CURRICULUM VITAE I. ACADEMIC BACKGROUND · 2020. 11. 30. · Khaled Barakat, PhD Curriculum Vitae – December 2018 1 CURRICULUM VITAE I. ACADEMIC BACKGROUND A. PERSONAL DATA Name:

KhaledBarakat,PhD CurriculumVitae–December2018

1

CURRICULUM VITAE

I. ACADEMIC BACKGROUND

A. PERSONAL DATA

Name: Khaled H. S. Barakat University Address: Faculty of Pharmacy & Pharmaceutical Sciences

02-20G Katz Group-Rexall Centre for Health Research University of Alberta, Edmonton, Alberta, Canada T6G 2E1 Phone : (+1) 780-492-5753

E-mail [email protected] Internet: https://www.ualberta.ca/pharmacy/about-us/contact-us-and-

people/people/khaled-barakat Nationality: Canadian Language: Fluent in English and Arabic

B. EDUCATION AND TRAINING 04/2012-01/2014: Post-doctoral fellow in Virology; The University of Alberta,

Edmonton (Alberta) Canada, under the supervision of Dr. Michael Houghton.

09/2007-03/2012: PhD in Biophysics, Department of Physics, Faculty of Science,

University of Alberta, Edmonton (Alberta) Canada, under the supervision of Dr. Jack Tuszynski.

09/2003-09/2006: M.Sc. Engineering Physics, Faculty of Engineering, Cairo

University, Cairo, Egypt, under the supervision of Dr. S. M. El-Sheikh and Dr. Noha. M. Salem.

09/2001-09/2003: Pre-Master Preparation Courses, Faculty of Engineering, Cairo

University, Cairo, Egypt. 05/1996- 05/2001 BS, Electrical Engineering, Faculty of Engineering, Cairo

University, Fayoum, Egypt.

C. ACADEMIC APPOINTMENTS 12/2015-present: Assistant Professor, Faculty of Pharmacy & Pharmaceutical

Sciences, University of Alberta, Edmonton (Alberta) Canada.


2

01/2014-12/2015: Research Assistant Professor, Faculty of Pharmacy & Pharmaceutical Sciences, University of Alberta, Edmonton (Alberta) Canada.

D. AWARDS AND HONORS 2013 - 2014 Canadian Institute of Health Research (CIHR) postdoctoral

fellowship, $40,000 + Research Allowance ($5000), for two years. 2012-2014 Alberta Innovates-Health Solutions (AIHS) postdoctoral

fellowship, $50,000 + Research Allowance ($5000), for three years.

2011-2012 Dissertation award, $22,000 + tuition fees ($4,500), for one year. 2009-2010 Alberta Cancer Research Institute Studentship, $20,000, for two

years. 1999 Faculty of Engineering Distinction Award, E£200, for one year. 1998 Faculty of Engineering Distinction Award, E£200, for one year. 1997 Faculty of Engineering Distinction Award, E£200, for one year.

E. PROFESSIONAL ORGANIZATION MEMBERSHIP

American Chemical Society (ACS). American Physical Society (APS). Biophysical Society (BPS). American Association for Cancer Research (AACR). Association of Professional Engineers and Geoscientists of Alberta (APEGA)

II. SERVICE

A. STUDENTS’ SUPERVISION:

Graduate Students:

Completed: Name Degree Period Thesis Title Current Position Francesco Gentile PhD 01/2014 –

12/2018 Computer-Aided Drug Design of DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease.

Postdoctoral Fellow, UBC's Vancouver Prostate Centre, Canada.


3

Horia Jalily Hasani MSc 01/2015-09/2017

A Comprehensive Dynamic Model for KCNQ1/KCNE1 Ion Channel: Structural & Functional Studies

Research Assistant, UofA, Canada.

Current:

Name Entry Date Degree Farag Mosa 06/2019 PhD

Yasser Tebana 01/2018 PhD Tianhua Feng 09/2016 MSc

Rui Chen 09/2017 MSc

Awards received by the students during their tenure:

Name Year Award Francesco Gentile 2019 Faculty of Science Dissertation Award, University of Alberta, Canada Francesco Gentile 2019 International High-Performance Computing Summer School

Scholarship, RIKEN Center for Computational Sciences, Kobe, Japan. Rui Chen 2019 Graduate Student Travel Support to CSPS and AFPC, 1250 CAD. Rui Chen 2018 Graduate Student Tuition Supplement, Winter Term, 850 CAD. Yasser Tabana 2018 Shire Canada Inc Graduate Scholarship, 2,700.00 CAD. Tianhua Feng 2018 Graduate Student Travel Support to CSPS and AFPC, 1250 CAD. Francesco Gentile 2018 Novartis Pharmaceuticals Canada Inc. Graduate Scholarship.

2,200CAD Francesco Gentile 2018 Alberta Innovates Graduate Student Scholarship. 31,500 CAD. Francesco Gentile 2018 SciNet HPC Summer School Scholarship (Declined). Francesco Gentile 2018 Canadian Cancer Society Travel Award. 726 CAD. Francesco Gentile 2017 Biophysical Society International Travel Award. 750 USD. Francesco Gentile 2017 University of Alberta Graduate Students’ Association Academic Travel

Award. 500 CAD Francesco Gentile 2016 University of Alberta Graduate Students’ Association Academic Travel

Award. 500 CAD Francesco Gentile 2016 University of Alberta Graduate Students’ Association Research

Assistant Award. 500 CAD. Francesco Gentile 2014 Alunni Meritevoli Award. 1,000 euros. Horia Jalily Hasani 2015 Mary Louise Imrie Graduate Student Award. Horia Jalily Hasani 2017 Finalist in the 3MT competition at the University of Alberta. Horia Jalily Hasani 2016 Novartis Pharmaceuticals Canada Inc Graduate Scholarship 1,800

CAD. Horia Jalily Hasani 2016 Graduate Poster Award , Faculty of Pharmacy and Pharmaceutical

Sciences Research Day Horia Jalily Hasani 2016 People’s Choice Poster Award, received at the Annual HPCS-

CANHEIT 2016 Conference ($100). Horia Jalily Hasani 2015 Antoine Noujaim Graduate Scholarship in Pharmaceutical Sciences.

This Scholarship is awarded on the basis of overall academic excellence and achievement ($6800)

Horia Jalily Hasani 2015 Graduate Student Tuition Award, Fall Term 2015 (September to December). ($1000)


4

Horia Jalily Hasani 2015 Mary Louise Imrie Graduate Student Award. This award is to recognize outstanding graduate students of the faculty. ($1100).

Horia Jalily Hasani 2016 Graduate Student Tuition Award, Winter Term 2016 (January to April). ($1000)

Tianhua Feng 2017 Shoppers Drug Mart Graduate Scholarship in Pharmacy and Pharmaceutical Sciences, 850 CAD.

Tianhua Feng 2016 Graduate Student Tuition Supplement, Winter Term, 850 CAD. Undergraduate & Intern Students:

Name Period Degree Current Position

Issar Arab 08/2019-11/2019 UARE Intern MSc, Germany Harsh Beesoon 07/2019-07/2019 HYRS High School Student Minwoo Ha 06/2019-08/2019 Summer student Science Undergraduate Student,

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

University of Alberta, Canada. Nawreen Henav 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. Guilherme Afonso 02/2018-05/2018 UARE Intern MSc Anna Jutlav 04/2018-09/2018 Summer Student Pharmacy Undergraduate Student,

University of Alberta, Canada. Nawreen Henav 01/2017-05/2017 Summer Student Science Undergraduate Student,

University of Alberta, Canada. Theinmozhi Arulraj 05/2017-08/2017 UARE Intern PhD Student, Germany. Gyan Darshan 05/2017-08/2017 UARE Intern MSc, India Nathalia Dumas 06/2017-09/2017 UARE Intern PhD student, Brazil 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, University of

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. Celment Vercil 06/2014-01/2015 Intern Student PhD, France Alessio Prunotto 03/2012-03/2012 Intern Student PhD, Italy

• UARE: University of Alberta Research Experience • CSC: China Scholarship Council • AUC: American University in Cairo • HYRS: Heritage Youth Researcher Summer (HYRS) Program • vJoined my research group more than one time as a summer student


5

Awards received by the undergraduate students during their tenure:

Name Year Award Anna Jutla 2019 Office of the Provost and VP (Academic) Summer Student Award

Anna Jutla 2019 Alberta Cancer Foundation (ACF) Undergraduate Summer Research

Studentship. Anna Jutla 2018 Faculty of Pharmacy and Pharmaceutical Sciences Undergraduate

Summer Research Studentship. Anna Jutla 2018 Alberta Innovates Health Solutions (AIHS) Undergraduate Summer

Research Studentship.

B. POSTDOCTORAL FELLOWS, RESEARCH ASSOCIATES & TECHNICIANS: Postdoctoral Fellows:

Completed:

Name Period Current Position Abdo Mohamed 02/2018 – 08/2018 Assistant Professor, Cairo University, Egypt. Marawan Ahmed 06/2014 – 10/2018 Senior data analyst, Alberta Health Services, Canada.

Current:

Name Period Aravindhan Ganesan 05/2015 – Present Subha Kalyaanamoorthy 06/2016 – Present

Awards received by postdoctoral fellows during their tenure:

Name Since Year

Award

Subha Kalyaanamoorthy 2019 Best basic science research award (Oral) at the 2019 Cardiac Society Research day, Edmonton, AB Canada.

Subha Kalyaanamoorthy 2018 NSERC post-doctoral fellowship, two years. Subha Kalyaanamoorthy 2017 Wu Hong Memorial Poster Prize; Faculty of Pharmacy Research Day. Marawan Ahmed 2016 Wu Hong Memorial Poster Prize; Faculty of Pharmacy Research Day. Marawan Ahmed 2016 Wu Hong Memorial Poster Prize; Faculty of Pharmacy Research Day.

Research Associates:

Name Period Tae Chul Moon 10/2015 – Present

Technicians:

Name Period Bethany Yoon 01/2016 – 03/2017


6

C. COMMITTEES:

At Faculty Level: July 2019 – July 2020 Chair of the Research Day Committee. July 2019 – July 2020 Member of the Awards Committee. July 2017 – July 2019 Member of the International Committee. July 2015 – July 2019 Member of the Research Day Committee. July 2015 – July 2017 Member of the Awards Committee. July 2014 – July 2015 Chair of the Space-Safety & IT Committee.

At University Level: March 2015 – March 2016 Member of the Environmental Health and Safety Senior

Administrator’s Committee at the University of Alberta.

D. CONSULTING SERVICES: External Expert, Li Ka Shing Applied Virology Institute (LKSAVI), Edmonton, Alberta, Canada.

E. TEACHING:

i. Undergraduate Courses: Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Canada (2014-2018):

Course (Lecture/Seminar/Lab) Contact Hours

Role

PHARM 301, “Introduction to Medicinal Chemistry” 8/0/0 Contributor PHARM 487, “Pulmonary” 1/0/0 Contributor PHARM 367, “Cardiology” 1/0/0 Contributor PHARM 437, “Bone and Joint” 1/0/0 Contributor

Faculty of Science, University of Alberta (2007-2011):


Role

PHYS 124, “Particles and Waves” 0/0/12 Contributor PHYS 126, “Fluids, Fields, and Radiation” 0/0/12 Contributor PHYS 130, “Wave Motion, Optics, and Sound” 0/0/12 Contributor ENPH 131, “Mechanics” 0/0/12 Contributor High School Physics lab 0/0/4 Contributor


7

Faculty of Science, American University in Cairo, Egypt (2006-2007):


Role

Introduction to Molecular Modelling 0/0/3 Contributor

Faculty of Engineering, Cairo University, Egypt (2001-2006):


Role

First Year General Physics 10/0/8 Contributor First Year Mathematics 20/0/0 Contributor First Year Classical Mechanics 20/0/0 Contributor

ii. Graduate Courses: Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Canada (2014-2018):

Course (Lecture/Seminar/Lab) Contact hours

Role

PHARM 580, “Computer Aided Drug Design” 22/8/12 Contributor PHARM 697, “Oral and Written Skill Development” 6/6/0 Contributor

iii. Developed Courses:

Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Canada (2014-2018):

Course Development Contribution 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.


8

iv. Workshops

Year Workshop 2014 3 lectures workshop on Computer Aided Drug Design. HAI-IDR Summer

School, University of Alberta, Canada. 2008 Molecular Docking, University of Alberta, Edmonton, Canada: A session among

the Biophysics workshop hosted by Professor Tuszynski’s PharmaMatrix group, University of Alberta, Canada.

2005 Introduction to Fortran, Fayoum University, Egypt: An introductory 2 weeks workshop on how to program using Fortran.

2004 Visual Basic Advanced Programming, Fayoum University, Egypt: An advanced 3 weeks workshop on managing the I/O ports using VB code.

III. RESEARCH AND SCHOLARLY ACTIVITIES

A. RESEARCH INTERESTS: My research stands at the multidisciplinary interface of physics, biology and computer science. Throughout the last few years, my lab has been focused on three main research points:

1- Developing novel immunotherapy drugs targeting the immune checkpoints proteins. Monoclonal antibodies (MABs) targeting the PD-1 and CTLA-4 have revolutionized cancer treatments over the last few years. My research group seeks to identify and develop small molecule blockers of the PD-1 and CTLA-4 pathways. In 2015, my research lab has been leading a world-class research team. The team is funded through a $5.4M over five years. Compared to available MAB therapies, small molecule immune checkpoints blockers can offer a more affordable, more easily administered, more easily controlled treatment that could treat a variety of cancers including advanced solid tumors and brain tumors.

2- Understanding the mechanism of action of transporters and ion channels. A major problem in drug discovery is the unexpected toxicity that can emerge from the interaction of drugs with unforeseen targets, such us ion channels and transporters. Cardiac ion channels form a major class of these proteins, which can interact with many drugs. These unwanted interactions can lead to cardiotoxicity and, eventually, sudden heart arrest. A major research focus in my group that is funded through a 5-year NSERC discovery grant, is to use computer simulations to predict the interaction of drugs with cardiac ion channels (e.g. hERG, NAV and CAV channels). The ultimate goal is to understand how the different drugs interact with these channels and provide hints on how to avoid these interactions.

3- Antiviral drug discovery. We focus on three viruses, namely, HCV, ZICA and Dengue

viruses. Computer simulations in my lab are used to design and identify novel antivirals for these targets.


9

B. RESEARCH EXPERTISE:

C. RESEARCH GRANTS

03/2015 –03/2021

Funding source: Natural Sciences and Engineering Research Council Program: Discovery Grant Title: Atomistic Computational Models To Evaluate Protein-Ligand Off-Target Interactions Role: Principal Applicant. Total funding: 150,000CDA. Status: Active

03/2015 – 03/2020

Funding source: Alberta Cancer Foundation & The Li Ka Shing Applied Virology Institute Program: Transformative Ideas Title: Developing Novel Cancer Immunotherapy Drugs: A Multidisciplinary Team Role: Principal Applicant. Total funding: 5,386,000 CDA. Status: Active.

07/2015 – 07/2018

Funding source: IC-IMPACTS Centres of Excellence Title: Identification of high affinity ligands against Dengue virus NS1 for the development of an affordable point-of-care diagnostic kit Program: Research Grant Role: Co-Applicant. Total funding: 400,000 USD. Status: Completed.

01/2015 – 01/2017

Funding source: Li Ka Shing Institute of Virology Title: Developing a novel combination therapy for Dengue virus infection Program: Translational Grant Role: Co-Applicant. Total funding: 100,000 CDA. Status: Completed.

01/2014 – 01/2016

Funding source: Li Ka Shing Institute of Virology Program: Start-up Fund Role: Principal Applicant. Total funding: 50,000 CDA. Status: Completed.

Molecular Modelling:

• Virtual Screening • Blind Docking • Protein-Protein Docking • Fragment-Based Drug

Design • Pharmacophore

Construction & Modelling

• Protein-Protein interaction

• Molecular dynamics simulations

• Mote Carlo simulations • Quantum Mechanics • Free energy calculations • Binding Energy Analysis

Computer Programming Methods:

• Visual Basic • C • Fortran • Python • TCL • Mathematica • Matlab • R

Bioinformatics:

• Sequence alignment • Homology modelling Systems Biology:

• Signal transduction pathway modelling

• Protein networks

Computer Architecture: • High Performance

Computing • Hardware Design • Software Design


10

10/2014 – 01/2015

Funding source: Alberta Cancer Foundation Program: Transformative Ideas (seed fund) Title: Developing Novel Cancer Immunotherapy Drugs: A Multidisciplinary Team Role: Principal Applicant. Total funding: 20,000 CDA. Status: Completed.

07/2014 – 08/2015

Funding source: Li Ka Shing Institute of Virology Title: Computational Discovery of Novel Hepatitis C Virus NS5A inhibitors. Program: Translational Grant Role: Principal Applicant. Total funding: 50,000 CDA. Status: Completed.

D. RESEARCH COMMUNITY

i. Editorial Boards:

Associate Editor, BMC Bioinformatics Editorial Board. Editorial board, Journal of Pharmaceutical Care & Health Systems. Editorial board, International Journal of Pharmaceutical Chemistry and Analysis.

ii. Grant applications’ Reviewer:

• Mitacs Accelerate • SHRF Collaborative Innovation Development • University of Sharjah, UAE • French National Research Agency (ANR) • National Science Center, Poland

iii. Reviewer for Journals:

Journal of Biophysical Chemistry PLOS ONE Journal of Molecular Graphics and Modelling BMC Clinical Pathology Journal of Molecular Modeling. Journal of Advanced Research. Viruses — Open Access Virology Journal Journal of pharmacy and pharmaceutical sciences. Drug Design, Development and Therapy. Journal of Medicinal Chemistry Current Drug Discovery Technologies Drug Design, Development and Therapy BMC Research Notes Journal of Biomolecular Structure & Dynamics BMC Systems Biology BMC Medical Genomics Scientific Reports World Journal of Gastroenterology

E. PUBLICATIONS i. Refereed Papers:

Published/In press: 1. 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", J Mol Graph Model. 2019 Jul;90:128-143.


11

2. Feng T, Kalyaanamoorthy S, Ganesan A, Barakat K, "Atomistic modeling and molecular dynamics analysis of human CaV1.2 channel using external electric field and ion pulling simulations", Biochim Biophys Acta Gen Subj. 2019 Jun;1863(6):1116-1126.

3. Elsayed NMY, Serya RAT, Tolba MF, Ahmed M, Barakat K, Abou El Ella DA5, Abouzid KAM, "Design, synthesis, biological evaluation and dynamics simulation of indazole derivatives with antiangiogenic and antiproliferative anticancer activity", Bioorg Chem. 2019 Feb;82:340-359.

4. Jody Groenendyk, Tautvydas Paskevicius, Hery Urra, Clement Viricel, Kui Wang, Khaled Barakat, Claudio Hetz, Lukasz Kurgan, Luis B Agellon, Marek Michalak,“Cyclosporine A binding to COX2 reveals a novel signaling pathway that activates the IRE1α unfolded protein response sensor”, Sci. Rep. 2018 Nov 12;8(1):16678.

5. A Ganesan, TC Moon, KH Barakat, “Revealing The Atomistic details behind the binding of B7–1 to CD28 and CTLA-4: A comprehensive protein-protein modelling study. Biochimica et Biophysica Acta (BBA)-General Subjects 2018, 1862 (12), 2764-2778.

6. Aravindhan Ganesan, Theinmozhi Arulraj, Tahir Choulli, and Khaled Barakat, ‘A mathematical modelling tool for unravelling the antibody-mediated effects on CTLA-4 interactions’, BMC medical informatics and decision making 2018, 18 (1), 37.

7. Francesco Gentile, Khaled H. Barakat, Jack A. Tuszynski, “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” Int. J. Mol. Sci. 2018, 19(5), 1328.

8. Feng T and Barakat K, “Molecular Dynamics Simulation and Prediction of Druggable Binding Sites.”, Methods Mol Biol. 2018, 1762:87-103.

9. Francesco Gentile, Jack A Tuszynski, Khaled H Barakat, “Investigating the Structure of the XPF-ERCC1 Functional Endonuclease using a Computational Approach”, Biophysical Journal, 2018, 114(3): 45a.

10. Francesco Gentile, Marco A Deriu, Khaled Barakat, Andrea Danani, Jack Tuszynski, “A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study”, Pharmaceuticals, 2018 11(1), 22.

11. Subha Kalyaanamoorthy, Khaled H Barakat, “Binding modes of hERG blockers: An unsolved mystery in the drug design arena”, Expert Opin Drug Discov. 2018 13(3), 207–210.

12. Marawan Ahmed, Khaled Barakat, “When theory meets experiment: the PD-1 challenge”, J Mol Graph Model., 2017 Nov 1; 23(11); 308.

13. HJ Hasani, A Ganesan, M Ahmed, KH Barakat, “Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel”, PloS one, 2018 13(2), e0191905.

14. Isobel S Okoye, Michael Houghton, Lorne Tyrrell, Khaled Barakat, Shokrollah Elahi, “Coinhibitory Receptor Expression and Immune Checkpoint Blockade: Maintaining a Balance in CD8+ T Cell Responses to Chronic Viral Infections and Cancer”, Frontiers in Immunology, 2017 Sep 29; 8; 1215.

15. HJ Hasani, M Ahmed, K Barakat, “A Comprehensive Structural Model For The Human Kcnq1/Kcne1 Ion Channel”, J Mol Graph Model., 2017 Sep 29, 29;78:26-47.


12

16. Marawan Ahmed, Khaled Barakat, “The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study”, Biochemistry, 2017 Sep 25, 56(40), 5428-5439.

17. Aravindhan Ganesan, Michelle L Coote, Khaled Barakat, Inside Cover Image, Volume 7, Issue 4, Wiley Interdisciplinary Reviews: Computational Molecular Science, 2017 July 1.

18. M Ahmed, HJ Hasani, A Ganesan, M Houghton, K Barakat, “Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade” Drug Des Devel Ther. 2017 Aug 4;11:2301-2324.

19. Aravindhan Ganesan & Khaled Barakat, “Applications of computer-aided approaches in the development of hepatitis C antiviral agents”, Expert Opin Drug Discov. 2017 Apr;12(4):407-425.

20. Marawan Ahmed, Abhishek Pal, Michael Houghton, and Khaled Barakat, “A Comprehensive Computational Analysis for the Binding Modes of Hepatitis C Virus NS5A Inhibitors: The Question of Symmetry”, ACS Infect Dis. 2016 Nov 11;2(11):872-881.

21. Aravindhan Ganesan, Michelle L. Coote and Khaled Barakat, “Molecular ‘time-machines’ to unravel key biological events for drug design”, WIREs Comput Mol Sci 2017, 7:e1306.

22. Horia H. Jalily and Khaled Barakat “Homology Modeling: An Overview of Fundamentals and Tools”, International Review on Modelling and Simulations (IREMOS) 2017, 10(2), 129.

23. Marawan Ahmed, Horia H. Jalily, Aravindhan Ganesan, Michael Houghton and Khaled Barakat “A Comprehensive Model of the Human Nav1.5 Sodium Channel: Structural and Mechanistic Insights of Ion Permeation & Drug Blockage” Drug Des Devel Ther. 2017 Aug 4;11:2301-2324.

24. Kalyaanamoorthy, S.Barakat, K. H., “Development of safe drugs: the hERG challenge” Med Res Rev., 2017, 38(2), 525-555.

25. Sheff, J. G.; Farshidfar, F.; Bathe, O. F.; Kopciuk, K.; Gentile, F.; Tuszynski, J.; Barakat, K.Schriemer, D. C.,Molecular & Cellular Proteomics 2017, mcp. M116. 064246.

26. Ganesan, A.; Coote, M. L.Barakat, ” Molecular ‘time-machines’ to unravel key biological events for drug design” K.,Wiley Interdisciplinary Reviews: Computational Molecular Science, 2017, 7(4), e1306.

27. Ganesan, A.Barakat, K., “Applications of computer-aided approaches in the development of hepatitis C antiviral agents”, Expert Opinion on Drug Discovery 2017, 12, 407-425.

28. Ganesan, A.; Coote, M. L.Barakat, K., “Molecular dynamics-driven drug discovery: leaping forward with confidence”, Drug discovery today 2017, 22, 249-269.

29. Syedbasha M, Linnik J, Santer D, O'Shea D, Barakat K, et al. “An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions”. JoVE (Journal of Visualized Experiments), 2016, e53575-e53575.

30. Gentile, F., Tuszynski, J. A. & Barakat, K. H. “Modelling DNA Repair Pathways: Recent Advances and Future Directions”, Curr. Pharm. Des, 2016, 22, 3527-46.

31. F Gentile, JA Tuszynski, KH Barakat, “New Design of Nucleotide Excision Repair (NER) Inhibitors for Combination Cancer Therapy”, J Mol Graph Model. 2016 Apr;65:71-82.


13

32. Ahmed M, Pal A, Houghton M, Barakat K (2016) A Comprehensive Computational Analysis for the Binding Modes of Hepatitis C Virus NS5A Inhibitors: The Question of Symmetry. ACS Infect Dis. 2016 Nov 11;2(11):872-881..

33. Eman M El-labbad, Mohammed AH Ismail, Abou Ei Ella, A Dalal, Marawan Ahmed, Feng Wang, Khaled H Barakat, Khaled AM Abouzid, “Discovery of Novel Peptidomimetics as Irreversible CHIKV NsP2 Protease Inhibitors Using Quantum Mechanical-Based Ligand Descriptors. Chemical biology & drug design”, 2015, 86(6), 1518-1527.

34. Ahmed M, Barakat K, “Baby Steps Toward Modelling The Full human Programmed Death-1 (PD-1) Pathway”, Receptors & Clinical Investigation, 2015, 2(3), 124.

35. Kassem S, Marawan A, El-Sheikh S, Barakat KH (2015) Entropy In Bimolecular Simulations: A Comprehensive Review Of Atomic Fluctuations-Based Methods. J Mol Graph Model. 2015 Nov;62:105-117.

36. Viricel C, Ahmed M, Barakat K, “Human PD-1 binds differently to its human ligands: A comprehensive modeling study”, J Mol Graph Model, 2015, 57C: 131-142.

37. Ahmed M, Wang F, Levin A, Le C, Eltayebi Y, et al., “Targeting the Achilles heel of the hepatitis B virus: a review of current treatments against covalently closed circular DNA”, Drug Discov Today. 2015 May;20(5):548-61.

38. Vos KJ, Martin AG, Trimboli MG, Forestell L, Barakat K, et al.,” A multi-compartment pharmacokinetic model of the interaction between paclitaxel and doxorubicin”, EPJ Nonlinear Biomedical Physics, 2014, 2: 1-40.

39. Hu G, Wang K, Groenendyk J, Barakat K, Mizianty MJ, et al.,”Human structural proteome-wide characterization of Cyclosporine A targets”, Bioinformatics, 2014, 30: 3561-3566.

40. Egli A, Santer DM, O'Shea D, Barakat K, Syedbasha M, et al.,”IL-28B is a Key Regulator of B- and T-Cell Vaccine Responses against Influenza”, PLoS Pathog, 2014, 10: e1004556.

41. Egli A, Santer D, Barakat K, Zand M, Levin A, et al.,”Vaccine adjuvants--understanding molecular mechanisms to improve vaccines”, Swiss Med Wkly, 2014, 144: w13940.

42. Egli A, Levin A, Santer DM, Joyce M, O'Shea D, et al. (2014) Immunomodulatory Function of Interleukin 28B during primary infection with cytomegalovirus. J Infect Dis 210: 717-727.

43. Barakat KH, Michael Houghton, Tyrrel DL, Tuszynski JA (2014) Rational Drug Design: One Target, Many Paths to It. 4: 59-85.

44. Barakat KH, Anwar-Mohamed A, Tuszynski JA, Robins MJ, Tyrrell DL, et al. (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.

45. Anwar-Mohamed A, Barakat KH, Bhat R, Noskov SY, Tyrrell DL, et al. (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.

46. Ribeiro AS, Borrelli R, Capobianco A, Peluso A, Gajewski MM, et al. (2013) Mg (II) and Zn (II) ions. Can J Chem 91.

47. Jordheim LP, Barakat KH, Heinrich-Balard L, Matera EL, Cros-Perrial E, et al. (2013) Small molecule inhibitors of ERCC1-XPF protein-protein


14

interaction synergize alkylating agents in cancer cells. Mol Pharmacol 84: 12-24.

48. Gajewski M, Tuszynski J, Barakat K, Huzil J, Klobukowski M (2013) Interactions of laulimalide, peloruside, and their derivatives with the isoforms of β-tubulin. Canadian Journal of Chemistry 91: 511-517.

49. Barakat KH, Law J, Prunotto A, Magee WC, Evans DH, 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.

50. Barakat KH, Huzil JT, Jordan KE, Evangelinos C, Houghton M, et al. (2013) A computational model for overcoming drug resistance using selective dual-inhibitors for aurora kinase A and its T217D variant. Mol Pharm 10: 4572-4589.

51. Barakat K, Tuszynski J (2013) Nucleotide Excision Repair Inhibitors: Still a Long Way to Go. In: Chen C, editor. New Research Directions in DNA Repair: INTECH.

52. Tuszynski JA, Craddock TJ, Mane JY, Barakat K, Tseng CY, et al. (2012) Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin. Pharm Res 29: 3007-3021.

53. K B, M G, J T (2012) DNA Repair Inhibitors: Our Last Disposal to Improve Cancer Therapy. Curr Top Med Chem.

54. Friesen DE, Barakat KH, Semenchenko V, Perez-Pineiro R, Fenske BW, et al. (2012) Discovery of small molecule inhibitors that interact with gamma-tubulin. Chem Biol Drug Des 79: 639-652.

55. Craddock TJ, St George M, Freedman H, Barakat KH, Damaraju S, et al. (2012) Computational predictions of volatile anesthetic interactions with the microtubule cytoskeleton: implications for side effects of general anesthesia. PLoS One 7: e37251.

56. Barakat KH, Jordheim LP, Perez-Pineiro R, Wishart D, Dumontet C, et al. (2012) Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction. PLoS One 7: e51329.

57. Barakat KH, Gajewski MM, Tuszynski JA (2012) DNA polymerase beta (pol beta) inhibitors: a comprehensive overview. Drug Discov Today 17: 913-920.

58. Barakat K, Gajewski M, Tuszynski JA (2012) DNA repair inhibitors: the next major step to improve cancer therapy. Curr Top Med Chem 12: 1376-1390.

59. Barakat K, Tuszynski J (2011) Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta. J Mol Graph Model 29: 702-716.

60. Barakat K, Issack BB, Stepanova M, Tuszynski J (2011) 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.

61. Bennett MJ, Barakat K, Huzil JT, Tuszynski J, Schriemer DC (2010) Discovery and characterization of the laulimalide-microtubule binding mode by mass shift perturbation mapping. Chem Biol 17: 725-734.

62. Barakat K, Mane J, Friesen D, Tuszynski J (2010) Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions. J Mol Graph Model 28: 555-568.

63. Huzil JT, Barakat K, Tuszynski JA (2009) Electrostatic contributions to colchicine binding within tubulin isotypes. Electromagn Biol Med 28: 355-364.

64. Barakat KH, Torin Huzil J, Luchko T, Jordheim L, Dumontet C, et al. (2009) Characterization of an inhibitory dynamic pharmacophore for the ERCC1-


15

XPA interaction using a combined molecular dynamics and virtual screening approach. J Mol Graph Model 28: 113-130.

65. El-Sheikh SM, Barakat K, Salem NM (2006) Phase transitions of methane using molecular dynamics simulations. J Chem Phys 124: 124517.

66. El-Sheikh S, Barakat K, Salem N, Ulivi L (2006) Phase transitions of carbon tetra-fluoride using raman spectroscopy and molecular dynamics simulations. High Pressure Research 26: 383-386.

ii. Book Chapters:

1. Tianhua Feng, Subha Kilannamorthy and Khaled Barakat (2018), “L-type

calcium channels: Structure and Functions”, Ion Channel, InTech open access publisher . DOI: 10.5772/intechopen.77305.

2. Hasani HJ, Barakat K (2016) “Protein-Protein Docking: Are We There Yet?”, Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery: IGI Global. pp. 173-195.

3. Barakat, K. H., Mane, J. Y., & Tuszynski, J. A. (2011). “Virtual Screening: An Overview on Methods and Applications”. In Liu, L. A., Wei, D., Li, Y., & Lei, H. (Eds.), Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications (1 vol). (pp. 28-60). doi:10.4018/978-1-60960-491-2.ch002.

4. Barakat, K. H. & Tuszynski, J. (2011), “Virtual Screening for DNA repair inhibitors”. InTech open access publisher (published Sep. 9, 2011)

5. Barakat, K. H. & Tuszynski, J. (2012), “Nucleotide Excision Repair Inhibitors: Still a Long Way to Go”. Biochemistry, Genetics and Molecular Biology » "New Research Directions in DNA Repair", book edited by Clark Chen, ISBN 978-953-51-1114-6.

iii. Editorial:

1. Khaled Barakat (2015) Editorial: Modelling Off-target Interactions (I): Cardiotoxicity. J Pharma Care Health Sys 2, e131.

2. Barakat K (2015) Editorial: Immune Checkpoints Inhibitors: The Search For A Single Antiviral & Anticancer Magic Bullet. J Pharma Care Health Sys. 2:e125.

3. Barakat K (2014) Editorial: Computer-Aided Drug Design. J Pharma Care Health Sys 1: 1000e1113.

4. Barakat K (2014) Editorial: Do We Need Small Molecule Inhibitors for the Immune Checkpoints? J Pharma Care Health Sys 1: 1000e1119.

iv. Abstracts/Poster Presentations:

1. Subha Kalyaanamoorthy, Shawn M. Lamothe, Xiaoqing (Ervin) Hou, Tae

Chul Moon,Harley T. Kurata, Michael Houghton, and Khaled H. Barakat. “Structure-based prediction of drug-induced hERG blockade”, 2019 Cardiac Society Research day, Edmonton, AB Canada.

2. Subha Kalyaanamoorthy, Justin Co, Khaled H. Barakat. “Computational study of the unbinding kinetics and mechanisms of hERG blockers”. 2019 Cardiac Society Research day, Edmonton, AB Canada.

3. Feng Tianhua, Subha Kalyaanamoorthy, Aravindhan Ganesan, Khaled Barakat “Atomistic modeling of the human CaV1.2 channel: structural and


16

mechanistic insights of cardiac ion permeation” 2019 Cardiac Society Research day, Edmonton, AB Canada.

4. Rui Chen, Elena Arutyunova, Aravindhan Ganesan, M. Joanne Lemieux, Khaled Barakat.“Recombinant B7-1 (CD80) Preparation Towards Probing the Druggable Sites of B7-1”, CSPS/CC-CRS 2019 Symposium, Vancouver, British Colombia, Canada.

5. Feng Tianhua, Subha Kalyaanamoorthy, Aravindhan Ganesan, and Khaled Barakat. "Atomistic modeling of the human CaV1.2 channel: structural and mechanistic insights of cardiac ion permeation" 2019 Cardiac Sciences Research Day, Edmonton, AB, Canada.

6. Feng Tianhua, Aravindhan Ganesan, Subha Kalyaanamoorthy, and Khaled Barakat. "Modeling the near-open conformation of human CaV1.2 using external electric field and ion pulling simulations " 2018 Faculty of Pharmacy Research Day, Edmonton, AB, Canada.

7. Rui Chen, Elena Arutyunova, Tae Chul Moon, Aravindhan Ganesan, M. Joanne Lemieux, Khaled Barakat. “Decoding the Druggable Sites of Human B7-1 for Targeting a Pyrazolocinnoline Series Small-molecule Inhibitor” 2018 CRINA Research Day, Edmonton, Alberta, Canada.

8. Feng Tianhua, Subha Kalyaanamoorthy, and Khaled Barakat. "Modeling the dynamic gating mechanism and small-molecule binding in the CaV1.2 channel" 2018 CSPS conference.

9. Francesco Gentile and Khaled Barakat, Computer-Aided Drug Design of ERCC1-XPF Inhibitors for Combination Cancer Therapy. Oral presentation at the Western Canadian Medicinal Chemistry Workshop - 6th WCMCW, Saskatoon, SK, Canada, September 22, 2018.

10. Yasser Tabana, Isobel S Okoye, Shima Shahbaz, Marawan Ahmed, Dinesh Babu, Shokrollah Elahi, Arno Siraki, Khaled Barakat, “Studying the immunostimulatory activity of heterocyclic small molecules ”, 2018, 5th Annual Cancer Research Institute of Northern Alberta (CRINA) Research Day, Edmonton, Canada.

11. Rui Chen, Elena Arutyunova, Aravindhan Ganesan, M. Joanne Lemieux, Khaled Barakat. “Does the IgC Domain of B7-1 (CD80) Impact Receptor Binding – A Key Process in T-cell Immunomodulation”, 2018 Faculty of Pharmacy and Pharmaceutical Sciences Research Day, Edmonton, AB, Canada.

12. Subha Kalyaanamoorthy and Khaled H. Barakat “Binding site and interaction analysis of Kv7 modulators on KCNQ1 and KCNQ3 channels”, CRINA-Research Day 2017, Edmonton, Alberta, Canada, November 2017. (Awarded the WU Hong Memorial Poster Prize for Runner-up for the Poster Group D Postdoctoral Fellow Award award).

13. Aravindhan Ganesan, Tae Chul Moon, Khaled Barakat. 2017. How do the co-stimulatory CD28/B7-1 interactions differ from the co-inhibitory interactions of CTLA/B7-1 for orchestrating T-cell immune responses? Cancer Research Institute of Northern Alberta 2017, Edmonton, Alberta, Canada. (Awarded top poster award).

14. Subha Kalyaanamoorthy and Khaled H. Barakat “Molecular determinants for blocking the hERG channel”, Faculty of Pharmacy and Pharmaceutical Sciences Research Day, University of Alberta (2017).

15. Horia Jalily Hasani, Aravindhan Ganesan, Marawan Ahmed, Khaled Barakat. 2017. The effects of protein-protein interactions and ligand-binding on the ion permeation through KCNQ1 channel revealed by computational simulations. Faculty of Pharmacy Research Day, University of Alberta, Edmonton, Alberta, Canada.


17

16. Aravindhan Ganesan, Theinmozhi Arulraj, Tahir Choulli, Khaled Barakat. 2017. Mathematical modelling and analyses of antibody-induced changes in the co-stimulatory interactions. Faculty of Pharmacy Research Day, University of Alberta, Edmonton, Alberta, Canada.

17. Marawan Ahmed, Anil Kumar, Tom Hobman, Khaled Barakat "Identification of High Affinity Ligands against Dengue Virus NS1 for the Development of an Affordable Point-of-care Diagnostic Kit" Faculty of Pharmacy and Pharmaceutical Sciences Research Day, University of Alberta (2017).

18. Francesco Gentile, Khaled H. Barakat, Jack A. Tuszynski , Rational design of inhibitors of the XPF-ERCC1 heterodimerization for combination cancer therapy. Oral and poster presentations at the Cancer Research Institute of Northern Alberta Research Day 2017, University of Alberta, Edmonton, AB, Canada, November 25, 2017.

19. Feng T., Subha Kalyaanamoorthy., Barakat K. “Modeling dynamic structure and investigating properties of the CaV1.2”, The Faculty of Pharmacy and Pharmaceutical Sciences Research Day 10/2017.

20. C.J. Mitran, A. Ganesan, S. Gnidehou, F. Ntumnia, J.H. Adams, K. Barakat, M. F. Good, and S. K. Yanow, ‘A structurally defined epitope in P. vivax PvDBP that may mediate antibody cross-reactivity to similar epitopes in VAR2CSA’, The Americal Society of Tropical Medicine & Hygine-2018, New Orleans, Louisiana, USA, October 28-November 1, 2018.

21. A. Ganesan, Khaled Barakat, ‘Structural bases of antibody-mediated effects on CTLA-4 revealed through molecular’, 101st Canadian Chemistry Conference and Exhibition, Edmonton, Alberta, Canada, 27-31 May 2018.

22. Subha Kilannamorthy, Khaled Barakat, ‘Structural basis for the PIP2-mediated pharmacology in KCNQ3 channels’, 101st Canadian Chemistry Conference and Exhibition, Edmonton, Alberta, Canada, 27-31 May 2018.

23. Marawan Ahmed, Anil Kumar, Tom Hobman, Khaled Barakat "High Affinity Ligands against Dengue Virus NS1" The 101st Canadian Chemistry Conference and Exhibition, Edmonton, AB (2018).

24. Feng T., Subha Kalyaanamoorthy., Barakat K. ‘Modeling the dynamic gating mechanism and small-molecule binding in the CaV1.2 channel’, The Canadian Society for Pharmaceutical Sciences Conference Toronto 05/2018.

25. Feng T., Subha Kalyaanamoorthy., Barakat K. ‘Modeling the dynamic gating mechanism and small-molecule binding in the CaV1.2 channel’, 101st Canadian Chemistry Conference and Exhibition, Edmonton, Alberta, Canada, 27-31 May 2018.

26. C. Mitran, A. Mena, A. Ganesan, A. Salanti, A. Maestre, F.S. Kano, L. Carvalho, K. Barakat, M. F. Good, and S. K. Yanow, ‘Defining a structural epitope within Plasmodium vivax PvDBP as a vaccine candidate against Plasmodium falciparum placental malaria’, 1st Malaria World Congress, Melbourne, Victoria, Australia, 1-5 July 2018.

27. Yasser M Tabana, Saad S Dahham, khaled Barakat, Amin MSA Majid "Anti-angiogenic effects of β-caryophyllene against Human Colorectal Cancer Xenografts", 27-31 May (2018) Canada “101st Canadian Chemistry Conference and Exhibition (CSC2018).

28. Francesco Gentile, Khaled H. Barakat, Jack A. Tuszynski ,Investigating the Structure of the XPF-ERCC1 Functional Endonuclease using a Computational Approach. Poster presentation at the Biophysical Society 62nd Annual Meeting Moscone Center, San Francisco, CA, United States of America, February 18, 2018.


18

29. Marawan Ahmed, Khaled Barakat "The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study" Canadian Cancer Research Conference (CCRC) November 5-7, 2017, Vancouver BC, Canada.

30. Francesco Gentile, Khaled H. Barakat, Jack A. Tuszynski, Virtual screening of DNA repair inhibitors targeting the XPF active site for combination cancer therapy. Poster presentation at the 4th Canadian Cancer Research Conference 2017, Vancouver Convention Center, Vancouver, BC, Canada, November 5, 2017.

31. Marawan Ahmed, Aravindhan Ganesan, Anil Kumar, Thomas Hobman, Khaled Barakat. 2017. Identification of high affinity ligands against dengue virus NS1 for the development of an affordable point-of-car diagnostic kit. IC-Impacts India Workshop Series, December 4-5 2017, Pune, Maharashtra, India.

32. A. Ganesan and K. Barakat, ‘ Modelling the interactions of CD28:B7-1 complexes: Towards understanding the control of immune responses against cancers’, CRINA-Research Day 2016, Edmonton, Alberta, Canada, 12 November 2016. (Awarded top poster award).

33. A. Ganesan, M. Ahmed, H. Horia and K. Barakat, ‘Exploration of sodium permeation in the human Nav1.5 channel’, Toxicology Symposium 2016, University of Alberta, Canada, 18 May 2016.

34. Marawan Ahmed, Shokrollah Elahi, James Nieman, Lai Xu, Isobel Okoye, Guangzhi Zhang, Appan Srinivas Kandadai, Mostofa Hena, Alexandr Belovodskiy, Seyedeh Nargess Hosseini, Elena Arutyunova, Tae Chul, Bethany Yoon, Justin Shields, Katharine Cheryl Agopsowicz, Nutan Srivastava, Fredrick West, Marry Hitt, John Walker, Michael Smylie, Joanne Lemieux, Arno Siraki, Lorne Tyrrell, Michael Houghton, Khaled Barakat "Rational Design and Validation of Of Small Molecular Inhibitors For The PD-1/PD-L1 Immune Checkpoint Pathway" CRINA research day (2016).

35. Marawan Ahmed, Shokrollah Elahi, James Nieman, Lai Xu, Isobel Okoye, Guangzhi Zhang, Appan Srinivas Kandadai, Mostofa Hena, Alexandr Belovodskiy, Seyedeh Nargess Hosseini, Elena Arutyunova, Tae Chul, Bethany Yoon, Justin Shields, Katharine Cheryl Agopsowicz, Nutan Srivastava, Fredrick West, Marry Hitt, John Walker, Michael Smylie, Joanne Lemieux, Arno Siraki, Lorne Tyrrell, Michael Houghton, Khaled Barakat "Rational Design and Validation of Of Small Molecular Inhibitors For The PD-1/PD-L1 Immune Checkpoint Pathway" Faculty of Pharmacy and Pharmaceutical Sciences Research Day, University of Alberta (2016).

36. Marawan Ahmed, Aravindhan Ganesan, Horia H. Jalily, Khaled Barakat "Investigating The Ion Permeation Pathway Of Nav1.5 Ion Channel" University of Alberta, Faculty of Pharmacy Toxicology symposium (2016).

37. Marawan Ahmed, Aravindhan Ganesan, Horia H. Jalily, Khaled Barakat "Investigating The Ion Permeation Pathway And Drug Blockade Of Nav1.5 Ion Channel" CANHEIT, HPCS (2016).

38. Francesco Gentile and Khaled Barakat “Computational Drug Design of Nucleotide Excision DNA Repair Inhibitors for Improved Cancer therapy”. Poster presentation at the American Society for Cell Biology 2016 Annual Meeting, Moscone Center, San Francisco, CA, United States, December 5, 2016.

39. Francesco Gentile and Khaled Barakat “Modeling the Human XPF Nuclease Domain for Structure-Based Drug Design of Nucleotide Excision Repair and Interstrand Crosslink Repair Inhibitors”. Poster presentation at the Pharmacy


19

Research Day 2016, University of Alberta Hospital, Edmonton, AB, Canada, November 25, 2016.

40. Marawan Ahmed, Abhishek Pal, Michael Houghton, Khaled Barakat “A Comprehensive Computational Analysis For The Binding Modes Of HCV NS5A Inhibitors: The Question Of Symmetry”, University Of Alberta - UARE Symposium, University of Alberta, Edmonton, AB, Canada, November 12, 2016.

41. Francesco Gentile and Khaled Barakat, “A Novel Model Of The Human XPF Nuclease Domain For The Rational Design Of DNA Repair Inhibitors”. Poster presentation at the Cancer Research Institute of Northern Alberta Research Day 2016, University of Alberta, Edmonton, AB, Canada, November 12, 2016.

42. Ganesan, A., Ahmed, M., Horia, H. J., and Barakat, K., “Revealing ion exchange mechanisms in Nav1.5 channel using steered molecular dynamics simulations”, CANHEIT-HPCS 2016, University of Alberta, Edmonton, Canada, 2016. (Oral presentation).

43. Heinzinger, M., Ganesan, A., Feng, T., and Barakat, K., “Taking protein-protein interactions to the maximum speed: Applying coarse-graining simulations”, CANHEIT-HPCS 2016, University of Alberta, Edmonton, Canada, 2016.

44. Ganesan, A., Ahmed, M., Horia, H. J., and Barakat, K., “Exploration of sodium permeation in the human Nav1.5 channel using steered molecular dynamics simulations”, Toxicology Symposium 2016, University of Alberta, Edmonton, Canada, 2016.

45. Marawan Ahmed, Abhishek Pal, Michael Houghton, Khaled Barakat "A Comprehensive Computational Analysis For The Binding Modes Of HCV NS5A Inhibitors: The Question Of Symmetry" University Of UARE Symposium.

46. Horia H. Jalily1, Marawan Ahmed, Khaled Barakat "Modelling the Human KCNQ1 Potassium ion Channel: Application of Computaional Approaches To Cardiotoxicity” CANHEIT, HPCS (2016).

47. Marawan Ahmed, Aravindhan Ganesan, Horia H. Jalily1, Khaled Barakat "Investigating The Ion Permeation Pathway And Drug Blockade Of Nav1.5 Ion Channel" CANHEIT, HPCS (2016).

48. Marawan Ahmed, Aravindhan Ganesan, Horia H. Jalily1, Khaled Barakat "Investigating The Ion Permeation Pathway Of Nav1.5 Ion Channel" University of Alberta, Faculty of Pharmacy Toxicology symposium (2016).

49. Gentile, F., Tuszynski, J. A. & Barakat, K. H. “Hybrid Ligand/Target-Based Virtual Screening Protocol to Identify Inhibitors for the XPA-ERCC1 Protein-Protein Interaction”. Pharmacy Research Day, November 27, 2015. University of Alberta Hospital, Edmonton, Canada.

50. Gentile, F., Tuszynski, J. A. & Barakat, K. H. “Identifying novel inhibitors for the XPA-ERCC1 protein-protein interaction”. Cancer Research Institute of Northern Alberta (CRINA) Research Day, November 14, 2015. University of Alberta, Edmonton, Canada.

51. Marawan Ahmed, Horia H. Jalily and Khaled Barakat " SHP2 Directly Interact With PD-1 In A Favoured Conformation: A Comprehensive Modelling Study" The Cancer Research Institute of Northern Alberta’s (CRINA) Research Day (November, 2015).

52. Horia H. Jalily, Marawan Ahmed and Khaled Barakat "Modelling The PD-L1:B7-1 Protein-Protein Interaction In The Tumor Microenvironment" The Cancer Research Institute of Northern Alberta’s (CRINA) Research Day


20

(November, 2015). 53. Marawan Ahmed, Horia H. Jalily and Khaled Barakat "A Comprehensive

Atomistic Model For The Human Nav1.5 Sodium Ion Channel: Toward Understanding The Molecular Origin Behind Cardiotoxicity" University of Alberta Faculty of Pharmacy and Pharmaceutical Sciences Research Day (November, 2015).

54. Marawan Ahmed, Horia Jalily Hasani and Khaled Barakat “A Comprehensive Atomistic Model For The Human Nav1.5 Sodium Ion Channel: Toward Understanding the Molecular Origin Behind Cardiotoxicity” July 2015, Ion Channel Retreat, Vancouver BC, Canada.

55. Horia Jilaly Hasani, Marawan Ahmed and Khaled Barakat “Knowledge-Based Flexible Docking Reveals A Comprehensive Model For Human PDL-1 Bound To Human B7-1” June 2015, HPCS 2015, Montreal, Québec, Canada.

56. Marawan Ahmed and Khaled Barakat “Toward A Full Model For The PD-1 Pathway: Modeling The Interaction Between PD-1 And SHP2.” June 2015, HPCS 2015, Montreal, Québec, Canada.

57. Marawan Ahmed and Khaled Barakat “Human PD-1 binds differently to its human ligands” June 2015, HPCS 2015, Montreal, Québec, Canada.

58. Khaled Barakat “Rational Design of Immune Checkpoints’ Small Molecule Inhibitors.” CIHR Institute Of Infection And Immunity New Investigator Forum, May 2015, LE MANOIR DU LAC DELAGE, QC, Canada.

59. Clement Viricel, Marawan Ahmed and Khaled H. Barakat “Rational Design of Small Molecule Immune Checkpoints’ Inhibitors” February 2015, Tumor Immunology: Multidisciplinary Science Driving Combination Therapy (J7).”

60. Khaled H. Barakat “Toward Potent Immunotherapy Drugs: Rational Design of Inhibitors of the PD-1 Pathway”, November 2014 CIHR, IG, ICR, ICRH New Principal Investigators 13th meeting.

61. Khaled H. Barakat, Lorne Tyrrell, David Evans and Michael Houghton, “Mode Of Binding of Daclatasvir”. HCV meeting, September 2014, Banff, Canada, Canada.

62. Khaled H. Barakat, John Law, Alessio Prunotto, Lorne Tyrrell, David Evans, Jack Tuszynski and Michael Houghton, “Computational Modeling of the HCV Polymerase active site and drug screening in silico”. 2nd Li Ka Shing Institute of Virology Symposium, May 2013, Edmonton, AB, Canada.

63. Anwar Anwar-Mohamed, Khaled H. Barakat, Darren Hockman, Bradley Thomas, D. Lorne Tyrrell, and Michael Houghton “MECHANISMS OF FATAL HUMAN CARDIOTOXICITY BY THE HCV DRUG BMS-986094” 2nd Li Ka Shing Institute of Virology Symposium, May 2013, Edmonton, AB, Canada.

64. Barakat, K. H., Lars Petter Jordheim, Michael Houghton, Charles Dumontet and “Virtual screening suggest novel inhibitors for the XPf-ERCC1 interaction”, 6th Drug Discovery and Medicinal Chemistry Conference, June 2012, San Diego, CA, USA.

65. Douglas Friesen, Barakat, K. H., Bruce Fenske, Jonathan Mane, Chih-Yuan Tseng and Jack Tuszynski. Identification of γ-tubulin Paclitaxel and Colchicine Binding Locations for Novel Dual Inhibitors of γ and βIII-tubulin. Poster presentation at the 17th Canadian Symposium on Theoretical Chemistry, University of Alberta, July 2010.

66. Barakat, K. H., Bilkiss Issack, Maria Stepanova and Jack Tuszynski. Effects of Temperature on the Binding Interactions and Collective Dynamics of p53-DNA: Comparing the Wild type to the R248Q Mutant. Poster presentation at


21

the 17th Canadian Symposium on Theoretical Chemistry, University of Alberta, July 2010.

67. D. Friesen, Barakat, K. H., and J. Tuszynski. “Blind docking predicts potential binding sites for Human Polynucleotide kinase inhibitors” Alberta Cancer Research Institute Meeting, November 2009, Banff, Edmonton, AB, Canada. The same poster was presented at the IGTC Summit, October 2010, Naramata Centre, Naramata, BC.

68. Barakat, K. H., and J. Tuszynski “Relaxed complex scheme predicts novel inhibitors for the lyase activity of DNA polymerase beta.” Alberta Cancer Research Institute Meeting, November 2009, Banff, Edmonton, AB, Canada.

69. Travis J. A. Craddock, Barakat, K. H., and Jack A. Tuszynski, “Computational Determination of Putative Binding Sites of Anesthetics to the Cytoskeleton”, Poster Presentation at The Seventh Canadian Computational Chemistry Conference. July 2009, Halifax, Nova Scotia, Canada.

70. Barakat, K. H., and Jack Tuszynski, “Ensemble Virtual Screening Reveals Potential Inhibitors for the MDM2-p53 Interaction”, Poster Presentation at The Seventh Canadian Computational Chemistry Conference in Halifax, Nova Scotia, Canada. July 2009, the abstract being included in the conference proceedings.

71. Barakat, K. H. and Jack Tuszynski, “Ensemble Virtual Screening Reveals Potential Inhibitors for the MDM2-p53 Interaction”, Poster Presentation at the Chemical Biophysics Symposium, Toronto, Canada, April 2009, the abstract being included in the conference proceedings.

72. Barakat, K. H., Huzil, J. T., and Tuszynski, J. A., "Virtual Screening and MD simulations suggest potential inhibitors of the Nucleotide Excision Repair pathway", Poster Presentation at the Western Canadian Medicinal Chemistry Workshop, at the University of Saskatchewan, Saskatoon, in September of 2008, the abstract being included in the conference proceedings.

v. Invited Speaker:

1. April 2019, “Computational Drug Discovery Of Membrane Proteins”, Northern lights seminar series, University of Alberta, Edmonton, AB, Canada.

2. November 2018, “Developing Small Molecule Immune Checkpoints Inhibitors”, LKS Translational Research Symposium, Edmonton (Alberta), Canada.

3. October 2018, “Atomistic Computational Models to Predict Drug-mediated Cardiotoxicity”, CVRC Seminar Series, Edmonton (Alberta), Canada.

4. September 2018, “New trends in Computational Drug Discovery”, Invited Talk, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt

5. April 2018, “Atomistic Computational Models To Predict Drug-mediated Cardiotoxicity”, Keynote Speaker, International Conference on Pharmacy and Pharmaceutical Sciences, Dubai, United Arab Emirates.

6. April 2018, “Atomistic Computational Models To Predict Drug-mediated Cardiotoxicity”, Visit to Al-Ain University, United Arab Emirates.

7. March 2018, “Rational Design And Development Of Small Molecule Inhibitors Of The Immune Checkpoints: A Slide Set Focused On A PD-1 & CTLA-4 Antagonists”, TecEdmonton Industrial day, Calgary, AB, Canada.

8. December 2017, “Identification Of High Affinity Ligands Against Dengue Virus NS1 For The Development Of An Affordable Point-of-care Diagnostic Kit”, 2017 Pune IC-IMPACTS workshop, Pune, India.


22

9. October 2017, “Rational Design Of Small Molecule Immune Checkpoints' Inhibitors: The PD-1 Challenge”, Keynote Speaker, Applied microbiology Conference, Toronto, Ontario, Canada.

10. May 2017, “Rational Design Of Small Molecule Immune Checkpoints' Inhibitors: The PD-1 Challenge”, Vaccine Innovation Conference, Montreal, QC, Canada.

11. April 2017, “HEKA THERAPEUTICS: Spin Off For The Immune Checkpoints Program At The University Of Alberta, Canada”, visit to Merck Research Labs (MRL), NJ, USA.

12. December 2016 “Computational Drug Discovery Applied To Cancer Immunotherapy And Hepatitis C Virus”, Keynote Speaker, ICDDDT-2016, Cairo, Egypt.

13. December 2016 “Computational Drug Discovery: A Candle In The Dark”, Invited Talk, Ain Shams University, Cairo, Egypt.

14. December 2016 “Computational Drug Discovery: A Candle In The Dark”, Invited Talk, American University in Cairo (AUC), Cairo, Egypt.

15. March 2016 “Toward Potent Immunotherapy Drugs: Rational Design of Inhibitors of the Immune Checkpoints Proteins” Keynote Speaker, 6th Euro  Virology Congress and Expo, Madrid, Spain.

16. February 2016 “Computational Drug Discovery: A Candle In The Dark”, Invited Talk, University of Sharjah, Sharjah, UAE.

17. February 2016 “Computational Drug Discovery: A Candle In The Dark”, Invited Talk, Al-Ain Univeristy, Al-Ain, UAE.

18. February 2016 “Computational Drug Discovery Applied To Cancer Immunotherapy And Hepatitis C Virus”, 7th International Conference on Drug Discovery and Therapy, University of Sharjah, Sharjah, UAE.

19. February 2016 “Computational Drug Discovery Applied To Cancer Immunotherapy And Hepatitis C Virus”, 7th International Conference on Drug Discovery and Therapy, University of Sharjah, Sharjah, UAE.

20. December 2015 “Rational Design Of Small Molecule Immune Checkpoints’ Inhibitors”, Virology 2015, Atlanta, GA, USA

21. April 2015 “Structure-Based Algorithms to Predict Drug-Mediated Toxicity” Bio-IT World, Boston, USA.

22. February 2015 “Rational Design of Small Molecule Immune Checkpoints’ Inhibitors” Short talk at the Tumor Immunology: Multidisciplinary Science Driving Combination Therapy (J7).

23. November 2014 “Toward Potent Immunotherapy Drugs: Rational Design of Inhibitors of the PD-1 Pathway” Short talk at the CIHR, IG, ICR, ICRH New Principal Investigators 13th meeting.

24. September 2014 “Computational Drug Discovery Applied to HCV” Plenary Speaker at the HCV meeting 2014.

25. June 2014, “Rational Drug Design” Department of Medical Genetics, University of Alberta, Edmonton, Canada.

26. September 2011, Virtual screening reveals dual inhibitors for the ERCC1-XPF interaction, 2nd Symposium on Graduate Physics Research, University of Alberta, Edmonton, AB, Canada.

27. May 2010, Sharcnet research day, York university, Toronto, Canada,” Ensemble-based virtual screening reveals dual-inhibitors of the p53-MDM2/MDMX interactions”.


23

28. November 2009, Northern Lights seminar series – University of Alberta, Edmonton, AB, Canada: “Molecular Drug Design: Receptor-Based Virtual Screening (RBVS)”.

29. October 2009, Graduate Biophysics Class – University of Alberta, Edmonton, AB, Canada: “A An introductory lecture on Bioinformatics and Bioinformatics tools”.

30. December 2006, Dept. of Engineering Physics, Cairo University, Egypt: "Phase transitions of tetrahedral molecules using molecular dynamics simulations".

31. October 2006, Physics Department, American University in Cairo, Egypt: "Phase transitions in solid Methane".

vi. Patents:

1. Khaled Barakat, Marawan Ahmed, Aravindhan Ganesan, Michael Houghton, Lorne

Tyrrell. U.S. Provisional Application Serial No. 62/371,675 Systems And Methods Of Selecting Compounds With Reduced Risk Of Cardiotoxicity Using Cardiac Sodium Ion Channel.

2. Michael Houghton, Jack A Tuszynski, Khaled Barakat, Anwar Mohamed. Chinese Patent Application No. 201480075454.3 Systems And Methods Of Selecting Compounds With Reduced Risk Of Cardiotoxicity.

3. Khaled Barakat, Marawan Ahmed, James Nieman, Michael Houghton, Lorne Tyrrel. U.S. Provisional Application No. 62/466,243 Entitled: Small Molecule Immunomodulators.

4. Egli A, Santer Dm, Levin Ay, Thomas Bs, Barakat Khs, Et Al. (2015) Immunomodulatory Peptides And Methods Of Use Thereof. Us Patent 20,150,307,590.

IV. VOLUNTEER AND PUBLIC SERVICE

Year Service 2015 Soccer coaching for minor kids. 2013 Chair of the “liver as an immune organ session” at the 2nd Li Ka Shing Institute

of Virology Symposium, May 2013, Edmonton, AB, Canada.

2011 President of Graduate Physics Student Association (GPSA) 2011 Vice President of Egyptian Student Association (ESA). 2006 Organized workshops on teaching how to read and write to how to use a computer

and write simple programs. 2005 Organized workshops for illiteracy to help people that cannot read or write

Arabic.

V. MEDIA INTERVIEWS

Vantage point: https://seekingalpha.com/article/4027531-vantage-point-going-small-hit-big Edmonton Sun: https://edmontonsun.com/2015/06/24/magic-cancer-drug-being-developed-by-university-of-alberta/wcm/cf843ea0-672a-45b1-8163-612961e79454 CTV National: http://www.ctvnews.ca/health/alberta-team-assembled-to-develop-cancer-curing-magic-drug-1.2439593


24

CTV Edmonton: http://edmonton.ctvnews.ca/the-fight-against-cancer-gets-multimillion-dollar-boost-1.2438643 Global Edmonton: http://globalnews.ca/news/2073234/edmonton-partnership-hopes-to-develop-magic-drug-for-cancer-patients/ Eureka alert: http://www.techienews.co.uk/9734974/researchers-take-the-fight-against-cancer-at-molecular-level/ Science News: https://www.sciencenews.org/article/new-cancer-drugs-wake-sleeping-killer-t-cells Dinner Television: http://www.dinnertelevision.ca/videos/4335349992001/ Leap Magazine: http://myleapmagazine.ca/2015/09/research-rock-star-the-beat-goes-on/ University of Alberta Website: http://pharm.ualberta.ca/news/2015/june/small-but-mighty-molecules

VI. SPIN OFF COMPANIES

Heka Therapeutics INC. Small molecule inhibitors for the immune checkpoints’

proteins.

Achlys Predicting off-target toxicity for small molecule drugs.

Documents

CURRICULUM VITAE I. ACADEMIC BACKGROUND · 2020. 11. 30. · Khaled Barakat, PhD Curriculum Vitae – December 2018 1 CURRICULUM VITAE I. ACADEMIC BACKGROUND A. PERSONAL DATA Name: