Discussion

OLCC S52 | Fri, 02/03/2017 - 08:46

Hi everybody, my name is Matea. I am currently in a 7 year dual degree program at St. Louis College of Pharmacy. I will be finishing my Bachelors degree in Health Science and continuing to work on my Doctorate of Pharmacy. I am hoping to get anything and everything out of this course. I hope to one day be able to use the information learned now into being able to have my own input in drug discovery in the future to prevent some undesirable effects in drugs that occur all through technology. A quote that stood out to me in "in Silico Medicinal Chemistry" book was "without careful thought and experimental design with appropriate controls, we will only find the wrong answers faster and still waste a great deal of time in physical experiments based on inappropriate predictions made using computation methods". This quote explains exactly what I am trying to do for our future, improve efficiently the methods of drug discovery.

I look forward to connecting with everyone on here!

OLCC S199 | Fri, 02/03/2017 - 07:55

Hello everyone. My name is Sooyah. I am an undergraduate student at the university of Arkansas at Little Rock, majoring in biology and minoring in Chemistry. I plan on furthering my career in pharmaceutical science, and look forward to learning more about cheminfomatics.

Nathan Brown's picture
Nathan Brown | Fri, 02/03/2017 - 06:12

Hi All, I'm Nathan Brown a Group Leader at The Institute of Cancer Research in London, UK. I've been involved in Chemoinformatics since 1999 when I started my PhD with Prof. Peter Willett in Sheffield. I currently run a research group at the ICR where we actively contribute to academic drug discovery programmes - a recent example is a drug I helped design using multiobjective de novo design methods I developed that has now entered two Phase I clinical trials.

I am a computer scientist by training, but switched to chemical information and chemoinformatics during my PhD. I have conducted research in academia (Sheffield, Erlangen-Nuremberg, ICR), biotech (Avantium Technologies, Amsterdam), and big pharma (Eli Lilly, and Novartis, Basel) during my career. In 2015 I published a new text book on Chemoinformatics methods, which I have shared with the course members at the bottom of this page.

My research interests are wide and varied. While I am now actively involved in around ten ongoing drug discovery projects, my original interests in the field were in algorithm development and implementing new methods. My coding is a little rusty now, but I still like to think I am a programmer, in my head at least.

If you want to find our more information about me and my research, please follow the links below. I am also quite active on Twitter, tweeting about our science and a number of other interests.

Personal Homepage: https://sites.google.com/site/nathanbroon/
ICR Homepage: http://www.icr.ac.uk/our-research/researchers-and-teams/dr-nathan-brown
Google Scholar: https://scholar.google.co.uk/citations?user=N0-4IgoAAAAJ&hl=en
Twitter: https://twitter.com/nathanbroon

Best wishes, Nath

Sunghwan Kim | Thu, 02/02/2017 - 22:24

Hi, all.

If you are not sure what to do for your projects or if you want to find one on your own, please visit the government's open data site (https://www.data.gov) to see what kind of information is publicly available on the web.

https://www.data.gov

This site has data sets generated by the federal, state, and local governments, many of which are related to chemicals in some way or another, in many different areas (including food & drug safety, environmental health, atmospheric science and so on). You can search this site using a simple text query like "chemicals", "drugs", "pesticides", and other chemistry related keywords. I hope that you can find some interesting data set or sets that you want to analyze for your projects. Even if you don't find any data set for your projects, you will realize that taxpayers' money has been used to generate a gazillion amount of data that reflects various aspects of our life, but that many people are not aware of the existence of these data in the public domain.

By the way, I think these two sites may interest you too.

https://www.healthdata.gov/
https://www.digitalgov.gov/

I hope you find them interesting.

Best,

Sunghwan,

OLCC S51 | Thu, 02/02/2017 - 20:16

Hello everyone! My name is Jeremy. I am currently in a 7 year dual degree program at St. Louis College of Pharmacy! I am finishing up my Bachelors degree in Health Science and progressing into working on my Doctorate of Pharmacy. I was originally interested in taking this course due to my love of computers and technology. I am hoping to simply learn about anything I can, and maybe eventually be able to incorporate that in my future career with my knowledge of pharmacy in some manner. I know that is somewhat broad in terms of what I hope to learn; however, I am mostly excited about data analysis. Especially when it involves drug design or designing specific molecules.

OLCC S51 | Thu, 02/02/2017 - 20:16

Hello everyone! My name is Jeremy. I am currently in a 7 year dual degree program at St. Louis College of Pharmacy! I am finishing up my Bachelors degree in Health Science and progressing into working on my Doctorate of Pharmacy. I was originally interested in taking this course due to my love of computers and technology. I am hoping to simply learn about anything I can, and maybe eventually be able to incorporate that in my future career with my knowledge of pharmacy in some manner. I know that is somewhat broad in terms of what I hope to learn; however, I am mostly excited about data analysis. Especially when it involves drug design or designing specific molecules.

Bob Hanson's picture
Bob Hanson | Thu, 02/02/2017 - 18:34

ps. As I am not able to read all messages to this list, I just ask that if you have a question specific to Jmol, please contact me directly at hansonr@stolaf.edu, not by leaving a message for me here. (I probably won't even see a reply to this message, actually...) Thanks! Looking forward to interacting! Looks like a great course.

Sunghwan Kim | Thu, 02/02/2017 - 17:58

If a drug gets a marketing authorization in Europe with orphan designation (meaning that it is approved for rare diseases), it will get a market exclusivity for 10 years (meaning that no "similar" drugs for the same indication cannot enter into the market). Please see this document for more details:

http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000392.jsp&mid=WC0b01ac058061f019

Therefore, the European Medical Agency, which is responsible for marketing authorization of medical products, requires the applicant of a new drug to submit a "similarity report", which compare the new drug with existing drugs in terms of molecular structure, mechanism of action, and indication. For more details, see Section 2.1 of this document:

http://ec.europa.eu/health//sites/health/files/files/orphanmp/doc/c_2008_4077_en.pdf

While the molecular structure similarity comparison is required for drug approval, molecular similarity is a very subjective concept, and no standard way to evaluate it.

For this reason, some papers have analyzed molecular similarity among approved drugs using several 2-D similarity methods:

http://jcheminf.springeropen.com/articles/10.1186/1758-2946-6-5
http://www.sciencedirect.com/science/article/pii/S1359644616304718

However, these studies evaluated molecular similarity using 2-D similarity methods, and if 3-D similarity methods are used, we will have some different insights on similarity assessment for EMA's orphan designations. This study will take the following steps:

(1) Get all approved orphan drugs from the European Medicines Agency
(2) Retrieve all known drugs from a public database (e.g., PubChem, DrugBank)
(3) Generate 3-D conformers for the drugs in (1) and (2)
(4) Compute 3-D similarity scores between the drugs, using the 3-D conformers generated in (3) and several 3-D similarity methods.
(5) Compute 2-D similarity scores between the drugs, using commonly used 2-D fingerprint methods.
(6) Identify drug-drug pairs with a low 2-D score but with a high 3-D score (meaning that the two drugs are similar in 3-D but not in 2-D).
(7) Identify drug-drug pairs with a high 2-D score but with a low 3-D score [that is, opposite to (6)].
(8) Discuss the difference between 2-D and 3-D similarity in recognizing molecular similarity.
(9) Discuss potential impacts of using 3-D similarity methods for EMA's similarity assessment for marketing authorization.
(10) Discuss how EMA's and FDA's regulations are different in terms of orphan drug marketing approval.

This project is quite straightforward, but would take more time than other projects, because 3-D similarity comparison takes longer than 2-D similarity comparison.

OLCC S197 | Thu, 02/02/2017 - 14:56

My name is chinenye from Nigeria .i am graduate student currently in chemistry department and i just joined the class not quite long .i have not heard of reaxys before until I joined this class. From the way things are going I think am enjoying the class and I am hoping to know more about reaxys database as time goes on.

Jennifer Muzyka | Thu, 02/02/2017 - 14:19

Hello Cheminformatics folk!
My name is Jennifer and I'm a faculty member at Centre College. I enjoyed participating in the fall 2015 course with a group of students. This time I have a few faculty/staff colleagues participating in these discussions. I look forward to learning more about retrieval of chemical information. I'm especially interested in seeing the projects that will develop as a result of this class.
Jennifer