Saturday, October 19, 2013

How does ARIAD's Ponatinib (Iclusig) Work

Mechanism of Action Series: Ponatinib

Ariad Pharmaceuticals' leukemia drug ponatinib has been in the news lately for major toxicity fears that can potentially derail its further clinical development. While these issues will be sorted out in coming months, it's a good time to review how does this drug work.

Ponatinib is a pan-inhibitor of native and T315I mutant forms of BCR-ABL kinase.

Philadelphia chromosome and BCR-ABL kinase

BCR-ABL kinase is a fusion product of BCR and ABL genes. In a subtype of chronic myeloid leukemia (CML) called Philadelphia chromosome-positive (Ph+) CML, chromosomal tranlocation t(9;22) results in a part of chromosome 22 containing the BCR gene at the breakpoint to fuse with a part of chromosome 9 with the ABL kinase gene. This hybrid chromosome is called Philadelphia chromosome, which now has the oncogenic BSR-ABL kinase gene.

(Image source: National Cancer Institute, NIH. [link])

Native and imatinib-resistant forms of BCR-ABL kinase

Imatinib (Gleevec; STI571 [Novartis]), the recommended first-line therapy for Ph+ CML, is a strong and effective inhibitor of BCR-ABL kinase. Imatinib blocks the binding of ATP to the kinase active site preventing phosphorylation of substrate molecules, and thus blocking the signaling cascade.

(Source: Frontiers in Bioscience. 2006, Jan 1;11:209-220 [link])

However, eventually imatinib-resistant forms of BCR-ABL emerge and patients relapse. These mutations in the ABL kinase domain affect imatinib binding to BCR-ABL protein.

Recently, second generation BCR-ABL kinase inhibitors have been approved by the FDA that work against imatinib-resitant BCR-ABL. These new drugs are nilotinib (Tasigna; AMN107, [Novartis]) and dasatinib (Sprycel; BMS-354825 [Bristol-Myers Squibb]).

While several mutations within the ABL binding site are known to interfere with the binding of these 3 drugs, one in particular called T315I is the most critical.

T315I gatekeeper mutation

The threonine amino acid at position 315 of BCR-ABL is also called "gatekeeper residue" as it forms hydrogen bond with these 3 kinase inhibitors and position the hydrophobic face of the inhibitor to the hydrophobic pocket of kinase located near T315. 

Mutation of this threonine to isoleucine (T315I) makes the BCR-ABL kinase resistant to all 3 kinase inhibitors by (1) being unable to hydrogen-bond, and (2) the bulky side-chain of isoleucine interferes with access of drug to the hydrophobic pocket.

(Imatinib and dasatinb in the ATP binding region of ABL kinase. 
Note: T315I [top in yellow] interfering with the fitting of these 
drugs in the binding region, [link])

The BCR-ABL gatekeeper mutation occurs in 15-20% of all imatinib-resistant BCR-ABL mutants. This mutant is also resistant to nilotinib and dasatinib.

How was ponatinib designed

ARIAD screened for compounds that satisfied two requirements: (1) the compound should tolerate the presence of isoleucine gatekeeper, and (2) it should maintain access and interaction with the hydrophobic pocket. 

The choice of a linear carbon-carbon triple bond (ie, ethylene bond) satisfied requirement #1. Thuis carbon-carbon bond is shown as "linker 1" in the image below. Rest of the structure was screened from the library.

(The carbon-carbon triple bond is indicated above as"Linker 1." A ring fits 
into the hydrophobic pocket. Source: Chem Biol Drug Des 2011; 77: 1–11)

How is ponatinib different from imatinib/nilotinib/dasatinib

The key structural feature of ponatinib is the linear carbon-carbon triple bond that allows the drug to skirt (or ignore) the presence of isoleucine amino acid (T315I) and fit past the bulky side-chain of isoleucine into the kinase hydrophobic pocket.

(Note: the isoleucine sidechain 315 (green spur on top left) lies adjacent to the stiff 
carbon-carbon triple bond of ponatinib, but is unable to displace the drug out of 
the kinase binding region. Source: Chem Biol Drug Des 2011; 77: 1–11.)

Ponatinib has very strong binding affinity for native or T315I BCR-ABL proteins: the IC50 is in low nM range. It inhibits Ba-F3 derived cell lines in vitro and increases survival of mice injected with Ba-F3 cells expressing BCR-ABL (T315I) forms. 

Ponatinib is a multikinase inhibitor

In addition to BCR-ABL, ponatinib also inhibits VEGFR and FGFR family of kinases. Both of these kinase families have valine amino acid as gatekeeper mutation. Similar to the mechanism in BCR-ABL, the stiff carbon-carbon triple bond interacts with valine gatekeeper residue, and allows the drug to bind and fit into the ATP-binding pockets of these kinases too.

Ponatinib also inhibits FLT3 kinase, thus it also has the potential to target FLT3-ITD driven acute myeloid leukemias.

  • Huang WS, Metcalf CA, Sundaramoorthi R, Wang Y, Zou D, Thomas RM, Zhu X, Cai L, Wen D, Liu S, Romero J, Qi J, Chen I, Banda G, Lentini SP, Das S, Xu Q, Keats J, Wang F, Wardwell S, Ning Y, Snodgrass JT, Broudy MI, Russian K, Zhou T, Commodore L, Narasimha (2010). Discovery of 3-[2-(imidazo[1,2-b]pyridazin-3-yl)ethynyl]-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide (AP24534), a potent, orally active pan-inhibitor of breakpoint cluster region-abelson (BCR-ABL) kinase including th J Med Chem, 53 (12), 4701-4719 DOI: 10.1021/jm100395q 

  • Dolgin E (2013). As leukemia options grow, drugs jockey to be first-line therapies. Nature medicine, 19 (1) PMID: 23295994 

  • Zhou T, Commodore L, Huang WS, Wang Y, Thomas M, Keats J, Xu Q, Rivera VM, Shakespeare WC, Clackson T, Dalgarno DC, & Zhu X (2011). Structural mechanism of the Pan-BCR-ABL inhibitor ponatinib (AP24534): lessons for overcoming kinase inhibitor resistance. Chemical biology & drug design, 77 (1), 1-11 PMID: 21118377 

  • O'Hare T, Shakespeare WC, Zhu X, Eide CA, Rivera VM, Wang F, Adrian LT, Zhou T, Huang WS, Xu Q, Metcalf CA 3rd, Tyner JW, Loriaux MM, Corbin AS, Wardwell S, Ning Y, Keats JA, Wang Y, Sundaramoorthi R, Thomas M, Zhou D, Snodgrass J, Commodore L, Sawyer TK, Dalgarno DC, Deininger MW, Druker BJ, & Clackson T (2009). AP24534, a pan-BCR-ABL inhibitor for chronic myeloid leukemia, potently inhibits the T315I mutant and overcomes mutation-based resistance. Cancer cell, 16 (5), 401-12 PMID: 19878872 

  • Gozgit JM, Wong MJ, Wardwell S, Tyner JW, Loriaux MM, Mohemmad QK, Narasimhan NI, Shakespeare WC, Wang F, Druker BJ, Clackson T, & Rivera VM (2011). Potent activity of ponatinib (AP24534) in models of FLT3-driven acute myeloid leukemia and other hematologic malignancies. Molecular cancer therapeutics, 10 (6), 1028-35 PMID: 21482694

Related Posts:
HiJAKing the JAKs in myeloproliferative disorders. February 25, 2011.


  1. A carbon-carbon triple bond could be described as 'an ethyne bond' but certainly not as 'an ethylene bond' which would be a carbon-carbon double bond. BKW