Khaled Barakat, PhD, MSc, EIT

Assistant Professor, Faculty of Pharmacy & Pharmaceutical Sciences

Contact

Assistant Professor, Faculty of Pharmacy & Pharmaceutical Sciences
Email
kbarakat@ualberta.ca

Overview

About

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. 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.

  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        

   

  


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.

Announcements

  • 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.

Courses

PHARM 697A - Graduate Seminar

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 of all MSc and PhD students.

Fall Term 2020
PHARM 697B - Graduate Seminar

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 of all MSc and PhD students.

Winter Term 2021

Browse more courses taught by Khaled Barakat

Publications

A comprehensive structural model for the human KCNQ1/KCNE1 ion channel
Author(s): Horia Jalily Hasani, Marawan Ahmed, Khaled Barakat
Publication: Journal of Molecular Graphics and Modelling
Volume: 78
Page Numbers: 26-47

A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study
Author(s): Francesco Gentile, Marco A Deriu, Khaled Barakat, Andrea Danani, Jack Tuszynski
Publication: Pharmaceuticals
Volume: 11
Issue: 1
Page Numbers: 22

A refined model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes
Author(s): Khaled H Barakat, Anwar Anwar-Mohamed, Jack A Tuszynski, Morris J Robins, D Lorne Tyrrell, Michael Houghton
Publication: J. Chem. Inf. Model
Volume: 55
Issue: 2
External Link: http://pubs.acs.org/doi/abs/10.1021/ci400631n
Applications of computer-aided approaches in the development of hepatitis C antiviral agents
Author(s): Aravindhan Ganesan, Khaled Barakat
Publication: Expert opinion on drug discovery
Volume: 12
Issue: 4

Baby Steps Toward Modelling The Full human Programmed Death-1 (PD-1) Pathway
Author(s): Marawan Ahmed and Khaled Barakat
Publication: Receptors & Clinical Investigation
Volume: 2
Issue: 3
External Link: http://www.smartscitech.com/index.php/rci/article/view/825
Binding modes of hERG blockers: An unsolved mystery in the drug design arena
Author(s): Subha Kalyaanamoorthy, Khaled H Barakat
Publication: Expert opinion on drug discovery
Volume: 13
Issue: 3
Page Numbers: 207–210

[HTML] from frontiersin.org Coinhibitory receptor expression and immune checkpoint blockade: Maintaining a balance in CD8+ T cell responses to chronic viral infections and cancer
Author(s): Isobel S Okoye, Michael Houghton, Lorne Tyrrell, Khaled Barakat, Shokrollah Elahi
Publication: Frontiers in immunology
Volume: 8
Page Numbers: 1215

Commentary: New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy
Author(s): Gentile Francesco, Tuszynski Jack A, Barakat Khaled H
Publication: Journal of Cancer Treatment and Diagnosis
Volume: 1
Issue: 1
Page Numbers: 1-3

Development of Safe Drugs: The hERG Challenge
Author(s): Subha Kalyaanamoorthy, Khaled H Barakat
Publication: Medicinal research reviews

Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel
Author(s): Horia Jalily Hasani, Aravindhan Ganesan, Marawan Ahmed, Khaled H Barakat
Publication: PloS one
Volume: 13
Issue: 2
Page Numbers: e0191905

Homology Modeling: an Overview of Fundamentals and Tools
Author(s): K. Jalily Hasani, H., Barakat
Publication: International Review on Modelling and Simulations (IREMOS)
Volume: 10
Issue: 2

Human PD-1 binds differently to its human ligands: A comprehensive modeling study
Author(s): Clement Viricel, Marawan Ahmed and Khaled Barakat
Publication: Journal of Molecular Graphics and Modelling
Volume: 57
Page Numbers: 131-142
External Link: http://www.sciencedirect.com/science/article/pii/S1093326315000340
Investigating the Structure of the XPF-ERCC1 Functional Endonuclease using a Computational Approach
Author(s): Francesco Gentile, Jack A Tuszynski, Khaled H Barakat
Publication: Biophysical Journal
Volume: 114
Issue: 3
Page Numbers: 45a

Modelling Off-target Interactions (I): Cardiotoxicity
Author(s): Khaled Barakat
Publication: J Pharma Care Health Sys
Volume: 2
Page Numbers: e131
External Link: http://www.omicsgroup.org/journals/modelling-offtarget-interactions-i-cardiotoxicity-2376-0419-1000e131.pdf
Molecular dynamics-driven drug discovery: leaping forward with confidence
Author(s): Aravindhan Ganesan, Michelle L Coote, Khaled Barakat
Publication: Drug discovery today
Volume: 22
Issue: 2
Page Numbers: 249-269

Molecular ‘time‐machines’ to unravel key biological events for drug design
Author(s): Aravindhan Ganesan, Michelle L Coote, Khaled Barakat
Publication: Wiley Interdisciplinary Reviews: Computational Molecular Science
Volume: 7
Issue: 4

Novel Allosteric Pathway of Eg5 Regulation Identified through Multivariate Statistical Analysis of Hydrogen-Exchange Mass Spectrometry (HX-MS) Ligand Screening Data
Author(s): oey G Sheff, Farshad Farshidfar, Oliver F Bathe, Karen Kopciuk, Francesco Gentile, Jack Tuszynski, Khaled Barakat, David C Schriemer
Publication: Molecular & Cellular Proteomics
Volume: 16
Issue: 3

Rational Design of Small Molecule Immune Checkpoints' Inhibitors: The PD-1 Challenge
Author(s): Khaled Barakat
Publication: JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES
Volume: 20
Page Numbers: 9S-10S

Targeting the Achilles heel of the hepatitis B virus: a review of current treatments against covalently closed circular DNA
Author(s): Marawan Ahmed, Feng Wang, Aviad Levin, Connie Le, Yomna Eltayebi, Michael Houghton, Lorne Tyrrell, Khaled Barakat
Publication: Drug discovery today
Volume: 20
Issue: 5
External Link: http://www.sciencedirect.com/science/article/pii/S1359644615000306
The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study
Author(s): Marawan Ahmed, Khaled Barakat
Publication: Biochemistry
Volume: 56
Issue: 40
Page Numbers: 5428-5439

When theory meets experiment: the PD-1 challenge
Author(s): Marawan Ahmed, Khaled Barakat
Publication: Journal of molecular modeling
Volume: 23
Issue: 11
Page Numbers: 308