24 - penicillin design i

Question 1

what is the functional part of the penicillin

Answer 1

• in the center of the molecule with the NO-square (b-lactam, functional part of the drug)
  
  • the rest of the drug helps the b-lactam get into the active site

Question 2

describe the mechanism and structure of the penicillin and how it compares to the normal peptide substrate

Answer 2

• the normal peptide substrate: the bond between the D-ala-d-ala is the one that is cut by the enzyme
  
  • carboxylate needs to have a negative charge into order for the substrate to bind into the pocket of transpeptidase
  • need to have 2 methyls attached to the backbone with a D configuration
  • d-aminopamilac acid + d-gluatomic acid = filler acid on the peptide strand
  • network of h-bond donors and acceptors that interact with the corresponding pieces on the enzyme
    
    • these all have a specific spacing and orientation which is determined by the d configuration of the alanine’s at the end
  • if we line up the bond that gets cut in penicilin and the bond that gets cut on the normal substrate, you see the parts of them line up with each other
    
    • carboxylate (both negatively charged at physiological pH)
    • core structure with methyl’s, h-bond donors, electrons
    • both have similar stereochemistry in their core
    • on the end of the penicillin, there is a non-polar side chain which mimics the non-polar chains you see on the normal substrate of the enzyme (the penicillin side chain is able to fill the pocket in the same way)
    • overall shape and network of intramolecular interactions present in penicillin makes it look like d-ala-d-ala that the enzyme usually accepts

Question 3

what is b-lactam carbonyl and why is it easy to break

Answer 3

• in b-lactam it is easy to break the amide bond because the amide is in a four membered ring
  
  • this creates ring strain which raises the energy of the functional group
  • also contribute to reactivity
  • by adding H2O, you can easily break open the ring

Question 4

what is penicillin G

Answer 4

• Isolated from mold

- Natural form

Question 5

what are the 4 significant limitations of penicillin G as a drug

Answer 5

• Acid sensitivity (very sensitive and if pH is too low, the drug wont work)
• Resistance (certain bacteria can be killed by it and others are resistant)
• Spectrum of action (two major families of bacteria, and penicillin only works on one family)
• Bioavailability (difficult to get the penicillin in in large amounts)

Question 6

why is acid sensitivity a limitation of penicillin g

Answer 6

• Stomach environment is very acid
• Drug must be given by i.v. injection
  
  • impossible to make a pill form
  • need to know why it is so sensitive to acid
• end up without a b-lactam → in presence of acid, penicillin is destroyed and cannot inhibit transpeptidase

Question 7

what is the goal for engineering acid resistance

Answer 7

if there is a way to make it less nucleophilic, the second reaction wont be able to happen. the O will just get protonated then deprotonated

Question 8

explain how heteroatoms contribute to acid resistance

Answer 8

• first strategy is to add a heteroatom
• add it between the aromatic ring and the CH2 group between the carbonyl
• use something like O or N, which or electronegative.
  
  • it will pull electrons away from the carbonyl = makes it less powerful
• b-lactam will still get protonated but no reaction will happen because the carbonyl is no longer a good Nu

Question 9

explain how charge contributes to acid resistance

Answer 9

• add a group that is going to put a charge on the side chain
• if you add a NH2 , it will act as a EWG
• any pH < 11, the NH2 is going to become NH3+ = super EWG
• the + N will draw the electrons out of the carbonyl = less nucleophilic

Question 10

what is semi-synthesis with respect to penicillin

Answer 10

• Penicillin “core” is very complex and difficult to synthesize
• Strategy
  
  • obtain the core from biological sources
  • use synthetic transformation to prepare new drug

Question 11

how is 6-apa made from penicillin G

Answer 11

• Grow penicillin mold
• Extract Penicillin G from mold, then purified and extracted
• Use amidase enzyme from E. coli to remove side chain
  
  • Modern versions have been optimized by genetic modification
• World-wide production over 20, 000 tons per year
• genetic engineering will just create the 6-apa for you