ligands, while the active compounds of tamarind leaves (Tamarindus indica L.) were used as the test ligands. There were 12 active compounds tested for drug-like properties based on the Lipinski Rule of Five, and 12 compounds met the criteria which were then tested through molecular docking using the PLANTS software. Based on the docking results, there were four compounds that had potential as anti-diabetic agents, namely linalool anthranilate, hexadecanol, pentadecanol, and benzyl benzoate, with docking scores of -85.889, -84.23032, -83.12325, and -81.54821 respectively. Although the docking scores of these compounds exceeded the score of the native ligand 5JNT, they did not exceed the score of the reference ligand glimepiride.
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Pratama, Mohammad Rizki Fadhil, Hadi Poerwono, and Siswandono Siswodihardjo. "Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions." Indonesian Journal of Biotechnology 26, no. 1 (March 30, 2021): 54. http://dx.doi.org/10.22146/ijbiotech.62194.
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Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained between the test and the reference ligands as the graph’s x‐axis. Meanwhile, the y‐axis contains the similarity of ligand‐receptor interactions, obtained from the ratio of amino acid residues and the types of interactions between the test and reference ligands. Docking result analysis was more straightforward because two critical parameters were presented in one graph. This graph could be used to support the analysis of the docking results.
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Rizma, Baiq Ressa Puspita, Yek Zen Mubarok, Dian Fathita Dwi Lestari, and Agus Dwi Ananto. "Molecular Study of Antiviral Compound of Indonesian Herbal Medicine as 3CLpro and PLpro Inhibitor in SARS-COV-2." Acta Chimica Asiana 4, no. 2 (October 29, 2021): 127–34. http://dx.doi.org/10.29303/aca.v4i2.74.
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Rapid transmission of COVID-19 disease and the fatal effects of the disease lead researchers to use various way to find potential anti-COVID-19 compounds, including using modern approaches. Molecular docking is one of the methods that can be used to analyse antiviral compounds and its molecular target from Indonesian herbs that are believed to have properties as anti-COVID-19. This study aims to analyse antiviral compounds from 5 herbs that have the potential as inhibitors of PLpro and 3CLpro, which both are a non-structural protein in SARS-CoV-2 by molecular docking approach using PLANTS. Remdesivir triphosphate, the active metabolite of remdesivir, was used as the comparison compound in studies. The results showed docking scores obtained from interactions between natural ligands, remdesivir trifospat, curcumin, demetoksikurkumin, bisdemetoksikurkumin, luteolin, apigenin, kuersetin, kaempferol, formononrtin-7-O-glucoronide, androgafolide, and neoandrogafolide with PLpro are as follows -111,441, -103,827, -103,609, -102,363, -100,27,-79,6655, -78.6901, -80.9337, -79.4686, -82.1124, -79.1789, and -97.2452.Combination between quercetin, neoandrographolide, bisdemethoxycurcumin, demetoxycurcumin, and curcumin showed a synergy effect by reduce its docking score. Meanwhile its interaction with the protein 3CLpro showed docking score for those compounds as follows 64.0074, -86.1811, -81.428, -87.1625, -78.2899, -73.4345,-70,3368, -71.5539, -68.4321, -72.0154, -75.9777 and -93.7746.Combination between andrographolide, neoandrographolide, bisdemethoxycurcumin, demetoxycurcumin and curcumin, also shows synegy effect in 3CLpro allow them to reduce the docking score.This study concludes that curcumin was known as the most potent compound that act as a PLpro inhibitor based on a docking score of -103,609, while in 3CLpro all the compound have a potential to inhibit 3CLpro with demethosxycurcumin and neoandrogafolide as the most potent compound with a docking score -87,126 and -93.7746.
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Mateev, Emilio Viktorov, Iva Valkova, Maya Georgieva, and Alexander Zlatkov. "Suitable Docking Protocol for the Design of Novel Coumarin Derivatives with Selective MAO-B Effects." Journal of Molecular Docking 1, no. 1 (June 30, 2021): 40–47. http://dx.doi.org/10.33084/jmd.v1i1.2357.
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Recently, the application of molecular docking is drastically increasing due to the rapid growth of resolved crystallographic receptors with co-crystallized ligands. However, the inability of docking softwares to correctly score the occurred interactions between ligands and receptors is still a relevant issue. This study examined the Pearson’s correlation coefficient between the experimental monoamine oxidase-B (MAO-B) inhibitory activity of 44 novel coumarins and the obtained GOLD 5.3 docking scores. Subsequently, optimization of the docking protocol was carried out to achieve the best possible pairwise correlation. Numerous modifications in the docking settings such as alteration in the scoring functions, size of the grid space, presence of active waters, and side-chain flexibility were conducted. Furthermore, ensemble docking simulations into two superimposed complexes were performed. The model was validated with a test set. A significant Pearson’s correlation coefficient of 0.8217 was obtained for the latter. In the final stage of our work, we observed the major interactions between the top-scored ligands and the active site of 1S3B.
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Bajusz, Dávid, Anita Rácz, and Károly Héberger. "Comparison of Data Fusion Methods as Consensus Scores for Ensemble Docking." Molecules 24, no. 15 (July 24, 2019): 2690. http://dx.doi.org/10.3390/molecules24152690.
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Ensemble docking is a widely applied concept in structure-based virtual screening—to at least partly account for protein flexibility—usually granting a significant performance gain at a modest cost of speed. From the individual, single-structure docking scores, a consensus score needs to be produced by data fusion: this is usually done by taking the best docking score from the available pool (in most cases— and in this study as well—this is the minimum score). Nonetheless, there are a number of other fusion rules that can be applied. We report here the results of a detailed statistical comparison of seven fusion rules for ensemble docking, on five case studies of current drug targets, based on four performance metrics. Sevenfold cross-validation and variance analysis (ANOVA) allowed us to highlight the best fusion rules. The results are presented in bubble plots, to unite the four performance metrics into a single, comprehensive image. Notably, we suggest the use of the geometric and harmonic means as better alternatives to the generally applied minimum fusion rule.
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Scobie, D. R., D. O'Connell, C. A. Morris, and S. M. Hickey. "A preliminary genetic analysis of breech and tail traits with the aim of improving the welfare of sheep." Australian Journal of Agricultural Research 58, no. 2 (2007): 161. http://dx.doi.org/10.1071/ar05444.
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The area of naturally bare skin around the perineum was scored at weaning in lambs (n = 2152) from a composite flock of New Zealand crossbred sheep. Breech bareness was scored on a range from 1, where wool was growing right to the edges of the anus, to 5, where a large bare area surrounded the perineum. Bareness on the under surface of the tail was measured on a linear scale at tail docking. Dag score (degree of breech soiling) was recorded at weaning, on a scale of 0–5, where an increasing score indicated more dags. Dag score was taken as a measure of the risk of flystrike in the breech. Female lambs tended to have slightly greater (P < 0.001) breech bareness score (mean score 2.7) than males (mean score 2.6), whereas mean dag score of females was lower than that of males (0.45 v. 0.53; P < 0.05). Breech bareness score had a heritability of 0.33 ± 0.06, and the length of bare skin under the tail had a heritability of 0.59 ± 0.06. The genetic correlation between breech bareness score at weaning and length of bare skin under the tail at docking was positive (0.35 ± 0.10). These 2 traits had phenotypic correlations with dag score of –0.17 ± 0.02 and –0.03 ± 0.03, respectively, and genetic correlations with dag score of –0.30 ± 0.13 and 0.03 ± 0.12, respectively; negative values indicated a favourable relationship. Tails were removed at docking, so the phenotypic correlation of about zero between tail data and dag score at weaning was of little utility. Our results suggest that selecting for these 2 bareness traits could reduce dag formation and the associated risk of breech strike.
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Feher, Miklos, and Christopher I. Williams. "Reducing Docking Score Variations Arising from Input Differences." Journal of Chemical Information and Modeling 50, no. 9 (August 10, 2010): 1549–60. http://dx.doi.org/10.1021/ci100204x.
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Batool, Majda, Affifa Tajammal, Firdous Farhat, Francis Verpoort, Zafar Khattak, Mehr-un-Nisa, Muhammad Shahid, et al. "Molecular Docking, Computational, and Antithrombotic Studies of Novel 1,3,4-Oxadiazole Derivatives." International Journal of Molecular Sciences 19, no. 11 (November 15, 2018): 3606. http://dx.doi.org/10.3390/ijms19113606.
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A new series of 1,3,4-oxadiazoles derivatives was synthesized, characterized, and evaluated for their in vitro and in vivo anti-thrombotic activity. Compounds (3a–3i) exhibited significant clot lysis with respect to reference drug streptokinase (30,000 IU), and enhanced clotting time (CT) values (130–342 s) than heparin (110 s). High affinity towards 1NFY with greater docking score was observed for the compounds (3a, 3i, 3e, 3d, and 3h) than the control ligand RPR200095. In addition, impressive inhibitory potential against factor Xa (F-Xa) was observed with higher docking scores (5612–6270) with Atomic Contact Energy (ACE) values (−189.68 to −352.28 kcal/mol) than the control ligand RPR200095 (Docking score 5192; ACE −197.81 kcal/mol). In vitro, in vivo, and in silico results proposed that these newly synthesized compounds might be used as anticoagulant agents.
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Steinmann, Casper, and Jan H. Jensen. "Using a genetic algorithm to find molecules with good docking scores." PeerJ Physical Chemistry 3 (May 17, 2021): e18. http://dx.doi.org/10.7717/peerj-pchem.18.
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A graph-based genetic algorithm (GA) is used to identify molecules (ligands) with high absolute docking scores as estimated by the Glide software package, starting from randomly chosen molecules from the ZINC database, for four different targets: Bacillus subtilis chorismate mutase (CM), human β2-adrenergic G protein-coupled receptor (β2AR), the DDR1 kinase domain (DDR1), and β-cyclodextrin (BCD). By the combined use of functional group filters and a score modifier based on a heuristic synthetic accessibility (SA) score our approach identifies between ca 500 and 6,000 structurally diverse molecules with scores better than known binders by screening a total of 400,000 molecules starting from 8,000 randomly selected molecules from the ZINC database. Screening 250,000 molecules from the ZINC database identifies significantly more molecules with better docking scores than known binders, with the exception of CM, where the conventional screening approach only identifies 60 compounds compared to 511 with GA+Filter+SA. In the case of β2AR and DDR1, the GA+Filter+SA approach finds significantly more molecules with docking scores lower than −9.0 and −10.0. The GA+Filters+SA docking methodology is thus effective in generating a large and diverse set of synthetically accessible molecules with very good docking scores for a particular target. An early incarnation of the GA+Filter+SA approach was used to identify potential binders to the COVID-19 main protease and submitted to the early stages of the COVID Moonshot project, a crowd-sourced initiative to accelerate the development of a COVID antiviral.
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Stefaniu, Amalia, Lucia Pintilie, Veronica Anastasoaie, and Eleonora-Mihaela Ungureanu. "In silico Evaluation of Antimicrobial Activity of Some Thiadiazoles Using Molecular Docking Approach." Chemistry Proceedings 3, no. 1 (November 14, 2020): 116. http://dx.doi.org/10.3390/ecsoc-24-08319.
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Molecular docking studies have been performed to assess the antimicrobial potential of three 1,3,4-thiadiazole derivatives containing azulene rings. The simulations were conducted on Mycobacterium tuberculosis DNA gyrase, Staphylococcus aureus DNA gyrase, and Escherichia coli DNA adenine methylase. The relationships between the structures of compounds and their potential antimicrobial activity were investigated. Interactions with amino acid residues from the active binding site were elucidated and the results of docking are reported in terms of docking score. Better docking scores are obtained for the investigated compounds than for the natural ligand, (4S)-2-methyl-2,4-pentanediol, in the case of the Mycobacterium tuberculosis. Two of the studied ligands present better binding affinities against Escherichia coli than the co-crystallized ones. Regarding S. aureus gyrase, the thiadiazole derivatives exhibit lower docking scores and fewer interactions than the aminobenzimidazole urea inhibitor. Our study can be useful to screen and design similar hybrid active compounds.
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Rizma, Baiq Ressa Puspita, Agus Dwi Ananto, and Anggit Listyacahyani Sunarwidhi. "The Study of Potential Antiviral Compounds from Indonesian Medicinal Plants as Anti-COVID-19 with Molecular Docking Approach." Journal of Molecular Docking 1, no. 1 (June 30, 2021): 32–39. http://dx.doi.org/10.33084/jmd.v1i1.2307.
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Corona Virus Disease 2019 (COVID-19) is a new strain of coronavirus called SARS-CoV-2, which was identified in Wuhan, China, in December 2019. The rapid transmission of COVID-19 from human to human forced researchers to find a potent drug by setting aside the time-consuming traditional method in drug development. The molecular docking approach is one a reliable method to screening compound from chemical drug or by finding a compound from Indonesian herbal plants. The present study aimed to assess the potency of compounds from five medicinal plants as potential inhibitors of PLpro and 3CLpro from SARS-CoV-2 using molecular study. The molecular docking was performed using Protein-Ligand Ant System (PLANTS) to analyze the potential compounds by the docking score. Remdesivir triphosphate was used as a standard for the comparison of the test compounds. The docking score obtained from the docking of PLpro with native ligand, remdesivir triphosphate, curcumin, demethoxycurcumin, bisdemethoxycurcumin, luteolin, apigenin, quercetin, kaempferol, formononetin-7-O-glucuronide, andrographolide, and neoandrographolide were -111.441, -103.827, -103.609, -102.363, -100.27, -79.6655, -78.6901, -80.9337, -79.4686, -82.1124, -79.1789, and -97.2452, respectively. Meanwhile, docking score with 3CLpro for the same ligand were -64.0074, -86.1811, -81.428, -87.1625, -78.2899, -73.4345, -70.3368, -71.5539, -68.4321, -72.0154, -75.9777, and -93.7746. The docking score data suggest that curcumin was the most potential as a PLpro inhibitor, while neoandrographolide was the best as a 3CLpro inhibitor.
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Kolageri, Shivanand, Siddaling Kamble, Viswanath S, Meganathan G, Khursid Alom, and Rajasekaran S. "Molecular Docking Study of Novel Nitrofuran Derivatives As Urinary Tract Anti Infectives." Asian Journal of Pharmaceutical Research and Development 10, no. 5 (October 14, 2022): 38–44. http://dx.doi.org/10.22270/ajprd.v10i5.1178.
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Modern drug design commonly uses molecular docking to understand drug-receptor interaction. For docking tests against 1YLU, an E. coli nitro-reductase, substituted furan derivatives were used in the current work. The study's primary goal is to dock the chosen nitrofuran derivatives onto the protein and compare the results to those of nitrofurantoin as a standard drug. PyRx and the discovery studio visualizer (DSV) application were used to carry out the molecular docking analysis, and E. coli nitro-reductase (1YLU) was retrieved from the protein data bank (PDB) website. All seven of the nitrofuran compounds docking scores were discovered to range between -5.9 and -8.8 Kcal/mol. Compound 2a received the highest binding score, with a score of -8.80 Kcal/mol.At the protein active site, compound 2a interacts with amino acids such as glutamic acid (GLU 165), arginine (ARG 10 & 207), serine (SER 39 & 12), glutamine (GLN 142), and lysine (LYS205).Numerous nitrofuran substituted compounds have been identified for the activity and the nitrofuran derivatives have been discovered to exhibit urinary tract anti-infective activities.
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Kim, Stephanie S., Melanie L. Aprahamian, and Steffen Lindert. "Improving inverse docking target identification with Z ‐score selection." Chemical Biology & Drug Design 93, no. 6 (January 2, 2019): 1105–16. http://dx.doi.org/10.1111/cbdd.13453.
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Xu, Siqi, Li Wang, and Xianchao Pan. "An evaluation of combined strategies for improving the performance of molecular docking." Journal of Bioinformatics and Computational Biology 19, no. 02 (February 27, 2021): 2150003. http://dx.doi.org/10.1142/s0219720021500037.
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Molecular docking is a fast and efficient computational method for the prediction of the binding mode and binding affinity between a ligand and a target protein at the atomic level. However, the performance of current docking programs is less than satisfactory. Herein, with a focus on free programs and scoring functions, the performances of LeDock and three standalone scoring functions were tested by 195 high-quality protein–ligand complexes. Results showed that the success rate for the best pose of the free available docking program LeDock achieved 89.20%, indicative of a strong sampling power. Based on the poses generated by LeDock, a comparative evaluation on other three non-commercial scoring functions, including DSX (DrugScore X), PoseScore and X-score was performed. Among all the evaluated scoring functions, DSX and X-score exhibited the best scoring power and ranking power, respectively. The performances of LeDock, DSX and X-score were similar in docking power test, which was much better than the PoseScore. Accordingly, it was suggested that the combination of pose sampling by LeDock with rescoring by DSX or X-score could improve the prediction accuracy of molecular docking and applied in the lead discovery.
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Yadav, Reena, and Jitender K. Malik. "In –Silico Approach for Assessment of Antimicrobial Potential of some Pyrazolidine-3, 5-Dione Derivatives." Global Academic Journal of Pharmacy and Drug Research 4, no. 3 (July 16, 2022): 51–58. http://dx.doi.org/10.36348/gajpdr.2022.v04i03.001.
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Background: Resistance to antibacterial drugs is a trouble in the worldwide public health that must be conquered immediately by finding new antibacterial drugs.Pyrazolidine-3, 5-dione derivatives of heterocyclic compounds were used as active agents against pathogenic microorganisms. This study has been carried out to rationally design three synthesized derivatives was assayed for antimicrobial potential by using in-silico molecular docking approach. Methods: Molecular docking of Isoleucyl-transfer RNA (tRNA) synthetase (IleRS) with three Pyrazolidine-3, 5-dione synthesized derivatives was carried out by AutoDock. Result: The molecular docking result revealed that synthesized compound 5(a-c) showed encouraging docking score as compared to standard ligand Gentamicin. The docking score found to be - 8.23, - 8.63, -6.89 &-8.30 kcal mol–1 respectively.
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Mali, Pooja, Shourya Pratap, Raghvendra S. Badhauria, and Himanshu Gurjar. "DOCKING STUDIES OF AMINOHYDANTOIN DERIVATIVES AS ANTIMALARIAL AGENTS." Journal of Drug Delivery and Therapeutics 8, no. 5-s (October 1, 2018): 322–26. http://dx.doi.org/10.22270/jddt.v8i5-s.1983.
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Objective: Docking studies of aminohydantoin derivatives as antimalarial agents. A novel derivative of aminohydantoins was selected from the literature. Method: in-silco studies using docking methodology. The compounds were sketched and energy minimized using Chem draw ultra and Chem 3D ultra respectively. Further, the compounds were docked into Plasmodium falciparum transferase inhibitor (3L7) using Molegro Virtual Platform. Twenty eight compounds were docked into the active site of Pf-lactate dehydrogenase cavity and all of them found to have similar binding interactions of a co-crystalized ligand. Result: The compounds were showed good docking score like moldock score and re-rank score. The finding of docking studies shows a typical molecular interaction pattern with lactate dehydrogenase. The binding interaction information derived from these molecules will be useful in future antimalarial agent design. Conclusion: From the docking study, it was observed that ligands bind to the electrostatic, hydrophobic clamp formed by the residues Asp 76(B), Tyr 190(B), Tyr 80(B) and Lys 72(B) which play an important role for Plasmodium falciparum inhibition. The binding affinity, grid calculation and RMSD percentage lower and upper parameters were calculated. Hence, the observable data indicated that, above compounds can serve as good leads for further modification and optimization in the of treatment malaria.
Keywords: Molegro, Chemdraw, aminohydantoins and docking, studies as Plasmodium falciparum, 4RAO, moldock score.
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Verma, Mohit, Preeti Jyoti, Devkant Sharma, and Anurag Bhargava. "Docking Studies of Histone Deacetylases Inhibitors." Asian Pacific Journal of Health Sciences 9, no. 4 (June 20, 2022): 13–18. http://dx.doi.org/10.21276/apjhs.2022.9.4.03.
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To augment hits from a high through put screening, a docking study on N-hydroxy phenyl acrylamides and N-hydroxy pyridine-derivatives was performed as histone deacetylases inhibitors. Twenty-nine ligands were docked inside the ligand-binding domain of protein data bank PDB ID: 1C3S utilizing Molegro version 4.02. All 29 compounds, compounds were found to embed in the hydrophobic pocket by forming hydrogen bonds. Almost all compounds were found to have highest MolDock score in comparison to reference or coexisting ligand in protein. The compounds that had highest MolDock score are generally considered better and can be used for further drug designing. The most potent compound was XXVIII having highest MolDock score. Compound XVI was found to have higher number of hydrogen bond interactions comparable to coexisting reference ligand.
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Khanal, Pukar, B. M. Patil, Jagdish Chand, and Yasmin Naaz. "Anthraquinone Derivatives as an Immune Booster and their Therapeutic Option Against COVID-19." Natural Products and Bioprospecting 10, no. 5 (August 8, 2020): 325–35. http://dx.doi.org/10.1007/s13659-020-00260-2.
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Abstract Anthraquinone derivatives are identified for their immune-boosting, anti-inflammatory, and anti-viral efficacy. Hence, the present study aimed to investigate the reported anthraquinone derivatives as immune booster molecules in COVID-19 infection and evaluate their binding affinity with three reported targets of novel coronavirus i.e. 3C-like protease, papain-like protease, and spike protein. The reported anthraquinone derivatives were retrieved from an open-source database and filtered based on a positive druglikeness score. Compounds with positive druglikeness scores were predicted for their targets using DIGEP-Pred and the interaction among modulated proteins was evaluated using STRING. Further, the associated pathways were recorded concerning the Kyoto Encyclopedia of Genes and Genomes pathway database. Finally, the docking was performed using autodock4 to identify the binding efficacy of anthraquinone derivatives with 3C-like protease, papain-like protease, and spike protein. After docking the pose of ligand scoring minimum binding energy was chosen to visualize the ligand–protein interaction. Among 101 bioactives, 36 scored positive druglikeness score and regulated multiple pathways concerned with immune modulation and (non-) infectious diseases. Similarly, docking study revealed torososide B to possess the highest binding affinity with papain-like protease and 3C-like protease and 1,3,6-trihydroxy-2-methyl-9,10-anthraquinone-3-O-(6′-O-acetyl)-β-d-xylopyranosyl-(1 → 2)-β-d-glucopyranoside with spike protein. Graphic Abstract
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Nabil-Adam, Asmaa, Mohamed L. Ashour, Tamer M. Tamer, Mohamed A. Shreadah, and Mohamed A. Hassan. "Interaction of Jania rubens Polyphenolic Extract as an Antidiabetic Agent with α-Amylase, Lipase, and Trypsin: In Vitro Evaluations and In Silico Studies." Catalysts 13, no. 2 (February 18, 2023): 443. http://dx.doi.org/10.3390/catal13020443.
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Jania rubens red seaweed has various bioactive compounds that can be used for several medicinal and pharmaceutical applications. In this study, we investigate the antidiabetic, anti-inflammatory, and antioxidant competency of Jania rubens polyphenolic extract (JRPE) by assessing their interactions with α-amylase, lipase, and trypsin enzymes. HPLC analysis revealed the dominance of twelve polyphenolic compounds. We performed computational analysis using α-amylase, lipase, and trypsin as target proteins for the polyphenols to explore their activities based on their predicted modes of binding sites following molecular modeling analysis. The molecular docking analysis demonstrated a good affinity score with a noticeable affinity to polyphenolic compositions of Jania rubens. The compounds with the highest affinity score for α-amylase (PDB: 4W93) were kaempferol, quercetin, and chlorogenic acid, with −8.4, −8.8 and −8 kcal/mol, respectively. Similarly, lipase (PDB: 1LPB) demonstrated high docking scores of −7.1, −7.4, and −7.2 kcal/mol for kaempferol, quercetin, and chlorogenic acid, respectively. Furthermore, for trypsin (PDB: 4DOQ) results, kaempferol, quercetin, and chlorogenic acid docking scores were −7.2, −7.2, and −7.1 kcal/mol, respectively. The docking findings were verified using in vitro evaluations, manifesting comparable results. Overall, these findings enlighten that the JRPE has antidiabetic, anti-inflammatory, and antioxidant properties using different diabetics’ enzymes that could be further studied using in vivo investigations for diabetes treatment.
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Rizqillah, Raihan Kenji, Jaka Fajar Fatriansyah, Fadilah, Sulhadi, Siti Wahyuni, Muhammad Arif Sudirman, Helya Chafshoh Nafisah, and Sukma Dewi Lestari. "In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease." BIO Web of Conferences 41 (2021): 07002. http://dx.doi.org/10.1051/bioconf/20214107002.
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In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone have comparable inhibition activity to SARS CoV-2 main protease in comparison to Remdesivir. 5-hydroxy7,8,2’,3’-tetramethoxyflavone has the lowest docking score, which was further validated by protein ligand contact fraction examination, although MMGBSA score is lowest for Remdesivir.
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Raj, Priya Durai, Palagati Rohith Kumar Reddy, Palaniyandi Thiruvanavukkarasu, Sindhu Rajesh, and Rajeswary Hari. "Anticancer Activity of Phyto Ligands from Carica papaya Leaves by Suppression of PI3CKA and BCL2 Proteins- An insilico Approach." Biomedical and Pharmacology Journal 15, no. 3 (September 29, 2022): 1289–98. http://dx.doi.org/10.13005/bpj/2466.
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The plant derived compounds possess several medicinal property including anticancer activities. In the present investigation molecular docking analysis was performed to identify a suitable antagonistic ligand from the phyto ligands of Carica pappya leaves which can inhibit the tumor progressive proteins PIK3CA, BCL 2. The molecular Docking analysis was performed using Autodock 4.2. The protein PIK3CA, BCL 2 structures were retrieved from PDB, and by GC-MS analysis the phyto molecules were identified. The ligand chemical structures were drawn using Chem sketch. The enzyme and ligand interaction were obtained as docking score using the Arguslabs server. Based on the docking score the best ligand was selected from the phyto constituents of Carica papaya ethanolic leaf extract and their inhibitory potential was analyzed in terms of their interactions with the amino acid residues present in the active site which were visualized and further confirmed by PYMOL. The standard drug Doxorubicin was also subjected to docking for comparison in the present study. Based on the docking score the phytochemicals namely Hexadecanoic acid, ethyl ester, Coumarine 3-(2,4-dinitrophenol), Androst-4-en-3-one,17-methoxy, 3-methoxime serves as the best antagonistic ligand in terms of their interaction with amino acids as well as inhibition of the particular tumour progressive proteins.
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Ejaz, Saima, Rehan Zafar Paracha, Sadaf Ejaz, and Zunera Jamal. "Antibody designing against IIIabc junction (JIIIabc) of HCV IRES through affinity maturation; RNA-Antibody docking and interaction analysis." PLOS ONE 18, no. 9 (September 8, 2023): e0291213. http://dx.doi.org/10.1371/journal.pone.0291213.
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Hepatitis C virus is a single-stranded RNA based virus which can cause chronic HCV and hepatocellular carcinoma. HCV genotype 3a has relatively higher rate of fibrosis progression, prevalence of steatosis and incidence of HCC. Despite HCVs variation in genomic sequence, the 5’ untranslated region containing internal ribosome entry site (IRES) is highly conserved among all genotypes. It is responsible for translation and initiation of the viral protein. In present study, IRES was targeted by designing variants of reported antigen binding fragment (Fab) through affinity maturation approach. Affinity maturation strategy allowed the rational antibody designing with better biophysical properties and antibody-antigen binding interactions. Complementarity determining regions of reported Fab (wild type) were assessed and docked with IRES. Best generated model of Fab was selected and subjected to alanine scanning Three sets of insilico mutations for variants (V) designing were selected; single (1-71), double (a-j) and triple (I-X). Redocking of IRES-Fab variants consequently enabled the discovery of three variants exhibiting better docking score as compared to the wild type Fab. V1, V39 and V4 exhibited docking scores of -446.51, -446.52 and-446.29 kcal/mol respectively which is better as compared to the wild type Fab that exhibited the docking score of -351.23 kcal/mol. Variants exhibiting better docking score were screened for aggregation propensity by assessing the aggregation prone regions in Fab structure. Total A3D scores of wild type Fab, V1, V4 and V39 were predicted as -315.325, -312.727, -316.967 and -317.545 respectively. It is manifested that solubility of V4 and V39 is comparable to wild type Fab. In future, development and invitro assessment of these promising Fab HCV3 variants is aimed.
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Saputri, Dwi, Triana Kusumaningtyas, Prismo Setiadi, and Rifki Febriansah. "Investigation of Moringa Leaf Compounds as Colon Anticancer Agents Using Bioinformatics and Molecular Docking Methods." Proceedings University of Muhammadiyah Yogyakarta Undergraduate Conference 2, no. 2 (June 30, 2022): 24–27. http://dx.doi.org/10.18196/umygrace.v2i2.421.
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Introduction - Colon cancer is a disease that has a high mortality rate. Cancer treatments such as chemotherapy can cause severe side effects. So, it is necessary to do research on herbal plants to minimize these side effects. The bioactive compounds in Moringa leaves (Moringa oleifera L.) are known to have antioxidant and anticancer activity, so they have the potential to be used as cancer treatment. Purpose – . This study aims to determine the potential of Moringa leaves as an anticancer agent in silico.
Methodology/Approach – The in silico test used is STITCH-STRING bioinformatics and molecular docking. STITCH-STRING bioinformatics was used to determine the target protein of the test compound, and molecular docking was used to determine the binding affinity between the test compound and cancer protein. Findings – In the STITCH-STRING bioinformatics test, the potential targets for kaempferol and quercetin were TP53-ESR1 and STAT3-EGFR, respectively.test Molecular docking on cancer protein showed that quercetin compound in EGFR protein had the best binding with a docking score of -9.2 kcal/mol. This shows good results because the docking score obtained is lower than the comparison drug (Fluorouracil) which has a docking score of -4.2 kcal/mol. These results indicate that compounds in Moringa leaves (Moringa oleifera L.) have the potential to be used as anticancer agents. Originality/ Value/ Implication – Moringa leaf research using bioinformatics and molecular docking methods is still rarely done, so this research can be used as further knowledge related to the search for moringa leaf compounds that have the potential for anticancer using bioinformatics and molecular docking methods
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Kumari, Uma, and Kartik Tripathi. "Computational Analysis and Molecular Docking Approach for Liver Cancer." International Journal for Research in Applied Science and Engineering Technology 11, no. 7 (July 31, 2023): 1628–33. http://dx.doi.org/10.22214/ijraset.2023.54927.
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Abstract: Liver cancer is a serious worldwide medical concern, with death rates that are alarmingly higher than those of other types of cancer. It kills roughly 700,000 people annually, necessitating immediate attention and effective strategies for prevention, diagnosis, and treatment. Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) are the most prevalent aggressive liver tumors, with uncommon variants such as fibrolamellar carcinoma and hepatoblastoma contributing to the disease burden. Computational analysis and molecular docking techniques are valuable tools in studying liver cancer. In this study, research was conducted via molecular docking analysis using the 3D structure of human ornithine aminotransferase with a bound intermediate molecule (PDB ID: 7JX9). This approach allows for the investigation of potential interactions between the target protein and ligands. Two ligands, Vinblastine and 5-Fluorouracil, were selected for molecular docking against the target protein. Vinblastine, derived from the plant Vincarosea Linnaeus, is an anticancer alkaloid that hinders microtubule development by interacting with tubulin. 5-Fluorouracil, a synthetic compound resembling the nucleobase uracil, functions as an antimetabolite and inhibits tumor growth. The docking analysis revealed that both ligands were able to bind to the target protein, and specific amino acid residues within the A-domain were identified as involved in the binding of Vinblastine. The docking results were visualized and analyzed using PyMol software. The analysis provided insights into the interactions between the target protein and ligands, shedding light on potential binding sites and affinity. The grid scoring was used in AutodockVina's docking procedure to determine how well the protein receptor might bind to the ligands. The calculated grid scores from the analysis showed that Vinblastine (with x-center = -38.8, y-center = -16.7 and z-center = -10.20) and 5- Fluorouracil (with x-center = -36.0, y-center = -19.7, z-center = -10.5).It was seen that the ligand with the lowest grid score is 5- Fluorouracil, with an x-center = -36.0, y-center = -19.7, z-center = -10.5.A ligand's binding energy is directly proportional to its grid score, meaning that a lower score indicates a higher binding energy. If the ligand has a lower grid score, it is predicted to have a stronger affinity for the protein.
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Santoso, Broto. "EXPLORING 3D MOLECULAR STUDIES OF DIKETOPIPERAZINE ANALOGUES ON Staphylococcus aureus DEHYDROSQUALENE SYNTHASE USING GLIDE-XP." Pharmacon: Jurnal Farmasi Indonesia 13, no. 2 (December 1, 2012): 77–86. http://dx.doi.org/10.23917/pharmacon.v13i2.14.
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There is a strong correlation between 3D molecular docking result with dehydrosqualene synthase protein and antibacterial activity against Staphylococcus aureus (S. aureus) of the pyrazoline analogues. The enzyme has been known as important protein for the synthesis of staphyloxanthin in S. aureus. Diketopiperazine analogues have similar structure to pyrazoline. Glide-XP, Schrodinger application that seeks for molecular docking screening between ligand and protein target is designed for speed, efficiency, and accuracy to conduct discovery efforts. The research report the three-dimension molecular studies diketopiperazine analogues for their antibacterial activity on dehydrosqualene synthase of S. aureus using Glide-XP. Analogues compound of diketopiperazine and curcumin has been calculated their geometry optimization using Gaussian-Density Functional Theory method. These 3D-optimized ligands along with reference ligands obtained from bindingDB database, MIMICs fingerprint shape screening and the compound from previous research were performed on dehydrosqualene synthase (2ZCO) for their docking score. The lowest values docking score were analyzed with multiple linear regressions. The results suggest that the diketopiperazine framework is a prospective template for modification and optimization to accomplish better potency of antibacterial activity in laboratory testing. Keywords: diketopiperazine, Glide-XP, docking score, Staphylococcus aureus, multiple linear regression.
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Rabar, Denis, Danijela Rabar, and Duško Pavletić. "Two-Step Manufacturing Process Measurement Model Using Qualitative and Quantitative Data—A Case of Newbuilding Dry-Docking." Journal of Marine Science and Engineering 9, no. 5 (April 25, 2021): 464. http://dx.doi.org/10.3390/jmse9050464.
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Newbuilding dry-docking is a part of the shipbuilding manufacturing process, common for vessels built on slipways. The subject of this research is steel-built vessels intended for non-restricted sea-going navigation. Based on former experience, the necessity of the dry-docking projects measurement has been noted as a managerial tool for performance estimation and project comparison. The dry-docking project is a complex task which includes the first self-propelled sea passage and the transfer of the manufacturing process to a remote place. The dry-docking result is a surveyed and coated vessel ready for sea trials and five-year service until the next dry-docking. This paper deals with a model which enables process measurement using the analytic hierarchy process (AHP) method for qualitative data related to the dry-docking places and data envelopment analysis (DEA) for quantitative data related to the vessels’ technical and cost data. The modelled data are collected from the completed dry-dockings, and the twenty-nine studied vessels represent the decision-making units (DMU) used in two-step process measurement calculations. The obtained results can distinguish the efficient DMUs, which create an efficient frontier as benchmarks or “the best practice units” in the given DMU set. For the non-efficient DMUs, the efficiency score and rate of improvements needed to reach the efficient frontier will be calculated, and the sources of inefficiency will be recognized.
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Zeb, Muhammad Aurang, Taj Ur Rahman, Muhammad Sajid, Weilie Xiao, Syed Ghulam Musharraf, Shabana Bibi, Takashiro Akitsu, and Wajiha Liaqat. "GC-MS Analysis and In Silico Approaches of Indigofera heterantha Root Oil Chemical Constituents." Compounds 1, no. 3 (September 28, 2021): 116–24. http://dx.doi.org/10.3390/compounds1030010.
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The phytochemical investigation on Indigofera heterantha root oil resulted in the identification of 121 phytochemicals using GC-MS analysis. These phytochemicals were docked against alpha-amylase, alpha-glucosidase enzymes. The docking results suggested that Hexacosyl acetate (121) possess alpha-amylase inhibitory potential with a docking score of −8.2944994 and the interaction with alpha-glucosidase enzyme was −9.73762512, followed by 9, 12, 15-Octadecatrienoic acid, 2, 3-dihydroxypropyl ester, (Z, Z, Z)-(83) with a docking score of −9.59869957, showed outstanding results in all the stages of the study and may be shown as the most auspicious phytochemical resulting from the docking studies of the new antidiabetic drug. Additionally, Pharmacokinetic and PASS studies revealed their drug-likeness, expected safety upon consumption, and likely pharmacological effects.
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Karnan, R., M. Sukumaran, and S. Velavan. "Correlation between Molecular Docking Score and Ligand Molar Mass: Statistical Approach." UTTAR PRADESH JOURNAL OF ZOOLOGY 44, no. 19 (September 2, 2023): 98–105. http://dx.doi.org/10.56557/upjoz/2023/v44i193623.
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In recent days, pharmacology researchers have studied secondary metabolic compounds because they are naturally produced by plants, bacteria, fungi, and marine sponges, leading to increased worldwide use of the computational technique of molecular modelling approaches to drug discovery. Flavonoids, which belong to secondary metabolic compounds, play a role in biological activity. In the present study, the flavonoids subclass of secondary metabolic compounds molecular docking binding energy was dependent on the compound's molecular weight on binding interaction with antioxidant proteins using the statistical approaches of correlation coefficient and cluster statistical analysis. To evaluate a strong negative relationship, higher molecular mass flavonoids compounds had high active properties and lower molecular mass flavonoids compounds had low active properties, as reported on antioxidant proteins in correlation (r = -0.76 to -0.91 for a strong relationship) and cluster analysis. Flavonoids subclass compounds molecular docking binding scores were based on ligand molecular mass and depended on a similarly strong negative relationship in molecular mass vs 1HD2, 1MFM, 2F8A, and 2HCK antioxidant proteins. In this study, statistical analysis concluded that molecular docking binding energy depends on ligand molecular mass. Overall, the higher molecular mass compounds have higher active properties may be used in biological activity.
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Nguyen, Duc Duy, and Guo-Wei Wei. "AGL-Score: Algebraic Graph Learning Score for Protein–Ligand Binding Scoring, Ranking, Docking, and Screening." Journal of Chemical Information and Modeling 59, no. 7 (June 18, 2019): 3291–304. http://dx.doi.org/10.1021/acs.jcim.9b00334.
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Breda, Ardala, Luiz Basso, Diogenes Santos, and Walter de Azevedo Jr. "Virtual Screening of Drugs: Score Functions, Docking, and Drug Design." Current Computer Aided-Drug Design 4, no. 4 (December 1, 2008): 265–72. http://dx.doi.org/10.2174/157340908786786047.
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Fukunishi, Yoshifumi, Satoshi Yamasaki, Isao Yasumatsu, Koh Takeuchi, Takashi Kurosawa, and Haruki Nakamura. "Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction." Molecular Informatics 36, no. 1-2 (April 29, 2016): 1600013. http://dx.doi.org/10.1002/minf.201600013.
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Maurya, Anil, and Jitender K. Malik. "Anti-Inflammatory Potential and Underlying Mechanistic of Phenolic Component from Ziziphus jujuba Fruit: A Molecular Docking Validation." EAS Journal of Pharmacy and Pharmacology 5, no. 03 (May 11, 2023): 43–48. http://dx.doi.org/10.36349/easjpp.2023.v05i03.001.
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The nutritious jujube fruit (Ziziphus jujube Mill.) is a member of the Rhamnaceous family and grows mainly in inland areas of Europe, southern and eastern Asia, Australia and especially northern China. Jujubes have a long history as fruit and medicinal. The main bioactive components are vitamin C, phenols, flavonoids, triterpenoids and polysaccharides. Chlorogenic acid (5-O-caffeoylquinic acid) is a phenolic compound of the hydroxycinnamic acid family found in the hydroethanolic fruit extract of Z.jujuba. This polyphenol has many health-enhancing properties, most of which are relevant for the treatment of metabolic syndrome, including antioxidant, anti-inflammatory, antilipidemic, antidiabetic, and antihypertensive effects. Methods: Molecular docking of COX2 with chlorogenic acid was carried out by AutoDock. Result: The molecular docking result revealed that chlorogenic acid showed encouraging docking score. The docking score found to be -5.15.
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Mourya, Brijendra, and Niyati Shrivastava. "Mechanistic Insights an Anti-Inflammatory Potential of Quercetin by Molecular Docking." Global Academic Journal of Pharmacy and Drug Research 4, no. 3 (July 30, 2022): 59–65. http://dx.doi.org/10.36348/gajpdr.2022.v04i03.002.
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Background: Inflammation is a biological response to a series of chemical reactions whose major function is protection from infection and the resolution of tissue damage caused by injury. There are several mediators released during the process of inflammation. Flavonoids are universal in photosynthesizing cells and are often found in vegetables, fruit, nuts, seeds, stems, tea, flowers, honey and wine preparations. This class of natural products is becoming the subject of anti-infective research, and many groups have isolated and identified the structures of flavonoids possessing, antiviral, antifungal antibacterial activity and anti-inflammatory activity. This study has been carried out to rationally design quercetin was assayed for anti-inflammatory potential by using in-silico molecular docking approach. Methods: Molecular docking of Phosphodiesterase 4 (PDE4) with quercetin was carried out by AutoDock. Result: The molecular docking result revealed that quercetin showed encouraging docking score. The docking score found to be -7.67 kcal mol–1 respectively.
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Lateef, Tooba, Sadaf Naeem, and Shamim A. Qureshi. "In-silico studies of HMG-Co A reductase inhibitors present in fruits of Withania coagulans Dunal (Solanaceae)." Tropical Journal of Pharmaceutical Research 19, no. 2 (April 9, 2020): 305–12. http://dx.doi.org/10.4314/tjpr.v19i2.13.
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Purpose: To evaluate the antihypercholesterolemic effect of chemical constituents of W. coagulans by determining inhibitory effect of the compounds against HMG-CoA reductase, using in-silico methods.
Method: Docking simulations of twenty-one chemical constituents, found in the fruits of W. coagulans were performed against HMGCR(PDB ID: 2Q1L) using Molegro Virtual Docker software. The best docked poses were then selected, based on the docking score and amino acids involved in the interaction within the ligand and active site of protein.
Results: Five compounds viz. Coagulin D (comp no. 11), Ergosta-5,25-diene-3β,24ε-diol (comp no. 13), Withacoagulin (comp no. 15), and Withaferin (comp no. 16), showed the highest MolDock scores. These compounds with highest docking score, also formed hydrogen bond interactions with His (752), Lys (692, 735), Asp (690), Glu (559) within the binding site of HMG-CoA reductase, thus, halting enzyme activity. Whereas, Withanolide D (comp no. 17) with high MolDock score did not show hydrogen bonding interactions.
Conclusion: The high MolDock score and maximum binding with catalytic region of the enzyme indicate that compounds selected from the fruits of W. coagulans are potential blockers of HMG-CoA reductase. Thus, the compounds may be useful for the management of hypercholesterolemia, which untreated, often leads to coronary artery disease.
Keywords: Withania coagulans, Coronary artery disease, HMG-CoA reductase, Molegro virtual docker, Hypercholesterolemia, In silico studies
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Hadi, Samsul, Amalia Khairunnisa, Sefa Nur Khalifah, Sintya Oktaviani, Sri Oktaviana Sari, and Umi Nur Hapifah. "Skrining Inhibitor NF-κB Combretum indicum dengan Metode Docking." Pharmacon: Jurnal Farmasi Indonesia 18, no. 2 (December 31, 2021): 157–63. http://dx.doi.org/10.23917/pharmacon.v18i2.15780.
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Nuclear factor kappa B (NF-κB) is a transcription factor that regulates the expression of genes important for innate and adaptive immune responses. NF-κB overactivation is associated with inflammatory diseases such as autoimmune, systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). This study aims to screen the chemical content of C.indicum against NF-κB-inducing kinase inhibitors. There are two methods used in this study, namely through PASSonline and docking. The docking method used was PLANTS. The results of PASSonline compounds that have P.a values above 0.7 weree arachidonic acid, linoleic acid, rutin, methyl urasolate, while the docking scores obtained were asquisqualic acid: -60.0382; arachidonic acid : -100,9410; linoleic acid: -93.8730; routine : -102,9320; methyl urasolate: -47,9166. This negative docking score indicates that the reaction between the compound and the target occurs easily. In conclusion, the compound predicted to have a potential as an inhibitor of NF-κB is Rutin.
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Tom, E. M., J. Rushen, I. J. H. Duncan, and A. M. de Passillé. "Behavioural, health and cortisol responses of young calves to tail docking using a rubber ring or docking iron." Canadian Journal of Animal Science 82, no. 1 (March 1, 2002): 1–9. http://dx.doi.org/10.4141/a01-053.
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The acute responses of thirty-six 7- to 17-d-old Holstein calves to tail docking using a rubber ring or a hot docking iron were examined. Plasma cortisol concentrations were measured on day 0 and day +1. Behaviour was examined on days –1, 0, +1, +2, and +5 after treatment. Milk intake, weight gain, body temperature and faeces scores were monitored. Rubber ring application caused an increase in tail grooming up to day +5 after treatment. Shorter standing and lying periods as well as higher frequencies of standing and lying on day 0 were seen in the rubber ring group. No significant differences in behaviour were observed between the control group and the docking iron group. No significant differences in plasma cortisol concentrations were found between any groups except for 60 min after treatment when the rubber ring group exhibited a significantly higher concentration than the control group. No differences in milk intake, weight gain, body temperature or faeces score were found. Tail docking with a rubber ring causes a more pronounced behavioural and physiological response than docking with a docking iron. However, long-term effects need to be investigated. Key words: Calves, tail docking, pain, behaviour, cortisol, stress
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Retna, A. Malar, P. Ethalsha, and J. Lydia. "DOCKING SCORE OF THE ISOLATED COMPOUND: 19-HYDROXY LOCHNERICINE - WITH DIFFERENT PROTEINS." Green Chemistry & Technology Letters 2, no. 1 (March 10, 2016): 31–34. http://dx.doi.org/10.18510/gctl.2015.216.
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It evaluates the inhibitory effect of the isolated compound with different drug targets for the anti-cancer activities. The present investigation analyses the docking score of the isolated compound with different proteins. Two types of proteins (Drug targets) were chosen against cancer namely Human Epidermal Growth Factor and Crystal structure of human placental aromatase cytochrome P450.This result reveals that the compound 19-Hydroxy lochnericine shows hydrogen interactions with the docking energy of – 7.41 and -7.15 –8.83 kcal/mol. This reveals a significant interaction between the target proteins and the selected compound. Hence, the compound may offer therapeutic advantages in the treatment and prevention of diabetes and breast cancer.
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Arner, Justin W., Edward S. Chang, Stephen Bayer, and James P. Bradley. "Direct Comparison of Modified Jobe and Docking Ulnar Collateral Ligament Reconstruction at Midterm Follow-up." American Journal of Sports Medicine 47, no. 1 (November 30, 2018): 144–50. http://dx.doi.org/10.1177/0363546518812421.
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Background: The modified Jobe and docking techniques are the 2 most commonly employed techniques for ulnar collateral ligament (UCL) reconstruction among overhead athletes. However, no study has directly compared these techniques performed by a single surgeon. Current comparisons of these techniques have relied solely on systematic reviews and biomechanical studies. Hypothesis: There will be no difference in outcomes or return to play between the modified Jobe and docking techniques in elbow UCL reconstruction surgery. Study Design: Cohort study; Level of evidence, 3. Methods: Twenty-five modified Jobe and 26 docking UCL-reconstructive surgical procedures were performed by a single surgeon, each with a minimum 2-year follow-up. Kerlan-Jobe Orthopaedic Clinic (KJOC) score, Conway Scale, years played, sex, handedness, sport, position, palmaris versus gracilis graft type, concomitant or future arm/shoulder injuries, and need for additional surgery were compared between the groups. Patients who underwent future shoulder or elbow surgery, no matter the cause, were included. Results: No difference was seen between the modified Jobe and docking reconstruction cases in regard to KJOC scores (mean ± SD: 78.4 ± 19.5 vs 72.0 ± 26.0, P = .44), Conway Scale (return to play, any level: 84% vs 82%, P = .61), years played (14.7 ± 6.2 vs 15.2 ± 5.8, P = .52), sex ( P = .67), handedness ( P ≥ .999), sport ( P = .44), position ( P = .60), level of competition ( P = .59), and future surgery (12% vs 4%, P = .35). Palmaris graft type had significantly higher KJOC scores than hamstring grafts (82.3 ± 20.0 vs 57.9 ± 21.2, P = .001). The mean follow-up was 6.1 years in the modified Jobe group and 7.3 years in the docking group (mean = 6.7, P = .47). Conclusion: The modified Jobe and docking techniques are both suitable surgical options for elbow UCL reconstruction. There was no statistically significant difference between the techniques in regard to return to play, KJOC score, or need for subsequent surgery at 6.7-year follow-up. This is the first direct clinical comparison of these 2 techniques by a single surgeon at midterm follow-up.
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Kolageri, Shivanand, Hemanth S, and Mahesh Parit. "In-silico ADME prediction and molecular docking study of novel benzimidazole-1,3,4-oxadiazole derivatives as CYP51 inhibitors for antimicrobial activity." Journal of Applied Pharmaceutical Research 10, no. 3 (September 30, 2022): 18–27. http://dx.doi.org/10.18231/j.joapr.2022.10.3.28.38.
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A class of innovative benzimidazole-1,3,4-Oxadiazole derivatives is a significant heterocyclic molecule for therapeutic development. In heterocyclic chemistry, the novel 1,3,4-Oxadiazole nucleus has a wide range of uses, including antibacterial, treatment. Molecular docking is frequently employed in contemporary drug design to comprehend drug-receptor interaction. Swiss dock, PyRx, and discovery studio visualizer (DSV) tools were used to predict in-silico ADME properties. In the current investigation, substituted benzimidazole-1,3,4-Oxadiazole derivatives were taken for docking studies against 6AYB an Naegleria fowleri CYP51-ketoconazole complex. The main objective of the study is to perform docking of the selected benzimidazole-1,3,4-oxadiazole derivatives on the protein and compare the docking score with standard ketoconazole. The molecular docking study was conducted using PyRx and the discovery studio visualizer (DSV) program, Naegleria fowleri CYP51-ketoconazole complex (6AYB) was obtained from the protein data bank (PDB) site. It was found that the docking score of all sixteen 1,3,4-Oxadiazole compounds ranged from -8.1 to -8.9 Kcal/mol. The novel benzimidazole with 1,3,4-Oxadiazole derivatives has been found to possess antibacterial properties, many substituted 1,3,4-Oxadiazole derivatives have been reported for the activity
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Kumar, Arvind, Rishu Yadav, Preeti Avasthi, and Shivani Thakur. "Ameliorative Role of In-Silico Study in Phytoconstituents of Cordyceps Used for PCOS." YMER Digital 21, no. 07 (July 29, 2022): 1225–39. http://dx.doi.org/10.37896/ymer21.07/a2.
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Background: Polycystic ovarian syndrome (PCOS) is a heterogeneous endocrine disease that impacts about one in 15 girls worldwide. It is a major sickness characterized through multiplied ranges of male hormones (androgens), acne and hirsutism. Objective: In silico study of different compounds from Cordyceps into active site of the target protein. (3RUK). Methods: Computer-aided drug plan principles should enhance the discovery of putative Cordyceps-derived medication inside much less time and low budget. The integration of computer-aided drug design techniques with experimental validation has contributed to the profitable discovery of novel drugs. Results: Results indicated that all the ligands have a strong binding affinity for the Human Cytochrome P450 CYP17A1 receptor as indicated by their docking score values that were found to be comparable with the docking score of the molecules1,6-di-o-glloyl-d-glucose (- 12.172) Isoquercitrin acid (-11.366) etc. Conclusion: It has been concluded that computer-aided drug design techniques could influence the multiple target-focused drug design, In silico studies were performed on the different compounds from Cordyceps into active site of the target protein. (3RUK). Compound 1,6-dio-glloyl-d-glucose was found to have highest affinity towards the Human Cytochrome P450 CYP17A1receptor(docking score = -12.172). Other different compounds from Cordyceps have also good dock scores. Keywords: PCOS, In-silico, Cytochrome P450 CYP17A1, Protein, Ligand.
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Shukla, Karuna S., Shailendra Pandey, and A. Pooja Chawla. "SYNTHESIS, BIOLOGICAL EVALUATION AND DOCKING STUDIES OF NON HEPATOTOXIC 5-SUBSTITUTED THIAZOLIDINE-2, 4-DIONES AS ANTIDIABETIC, ANTI-HYPERLIPIDEMIC, ANTI-OXIDANT AND CYTOTOXIC AGENTS." INDIAN DRUGS 57, no. 09 (November 5, 2020): 19–37. http://dx.doi.org/10.53879/id.57.09.12186.
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A series of eleven thiazolidine-2, 4-dione (TZD) derivatives, were synthesized and characterized by FT-IR, 1 H NMR and mass spectral analysis. All the synthesized TZD derivatives were screened for their in vitro and in vivo anti-diabetic and antioxidant, activities and cytotoxicity. In vivo antihyperglycemic effect was assessed by measuring plasma glucose (PG) levels in alloxan-induced type II diabetic rat models. The compound 4h exhibited better blood glucose lowering activity than the standard drug rosiglitazone. The synthesized TZD derivatives were evaluated for hepatotoxicity and pancreatic tissue studies. Antioxidant activity was evaluated by DPPH method and H2 O2 method. Compounds 4a and 4b exhibited potent antioxidant activity. Among the tested compounds for cytotoxicity using MTT assay method, compound 4i exhibited better viability and cytotoxicity activity. Thiazolidinedione derivatives were evaluated for their affinity towards target PPARg, using rosiglitazone as the reference compound molecular docking visualization through FlexX docking program. From selected anti-diabetic targets, the proposed derivatives exhibited better interaction with PPARγ receptor, where rosiglitazone showed docking score of -19.891 kJ/ mol, compound 4h exhibited highest docking score of -31.6068 kJ/mol. The study showed that all the studied compounds were showing higher docking score when compared to control drug rosiglitazone and it could be a remarkable starting point to evaluate structure activity relationships to develop new lead molecules with potential anti-diabetic activities.
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Vidhya Rekha, Umapathy. "Molecular docking analysis of bioactive compounds from Plectranthus amboinicus with glucokinase." Bioinformation 18, no. 3 (March 31, 2022): 261–64. http://dx.doi.org/10.6026/97320630018261.
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Natural remedies from medicinal plants are known to be effective and reliable appropriate medicine for illnesses. The current research examined Plectranthus amboinicus’ anti diabetic property by docking the bioactive compounds of certain target proteins. We document the molecular docking analysis of bioactive compounds from Plectranthus amboinicus with protein Glucokinase. Molecular docking experiments were carried out in PyRx software. Results of these docking experiments showed that most of the compounds showed very strong interaction with the target protein Glucokinase. Based on the scoring parameters we have selected best four compounds (Rutin, Salvianolic acid, Luteolin and Salvigenin) which showed very good docking score and hydrogen bond interaction for diabetics.
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Rajendran, Sudha, Nithya G, Brindha Devi P, and Charles C. Kanakam. "DOCKING ANTIOXIDANT ACTIVITY ON HYDROXY (DIPHENYL) ACETICACID AND ITS DERIVATIVES." Asian Journal of Pharmaceutical and Clinical Research 10, no. 7 (July 1, 2017): 263. http://dx.doi.org/10.22159/ajpcr.2017.v10i7.18299.
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Objectives: The antioxidant activity of the synthesized compounds along with the standard compound for comparison is reported. There is comparison of binding analysis and the ligand interaction of the compound. Methods: The protein crystal structure complexed with 4-methyl-6-[2-(5-morpholin-4-ylpyridin-3-yl)ethyl]pyridin-2-amine inhibitor was selected from Protein Data Bank (5FVP) for our study. Results: The docking studies and structure-activity relationship reveals that the compound 2’-chloro-4-methoxy-3nitro benzilic acid after three different docking strategies reveals that the score was found to be higher compared with others.Conclusion: Based on the in vitro antioxidant results, the compounds synthesized were investigated for the molecular docking study to identify the amino acid interactions in the active site pocket of nitric oxide synthase enzyme. Based on the docking score results, all the compounds were oriented toward the active site pocket occupied by the cocrystallized ligand
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Bano, Shayara, and Jitender K. Malik. "Chlorogenic Acid a Potent Anti-inflammatory Agent: In-Silico Molecular Docking approach." Middle East Research Journal of Pharmaceutical Sciences 2, no. 1 (December 27, 2021): 10–20. http://dx.doi.org/10.36348/merjps.2022.v02i01.002.
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Abstract: Chlorogenic acid (5-O-caffeoylquinic acid) is a phenolic compound of the hydroxycinnamic acid family. This polyphenol has many health-enhancing properties, most of which are relevant for the treatment of metabolic syndrome, including antioxidant, anti-inflammatory, antilipidemic, antidiabetic, and antihypertensive effects. In addition, chlorogenic acid has antioxidant properties, especially against lipid oxidation. Protective properties against degradation and prebiotic activity of other bioactive compounds present in foods. In addition, chlorogenic acid has antioxidant properties, especially against lipid oxidation. Protective properties against degradation and prebiotic activity of other bioactive compounds present in foods. In addition, chlorogenic acid has antioxidant properties, especially against lipid oxidation. Protective properties against degradation of other bioactive compounds present in food and prebiotic activity. Methods: Molecular docking of COX2, NF-κB inducing kinase (NIK) & PhospholipaseA2 (PLA2) with chlorogenic acid was carried out by AutoDock. Result: The molecular docking result revealed that chlorogenic acid showed encouraging docking score. The docking score found to be -6.71, -6.31 & -4.43 kcal mol–1 respectively.
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Shakeel, Areeba, and Bashah Javed. "Plant-derived antiviral compounds study for drug designing against replicase polyprotein1ab of SARS-COV2: silico- approach." Science Progress and Research 2, no. 1 (January 10, 2022): 392–401. http://dx.doi.org/10.52152/spr/2022.167.
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Covid-19 is caused by severe acute respiratory syndrome (SARS) and that leads to millions of death around the World so indeed there are over 90 vaccines are designed against it. For drug designing, we used Bioinformatics technology and the target is one of the important proteins of covid-19 i.e, Replication Poly- protein 1ab which is 7096 amino acids long and 794,058 Da in weight and one of its important domains is host translation inhibitor nsp1which inhibits host translation by associating with the open head conformation of the 40S subunit. For this experiment, we collected data of 50 antiviral compounds from various medicinal plants. Docking was performed with these compounds, combined with our target i.e, protein of the virus. Docking was done by using MVD followed by virtualization of the compound’s 3D structure on Pymol. After getting all the results, select the result having the best docking score that means compounds having the lowest docking score for further steps of drug designing.
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Thakur, Monica, Hyacinth Highland, and Linz-Buoy George. "IN SILICO EVIDENCE OF THE EFFICACY OF PHYTOCOMPONENTS AS COMPETITIVE INHIBITORS AGAINST A TOBACCO SMOKE CARCINOGEN IN NON-SMALL CELL LUNG CANCER." International Association of Biologicals and Computational Digest 1, no. 2 (October 5, 2022): 69–74. http://dx.doi.org/10.56588/iabcd.v1i2.46.
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Cigarette smoke is a major risk factor in the development of Non-small cell lung cancer (NSCLC). Nicotine- derived nitrosamine ketone (NNK) is an important carcinogen present in cigarette smoke that induces tumor metastasis by activation of a protein kinase cascade, including Focal adhesion kinase (FAK). The present investigation was aimed at employing molecular docking studies to establish binding interactions and comparison of phytocomponents from different herbs and selected Rosmarinic acid derivatives against the target protein FAK with the purpose of blocking the binding of Nicotine-derived nitrosamine ketone (NNK). Molegro virtual docker (MMV) and Hex (version 8.0.0) software was used as docking tool for investigating the interaction of the protein active site residues with the phytocomponents. Molegro molecular viewer (MMV) and Biovia Discovery studio 2017 R2 visualizer were used to identify the amino acid interactions between phytocomponents and protein and also to calculate binding scores. The molecular interaction of NNK with the target protein was also done to obtain the binding energy of this carcinogen with the protein. Rosmarinic acid derivatives manifested the highest docking score with the target protein FAK. In comparison, NNK showed weaker binding score with FAK. In addition the derivatives showed common interacting amino acids. Hence, docking studies indicated that phytocomponents and certain derivatives could effectively bind to the same active site of FAK and block its interaction with NNK. Thus, in nicotine exposed NSCLC patients, Rosmarinic acid derivatives may work as effective competitive binders.
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Mustafa, Ghulam, Hafiza Salaha Mahrosh, Mahwish Salman, Sumaira Sharif, Raheela Jabeen, Tanveer Majeed, and Hafsah Tahir. "Identification of Peptides as Novel Inhibitors to Target IFN-γ, IL-3, and TNF-α in Systemic Lupus Erythematosus." BioMed Research International 2021 (November 13, 2021): 1–11. http://dx.doi.org/10.1155/2021/1124055.
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Autoimmune disorder is a chronic immune imbalance which is developed through a series of pathways. The defect in B cells, T cells, and lack of self-tolerance has been greatly associated with the onset of many types of autoimmune complications including rheumatoid arthritis, systemic lupus erythematosus (SLE), multiple sclerosis, and chronic inflammatory demyelinating polyneuropathy. The SLE is an autoimmune disease with a common type of lupus that causes tissue and organ damage due to the wide spread of inflammation. In the current study, twenty anti-inflammatory peptides derived from plant and animal sources were docked as ligands or peptides counter to proinflammatory cytokines. Interferon gamma (IFN-γ), interleukin 3 (IL-3), and tumor necrosis factor alpha (TNF-α) were targeted in this study as these are involved in the pathogenesis of SLE in many clinical studies. Two docking approaches (i.e., protein-ligand docking and peptide-protein docking) were employed in this study using Molecular Operating Environment (MOE) software and HADDOCK web server, respectively. Amongst docked twenty peptides, the peptide DEDTQAMMPFR with S -score of -11.3018 and HADDOCK score of − 10.3 ± 2.5 kcal/mol showed the best binding interactions and energy validation with active amino acids of IFN-γ protein in both docking approaches. Depending upon these results, this peptide could be used as a potential drug candidate to target IFN-γ, IL-3, and TNF-α proteins to control inflammatory events. Other peptides (i.e., QEPQESQQ and FRDEHKK) also revealed good binding affinity with IFN-γ with S -scores of -10.98 and -10.55, respectively. Similarly, the peptides KHDRGDEF, FRDEHKK, and QEPQESQQ showed best binding interactions with IL-3 with S -scores of -8.81, -8.64, and -8.17, respectively.
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Yadav, Manisha, Swasti Dhagat, and Jujjavarapu S. Eswari. "Structure Based Drug Design and Molecular Docking Studies of Anticancer Molecules Paclitaxel, Etoposide and Topotecan using Novel Ligands." Current Drug Discovery Technologies 17, no. 2 (June 19, 2020): 183–90. http://dx.doi.org/10.2174/1570163816666190307102033.
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Background: Tubulin is the biochemical target for several clinically used anticancer drugs as it helps in the formation of mitotic spindle during mitosis stage of cell division. Many of the anti-cancer drugs are known to interact with tubulin and microtubules including some plant alkaloids, such as paclitaxel, etoposide and topotecan. In silico drug design of these molecules were performed prior to testing these drugs in vitro. In silico drug design of these anti-cancer drugs becomes a challenge due to the complex structure of target protein. This challenge was overcome by predicting the structure of the target protein (tubulin) by homology modeling. Methods: In this study, computer aided drug designing approach was applied to predict the suitable docking site in target protein and the interaction of tubulin protein with paclitaxel, etoposide and topotecan was explored by molecular docking using Schrödinger software. Docking score and glide energy were determined with ligands to validate their anticancer properties. Results: The results indicate that etoposide is the best drug for tubulin with a docking score of - 4.916 and glide energy of -46.470 kcal/mol compared to paclitaxel and topotecan. Conclusion: The testing of these drugs in silico provides an alternate to in vitro testing of these molecules on cancer cell lines which is a time and cost intensive process. The in silico study of parameters, such as docking score and glide energy, will help pharmacists in developing new molecules as targets for cancers in a time and cost-effective manner.