This is a new weblog. You can replace this text with an introduction to your blog, or just delete it if you wish. To add an entry to the weblog, add a new page using the “Pages” button in the toolbar. For more information on blogging with Sandvox, please have a look through our help guide.
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)
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.
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.
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.
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.
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.
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.
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!
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.
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.
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.
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.
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.
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!