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Weekly Units
Week 1: Introduction to Medicinal Chemistry
During this week, you will be presented with a "big picture" overview about the field of medicinal chemistry -- what it is, what medicinal chemists do, and the types of knowledge and skills that one needs to master to be a medicinal chemist. This week's activities are designed to prepare you for the specific topics that will be presented in subsequent weeks. We will also start learning some organic chemistry!
Week 2: Pharmacology -- Organic Chemistry I
Organic chemistry, the study of carbon-based compounds, is the basis for an understanding of medicinal chemistry. Virtually all drugs are organic compounds. This week provides you with a "crash course" on organic chemistry, with a focus on learning how organic compounds are structured and named. In addition to basic structures and nomenclature, you'll be provided with a brief introduction to functional groups, to be continued in Week 3. THIS IS ALSO THE FIRST RESIDENTIAL WEEKEND (January 30-Feb 1)
Week 3: Pharmacology -- Organic Chemistry II
We continue our "short course" on organic chemistry, focusing heavily on functional groups -- alcohols, aldehydes, esters, ketones, ethers, and carboxylic acids. We'll also talk about some of the reactions of organic compounds, with examples from pharmacology.
Week 4: Pharmacology -- Drug Solubility
During this week, we'll take a look at getting a drug into the body, primarily through oral means. To do this, we need to understand about drug solubilities, or the ability of the drug to dissolve in water-based (aqueous) or lipid (fat)-based environments. This unit, like many in drug chemistry, makes use of statistical techniques to evaluate and understand drug behavior.
Week 5: Pharmacology -- Acid-Base Chemistry in Drug Design
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As the title of this session suggests, we'll review (or be introduced to) some basic acid-base chemistry, with a specific eye towards drug design chemistry. Drugs can be classified as acidic or basic. When introduced into the body, drugs travel to acidic (pH<7) and/or basic (pH>) environments. An understanding of that chemistry will be critically important for the remainder of the course.
Week 6: Drug Design -- QSAR I
QSAR -- quantitative structure activity relationships -- is one of the fundamental tools for the medicinal chemist. QSAR is a statistical technique, so it's time to dust off your mathematics skills! During this session, we'll explore the background theory of QSAR, talk about its strengths and limitations, and do some simple QSAR calculations.
Week 7: Drug Design -- ADME
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During this session, we'll look at the how drugs are absorbed, distributed, metabolized, and excreted (ADME) in a little more detail. We've spent the majority of our time so far looking at getting the drug into the body (absorption); now we'll spend some time thinking about how the drug is distributed, metabolized, and eventually excreted.
Week 8: Drug Design -- Drug Synthesis
In this week's activities, we'll look at some of the basic organic synthesis methods that are used to create complex molecules, like drugs. We'll talk about retrosynthetic mechanisms and other named (and unnamed) organic reaction mechanicsms.
Week 9: Drug Design -- Pharmacokinetic Modeling
During this week (residential weekend!), we will look at one of the basic guiding principles of pharmacology and drug design -- ADME(T) -- absorption, distribution, metabolism, excretion, and toxicology. During the residential weekend, you will construct, from scratch, a pharmacokinetics (pharm=drug; kinetics=speed) model. This model will allow you to play the role of a physician, looking to determine the correct dosing regimen for a patient with an illness. Try not to kill your patient!
Week 10: Pharmacodynamics -- Introduction to Protein Structure
Drugs interact with targets in the body, and the majority of those targets are proteins. In order to understand how drugs interact with proteins, it is imperative to understand the basic structures of proteins. During this week we'll investigate protein structures and spend some time looking at protein-ligand (drug) interactions.
Week 11: Pharmacodynamics -- Protein Structure II
During this week, we'll continue to look at protein structures, with an eye towards beginning to understand how protein receptors interact with drug ligands.
Week 12: Pharmacodynamics -- Intro to Bioinformatics
Bioinformatics, also known as computational biology, is one of the primary computational tools used by the medicinal chemist. Bioinformatics tools allow the researcher to explore a wide variety of structures, properties, and activities of proteins, genes, and related structures.
Week 13: Pharmacodynammics -- Bioinformatics II
During this session, we'll look at a variety of specific bioinformatics resources (Ensembl, Biology Workbench, OMIM, and HGMD) and explore the use of bioinformatics tools (such as CLUSTAL, AASTATS, and PELE) used in the practice of medicinal chemistry.
Week 14: Pharmacodynamics -- Protein Docking I
Protein docking is the process by which drugs (known as "ligands") are inserted into receptor molecules, which are typically proteins found in the organism. During this week's discussions, we will set the stage for learning how to dock a ligand into a protein receptor.
Week 16/17/18: Final Project
The final project consists of a large case study: your "company" of three consultants is "hired" to provide technical advise to a large pharmaceutical company. You will prepare a technical report on a lead drug, discussing its chemical and molecular properties, its pharmacokinetics, and its pharmacogenomic effects. Each person in the team will have a role, and part of the activity is to help you learn how to work together towards a common goal!