Sandbox Reserved 425

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[[Student Projects for UMass Chemistry 423 Spring 2016]]
[[Student Projects for UMass Chemistry 423 Spring 2016]]
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<StructureSection load='4uxq' size='350' side='right' caption='FGFR in complex with Ponatinib is a highly effective inhibitory treatment for CML ([[4uxq]])' scene=''>
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<StructureSection load='4uxq' size='350' side='right' caption='The Ponatinib-FGFR complex is highly effective for treating CML ([[4uxq]])' scene=''>
==Introduction==
==Introduction==
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==Binding Interactions==
==Binding Interactions==
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Kinases are the largest drug targets currently being tested in clinical trials. All kinases possess a biolobal fold that is a smaller N-terminal and a larger C-terminal lobe joined together by a “hinge.” The cofactor ATP binds deeply into a pocket between the lobes and binds to the hinge region. The imposition of any other residue in this ATP-binding pocket controls access to the hydrophobic pocket by separating the adenine binding site from an adjacent hydrophobic pocket. Such residues are termed “gatekeepers,” and are critical considerations in the development of drugs to treat CML because of the mutations that these residues can ensue. Gatekeeper mutations that convert a small hydrophilic residue into a large hydrophobic residue are one example of what has been shown to result in drug resistance, specifically to the most well-known ABL inhibitors like imatinib (Gleevec)<ref name="four">PMID: 25317566</ref>. Ponatinib is a third generation type II pan-BCR-ABL kinase inhibitor, which allows it to bind even with the presence of gatekeeper mutations<ref name="five">PMID: 25219510</ref>. Type II inhibitors are classified by binding to the hydrophobic and allosteric pocket that is only accessible in the DFG-out conformation and that is next to the ATP binding pocket. Additionally, type II inhibitors extend deep into the adenine pocket and hydrogen bond with the hinge region<ref name="four" />. This unique property is caused by ponatinib’s ability to overcome resistances of the BCR-ABL gatekeeper mutant T315I at low concentrations (low IC50s ranging from 0.5 nM to 36 nM) by an ethynyl linker in the <scene name='48/483882/Active_sitezoom/1'>DFG-out</scene> conformation (see color chart below)<ref name="five" /> <ref name="six" />. The T315I mutation accounts for 15-20% of all clinically observed mutations and it is resistant to all previous generation drugs (imatinib, nilotinib, dasatinib). Additionally, ponatinib has a very high potency against native ABL which allows the binding energy to be distributed over many protein residues<ref name="five" />.
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Kinases 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<ref name="four">PMID: 25317566</ref>. 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<ref name="five">PMID: 25219510</ref>. This class of inhibitors can bind deep within the hydrophobic and allosteric pocket that is only accessible in the <scene name='48/483882/Active_sitezoom/1'>DFG-out</scene> conformation (see color chart) which consists of Asp630, Phe631, and Glu632<ref name="four" />.
<center><big>{{Template:ColorKey_N52C3Rainbow}}.</big></center>
<center><big>{{Template:ColorKey_N52C3Rainbow}}.</big></center>
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The specific binding of ponatinib can be categorized into and explained by five major chemical components, they are: (1) the template that interacts with the hinge region; (2) the A ring that occupies the hydrophobic pocket behind the gatekeeper residue; (3) the key ethynyl linker that joins the template and A ring, and that interacts with the gatekeeper residue (linker 1); (4) the A-B ring linker (linker 2); and (5) the B ring that binds to the DFG-out pocket<ref name="five" />.
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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 <scene name='48/483882/Hinge/1'>hinge</scene> (<font color='cyan'><b>cyan</b></font>) 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 <scene name='48/483882/Hingehbond/1'>hydrogen bond</scene> with the amide nitrogen atom of Ala553 (<font color='magenta'><b>magenta</b></font>) in the hinge<ref name="seven" />. 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 <scene name='48/483882/Gatekeeper/1'>gatekeeper</scene> in <font color='yellow'><b>yellow</b></font>), 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<ref name="seven" />.
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Ponatinib binds into the ATP binding pocket between the N and C lobes to induce a shift from the DFG-in to the DFG-out conformation. It covers an immense region that spans from the kinase <scene name='48/483882/Hinge/1'>hinge</scene> (in <font color='cyan'><b>cyan</b></font>) region (back of kinase) to the catalytic pocket (front of kinase). Three sites are engaged in the ATP binding cleft by ponatinib’s aromatic rings. In the first site, the imidazo[1,2b]pyridazine scaffold takes up the same space as the adenine ring of ATP and it is able to form one <scene name='48/483882/Hingehbond/1'>hydrogen bond</scene> with the backbone amide nitrogen atom of Ala553 (in <font color='magenta'><b>magenta</b></font>) in the hinge <ref name="seven" />. Both of its rings form several Van der Waals contacts with residues in the N and C lobes of the adenine binding site as well<ref name="five" />. Rigid acetylene linkage drives the rest of the drug into the back of the ATP binding pocket. In the second site, the methylphenyl group displaces the side chain of the catalytic Lys503 and its aromatic ring binds to the hydrophobic pocket that is formed by Val550, the <scene name='48/483882/Gatekeeper/1'>gatekeeper</scene> residue (in <font color='yellow'><b>yellow</b></font>), and Met524<ref name="seven" />. Val550 is stabilized by the benzimide group<ref name="six">PMID: 25478866</ref>. This displacement allows Glu520 in the αC helix to hydrogen bond with the amide linkage between the aromatic rings in ponatinib. In the third site, Phe631 of DFG is expelled out of the cleft by ponatinib’s 3-trifluoromethylphenyl moiety, which takes the place of Phe631. Phe631’s new position enables it to make hydrophobic contact with the drug’s scaffold and acetylene linker. Also, Asp630 of DFG becomes available for hydrogen bonding with the amide linkage between the aromatic rings in ponatinib. This also puts the piperazine ring in the position to engage in hydrogen bonding with the catalytic loop. This is shift forms the DFG-out conformation<ref name="seven" />.
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Other inhibitors are not as potent as ponatinib against FGFR kinases because they are unable to penetrate far enough to access the third site and cannot assume the DFG-out conformation<ref name="seven" />.
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==Additional Features==
==Additional Features==
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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<ref>FDA Drug Safety Communication: FDA investigating leukemia drug Iclusig (ponatinib) after increased reports of serious blood clots in arteries and veins; Drug Safety and Availability; United States Food and Drug Administration (2013). Web. [http://www.fda.gov/Drugs/DrugSafety/ucm370945.htm]</ref>.
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<ref>FDA Drug Safety Communication: FDA investigating leukemia drug Iclusig (ponatinib) after increased reports of serious blood clots in arteries and veins; Drug Safety and Availability; United States Food and Drug Administration (2013). Web. [http://www.fda.gov/Drugs/DrugSafety/ucm370945.htm]</ref>.
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FGFR-4 is abundantly present in human prostate cancer observed in vitro and in mouse model simulations<ref name="nine">PMID: 22573348</ref>. A <scene name='48/483882/Variant/4'>variant</scene> of FGFR-4 with (Arg(388)) replacing (Gly(388)) is associated with increased human prostate cancer. This causes increased receptor stability and activation<ref name="ten">PMID:18670643</ref>. A study revealed that the inhibition of FGFR-4 signaling completely curtailed prostate cancer cell lines that were responsible for tumor growth<ref name="nine">PMID: 22573348</ref>. 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.
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FGFR-4 is abundantly present in human prostate cancer observed in vitro and in mouse model simulations<ref name="nine">PMID: 22573348</ref>. A <scene name='48/483882/Variant/9'>variant</scene> of FGFR-4 with Arg388 replacing Gly388 is implicated with increased human prostate cancer. This variation causes increased receptor stability and activation<ref name="ten">PMID:18670643</ref>. A study revealed that the <scene name='48/483882/Inhibition/1'>inhibition</scene> of FGFR-4 signaling completely curtailed prostate cancer cell lines that were responsible for tumor growth<ref name="nine">PMID: 22573348</ref>. 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.
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==Quiz Question 1==
==Quiz Question 1==
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Ponatinib 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 structure characteristics would the inhibitor need to posses? Consider the unique binding methods of Ponatinib and the <scene name='48/483882/Active_sitezoom/1'>DFG-out</scene> conformation.
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Ponatinib 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 <scene name='48/483882/Active_sitezoom/1'>DFG-out</scene> conformation.
a. Small, fully conjugated aromatic system with no electronegative substituents, to prevent unwanted hydrogen bonding.
a. Small, fully conjugated aromatic system with no electronegative substituents, to prevent unwanted hydrogen bonding.

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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

The Ponatinib-FGFR complex is highly effective for treating CML (4uxq)

Drag the structure with the mouse to rotate
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