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| This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439. |
Fibroblast Growth Factor Receptor/Ponatinib (4uxq) [1]
by Julie Boshar, Emily Boyle, Nicole Kirby, Cory Thomas, Connor Walsh
Student Projects for UMass Chemistry 423 Spring 2016
IntroductionPotatinib was developed as a treatment option for chronic myeloid leukemia (CML) as other inhibitors in treatment have become ineffective. BCR-ABL is a kinase with a cancerous genetic mutation in chromosome 22 that leaves it always active. Further mutations in BCR-ABL have left earlier drugs that inhibit tyrosine kinases unable to bind in almost 30% of cases after five years of treatment. The newer, mutant BCR-ABL kinase’s ability to develop new resistances has pushed for newer developments in inhibitors, such as Potatinib[2]. Fibroblast growth factor (FGFR) signaling is the factor that normally activates the BCR-ABL kinase. Also, it is the protein behind both tissue development and repair, the disruption of FGFR leads to tumor growth. The activation of BCR-ABL happens through a series of cascading signals that induce proliferation and migration in cells. Mutations in the regulation of the FGFR tyrosine kinases can be diresctly correlated to malignant tumor growth[1]. The tyrosine kinase inhibitor Ponatinib has been used to to the mutant version of kinase BCR-ABL by the enzyme's specific "DFG-out" conformation (in turquoise). This conformation has the phenylalanine group of BCR-ABL flipped out of its hydrophobic binding site. Ponatinib is the first of its kind to be able to inhibit this specific mutation in BCR-ABL of the "DGF-out" conformation[2]. Ponatinib's harmful side effects have caused it to fall under scrutiny from the U.S. Food and Drug Administration (FDA). It has shown to increase chances of deadly blood clotting and restenosis in both arteries and veins with a rate of about 1 in 5 patients. The drug has also shown to increase risk of heart attack and overall worsening of heart disease in patients[2].
Overall StructureIn terms of , FGFR in complex with Ponatinib consists of two domains, which is the characteristic structure exhibited by kinases. The N-terminal domain is the smaller of the two, and it contains a five-stranded beta sheet and an alpha carbon helix. The larger C-terminal domain is primarily alpha helical in structure. The alpha helices are shown in fuchsia and the beta strands are shown in orange. A hinge links the two regions. A network of hydrogen-bonds between three conserved residues – Glu551, Asn535, and Lys627 – exists in the hinge region. This hydrogen-bonding controls the kinase activity of FGFR. In its active form, FGFR is dimerized and contains two activated intracellular substrates. The binding of a coreceptor, β-Klotho, stabilizes the activated complex. A DFG moiety is found in BCR-ABL, the conformation of which plays a key role in binding Ponatinib. Another defining feature of active FGFR is its . Four residues in the spine – Leu536, Met524, His610, and Phe631 (in orange) – are highly conserved. A gatekeeper residue is present at the beginning of the hinge, and interactions among the four hydrophobic spine residues link the gatekeeper to Tyr643 in the activation loop. This activation loop is glycine-rich and found in the kinase domain of FGFR[1]. The structure of Ponatinib is shown as follows:
Binding InteractionsKinases are the largest drug targets being tested. All kinases possess a biolobal fold that connects the N and C termini by a “hinge” that binds ATP. “Gatekeepers” are other residues that are in the hinge and alter binding capabilities. Mutations to gatekeepers are critical considerations in drug development because they can result in drug resistances[3]. Ponatinib can bind even in the presence of gatekeeper mutations, like T315I which accounts for 15-20% of all clinically observed mutations and is resistant to all previous generation drugs[4]. This class of inhibitors can bind deep within the hydrophobic and allosteric pocket that is only accessible in the conformation (see color chart) which consists of Asp630, Phe631, and Glu632[3].
Ponatinib binds to the ATP binding pocket between the N and C lobes to shift from the DFG-in to the DFG-out conformation. It spans from the (cyan) to the front catalytic pocket. Three sites are engaged in the ATP binding cleft by ponatinib’s aromatic rings. First, imidazo[1,2b]pyridazine occupies the same space as the adenine ring of ATP and forms a with the amide nitrogen atom of Ala553 (magenta) in the hinge[2]. Multiple triple bonds help the rest of ponatinib to move further in to the ATP binding pocket. Second, the methylphenyl group displaces the side chain of Lys503 and its aromatic ring binds to the hydrophobic pocket that is formed by Val550 (the in yellow), and Met524. This allows Glu520 to hydrogen bond with the amide linkage between the aromatic rings in ponatinib. Third, Phe631 is replaced by ponatinib’s 3-trifluoromethylphenyl group. Asp630 becomes available for hydrogen bonding with the amide linkage between ponatinib’s aromatic rings and lets the piperazine ring hydrogen bond with the catalytic loop which forms the DFG-out conformation[2]. Additional FeaturesPonatinib is an orally ingested tyrosine kinase inhibitor that has revealed successful avenues of treatment for counteracting the effects of angiogenesis in tumor growth. Besides the inhibition of FGFRs, this agent inhibits tyrosine kinases involved in vascular endothelial growth factor receptors. Ponatinib is considered a third generation TKI that can treat even the most drug-therapy resistant mutations that previous TKIs were incapable of treating[5]. The brand name for ponatinib is Iclusig. Iclusig received an accelerated approval grant through the Food and Drug Administration. It was mainly prescribed to patients suffering from Chronic Myeloid Leukemia or Acute Lymphoblastic Leukemia who did not make any progress with the first and second generation TKIs. However, the clinical trials data displayed a spike in adverse effects. These consequences include heart failure, stroke, coronary artery disease, loss of blood flow to body parts leading to amputation amongst other narrowing of blood vessels[6]. FGFR-4 is abundantly present in human prostate cancer observed in vitro and in mouse model simulations[7]. A of FGFR-4 with Arg388 replacing Gly388 is implicated with increased human prostate cancer. This variation causes increased receptor stability and activation[8]. A study revealed that the of FGFR-4 signaling completely curtailed prostate cancer cell lines that were responsible for tumor growth[7]. Due to the significant results of diminished cell growth in treated tumors, targeting fibroblast growth factor signaling appears to provide a promising step towards combating aggressive prostate cancer.
Quiz Question 1Ponatinib is unique in it's ability to bind to the mutated BCR-ABL because of it's preference to shift to the DFG-out conformation. In theory, if a competitive inhibitor was created by nature to prevent Ponatinib from binding to BCR-ABL to further its drug resistance, what specific structural characteristics would the inhibitor need to possess? Consider the unique binding methods of Ponatinib and the conformation. a. Small, fully conjugated aromatic system with no electronegative substituents, to prevent unwanted hydrogen bonding. b. Multiple ring system, one ring particularly for hydrogen bonding and another capable of binding in a hydrophobic pocket. c. Polymer chain with an ester linkage and a hydroxyl end group . d. Metal center that binds four large, nonpolar hydrocarbon ligands that exhibit significant steric hindrance. See AlsoCreditsIntroduction - Emily & Cory* Overall Structure - Nicole* & Connor Drug Binding Site - Julie* & Cory Additional Features - Connor* & Nicole Quiz Question 1 - Julie & Emily* References
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