3. modern chemotherapy -protein-protein interactions

what are protein-protein interactions

the interaction of 2 proteins at their domain interfaces that regulates the function of protein complex

what are 6 potential problems with using protein-protein interactions

1. affinity acheived from the accumulation of numerous weak interactions

2. small molecule compared to protein

3. protein surfaces often flat & featureless

4. buried surface

5. hydrophobic nature results in drug that large and hydrophobic - can’t cross BBB

6. PPPis invlove large S.A - hard to design

what is the Bcl-2 family

• B-cell lymphoma 2 family

• key regulators in cell apoptosis

• some members are pro-survival (Bcl-2, Bcl-x, MCl-1P

• some members are pro-death (BAX, BID, BIM, BAD)

what happens with the Bcl-2 family members in cancer

• over-expression of pro-survival proteins

• prevents pro-death proteins from triggering caspase activation therefore prevents apoptosis

what is the overall aim of targeting the bcl-2 family in cancer

use a small molecule to bind to and inhibit the pro-survival protein therefore restoring apoptosis pathway how

how would we target the BCL-2 family (what technique, binding site)

3D NMR studies reveal the presence of hydrophobic groove on anti-apoptotic pathway

binding site to the a-helicall peptide of pro-apoptotic members w

what are the 3 types of fragment elaboration technique

1. Elaboration of HTS hit

2. fragment growing

3. fragment linking

4 features of fragment based drug discovery

• screen low affinity fragments at high concentrations

• uses structural information to determine bindin mode

• less synthetic steps

• quick SAR

What is ABT-377

• Discovered through high throughput NMR based screen & parallel synthesis

• aims to identify small molecules that bind to the hydrophobic grrow of Bcl-2

how does the structure of ABL-377 enable it to bind to the bidnign site

• has a polar group in solvent exposed areas - aids water solubitiy

• has a long side chain of chloro-biphenyl group- hydrophobic space

what are the effects of a loss or mutation in P53 protein

• accumulation of cancer promoting mutations

• uncontrolled proliferation

• apoptosis evasion

• neoangiogenesis

• DNA instability

how does MDM2 block P53

1. Direct Binding and Inhibition:

   • interferes with the interaction of p53 with transcriptional co-activators and RNA polymerase, inhibiting p53-mediated gene expression.

2. Ubiquitination and Degradation:

   • MDM2 has E3 ubiquitin ligase activity, which allows it to ubiquitinate p53.

   • Ubiquitinated p53 is targeted for degradation by the proteasome, leading to decreased levels of p53 protein in the cell.

3. Nuclear Export:

   • MDM2 can shuttle p53 out of the nucleus into the cytoplasm, where p53 is more susceptible to degradation by the proteasome, further reducing its transcriptional activity.

   • Phosphorylation of MDM2 or p53 at specific sites can disrupt their binding, leading to activation of p53 and induction of its target genes.

How does P53 bind to MDM2

• Binding site on MDM2; deep, hydrophobic groove

• P53 binds in a-helical manner

• P53 forms 3 critical contacts through the side chains of Phe19, Try23, Leu26

what s the role of the nutrlins

• mimics the interaction of p53

• displaces P53 from MDM2 w. nanomoleculer affinity

• cis-imidizolines

how does the cis-imidazoline interact with P53

• one bromophenyl group sits deeply in the Try23 pocket, other occupies Leu26

• Ethyl ether side chain is directed towards Phe19

• scaffold replaes the helical backbone on P53 projecting the groups into correct pockets