Dr. Khaled Hassan Barakat

Assistant Professor
University of Alberta, Canada

Highest Degree
Ph.D. in Biophysics from University of Alberta, Canada

My URL
https://livedna.org/20.9842

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Biography

Dr. Khaled H. S. Barakat is currently working as Research Assistant Professor, Faculty of Pharmacy & Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada. He obtained his PhD in Biophysics from same University in 2012. His area of research expertise includes Molecular Modeling, Bioinformatics, Computer Architecture, and Computer Programming Method. He is supervising a number of PhD and Masters Students under his active supervision. He is Guest Reviewer for the Scientific Journals. He is member of editorial board in many journals. He is also professional member of American Chemical Society. He has published (35) peer review papers in journals, (3) chapters in books, (14) poster presentations, (7) patent contributed as writer/co-writer.

Area of Interest:

Pharmacology and Toxicology
Molecular Modeling
Drug Design
Virology
Biophysics

Selected Publications

  1. Syedbasha, M., J. Linnik, D. Santer, D. O`Shea and K. Barakat, et al., 2016. An ELISA based binding and competition method to rapidly determine ligand-receptor interactions. J. Visualized Exp., 109: e53575-e53575.
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  2. Hasani, H.J. and K. Barakat, 2016. Protein-Protein Docking: Are We There Yet? In: Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery. Siavoush, D., (Ed.). IGI Global, USA, pp. 173-195.

  3. Gentile, F., J.A. Tuszynski and K.H. Barakat, 2016. New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy. J. Mol. Graphics Modell., 65: 71-82.
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  4. Gentile, F., J.A. Tuszynski and K.H. Barakat, 2016. Modelling DNA repair Pathways: Recent advances and future directions. Curr. Pharm. Des., 22: 3527-3546.
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  5. Ganesan, A. and K. Barakat, 2016. Target fishing: a key to unlock the one-to-many puzzle in drug discovery. J. Pharm. Care Health Syst., .
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  6. Ahmed, M., A. Pal, M. Houghton and K. Barakat, 2016. A comprehensive computational analysis for the binding modes of hepatitis C virus NS5A Inhibitors: The question of symmetry. ACS Infect. Dis., .
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  7. Viricel, C., M. Ahmed and K. Barakat, 2015. Human PD-1 binds differently to its human ligands: a comprehensive modeling study. J. Mol. Graphics Modell., 57: 131-142.
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  8. Kassem, S., M. Ahmed, S. El Sheikh and K.H. Barakat, 2015. Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods. J. Mol. Graphics Modell., 62: 105-117.
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  9. El labbad, E.M., M.A. Ismail, A.E. Ella, A. Dalal and M. Ahmed, et al., 2015. Discovery of novel peptidomimetics as irreversible CHIKV NsP2 protease inhibitors using quantum mechanical‐based ligand descriptors. Chem. Biol. Drug Des., 86: 1518-1527.

  10. Barakat, K., 2015. Editorial: Modelling off-target interactions (I): Cardiotoxicity. J. Pharm. Care Health Syst., .

  11. Barakat, K., 2015. Editorial: Immune checkpoints Inhibitors: The search for a single antiviral & anticancer magic bullet. J. Pharm. Care Health Syst., .

  12. Barakat, K and M. Ahmed, 2015. Baby steps toward modelling the full human programmed death-1 (pd-1) pathway. Recept. Clin. Invest., 10.14800/rci.825.
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  13. Ahmed, M., F. Wang, A. Levin, C. Le and Y. Eltayebi et al., 2015. Targeting the Achilles heel of the hepatitis B virus: A review of current treatments against covalently closed circular DNA. Drug Discov. Today, 20: 548-561.
    CrossRef  |  

  14. Vos, K.J., A.G. Martin, M.G. Trimboli, L. Forestell, K. Barakat and J.A. Tuszynski, 2014. A multi-compartment pharmacokinetic model of the interaction between paclitaxel and doxorubicin. EPJ Nonlinear Biomed. Phys., 2: 1-40.
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  15. Hu, G., K. Wang, J. Groenendyk, K. Barakat and M.J. Mizianty, 2014. Human structural proteome-wide characterization of cyclosporine a targets. Bioinf., 30: 3561-3566.
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  16. Egli, A., D.M. Santer, D. O`Shea, K. Barakat, M. Syedbasha, M. Vollmer and D. Kumar, 2014. IL-28B is a key regulator of B-and T-cell vaccine responses against Influenza. PLoS Pathog., 10.1371/journal.ppat.1004556.
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  17. Egli, A., D. Santer, K. Arakat, M. Zand, A. Levin, M. Vollmer and D. O`Shea, 2014. Vaccine adjuvants-understanding molecular mechanisms to improve vaccines. Swiss Med. Wkly, 10.4414/smw.2014.13940.
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  18. Egli, A., A. Levin, D.M. Santer, M. Joyce and D. O`Shea et al., 2014. Immunomodulatory Function of Interleukin 28B during primary infection with cytomegalovirus. J. Infect Dis., 210: 717-727.
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  19. Barakat, K.H., M. Houghton, D.L. Tyrrel and J.A. Tuszynski, 2014. Rational drug design: one target, many paths to it. Int. J. Comput. Models Algorithms Med., 4: 59-85.
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  20. Barakat, K.H., A. Anwar-Mohamed, J.A. Tuszynski, M.J. Robins, D.L. Tyrrell and M. Houghton, 2014. A refined model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes. J. Chem. Inf. Model., 55: 362-373.
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  21. Barakat, K., 2014. Editorial: Computer-aided drug design. J. Pharm. Care Health Sysy., .

  22. Barakat, K., 2014. Do we need small molecule inhibitors for the immune checkpoints? J. Pharm. Care Health Syst., .
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  23. Anwar, M.A., K.H. Barakat, R. Bhat, S.Y. Noskov, D.L. Tyrrell, J.A. Tuszynski and M. Houghton, 2014. A human ether-a-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity. Toxicol. Lett., 230: 382-392.
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  24. Jordheim, L.P., K.H. Barakat, L. Heinrich-Balard, E.L. Matera and E. Cros-Perrial, 2013. Small molecule inhibitors of ERCC1-XPF protein-protein interaction synergize alkylating agents in cancer cells. Mol. Pharmacol., 84: 12-24.
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  25. Gajewski, M.M., J.A. Tuszynski, K. Barakat, J.T. Huzil and M. Klobukowski, 2013. Interactions of laulimalide, peloruside, and their derivatives with the isoforms of β-tubulin. Can. J. Chem., 91: 511-517.
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  26. Barakat, K.H., J.T. Huzil, K.E. Jordan, C. Evangelinos, M. Houghton and J. Tuszynski, 2013. A computational model for overcoming drug resistance using selective dual-inhibitors for aurora kinase A and its T217D variant. Mol. Pharmacol., 10: 4572-4589.
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  27. Barakat, K.H., J. Law, A. Prunotto, W.C. Magee and D.H. Evans et al., 2013. Detailed computational study of the active site of the hepatitis C viral RNA polymerase to aid novel drug design. J. Chem. Inf. Model., 53: 3031-3043.
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  28. Tuszynski, J.A., T.J. Craddock, J.Y. Mane, K. Barakat and C.Y. Tseng et al., 2012. Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin. Pharm. Res., 29: 3007-3021.
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  29. Friesen, D.E., K.H. Barakat, V. Semenchenko, R. Perez-Pineiro and B.W. Fenske et al., 2012. Discovery of small molecule inhibitors that interact with γ-tubulin. Chem. Biol. Drug Des., 79: 639-652.
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  30. Craddock, T.J., M.S. George, H. Freedman, K.H. Barakat, S. Damaraju, S. Hameroff and J.A. Tuszynski, 2012. Computational predictions of volatile anesthetic interactions with the microtubule cytoskeleton: Implications for side effects of general anesthesia. PLoS One, .
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  31. Barakat, K.H., M.M. Gajewski and J.A. Tuszynski, 2012. DNA polymerase beta (pol β) inhibitors: a comprehensive overview. Drug Discovery Today, 17: 913-920.
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  32. Barakat, K.H., L.P. Jordheim, R. Perez Pineiro, D. Wishart, C. Dumontet and J.A. Tuszynski, 2012. Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction. PloS one, .
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  33. Barakat, K., M. Gajewski and J.A. Tuszynski, 2012. DNA repair inhibitors: the next major step to improve cancer therapy. Curr. Top. Med. Chem., 12: 1376-1390.
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  34. Barakat, K., M. Gajewski and J. Tuszynski, 2012. DNA repair Inhibitors: Our last disposal to improve cancer therapy. Curr. Top. Med. Chem., .
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  35. Barakat, K.H., J.Y. Mane and J.A. Tuszynski, 2011. Virtual Screening: An Overview on Methods and Applications. In: Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications. Liu and L. Angela, (Ed.)., Medical Information Science Reference, Canada, pp: 28-60.

  36. Barakat, K.H. and J. Tuszynski, 2011. Virtual Screening for DNA repair inhibitors. InTech open access publisher, China, Pages: 28.

  37. Barakat, K., B.B. Issack, M. Stepanova and J. Tuszynski, 2011. Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant. PloS One, 10.1371/journal.pone.0027651.
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  38. Barakat, K and J. Tuszynski, 2011. Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta. J. Mol. Graphics Modell., 29: 702-716.
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  39. Bennett, M.J., K. Barakat, J.T. Huzil, J. Tuszynski and D.C. Schriemer, 2010. Discovery and characterization of the laulimalide-microtubule binding mode by mass shift perturbation mapping. Chem. Biol., 17: 725-734.
    CrossRef  |  

  40. Barakat, K., J. Mane, D. Friesen and J. Tuszynski, 2010. Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions. J. Mol. Graphics Modell., 28: 555-568.
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  41. Huzil, J.T., K. Barakat and J.A. Tuszynski, 2009. Electrostatic contributions to colchicine binding within tubulin isotypes. Electromagn. Biol. Med., 28: 355-364.
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  42. Barakat, K.H., T.J. Huzil, T. Luchko, L. Jordheim, C. Dumontet and J. Tuszynski, 2009. Characterization of an inhibitory dynamic pharmacophore for the ERCC1-XPA interaction using a combined molecular dynamics and virtual screening approach. J. Mol. Graphics Modell., 28: 113-130.
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  43. El-Sheikh, S.M., K. Barakat, N.M. Salem and L. Ulivi, 2006. Phase transitions of carbon tetra-fluoride using raman spectroscopy and molecular dynamics simulations. High Pressure Res. Int. J., 26: 383-386.
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  44. El-Sheikh, S.M., K. Barakat and N.M. Salem, 2006. Phase transitions of methane using molecular dynamics simulations. J. Chem. Phys., 124: 124517-124517.
Member since October, 2017