Khaled Barakat, PhD, MSc, EIT

About

Dr. Barakat received his PhD in biophysics from the University of Alberta in 2012 followed by a postdoctoral fellowship in the lab of the Nobel Laureate, Professor Michael Houghton, 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

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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. Aravindhan Ganesan, Postdoctoral Fellow (May 2015 - September 2019): Research Assistant Professor, School of Pharmacy, University of Waterloo.
• Dr. Subha Kalyaanamoorthy, Postdoctoral Fellow (June 2016 - September 2019): Assistant Professor, Department of Chemistry, University of Waterloo.
• 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.
• Tianhua Feng, Master student. Current position: R&D technician at Neova Technology Inc., BC, Canada.
• Rui Chen, Master student. Current position: Research Assistant, UofA, Canada.
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  Internship & Summer Students:  

 Name                Period                    Degree              Current Position

Minwoo Ha 06/2019-08/2019 Summer student Science Undergraduate Student, University of Alberta, Canada.

Anna Jutla 06/2019-08/2019 Summer student Pharmacy Undergraduate Student, University of Alberta, Canada.

Nawreen Hena 06/2019-08/2019 Summer student Science Undergraduate Student, University of Alberta, Canada.

Simaranjit Grewal 06/2019-08/2019 Summer student Science Undergraduate Student, University of Alberta, Canada.

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 

                    

High School Students:

 Name                Period            Degree           

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

              

                                 Current Lab Members:

Research Associates:

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

Postdoctoral Fellows:

• Dr. Surya Narayanan, Postdoctoral Fellow (October 2019- Present).

Graduate Students:

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

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

  

Internship & Summer Students:

   Name               Period           Position               

   Minwoo Ha        05/2020-09/2020   Summer student       

   Anna Jutla        06/2020-09/2020   Summer student        

   

  

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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.

• Congratulations, Anna Jutla, for receiving the Alberta Innovates Summer Research Studentship
• Congratulations, Minwoo Ha, for receiving the NSERC Undergraduate Student Research Assistantship Award
• Congratulations, Dr. Subha Kalyaanamoorthy, for being appointed as an Assistant Professor at the Department of Chemistry, University of Waterloo.
• Congratulations, Dr. Aravindhan Ganesan, for being appointed as a Research Assistant Professor, School of Pharmacy, University of Waterloo.
• Congratulations, Yasser Tabana, for receiving the Alberta Graduate Excellence Scholarship
• Congratulations, Yasser Tabana, for receiving the Antoine Noujaim Graduate Scholarship in Pharmaceutical Sciences.
• Congratulations, Yasser Tabana, for receiving the Shire Canada Inc Graduate Scholarship.
• Congratulations, Yasser Tabana, for receiving the Shire Canada Inc Graduate Scholarship.
• Congratulations, Rui Chen, for receiving the Shire Canada Inc Graduate Scholarship.
• Congratulations, Frnacesco, for receiving a CIHR postdoctoral fellowship to join the University of British Colombia Prostate Cancer Centre.
• Congratulations Crystal for being accepted at the Faculty of Medicine, UofC
• Congratulations, Frnacesco, for being awarded the Canadian Cancer Society (CCS) Travel Award for 2018. 
• Summer Internships Are Available In Barakat's Lab for 2018 - Please send your CV to Dr. Aravindhan Ganesan (aganesan@ualberta.ca).
• Congratulations, Frnacesco, for passing your Candidacy exam.
• Congratulations, Dr. Subha Kalyaanamoorthy, for being awarded the NSERC PostDoctoral Fellowship for 2018/2019.
• Congratulations, Francesco, for being awarded the prestigious Alberta Innovates studentship for 2018.
• Congratulations, Fitch, for receiving financial support to attend and present an abstract at the upcoming CSPS/CSPT/CC-CRS Joint Conference "Translating Innovative Technology to Patient Care", being held on May 22-25, 2018, Toronto, ON.
• Congratulations, Horia, for completed your Master's degree.
• Congratulations, Dr. Marawan Ahmed, for receiving the CRINA-ACF CCRC Travel award.
• Congratulations, Dr. Aravindhan Ganesan, for being awarded the best poster award in the CRINA research day.
• Congratulations, Horia, for being a finalist at the 3MT competition in 2017.

PHARM 201 - Principles of Medicinal Chemistry

Introduces students to fundamental principles in medicinal chemistry necessary to understand the relationship between drug structure and drug action. The clinical relevance of medicinal chemistry will be explored through examination of drug structure, properties, classification, cell targets, and selected design/development strategies. (Restricted to Pharmacy students.)

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PHARM 694 - Directed Project

Directed studies in pharmaceutical research, using one or more techniques of special interest to individual students. Prerequisites: consent of the Faculty and the supervising faculty member.

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PHARM 697A - Advanced Oral, & Written Skills in Graduate Training

This course develops students in the critical written and oral communication skills required for successful graduate training, with particular emphasis on writing abstracts, creating research posters, and presenting research orally. All students deliver a 20-min oral presentation in the Winter term. Required of all MSc and PhD students.

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PHARM 697B - Advanced Oral, & Written Skills in Graduate Training

This course develops students in the critical written and oral communication skills required for successful graduate training, with particular emphasis on writing abstracts, creating research posters, and presenting research orally. All students deliver a 20-min oral presentation in the Winter term. Required of all MSc and PhD students.

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Browse more courses taught by Khaled Barakat

1. Mosa, FES, , Suryanarayanan, C., Feng, T. and Baraka, K.*

2020 November; 102

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Kalyaanamoorthy, S.,Lamothe, S.,Hou, X.,Moon, T., Kurata,H., Houghton, M., Barakat, K.*

2020 October; 10 (1):1-18

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Clement Viricel, Marawan Ahmed and Khaled Barakat

Journal of Molecular Graphics and Modelling. 57

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Marawan Ahmed, Khaled Barakat

Journal of molecular modeling. 23 (11):308

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Marawan Ahmed, Khaled Barakat

Biochemistry. 56 (40):5428-5439

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Marawan Ahmed, Feng Wang, Aviad Levin, Connie Le, Yomna Eltayebi, Michael Houghton, Lorne Tyrrell, Khaled Barakat

Drug discovery today. 20 (5)

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Khaled Barakat

JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES. 20

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oey G Sheff, Farshad Farshidfar, Oliver F Bathe, Karen Kopciuk, Francesco Gentile, Jack Tuszynski, Khaled Barakat, David C Schriemer

Molecular & Cellular Proteomics. 16 (3)

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Aravindhan Ganesan, Michelle L Coote, Khaled Barakat

Wiley Interdisciplinary Reviews: Computational Molecular Science. 7 (4)

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Aravindhan Ganesan, Michelle L Coote, Khaled Barakat

Drug discovery today. 22 (2):249-269

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Khaled Barakat

J Pharma Care Health Sys. 2

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Francesco Gentile, Jack A Tuszynski, Khaled H Barakat

Biophysical Journal. 114 (3):45a

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Horia Jalily Hasani, Marawan Ahmed, Khaled Barakat

Journal of Molecular Graphics and Modelling. 78

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K. Jalily Hasani, H., Barakat

International Review on Modelling and Simulations (IREMOS). 10 (2)

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Horia Jalily Hasani, Aravindhan Ganesan, Marawan Ahmed, Khaled H Barakat

PloS one. 13 (2):e0191905

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Subha Kalyaanamoorthy, Khaled H Barakat

Medicinal research reviews.

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Gentile Francesco, Tuszynski Jack A, Barakat Khaled H

Journal of Cancer Treatment and Diagnosis. 1 (1):1-3

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Isobel S Okoye, Michael Houghton, Lorne Tyrrell, Khaled Barakat, Shokrollah Elahi

Frontiers in immunology. 8

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Subha Kalyaanamoorthy, Khaled H Barakat

Expert opinion on drug discovery. 13 (3):207–210

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Marawan Ahmed and Khaled Barakat

Receptors & Clinical Investigation. 2 (3)

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Aravindhan Ganesan, Khaled Barakat

Expert opinion on drug discovery. 12 (4)

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Khaled H Barakat, Anwar Anwar-Mohamed, Jack A Tuszynski, Morris J Robins, D Lorne Tyrrell, Michael Houghton

J. Chem. Inf. Model. 55 (2)

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Francesco Gentile, Marco A Deriu, Khaled Barakat, Andrea Danani, Jack Tuszynski

Pharmaceuticals. 11 (1):22