Course Syllabus

Medicinal Chemistry: Transforming Molecules into Medicines

This is a draft syllabus 

Semester & Location:	Spring 2027 - DIS Copenhagen
Type & Credits:	Elective Course - 3 credits
Major Disciplines:	Biomedicine / Biotechnology, Chemistry / Biochemistry
Prerequisites:	One year each of biology and chemistry at university level (including at least one semester of Organic Chemistry).
Faculty Member:	Amy Dounay (visiting faculty) (current students please use the canvas inbox to contact)
Program contact:	Science and Health Department shsupport@dis.dk
Program Director:	Susana Dietrich
Time & Place:	TBD

 

Faculty

Amy Dounay Professor, Department of Chemistry and Biochemistry, Colorado College

 
Course Description

This course introduces the principles and practice of medicinal chemistry. Students will explore how new small molecule drugs are designed and how their pharmacological, metabolic, and toxicological properties are optimized. The course provides an overview of the drug discovery, development, and approval process, supported by case studies of successful and failed drug candidates. Through in-depth analysis of primary literature and case studies, students will examine how emerging technologies drive modern drug discovery. 

 

Expected Learning Outcomes

 After successful completion of this course, students will be able to:

• Propose strategies to optimize the pharmacological, metabolic, and toxicological properties of drug leads and candidates.
• Evaluate and explain the biological rationale for targeting specific enzymes or receptors in disease.
• Apply principles of biochemistry, molecular biology, and organic chemistry to interpret and critique recent primary medicinal chemistry literature.
• Critically assess how pharmaceutical research and development is represented in the press and popular media.
• Analyze how drug discovery and development practices have benefited or marginalized particular identity groups.
• Deliver a professional-quality presentation on medicinal chemistry advances underlying a recently approved drug.

The following topics will be covered in this course:

Unit 1: Introduction and Foundational Topics

• Drug Discovery Overview
• Organic Chemistry: Fundamentals for Drug Design
• Biochemistry: Fundamentals for Drug Design
• Pharmacology: Basics on Receptors and Enzymes as Drug Targets

Unit 2: Medicinal Chemistry Strategies and Tactics

• Drug Design Metrics: Ligand Efficiency and Lipophilic Efficiency
• Lead Identification: High-Throughput Screening (HTS)
• Lead Optimization: Structure-Activity Relationships (SAR)
• Intro to ADME (Absorption, Distribution, Metabolism, and Excretion)
• Optimization of Drug Metabolism and Safety
• Drug-Drug Interactions (DDI)
• Structure-Based Drug Design
• Case Study: Boceprevir

Unit 3: New Directions, Challenges, and Opportunities in Medicinal Chemistry

• Intellectual Property for Pharmaceuticals
• Green Chemistry in Drug Discovery and Production
• Drug Safety, Clinical Trials, and 21^st Century approaches
• New Breakthroughs: Small Molecule GLP1 agonists for Diabetes and Obesity

 

Classroom learning environment and expectations

This course is designed around active, student-centered learning rather than traditional lectures. Class time will primarily involve interactive activities, group work, and discussions aimed at maximizing understanding and application of key concepts. To make the most of this approach, students are expected to come to class prepared and ready to actively engage with both the material and their peers.

Description of Assignments, Testing and Grading

Evaluation 

To be eligible for a passing grade in this class all of the assigned work must be completed.

The factors influencing the final grade and their weights are tentative and will be updated before registration opens.

Guided reading questions (Canvas)		15%
Literature analysis assignment		15%
Journal club: student-led literature discussion		15%
Discussion forums (Canvas)		10%
Class attendance and participation		10%
Individualized goals and reflection		5%
New Drug Project	Annotated bibliography, draft slides, peer feedback	10%
	Oral presentation	20%

 Assignment Descriptions:

 

Guided Reading Questions (Canvas)

Throughout the semester, you will complete several guided reading question assignments based on textbook chapters or articles. These open-book, individual assignments help you deepen your understanding of key concepts and allow me to focus class time on areas where clarification is needed. Work independently and support your answers with specific examples from the readings. To get the most out of this exercise, you will focus on developing your own thinking and explanations rather than relying on AI tools like ChatGPT. Writing for this assignment is primarily a way to clarify your understanding, and feedback will focus on content rather than writing style. You may use bullet points or full sentences, but clear organization will help you process and retain the material.

Literature Analysis Assignment

You will read a primary medicinal chemistry article and answer questions provided by the instructor. This open-book assignment encourages you to use the article, your class notes, and relevant textbook or cited references to develop your skills in critical reading, data interpretation, and analysis of current research.

Journal Club

You will participate in student-led presentations followed by class discussions on recent primary literature or review articles. These sessions help you develop critical thinking, scientific reading, collaboration, and presentation skills. If you are presenting, you will lead the discussion; if not, you should read the assigned paper in advance and prepare questions. Presentations should clearly summarize key findings, highlight broader implications, and explain original data to support understanding and critical evaluation.

Canvas Discussion Forums

Throughout the semester, you will participate in online discussion forums on Canvas to reflect on readings, class discussions, and field study experiences. You will be graded on thoughtful contributions and active engagement with your classmates. This means sharing your own ideas and responding to others in ways that encourage meaningful dialogue and help everyone deepen their understanding of the course material.

New Drug Project: Presentation

You will deliver a professional-quality presentation on a recently approved drug, with topics approved by the instructor. Your presentation should explain the therapeutic background, preclinical research, and key properties of the compound, focusing on how medicinal chemists used structure-activity relationship (SAR) studies to optimize the molecule. You will rely extensively on primary scientific literature and patents as source material. The assignment is scaffolded: you will complete an annotated bibliography and receive feedback on draft slides from peers and the instructor before the final presentation. This project helps you synthesize course concepts in a real-world context while presenting clearly, engaging the audience, and responding thoughtfully to questions.

Individualized Goals and Reflection

At the start of the course, you will set your own learning goals related to the course material, skills you want to develop, and your longer-term educational or career plans. Throughout the semester, you will track your progress through assignments, discussions, and field study experiences. At the end of the semester, you will write a reflection on what you’ve learned, the progress you’ve made toward your goals, and any challenges you encountered. Reflection prompts will help you connect your experiences to course objectives, presentations, and personal growth, encouraging you to think critically about your learning and how it applies to your future.

Participation
Your participation is an important part of our shared learning environment. This includes coming to class prepared, engaging actively in discussions, contributing during group work, and participating fully in field studies. To earn full participation credit, plan to attend all scheduled class meetings and take an active role in our conversations and activities.

 

 

 

Field Studies

This course will be accompanied by field studies. Field studies are typically a half-day excursion.

Two field studies will take place during the semester.

 

Required Readings

• Textbook: Patrick, G. L. An Introduction to Medicinal Chemistry, 7^th edition, Oxford University Press, 2023.
• Additional primary literature, review articles, and supplemental readings will be posted on Canvas.

 

Policies

Absences

As a common courtesy, and to help me help you, please email me if you will miss any class session.  I appreciate knowing in advance of class, if possible; otherwise, please let me know as soon as possible.

If you miss a class for any reason, arrange to get notes from a classmate. Due to the format of the class and extensive group work in class, Zoom will not generally be available as an option. Students who miss a class will still be expected to learn the content, as it will be needed on future assignments. 

AI Generative AI tools such as ChatGTP, can only be used under defined circumstances in the classroom and not for homework assignments or online exams.

Use of Laptops or Phones in Class

Use of laptop computers or tablets in class is limited and only allowed for taking notes, completing group work, and ad hoc research within the class discussions and exercises. Cell phones should be turned off and put away.

Late Work Policy

Late assignments will be accepted, but your grade for the paper will be reduced by 10% for each day that it is late.

Questions and feedback

If you have questions about the readings, lectures, or assignments, you are always welcome to contact me (email preferred).

 

 

Academic Regulations  

Please make sure to read the Academic Regulations on the DIS website. There you will find regulations on: 

• Course Enrollment and Grading  
• Academic Expectations and Honor Code 

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