CHEM 731/7310-02 - Rational Drug Design

Semester: Fall 2023

Professor: S. Kalyaanamoorthy | Discipline: Biochemistry | Campus: Waterloo


The objective of this course is to provide an introduction to strategies for design of drug candidates, including structure-based and ligand-based drug discovery.  It builds upon molecular modelling principles introduced in CHEM 340 and will apply them to specific problems in drug design. Specific topics includes molecular modelling, and molecular dynamics using molecular mechanics principles, molecular docking and virtual screening of drug molecules to target proteins, computational analysis of drug-receptor interactions, lead modification for improved biochemical activity and the role of artificial intelligence (AI) in the drug discovery process.


By the end of this course students should be able to:

Understand the drug discovery cycle, and different concepts in drug discovery
Learn about different computational drug discovery methods and their usage and applications
Gain hands-on experience on different software programs that can be used for drug discovery applications
Learn the basics of programming using Unix-based commands and TCL scripts


Title / Name Notes / Comments Required
Laptop/Desktop computer Yes
Software: Visual Molecular Dynamics, ChemAxon Marvin, Autodock MGL Tools, Autodock Vina, Autogrow, NAMD Yes

Additional reading:

  • Andrew Leach, Molecular Modelling: principles and Applications, Prentice Hall, 2001
  • Hans-Dieter Holtje, Wolfgang Sippl, Didier Rognan, Gerd Folkers, Molecular Modeling: Basic Principles and Applications, Wiley-VCH Verlga GmbH, 2008
  • Daan Frenkel, Berend Smit, Understanding Molecular Simulation From Algorithms to Applications, Academic Press, 2001


Component Value
Project proposal 10%
Research Project (Presentation and Report) 30% (=>15% presentation and 15% project report)
Assignments/Lab reports (3-4) 40%
Literature review (Discussion/report) 10%
Quiz 10%


Text matching software (Turnitin) will be used to screen project reports in this course. This is being done to verify that use of all material and sources in report is documented. In the first week of the term, details will be provided about the arrangements for the use of Turnitin and alternatives in this course. See Administrative Policy below for more information and links.


Activities for this course involve recording, in partial fulfillment of the course learning outcomes.  You will receive notification of recording via at least one of the following mechanisms: within the Learning Management System (LEARN), a message from your course instructor, course syllabus/website, or other means. Some technologies may also provide a recording indicator. Images, audio, text/chat messaging that have been recorded may be used and/or made available by the University to the Professor, Professor’s research team, Classmates, Project group  for the purpose of materials review and assessments. Recordings will be managed according to the University records classification scheme, WatClass, and will be securely destroyed when no longer needed by the University. Your personal information is protected in accordance with the Freedom of Information and Protection of Privacy Act, as well as University policies and guidelines and may be subject to disclosure where required by law.

The University will use reasonable means to protect the security and confidentiality of the recorded information, but cannot provide a guarantee of such due to factors beyond the University’s control, such as recordings being forwarded, copied, intercepted, circulated, disclosed, or stored without the University’s knowledge or permission or the introduction of malware into computer system which could potentially damage or disrupt the computer, networks, and security settings. The University is not responsible for connectivity/technical difficulties or loss of data associated with your hardware, software or Internet connection.

By engaging in course activities that involve recording, you are consenting to the use of your appearance, image, text/chat messaging, and voice and/or likeness in the manner and under the conditions specified herein. (In the case of a live stream event, if you choose not to have your image or audio recorded, you may disable the audio and video functionality. Instructions to participate using a pseudonym instead of your real name are included where the feature exists; however, you must disclose the pseudonym to your instructor in advance in order to facilitate class participation.) If you choose not to be recorded, this notice serves as confirmation of your understanding that to view the recording later and ask questions in the MSTeams discussion forum/email.

You are not permitted to disclose the link to/URL of an event or an event session recording or copies of recording to anyone, for any reason. Recordings are available only to authorized individuals who have been directly provided the above instructions/link for their use. Recordings for personal use, required to facilitate your learning and preparation of personal course/lecture notes, should not be shared with others without the permission of the instructor or event coordinator. Review the University’s guidelines for faculty, staff and students entering relationships with external organizations offering access to course materials for more information on your obligations with respect to keeping copies of course materials. For more information about accessibility, connect with AccessAbility Services.


  • Mon: 12:30 pm - 1:20 pm in QNC 2501
  • Wed: 12:30 pm - 1:20 pm in QNC 2501
  • Fri: 12:30 pm - 1:20 pm in QNC 2501

Office Hours

Office: ESC 234 Office Hours: In person or Teams