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Khaled Barakat, PhD, MSc, EIT

Assistant Professor

Pharmacy and Pharmaceutical Sciences

About Me

Dr. Barakat received his PhD in biophysics from the University of Alberta in 2012 followed by a postdoctoral fellowship in Professor Michael Houghton’s Lab for two years. During his career, Dr. Barakat received numerous awards including the CIHR and AIHS postdoctoral fellowships, the prestigious UofA dissertation award, the ACRI Studentship and many distinction awards throughout his undergraduate and graduate studies. Dr. Barakat is also the editor of a number of journals. Dr. Barakat's lab is supported by different funding agencies including the Alberta Cancer Foundation, Li Ka Shing Applied Virology Institute, Natural Sciences and Engineering Research Council (NSERC), Li Ka Shing Institute of Virology and IC-IMPACTS Centres of Excellence. Dr. Barakat is also the CEO & co-founder of HEKA Therapeutics Inc. and co-founder of ACHLYS; two spinoff companies devoted to drug discovery of immune checkpoints small molecule inhibitors and predicting off-target toxicity of new compounds in drug discovery.  

For more information, please check recent media coverage about Barakat's lab:

Edmonton Journal    Edmonton Sun      CTV National     CTV Edmonton          

Global Edmonton     TechieNews           Pharmpro          Science News

UofA                         Dinner Television   Leap Magazine


Research

The major research focus in my lab is to apply state-of-the-art computational drug discovery tools to discover new antiviral and immune checkpoints’ small molecule drugs. Our lab specializes in understanding the nature and biophysical processes underlying protein-drug interaction, protein-protein interactions, protein-DNA interactions, drug off-target interactions and predicting drug-mediated toxicity. My laboratory has been growing and evolving into a multidisciplinary team, which comprises members with expertise in computer software design, pharmaceutics, chemistry, biophysics and computer science. We also have our own contemporary computer cluster as well as allocated resources from compute Canada and the IBM Blue Gene/Q supercomputer. In addition to the computational framework in our group, we also carry out different wet-lab experimental techniques to validate our modelling hypothesis and optimize our calculations. Our experiments are devoted to the characterization of protein-small molecules and  protein-protein interactions.

My lab has managed to:

• Build innovative computer models for the immune checkpoints proteins.

• Design small molecule inhibitors for the PD-1 and CTLA-4 pathways.

• Build comprehensive models for protein ion channels and membrane proteins.

• Develope new technologies to predict protein-protein and protein-drug interactions.

• Build robust mathematical models for different immune checkpoints pathways.

• Develope novel inhibitors for the RNA polymerase NS5B of HCV.

• Develope three novel classes of inhibitors for the HCV viral protein NS5A.

• Discover the first inhibitor of the ERCC1-XPA protein-protein interaction.

• Discover inhibitors for the ERCC1-XPF protein-protein interaction.

• Discover dual inhibitors for the p53-MDM2/MDM4 protein-protein interactions.

• Identify the binding site of Laulimalide within tubulin protein.


                                              Past Lab Members (where do our trainees go?):

  Postdoctoral Fellows:

  • Dr. Marawan Ahmed, Postdoctoral Fellow (June 2014 - June 2018): Current position: Senior data analyst at Alberta Health Services (AHS) 
  • Dr. Abdo Ahmed, Postdoctoral Fellow (February 2018 - August 2018). Current position: Assistant professor, Cairo University, Egypt. 

  Graduate Students:

  • Francesco Gentile, PhD student. Current position: Postdoctoral fellow, University of British Colombia, Canada.
  • Horia Jalily, Master Student. Current position: Research Assistant, University of Alberta, Canada.
  • Clement Viricel, Master student. Current position: PhD student, University of Lyon, France.

   Internship & Summer Students:  

 Name                               Period                                        Degree                           Current Position

Jiay Tong                   03/2019-05/2019                           UARE Intern                         MSc, Germany

Yanping Yang            01/2019-03/2019                           UARE Intern                          MSc, China

Ziwen Chen              10/2018-12/2018                            CSC Intern                            MSc, China.

Anna Jutla                 04/2018-09/2018                         Summer Student     Pharmacy Undergraduate Student, Uof Alberta, Canada.

Nawreen Hena          01/2017-05/2017                         Summer Student     Science Undergraduate Student, Uof Alberta, Canada.

Theinmozhi Arulraj    05/2017-08/2017                           UARE Intern                          PhD Student, Germany. 

Gyan Darshan           05/2017-08/2017                           UARE Intern                          MSc, India

Min-haung chiang    01/2017-05/2017                            UARE Intern                          PhD student, New Zealand

Abhishek Pal            05/2016-08/2016                            UARE Intern                          MSc, India

 Crystal Lui                01/2016-05/2016                         Summer Student                    Faculty of Medicine, Uof Calgary, Canada.  

Michael Heinzinger  01/2016-03/2016                            UARE Intern                          PhD student, Germany. 

Amanda Ngo           05/2015-09/2015                          Summer Student                     Pharmacist, Edmonton, AB, Canada.

Jeffery Chow           05/2015-09/2015                          Summer Student                     Pharmacist, Edmonton, AB, Canada.

Tianhua Feng           04/2015-07/2015                            CSC intern                            MSc, University of Alberta, Canada.

Summer Kassem     09/2014-01/2015                          Intern Student                         PhD, AUC, Egypt.

Alessio Prunotto      03/2012-03/2012                          Intern Student                         PhD, Italy 

                                                                  

                                                                 Current Lab Members:

Research Associates:

  • Dr. Tae Chul Moon, Research Associate (July 2015 - Present).

Postdoctoral Fellows:

  • Dr. Aravindhan Ganesan, Postdoctoral Fellow (August 2015- August 2019).
  • Dr. Subha Kalyaanamoorthy, Postdoctoral Fellow (June 2016- August 2019) - (Awardee of the prestigious NSERC postdoctoral fellowship).

Graduate Students:

      • Farag Mosa, PhD Student (June 2019 - Present).

      • Yasser Tebana, PhD Student (January 2018 - Present).

      • Tianhua Feng, Master Student (September 2016 - Present)

      • Rui Chen, Master Student (September 2017 - Present).

Internship & Summer Students:

     Name                             Period                     Degree                     

     Issar Arab                 08/2019-11/2019         UARE Intern                 

     Minwoo Ha               06/2019-08/2019      Summer student            

     Anna Jutla                06/2019-08/2019      Summer student              

     Nawreen Hena         06/2019-08/2019      Summer student              

     Simaranjit Grewal    06/2019-08/2019      Summer student          

High School Students:

 Name                               Period                       Degree                     

Harsh Beesoon             07/2019-08/2019          Heritage Youth Researcher Summer (HYRS) Program

   


Teaching

  • PHARM 301- Medicinal Chemistry  
           Introduction to Medicinal Chemistry: Principles of Drug Action and Disposition. My Lectures are focused on drug binding interactions and structure-activity relationships.  

  • PHARM 437 - Bone and Joint 

           A Lecture on Drugs For Rheumatoid Arthritis, Gout & Hyperuricemia.

  • PHARM 367 - Cardiology

          A Lecture on Medicinal Chemistry Of Antiarrythmic Drugs.

  • PHARM 487 - Pulmonary

           A Lecture on Medicinal Chemistry of Adrenergic β2-agonists

  • PHARM580 Computer Aided Drug Design – Graduate Course

          This introductory graduate-level course was designed to provide students with the background and a hands-on understanding of basic techniques involved in computer-aided drug design. The course introduced students to different tools including chemoinformatics, bioinformatics, molecular modeling, homology modeling, molecular dynamics simulation, molecular docking, QSAR, pharmacophore modelling, in silico ADME prediction and case studies highlighting recent successes. Lectures on course concepts were closely combined with hands-on tutorials that allowed the practical application of computational methods and statistical data analysis in a project-based format. Students recognized the strengths and challenges in computer-aided drug design approaches and learned how in silico methods can be complemented with experimental studies in concrete ligand discovery and design projects. Students were granted access to high performance computing resources to run their simulations and analyze the resulting data.


  • PHARM 697/698 - Graduate Course  

          This course is focused on seminar training and short seminar presentations on topics related to the student’s field of research. Normally, the seminar will be presented during the student’s second or third term. Required for all MSc and PhD students.