4- discovery leads part I

Question 1

what are the five different methods to identify leads?

Answer 1

high throughput screening, rational drug design, natural products, combinatorial chemistry, de-novo design

Question 2

what are the most common to least common methods of identifying leads?

Answer 2

• high throughput screening
• rational drug design
• natural products
• combinatorial chemistry
• de-novo design

Question 3

what is high throughput screening? what kind of assay is needed, and what happens?

Answer 3

thousands of compounds are tested for activity. requires biological assay that is easily automated. modern robots screen >200,000 compounds per week (compounds showing activity (hits) test more carefully)

Question 4

what are the 4 reasons it important to test a variety of compounds?

Answer 4

• no way to know which compounds will work
• lots of ways that drugs and biological molecules interact
• don’t want to just test versions of the same compound
• large variety of structures and chemical types

Question 5

what dose are HTS tested at?

Answer 5

typical 30 μM

Question 6

explain the four detailed steps of the HTS

Answer 6

• compounds are tested one-at-a-time
• biological assay (test) gives yes/no answer
• counter-screen used to sort false positives (want compounds that are specific → only active in one assay)
• good HTS generates approximately 500 hits

Question 7

how many hits are usually false in the HTS method? how come? list the 4 reasons why

Answer 7

> 99% are false. reasons: impurity, decomposition, compound reactivity (detergent, redox reaction, strong electrophile or nucleophile), interference with assay (hydrophobic, assay measurement, solubility).

Question 8

what are pan assay interference compounds?

Answer 8

promiscuous bioactive compounds (show activity in virtually any biological test)

Question 9

why do certain chemical structures react nonspecifically with PAINS? list four reasons

Answer 9

redox activity, strong acid/base, strong nucleophile/electrophile, highly lipophilic

Question 10

what are re-testing hits? what kind of concentration are they tested at?

Answer 10

re-test using purified samples (more accurate assay → recover from the compound, re-purify, re-synthesize). test at multiple concentrations (look for increase in reactivity with an increase in the concentration of the drug).

Question 11

what kind of a graph is shown for the re-testing hits?

Answer 11

sigmoidal graph (tells you that you have an equilibrium happening)

Question 12

what does it mean when a molecule tests positive in many assays?

Answer 12

it will have many side affects

Question 13

what is done for the confirmation of the structure? why is this done?

Answer 13

• spectroscopy and independent synthesis (determine the structure of the compound)
• many compounds in collections are very old (re-identify them)
• synthesize, purify, confirm structure and test
• test a series of compounds with related structures

Question 14

what is the purpose of testing a series of compounds with related structures?

Answer 14

to check that they all do what you want them to do BUT in a slightly different way

Question 15

how long does hit to lead take? what is the process in terms of hits and rejecting?

Answer 15

• takes 3 to 6 months
• > 500,000 compounds → 5000 hits (reject non-specific) → 500 hits (reject PAINS) → 300 hits (reject compounds that do not show dose-response) → 10 hits (reject compounds that mis-behave → 3 hits (reject compounds that do not show SAR → 1 hit

Question 16

what are some drugs developed by HTS?

Answer 16

Nevirapine, Gleevec, Quinolones

Question 17

what are patterns found in HTS discovered drugs?

Answer 17

tend to be aromatic compounds (relatively easy to work with), no stereocenters present (stereochemistry is very difficult to work with → cannot control them)

Question 18

what are natural products? in terms of metabolites?

Answer 18

chemicals not directly required for life, they are produced by the organism for secondary purpose

Question 19

what is done during the search for natural products? list 5 things

Answer 19

• collect large amount of a source organism
• isolate and purify substances showing biological activity
• determine chemical structure
• confirm biological activity
• may use info about biological source to narrow search

Question 20

what are some problems that arise from natural product leads? list three

Answer 20

• isolated from living things (logistic problem), often difficult to perform SAR (feasibilty problem, done in academic labs only

Question 21

what are three examples of natural product structures?

Answer 21

penicillin, taxol, digoxin

Question 22

what are the patterns in natural product leads? list 3

Answer 22

aliphatic (sp3), lots of stereocenters, large

Question 23

what is a requirement for natural products to be in industrial quantities?

Answer 23

the organism that the molecule is taken from must be producing it on a large scale

Question 24

explain the spongistatin example

Answer 24

found to be one of the most potent tumor-growth inhibitors ever discovered. attempt to isolate the compound was unsuccessful three times. went extinct → will never become available as a successful product.

Question 25

what is a rational drug design? what is it designed for, and what can it reduce?

Answer 25

design a lead using a known chemical structure (enzyme substrate, natural inhibitor, ligand for a biological receptor, existing drug) OR knowledge of the mechanism of action. designed for improved properties. can reduce the amount of trial and error.

Question 26

explain the example of captopril and snake venom

Answer 26

captopril is used to regulate blood pressure. snake venom has an effect of lowering the blood pressure of its bite victims. designed captopril based on the part of the snake venom molecule that regulates blood pressure.

Question 27

explain the example of acyclovir and guanine?

Answer 27

acyclovir is used to treat herpes virus infections. acyclovir is constituted from a part of the guanine molecule (eliminated a sugar part of the guanine). used information of how guanine works with respect to the lifecycle of the herpes virus

Question 28

what are three examples of rationally designed drugs?

Answer 28

Captopril, Acyclovir, Indinavir

Question 29

what are two features of rationally designed drugs?

Answer 29

aromatic or aliphatic, limited stereochemistry present