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Khaled H. Barakat, Ph.D. - Publications

Affiliations: 
2012 Physics University of Alberta, Edmonton, Alberta, Canada 
Area:
General Biophysics, Bioinformatics Biology
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48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Weilbeer C, Jay D, Donnelly JC, Gentile F, Karimi-Busheri F, Yang X, Mani RS, Yu Y, Elmenoufy AH, Barakat KH, Tuszynski JA, Weinfeld M, West FG. Modulation of ERCC1-XPF Heterodimerization Inhibition Structural Modification of Small Molecule Inhibitor Side-Chains. Frontiers in Oncology. 12: 819172. PMID 35372043 DOI: 10.3389/fonc.2022.819172  0.558
2019 Gentile F, Elmenoufy AH, Ciniero G, Jay D, Karimi-Busheri F, Barakat KH, Weinfeld M, West FG, Tuszynski JA. Computer-Aided Drug Design of Small Molecule Inhibitors of the ERCC1-XPF Protein-Protein Interaction. Chemical Biology & Drug Design. PMID 31891209 DOI: 10.1111/Cbdd.13660  0.628
2019 Jaballah MY, Serya RAT, Saad N, Khojah SM, Ahmed M, Barakat K, Abouzid KAM. Towards discovery of novel scaffold with potent antiangiogenic activity; design, synthesis of pyridazine based compounds, impact of hinge interaction, and accessibility of their bioactive conformation on VEGFR-2 activities. Journal of Enzyme Inhibition and Medicinal Chemistry. 34: 1573-1589. PMID 31852269 DOI: 10.1080/14756366.2019.1651723  0.301
2019 Chen R, Ganesan A, Okoye I, Arutyunova E, Elahi S, Lemieux MJ, Barakat K. Targeting B7-1 in immunotherapy. Medicinal Research Reviews. PMID 31448437 DOI: 10.1002/Med.21632  0.302
2019 Elmenoufy A, Gentile F, Jay D, Karimi-Busheri F, Yang X, Soueidan OM, Weilbeer C, Mani RS, Barakat KH, Tuszynski J, Weinfeld M, West FG. Targeting DNA Repair in Tumor Cells via Inhibition of ERCC1-XPF. Journal of Medicinal Chemistry. PMID 31369707 DOI: 10.1021/Acs.Jmedchem.9B00326  0.586
2019 Ahmed M, Kumar A, Hobman TC, Barakat K. Structure-based screening and validation of potential dengue virus inhibitors through classical and QM/MM affinity estimation. Journal of Molecular Graphics & Modelling. 90: 128-143. PMID 31082639 DOI: 10.1016/J.Jmgm.2019.04.010  0.338
2018 Elsayed NMY, Serya RAT, Tolba MF, Ahmed M, Barakat K, Abou El Ella DA, Abouzid KAM. Design, synthesis, biological evaluation and dynamics simulation of indazole derivatives with antiangiogenic and antiproliferative anticancer activity. Bioorganic Chemistry. 82: 340-359. PMID 30428414 DOI: 10.1016/J.Bioorg.2018.10.071  0.333
2018 Groenendyk J, Paskevicius T, Urra H, Viricel C, Wang K, Barakat K, Hetz C, Kurgan L, Agellon LB, Michalak M. Cyclosporine A binding to COX-2 reveals a novel signaling pathway that activates the IRE1α unfolded protein response sensor. Scientific Reports. 8: 16678. PMID 30420769 DOI: 10.1038/S41598-018-34891-W  0.31
2018 Gentile F, Barakat KH, Tuszynski JA. Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease. International Journal of Molecular Sciences. 19. PMID 29710850 DOI: 10.3390/Ijms19051328  0.63
2018 Feng T, Barakat K. Molecular Dynamics Simulation and Prediction of Druggable Binding Sites. Methods in Molecular Biology (Clifton, N.J.). 1762: 87-103. PMID 29594769 DOI: 10.1007/978-1-4939-7756-7_6  0.328
2018 Gentile F, Deriu MA, Barakat K, Danani A, Tuszynski J. A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study. Pharmaceuticals (Basel, Switzerland). 11. PMID 29462934 DOI: 10.3390/Ph11010022  0.491
2018 Barakat K. Abstract 2503: Rational design of small-molecule immune checkpoints' inhibitors Cancer Research. 78: 2503-2503. DOI: 10.1158/1538-7445.Am2018-2503  0.328
2018 Gentile F, Tuszynski JA, Barakat KH. Investigating the Structure of the XPF-ERCC1 Functional Endonuclease using a Computational Approach Biophysical Journal. 114: 45a. DOI: 10.1016/J.Bpj.2017.11.300  0.424
2017 Kalyaanamoorthy S, Barakat KH. Binding modes of hERG blockers: an unsolved mystery in the drug design arena. Expert Opinion On Drug Discovery. 1-4. PMID 29240515 DOI: 10.1080/17460441.2018.1418319  0.303
2017 Ahmed M, Barakat K. When theory meets experiment: the PD-1 challenge. Journal of Molecular Modeling. 23: 308. PMID 29019005 DOI: 10.1007/S00894-017-3482-X  0.306
2017 Kalyaanamoorthy S, Barakat KH. Development of Safe Drugs: The hERG Challenge. Medicinal Research Reviews. PMID 28467598 DOI: 10.1002/Med.21445  0.357
2017 Sheff JG, Farshidfar F, Bathe OF, Kopciuk K, Gentile F, Tuszynski J, Barakat K, Schriemer DC. Novel allosteric pathway of Eg5 regulation identified through multivariate statistical analysis of HX-MS ligand screening data. Molecular & Cellular Proteomics : McP. PMID 28062800 DOI: 10.1074/Mcp.M116.064246  0.518
2017 Ganesan A, Coote ML, Barakat K. Molecular ‘time-machines’ to unravel key biological events for drug design Wiley Interdisciplinary Reviews: Computational Molecular Science. 7. DOI: 10.1002/Wcms.1306  0.315
2016 Ahmed M, Pal A, Houghton M, Barakat K. A Comprehensive Computational Analysis for the Binding Modes of Hepatitis C Virus NS5A Inhibitors: The Question of Symmetry. Acs Infectious Diseases. 2: 872-881. PMID 27933783 DOI: 10.1021/Acsinfecdis.6B00113  0.379
2016 Ganesan A, Coote ML, Barakat K. Molecular dynamics-driven drug discovery: Leaping forward with confidence. Drug Discovery Today. PMID 27890821 DOI: 10.1016/J.Drudis.2016.11.001  0.334
2016 Gentile F, Tuszynski JA, Barakat KH. Modelling DNA Repair Pathways: Recent Advances and Future Directions. Current Pharmaceutical Design. PMID 27093954 DOI: 10.2174/1381612822666160420141435  0.617
2016 Gentile F, Tuszynski JA, Barakat KH. New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy. Journal of Molecular Graphics & Modelling. 65: 71-82. PMID 26939044 DOI: 10.1016/J.Jmgm.2016.02.010  0.641
2015 El-Labbad EM, Ismail MA, Abou El Ella DA, Ahmed M, Wang F, Barakat K, Abouzid KA. Discovery of novel peptidomimetics as irreversible CHIKV nsP2 protease inhibitors using quantum mechanical based ligand descriptors". Chemical Biology & Drug Design. PMID 26212366 DOI: 10.1111/Cbdd.12621  0.341
2015 Ahmed M, Wang F, Levin A, Le C, Eltayebi Y, Houghton M, Tyrrell L, Barakat K. Targeting the Achilles heel of the hepatitis B virus: a review of current treatments against covalently closed circular DNA. Drug Discovery Today. 20: 548-61. PMID 25622780 DOI: 10.1016/J.Drudis.2015.01.008  0.303
2015 Barakat KH, Anwar-Mohamed A, Tuszynski JA, Robins MJ, Tyrrell DL, Houghton M. A Refined Model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes. Journal of Chemical Information and Modeling. 55: 362-73. PMID 24730573 DOI: 10.1021/Ci400631N  0.496
2015 Barakat K. Immune Checkpoints Inhibitors: A Single Antiviral and Anticancer Magic Bullet Journal of Pharmaceutical Care & Health Systems. 2: 1-2. DOI: 10.4172/2376-0419.1000E127  0.325
2015 Ahmed M, Barakat K. Baby Steps Toward Modelling The Full human Programmed Death-1 (PD-1) Pathway Receptors and Clinical Investigation. 2. DOI: 10.14800/Rci.825  0.381
2014 Hu G, Wang K, Groenendyk J, Barakat K, Mizianty MJ, Ruan J, Michalak M, Kurgan L. Human structural proteome-wide characterization of Cyclosporine A targets. Bioinformatics (Oxford, England). 30: 3561-6. PMID 25172926 DOI: 10.1093/Bioinformatics/Btu581  0.353
2014 Anwar-Mohamed A, Barakat KH, Bhat R, Noskov SY, Tyrrell DL, Tuszynski JA, Houghton M. A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity. Toxicology Letters. 230: 382-92. PMID 25127758 DOI: 10.1016/J.Toxlet.2014.08.007  0.502
2014 Barakat K. Do We Need Small Molecule Inhibitors for the Immune Checkpoints Journal of Pharmaceutical Care & Health Systems. 1: 1-2. DOI: 10.4172/2376-0419.1000E119  0.311
2014 Barakat KH, Houghton M, Tyrrel DL, Tuszynski JA. Rational Drug Design International Journal of Computational Models and Algorithms in Medicine. 4: 59-85. DOI: 10.4018/Ijcmam.2014010104  0.51
2013 Barakat KH, Law J, Prunotto A, Magee WC, Evans DH, Tyrrell DL, Tuszynski J, Houghton M. Detailed computational study of the active site of the hepatitis C viral RNA polymerase to aid novel drug design. Journal of Chemical Information and Modeling. 53: 3031-43. PMID 24116674 DOI: 10.1021/Ci4003969  0.517
2013 Barakat KH, Huzil JT, Jordan KE, Evangelinos C, Houghton M, Tuszynski J. A computational model for overcoming drug resistance using selective dual-inhibitors for aurora kinase A and its T217D variant. Molecular Pharmaceutics. 10: 4572-89. PMID 24094068 DOI: 10.1021/Mp4003893  0.529
2013 Jordheim LP, Barakat KH, Heinrich-Balard L, Matera EL, Cros-Perrial E, Bouledrak K, El Sabeh R, Perez-Pineiro R, Wishart DS, Cohen R, Tuszynski J, Dumontet C. Small molecule inhibitors of ERCC1-XPF protein-protein interaction synergize alkylating agents in cancer cells. Molecular Pharmacology. 84: 12-24. PMID 23580445 DOI: 10.1124/Mol.112.082347  0.591
2012 Barakat KH, Jordheim LP, Perez-Pineiro R, Wishart D, Dumontet C, Tuszynski JA. Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction. Plos One. 7: e51329. PMID 23272099 DOI: 10.1371/Journal.Pone.0051329  0.564
2012 Tuszynski JA, Craddock TJ, Mane JY, Barakat K, Tseng CY, Gajewski M, Winter P, Alisaraie L, Patterson J, Carpenter E, Wang W, Deyholos MK, Li L, Sun X, Zhang Y, et al. Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin. Pharmaceutical Research. 29: 3007-21. PMID 22833053 DOI: 10.1007/S11095-012-0829-Y  0.71
2012 Barakat K, Gajewski M, Tuszynski JA. DNA repair inhibitors: the next major step to improve cancer therapy. Current Topics in Medicinal Chemistry. 12: 1376-90. PMID 22794314 DOI: 10.2174/156802612801319070  0.764
2012 Craddock TJ, St George M, Freedman H, Barakat KH, Damaraju S, Hameroff S, Tuszynski JA. Computational predictions of volatile anesthetic interactions with the microtubule cytoskeleton: implications for side effects of general anesthesia. Plos One. 7: e37251. PMID 22761654 DOI: 10.1371/Journal.Pone.0037251  0.462
2012 Barakat K, Gajewski M, Tuszynski J. DNA Repair Inhibitors: Our Last Disposal to Improve Cancer Therapy. Current Topics in Medicinal Chemistry. PMID 22690684  0.767
2012 Barakat KH, Gajewski MM, Tuszynski JA. DNA polymerase beta (pol β) inhibitors: a comprehensive overview. Drug Discovery Today. 17: 913-20. PMID 22561893 DOI: 10.1016/J.Drudis.2012.04.008  0.75
2012 Friesen DE, Barakat KH, Semenchenko V, Perez-Pineiro R, Fenske BW, Mane J, Wishart DS, Tuszynski JA. Discovery of small molecule inhibitors that interact with γ-tubulin. Chemical Biology & Drug Design. 79: 639-52. PMID 22268380 DOI: 10.1111/J.1747-0285.2012.01340.X  0.547
2011 Barakat K, Issack BB, Stepanova M, Tuszynski J. Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant. Plos One. 6: e27651. PMID 22110706 DOI: 10.1371/Journal.Pone.0027651  0.527
2011 Barakat KH, Mane JY, Tuszynski JA. Virtual screening: An overview on methods and applications Handbook of Research On Computational and Systems Biology: Interdisciplinary Applications. 28-60. DOI: 10.4018/978-1-60960-491-2.ch002  0.425
2010 Barakat K, Tuszynski J. Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta. Journal of Molecular Graphics & Modelling. 29: 702-16. PMID 21194999 DOI: 10.1016/J.Jmgm.2010.12.003  0.591
2010 Bennett MJ, Barakat K, Huzil JT, Tuszynski J, Schriemer DC. Discovery and characterization of the laulimalide-microtubule binding mode by mass shift perturbation mapping. Chemistry & Biology. 17: 725-34. PMID 20659685 DOI: 10.1016/J.Chembiol.2010.05.019  0.458
2010 Barakat K, Mane J, Friesen D, Tuszynski J. Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions Journal of Molecular Graphics and Modelling. 28: 555-568. PMID 20056466 DOI: 10.1016/J.Jmgm.2009.12.003  0.499
2009 Huzil JT, Barakat K, Tuszynski JA. Electrostatic contributions to colchicine binding within tubulin isotypes. Electromagnetic Biology and Medicine. 28: 355-64. PMID 20017626 DOI: 10.3109/15368370903206606  0.509
2009 Barakat KH, Torin Huzil J, Luchko T, Jordheim L, Dumontet C, Tuszynski J. Characterization of an inhibitory dynamic pharmacophore for the ERCC1-XPA interaction using a combined molecular dynamics and virtual screening approach. Journal of Molecular Graphics & Modelling. 28: 113-30. PMID 19473860 DOI: 10.1016/J.Jmgm.2009.04.009  0.598
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