Relevant bibliographies by topics / CB-DOCK

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Academic literature on the topic 'CB-DOCK'

Author: Grafiati
Published: 11 September 2023

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Journal articles on the topic "CB-DOCK"

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Pandey, Pratibha, Fahad Khan, Kiran Yadav, Kartikey Singh, Akhlakur Rehman, Avijit Mazumder, and Minhaj Ahmad Khan. "Screen natural terpenoids to identify potential Jab1 inhibitors for treating breast cancer." Trends in Immunotherapy 7, no. 1 (June 29, 2023): 2055. http://dx.doi.org/10.24294/ti.v7.i1.2055.

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Jab1 (c-Jun activation domain-binding protein-1) overexpression has been extensively linked to cancer development (or metastasis) in various malignancies by positively regulating cancer cell proliferation or inactivating several tumor suppressors. Recent research has focused on utilizing plant products to target crucial elements of dysregulated signaling pathways to elucidate a potent cancer therapeutic approach. Terpenoids have shown significant anti-inflammatory and anti-cancerous properties in a broader range of carcinomas by inducing apoptosis. Through an extensive literature search, we have selected only those terpenoids (from the NPACT database) that have not been explored against Jab1 (CSN5, COP9 signalosome subunit 5) in breast cancer for our research study. We have used two docking servers, PATCH DOCK, and CB DOCK, to find the binding interaction between selected terpenoids and Jab1. Further, we have also used SWISS ADME to investigate the pharmacokinetics of selected ligands. Amongst all selected ligands, lutein (belongs to the xanthophylls class) has displayed maximum binding energy in both CB Dock and Patch Dock analysis. Hence, our preliminary in silico results have shown lutein as the potent lead candidate for developing a better drug against breast cancer. However, more in silico and in vitro studies are still needed to validate the inhibitory potential of lutein terpenoid against Jab1 in breast cancer.
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Avezov, Hasan Tilloyevich, Baxtiyor Shukurulloevich Ganiyev, Gulyayra Qo`ldoshevna Xoliqova, Furqat G'ayrat o'g`li Salimov, and Ferangiz Sadilloevna Aslonova. "SIANUR KISLOTANING MOCHEVINA ALMASHINGAN HOSILALARINING ONLINE MOLEKULYAR DOKINGI VA PASS ANALIZI." Журнал химии товаров и народной медицины 1, no. 3 (July 26, 2022): 82–94. http://dx.doi.org/10.55475/jcgtm/vol1.iss3.2022.53.

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Ushbu maqolada CB-Dock va PASS onlayn prognozli dasturiy ta'minotidan foydalangan holda sianur kislotaning mochevina almashingan hosilalari molekulyar doking natijalari, shuningdek, biologik faollik nuqtai nazaridan ularni qo’llashning mumkin bo’lgan sohalari haqida ma’lumotlar keltirilgan.
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Liu, Yang, Maximilian Grimm, Wen-tao Dai, Mu-chun Hou, Zhi-Xiong Xiao, and Yang Cao. "CB-Dock: a web server for cavity detection-guided protein–ligand blind docking." Acta Pharmacologica Sinica 41, no. 1 (July 1, 2019): 138–44. http://dx.doi.org/10.1038/s41401-019-0228-6.

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De Zotti, R., V. Patussi, A. Fiorito, and F. Larese. "Sensitization to green coffee bean (GCB) and castor bean (CB) allergens among dock workers." International Archives of Occupational and Environmental Health 61, no. 1-2 (October 1988): 7–12. http://dx.doi.org/10.1007/bf00381601.

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Balansa, Walter, Lis C. Lukas, Frets J. Rieuwpassa, and Aprelia M. Tomasoa. "Aktivitas Antibakteri Sponge Agelas Nakamurai Terhadap Bakteri Gram Negative: Study In Vitro dan In Silico." Samakia : Jurnal Ilmu Perikanan 14, no. 1 (May 6, 2023): 76–84. http://dx.doi.org/10.35316/jsapi.v14i1.3012.

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Bakteri gram negatif tetap menjadi ancaman serius bagi akuakultur, ekonomi, dan kesehatan manusia. Ironisnya, sementara antibiotik yang efektif belum ditemukan, resistensi bakteri ini terhadap berbagai antibiotik meningkat dengan kecepatan yang mengkhawatirkan. Hal ini menunjukkan urgensi penemuan antibiotik baru, terutama antibiotik yang dapat menghambat replikasi enzim seperti DNA gyrase atau topoisomerase IV, yang saat ini menjadi target baru penemuan antibiotik. Tujuan dari penelitian ini adalah untuk mengetahui potensi antibakteri Agelas nakamurai terhadap A. hydrophila, A. salmonicida dan E. tarda menggunakan ekstrak spons (1, 10, dan 100) mg/mL dan tetrasiklin (1 mg/mL) sebagai kontrol positif dan memprediksi potensi antibakteri dari agelasine A-F (1-6) dan agelasidine A (7) dari A. nakamurai dari Kepulauan Sangihe terhadap protein topoisomerase IV melalui docking molekuler. Uji in vitro dilakukan dengan menggunakan metode Kirby Bauer dengan sedikit modifikasi dan studi in silico menggunakan CB-dock 2 dan Protein Ligand Interaction Profiler. Meskipun ekstrak menunjukkan aktivitas antibakteri yang lebih lemah terhadap A. hydrophila, A. salmonicida dan E. tarda dibandingkan tetrasiklin, molekul docking dengan CB-dock 2 menunjukkan bahwa agelasine A-F (1-6) dan agelasidin A (7) memiliki afinitas pengikatan yang lebih kuat (-7.1). hingga -8,6 kJ/mol) daripada tetrasiklin (10), ciprofloksasin (11) atau levofloksasin (12) (-6,6 hingga -8,3 kJ/mol). Docking molekuler pada agelasidin C (9) dan D (10) juga menunjukkan afinitas pengikatan yang kuat (-8,3 dan -8,8 kJ/mol) ke protein target 1S16 terutama akibat ikatan hidrogen dan interaksi hidrofobik. Secara kolektif, hasil ini menunjukkan potensi agelasidin A, C dan D sebagai modulator dari target antibiotik baru, enzim topoisomerase IV.
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Aung, Thet Htwe. "Proximicin A-C as prospective HER2-positive and negative breast cancer drugs: Molecular docking and in silico ADME modeling." IPS Journal of Molecular Docking Simulations 1, no. 1 (May 18, 2022): 1–11. http://dx.doi.org/10.54117/ijmds.v1i1.9.

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Breast cancer is the second leading cause of cancer-related death among women worldwide. Proximicin A-C are bioactive chemicals produced by the marine Verrucosispora strain, which have been shown to have potent cytostatic effect against human breast cancer [MCF 7]. HER2 (Human epidermal growth factor receptor 2) is a gene that has been linked to breast cancer development. The study’s goals are to (1) forecast the intensity of binding affinity and interactions between HER2 and proximicin A-C, and (2) analyze ADME characteristics of proximicin A-C (Absorption, Distribution, Metabolism, and Excretion). The CB-Dock web service was used to dock proximicin A-C and commonly used breast cancer medicines Neratinib (Nerlynx) and Talazoparib against HER2, and protein-ligand interaction findings were collected via the protein-ligand interaction profiler (PLP) web server. The SwissADME web server was used to investigate ADME properties of the substances. In terms of docking, proximicin A has a vina score of -8.6, proximicin B and C has a score of -10, Talazoparib has a vina score of -8.5, and Neratinib (Nerlynx) has a vina score of -10.2 on CB-Dock. This means that proximicin B and C bind to HER2 more strongly than proximicin A and Talazoparib. Furthermore, their high binding affinity is nearly equivalent to Neratinibs (Nerlynx). Talazoparib has a lower binding affinity for HER2 than proximicin A. With HER2, all three chemicals have a strong hydrogen bond and hydrophobic contact. SwissADME estimated that all three substances follow the Lipinski rule (RO5) and have a bioavailability score of 0.55. They don’t have any structural issue in medicinal chemistry (no alerts in PAINS and Brenk forecasts), and their synthetic accessibility scales range from 3 to 3.5. Only proximicin A, on the other hand, has the leadlikeness feature. All three drugs failed to cross the blood-brain barrier (BBB) in terms of pharmacokinetics. Proximicin A has a high absorption rate in the GI tract, whereas proximicin B-C has a low absorption rate in the GI tract (GI). Similarly, proximicin A is neither a P-gp substrate nor a CYP1A2, CYP2C19, CYP2C9, CYP2D6, or CYP3A4 inhibitor. Proximicin B-C, on the other hand, are P-gp substrates, and proximicin C is an inhibitor of all provided CYP enzymes, whilst proximicin B inhibits only three. Overall, proximicin A-C could be used as a possible breast cancer therapeutic candidate. Proximicin B-C will outperform proximicin A in terms of therapeutic efficacy. Proximicin A, on the other hand, will have better ADME qualities than Proximicin B-C. This study will provide the lead information for developing a new breast cancer medication with a good pharmacological profile.
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Sharma, Arun Dev, and Inderjeet Kaur. "Chemical Profile and in-silico Docking Studies on Bioactives from Essential Oil of Cymbopogan pendulus Targeting Penicillin Binding Proteins (PBPs) in Bacteria." Biology, Medicine, & Natural Product Chemistry 12, no. 1 (February 17, 2023): 225–32. http://dx.doi.org/10.14421/biomedich.2023.121.225-232.

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Antibiotic resistance in bacteria is the major concern worldwide. PBP (Penicillin binding proteins) have been cited as an appropriate target for therapeutic drug design. In the present study molecular docking followed by wet lab validation was designed to estimate the effect of potent bioactive molecules from Cymbopogan pendulus essential oil against PBP5 protein. GC-FID (gas chromatography with flame-ionization detection) based composition profile, and in-silico docking study was conducted by using CB-dock 2 analysis followed by 2D and 3D interactions. GC-FID revealed Limonene, Neral, Geranial, Linalool, Myrcene as major and minor compounds in Cymbopogan pendulus essential oil. The docking score indicated effective binding of ligands to PBP5. Interactions results indicated that, PBP5/ligand complexes form hydrogen and hydrophobic interactions. Wet lab study validated the anti-bacterial potential of oil against gram-positive and gram-negative bacteria. Therefore, essential oil from Cymbopogan pendulus essential oil may represent potential herbal treatment to mitigate bacterial infections.
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Dilshad, Erum, Muhammad Maaz, Suliman, and Naeem Mehmood Ashraf. "Identification of Anti-inflammatory Metabolites from Trigonella foenum-greacum using Computational Approaches." Current Trends in OMICS 2, no. 1 (June 28, 2022): 55–88. http://dx.doi.org/10.32350/cto.21.04.

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Human disease prevalence has increased as a result of modern lifestyles, stress, and toxic waste. Worldwide, researchers aim to discover therapeutic compounds which may cure and prevent the onset of diseases. So, this study was planned to discover potential anti-inflammatory metabolites from Trigonella foenum-graecum. It is an annual plant within the family Fabaceae. This plant is used as a spice throughout the world and has many beneficial medicinal effects. It is commonly grown in Pakistan, India, and some Middle Eastern countries. Ten bioactive compounds representative of all classes, namely alkaloid, flavonoid, phytic acid, 4-hydroxy isoleucine, sapogenin, quercetin, trigonelline, tricin, naringenin, and flavonol were selected. Molecular docking of these ligands was carried out against drug targets namely cyclooxygenase-2, Human Neutrophil Elastase (HNE), microsomal PGES-2, and tyrosinase by using CB Dock and AMDock software. Further refining by screening filters produced sapogenin as the lead compound. All the visualization analysis and interaction studies were performed using PyMol molecular visualization tool and Ligplot+. Celebrex was used as the standard for comparison. The comparison between sapogenin and Celebrex showed that the former is much more active than the standard drug. This is a novel finding. So, it might be explored further as a drug candidate to treat chronic inflammatory diseases in the future.
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Alavi, Mehran, M. R. Mozafari, Saba Ghaemi, Morahem Ashengroph, Fatemeh Hasanzadeh Davarani, and Mohammadreza Mohammadabadi. "Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study." Biomedicines 10, no. 12 (November 29, 2022): 3074. http://dx.doi.org/10.3390/biomedicines10123074.

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Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of −9.9 and −8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.
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Ashraf, Huma, Erum Dilshad, Tayyaba Afsar, Ali Almajwal, Huma Shafique, and Suhail Razak. "Molecular Screening of Bioactive Compounds of Garlic for Therapeutic Effects against COVID-19." Biomedicines 11, no. 2 (February 20, 2023): 643. http://dx.doi.org/10.3390/biomedicines11020643.

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An outbreak of pneumonia occurred on December 2019 in Wuhan, China, which caused a serious public health emergency by spreading around the globe. Globally, natural products are being focused on more than synthetic ones. So, keeping that in view, the current study was conducted to discover potential antiviral compounds from Allium sativum. Twenty-five phytocompounds of this plant were selected from the literature and databases including 3-(Allylsulphinyl)-L-alanine, Allicin, Diallyl sulfide, Diallyl disulfide, Diallyl trisulfide, Glutathione, L-Cysteine, S-allyl-mercapto-glutathione, Quercetin, Myricetin, Thiocysteine, Gamma-glutamyl-Lcysteine, Gamma-glutamylallyl-cysteine, Fructan, Lauricacid, Linoleicacid, Allixin, Ajoene, Diazinon Kaempferol, Levamisole, Caffeicacid, Ethyl linoleate, Scutellarein, and S-allylcysteine methyl-ester. Virtual screening of these selected ligands was carried out against drug target 3CL protease by CB-dock. Pharmacokinetic and pharmacodynamic properties defined the final destiny of compounds as drug or non-drug molecules. The best five compounds screened were Allicin, Diallyl Sulfide, Diallyl Disulfide, Diallyl Trisulfide, Ajoene, and Levamisole, which showed themselves as hit compounds. Further refining by screening filters represented Levamisole as a lead compound. All the interaction visualization analysis studies were performed using the PyMol molecular visualization tool and LigPlot+. Conclusively, Levamisole was screened as a likely antiviral compound which might be a drug candidate to treat SARS-CoV-2 in the future. Nevertheless, further research needs to be carried out to study their potential medicinal use.
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Dissertations / Theses on the topic "CB-DOCK"

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NAVNEET. "AN APPROACH TO TARGET ALZHEIMER'S DISEASE THROUGH MOLECULAR DOCKING." Thesis, 2022. http://dspace.dtu.ac.in:8080/jspui/handle/repository/19052.

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Alzheimer's disease is described as a nervous system illness that worsens with time. In the world's increasing aging people, it is the most common cause of dementia. The increasing number of Alzheimer’s disease cases poses a massive load on families or communities. Despite different attempts to study more about the genesis of Alzheimer's disease, little progress has been made till now. And for the detection and prognosis of Alzheimer’s disease, circulatory miRNAs are the most specific favorable prospects in the search for simply attainable and non-invasive biomarkers. Few of them have been recognized as AD-specific miRNAs, and their targets appear to be involved in pathophysiological processes that underpin AD. And now the currently available drugs are very limited for the effective therapy of Alzheimer’s disease thus the discovery of new & effective therapeutics is required for AD. Recent computational endeavors to predict novel and effective drugs and targets are reliable and less time-consuming. In computer-assisted drug design, molecular docking is an important technology. PB-DOCK online site gives the detailed docking result and confers how the ligands make a bond with the specific target, which is invaluable in lead molecule optimization. In CB-DOCK, I have used target protein 1sgz Beta-Secretase from AD, which is collected from RCSC PDB databank in PDB format, and then carried CB-DOCK dockings with the test ligands collected from PubChem in SDF-MDL MOL format then converted into PDB format through Open Bable GUI software, which is freely available on the internet. After that, I proceeded with the docking of the rasagiline, Entacapone, and mirtazapine drugs. Results further indicated that these test ligands bind significantly to the Beta-secretase and may play a role in its inhibition. These ligands have been identified as potential beta-secretase inhibitors and new anti-Alzheimer drugs in this study.
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