26 Jun What will be your strategy to search for the lead small
Question
Apr. 30, 2014 Name__________________________________
Due: Friday, May 6
1. Choose questions to get total of 24 points
2. No examples, please, think about the answers that would be applicable to any related processes and small/macromolecules interactions.
#1. 6 points total
A new macromolecule was identified that seems to be common in patients having a certain type of tumors, and you are searching for an inhibitor. The functions and structure of the macromolecule are unknown and you do not have time/resources to investigate them
1.1. What will be your strategy to search for the lead small molecule inhibitor? – 2 points
1.2. What are some of the advantages (name at least 3) and disadvantages (name at least 3) of the approach you suggested to use in 1.1.? – 4 points
(Be brief but specific in your answers, please)
#2. 4 points
You have solved a crystal structure of your target membrane receptor and plan to use computer-aided drug design methods to search for a small molecule inhibitor binding to the receptor. What could be the problems of this approach leading to discovery of the molecules that fail in further studies? (please, list the problems using the bullet points providing only minimum necessarily explanation)
#3. 4 points
Computer-aided drug discovery approaches utilize information about steric, electronic, hydrophobic, and H-bonding effects. What is the importance of each of these effects in rational drug design? (Please provide separate answers and list as many factors as you can. Be brief, no full sentences are needed, and do not copy or try to rephrase the definitions from the class material!):
· Steric
· Electronic
· Hydrophobic
· H-bonding
#4. 6 points
For what purposes would someone consider designing a small molecule enzyme inhibitor? (Not more than 3 short but meaningful sentences, please. Saying that “enzymes are important are they are everywhere” is not enough. Be specific and think about the best answer for this question, no examples, please).
# 5. 4 points
Working with a particular harmful microorganism, you recently identified a protein (e.g. an enzyme) and think it may become an important drug design target. However, the protein was also found in mammals. How would you proceed with an inhibitor search for this enzyme? (Not more than 3 short but meaningful sentences, please. Removing this protein from the target list is not an option).
# 6. 2 points
In your design of a DNA intercalating drug, what would be the structural features needed to be incorporated into the molecule? (A brief answer, please, only talk about the structural details)
#7. 4 points
You designed and marketed a DNA alkylating agent, which was soon found to lead to cancer cell resistance. The mechanism of the resistance included formation of a new enzyme effectively repairing the modified DNA. How would you deal with this problem? (This is a scientific but not commercial question, please be brief and specifically talk about a scientific solution only).
# 8. (4 points)
In mid-20th century, electric engineers faced a problem called a “tyranny of data”. Are we facing it right now in drug development field? If so, are there any ways to deal with this problem? (Feel free to write as much as you want but be field-specific.)
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