WK4- Modern Chemotherapy - ribs & nibs

What does PARP stand for?

Poly(ADP-ribose) polymerase – an enzyme that repairs single-strand DNA breaks.

What type of DNA damage does PARP repair?

Single-strand breaks (via base excision repair, BER).

What type of DNA damage do BRCA1 and BRCA2 repair?

Double-strand breaks (via homologous recombination).

What is synthetic lethality?

Two non-lethal events together cause cell death. BRCA mutation + PARP inhibition = cancer cell death.

Why are PARP inhibitors effective in BRCA-mutant cancers?

BRCA-mutant cells cannot repair double-strand breaks. PARP inhibitors cause single-strand breaks to become double-strand breaks. The cancer cell dies (synthetic lethality). Normal cells have working BRCA and survive.

What is the first PARP inhibitor licensed in Europe?

Olaparib – for BRCA-mutant ovarian, fallopian tube, and peritoneal cancer.

What happens when PARP is inhibited (Slide 7 diagram)?

Single-strand breaks collapse into double-strand breaks during replication. Without functional BRCA, the cell cannot repair them and dies.

What is the Philadelphia chromosome?

A translocation between chromosome 9 and 22 (t(9;22)) that creates the BCR-ABL fusion gene.

What cancer is associated with the Philadelphia chromosome?

Chronic Myelogenous Leukaemia (CML).

What is the BCR-ABL fusion protein?

A tyrosine kinase that is constitutively active (always ON). It constantly sends growth signals, causing uncontrolled proliferation of white blood cells.

What drug targets BCR-ABL?

Imatinib (Gleevec/Glivec) – a tyrosine kinase inhibitor.

Why did scientists originally think kinases were poor drug targets?

All kinases have a similar ATP-binding site, and there are over 500 kinases in the body. Selectivity was thought to be impossible.

How did Imatinib achieve selectivity?

It binds to the inactive conformation of BCR-ABL, not just the ATP-binding site common to all kinases.

What is the BRAF V600E mutation?

A point mutation (T to A at nucleotide 1799) changing valine (V) to glutamic acid (E) at position 600 of BRAF. Found in many melanomas.

How does BRAF V600E cause cancer?

The mutation makes BRAF constitutively active (always ON). It sends constant growth signals without needing upstream activation (Ras). This leads to uncontrolled proliferation of melanocytes (melanoma).

What drug targets BRAF V600E?

Vemurafenib – a selective BRAF inhibitor.

What interaction does vemurafenib make with glutamic acid (E) that it cannot make with valine (V)?

Glutamic acid has a negatively charged carboxylic acid side chain (COO⁻). It forms ionic and H-bond interactions with vemurafenib. Valine is hydrophobic – no ionic or H-bond interactions.

Why does vemurafenib not work on BRAF V600K?

V600K changes valine to lysine (K). Lysine has a positively charged bulky side chain (NH₃⁺) that either physically blocks vemurafenib (steric clash) or repels it (charge repulsion).

What drug works on both BRAF V600E and BRAF V600K?

Dabrafenib – it has a different chemical structure that fits around the lysine side chain.

What are two common resistance mechanisms to tyrosine kinase inhibitors?

1) Upregulation of other growth-related tyrosine kinases (bypass pathway). 2) Site mutations in the binding site of the target kinase (prevents drug binding).

What are the 4 types of drug-protein interactions?

1) Hydrophobic (water-hating groups stick together), 2) Pi-stacking (flat rings stack), 3) Hydrogen bonding (H sticks to O or N), 4) Ionic (positive and negative attract).

What functional groups on a drug do hydrophobic interactions?

Alkyl groups (CH₃, CH₂, CH), aromatic rings, CF₃ (trifluoromethyl), alkynes (C≡C), alkenes (C=C), halogens (F, Cl, Br, I).

What functional groups on a drug do pi-stacking interactions?

Aromatic rings (benzene, pyridine, etc.) – flat rings stack on each other.

What functional groups on a drug do hydrogen bonding?

NH (amines, amides, pyrrole), OH (alcohols), C=O (amides, ketones, aldehydes), N (pyridine, nitriles). NH and OH are H-bond donors. C=O and N lone pairs are H-bond acceptors.

What functional groups on a drug do ionic interactions?

Protonated amines (NH₃⁺ – positive charge) and deprotonated carboxylic acids (COO⁻ – negative charge). At pH 7.4, amines are often protonated, carboxylic acids are deprotonated.

What is the difference between valine (V) and glutamic acid (E) side chains?

Valine = hydrophobic alkyl (CH(CH₃)₂). Glutamic acid = negatively charged carboxylic acid (CH₂-CH₂-COO⁻).

What is the difference between valine (V) and lysine (K) side chains?

Valine = hydrophobic alkyl (CH(CH₃)₂). Lysine = positively charged amine (CH₂-CH₂-CH₂-CH₂-NH₃⁺).

What are the 8 functional groups in ponatinib?

Tertiary amines, pyridine nitrogens (2), pyrrole nitrogen, alkyne, amide, aromatic rings, alkyl substituents, trifluoromethyl (CF₃).

Complete the sentence: "Glutamic acid has a ___________ side chain that forms ionic and H-bond interactions with vemurafenib."

negatively charged (COO⁻)

Complete the sentence: "Valine has a ___________ side chain that cannot form ionic or H-bond interactions."

hydrophobic

Complete the sentence: "Lysine has a ___________ side chain that blocks vemurafenib binding due to steric clash or charge repulsion."

positively charged (NH₃⁺)

What is the difference between vemurafenib and dabrafenib?

Vemurafenib only works on BRAF V600E. Dabrafenib works on both BRAF V600E and V600K.

What is the T315I mutation?

A common resistance mutation in BCR-ABL (gatekeeper mutation). Threonine (T) to isoleucine (I) blocks imatinib binding.

What other cancer is imatinib used for besides CML?

Gastrointestinal Stromal Tumours (GIST) – driven by c-KIT mutation.