Sandbox Reserved 432

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(→'''1-JVQ: Devourer of Memories''')
Current revision (03:46, 11 April 2016) (edit) (undo)
(→'''Protein complex with cancer drug Alecensa-Alectinib (4uxl)<ref>PMID: 25733882 </ref>''')
 
(184 intermediate revisions not shown.)
Line 3: Line 3:
<!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE -->
<!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE -->
-
=='''1-JVQ: Devourer of Memories'''==
+
=='''Protein complex with cancer drug Alecensa-Alectinib (4uxl)<ref>PMID: 25733882 </ref>'''==
 +
by Laura Feeley, Katie Kwan, Daniel Peters, Ishtiaq Rafiyu, Luke Ruksnaitis
-
===Introduction===
+
[[Student Projects for UMass Chemistry 423 Spring 2016]]
-
<Structure load='1jvq' size='500' frame='true' align='right' caption='Antithrombin III' scene='Insert optional scene name here' />
+
<StructureSection load='4uxl' size='350' side='right' caption='Alectinib- an anaplastic lymphoma kinase inhibitor used to treat non-small-cell lung cancer (PDB entry [[4uxl]])' scene=''>
-
+
-
Slowly losing one's mind is a terrible experience, and it is especially hard on those who have to watch it happen to one of their loved ones. We can all agree that dementia is a disease worth curing: to do that we must first determine its cause.
+
-
The most likely culprit for the cause of some dementias are a group of protease inhibitors called serpins. Serpins are an unusual group as inhibitors go because while most inhibitors simply block the binding site, serpins undergo conformational changes when they bind. Mutations can alter those conformational changes. When this happens, the serpins can no longer function as inhibitors, and instead polymerize to form long chains of worthless protein. These chains eventually grow so long that they destroy the cell and spread into the surrounding tissue, causing further damage and eventually resulting in organ failure. Mutations in the conformational structure of neuroserpin, a serpin found in neurons, has been blamed for the deterioration of brain function seen in dementia.
+
-
<scene name='Sandbox_Reserved_432/1jvq/2'>Dimensions of Dementia</scene>
+
==Introduction==
 +
<scene name='48/483889/Alectinibintro/6'>Alectinib</scene>, otherwise known as Alecensa, is an FDA approved second generation drug that is used to primarily target non-small-cell lung cancer. It functions as an anaplastic lymphoma kinase(ALK) and Oncogenic c-ros oncogene1 (ROS1) fusion kinase inhibitor. Alectinib was approved by the FDA for immediate release in December of 2015. It is prescribed when anaplastic lymphoma kinase gene mutations occur as a response to the first generation drug, crizotinib, and pose a risk of spreading to the brain. Alectinib inhibits the gatekeeper L1196M mutation that occurs in response to crizotinib.<ref>DOI: 10.18632/oncotarget.2055</ref>
 +
The ligand (in green) for the ROS1 kinase complex was found to be (10R)-7-amino-12-fluoro-2,10,16-trimethyl- 15-oxo-10,15,16,17-tetrahydro-2H-8,4-(metheno)pyrazolo[4,3- h][2,5,11]benzoxadiazacyclotetradecine-3- carbonitrile, although identifying ligands for receptor ALK is a topic of on going research.<ref>http://dx.doi.org/10.2210/pdb4uxl/pdb</ref> The <scene name='48/483889/Alectinibintroligand/1'>ligand</scene> bound complex aims to inhibit pathways that are activated through phosphorylation, and in turn stop uncontrolled growth of the point mutations created from a resistance to crizotinib.
 +
Alectinib is utilized in patients when the first generation drug, crizotinib, also an anaplastic lymphoma kinase inhibitor, has failed to work. Crizotinib did have a sixty percent tumor response but the side effects included diarrhea, nausea, vomiting, and constipation.<ref>http://www.cancer.gov/news-events/cancer-currents-blog/2016/fda-alectinib-nsclc</ref>. Alectitinib aims to have a successful inhibitory response but also to reduce the magnitude of these side effects. The success of alectinib is the result of its effectiveness against the mutations created in response to the first generation drug crizotinib.
 +
In the two clinical trials that have been conducted, there were tumor reductions in thirty-eight percent of patients which then increased to forty-four percent in the second trial. It was found in a trial of patients with brain metastases that sixty percent had a complete or partial reduction of tumors.
 +
 +
==Overall Structure==
 +
Alectinib is an anaplastic lymphoma kinase (ALK) inhibitor with a 5H-benzo[b]carbazol-11(6H)-one structural scaffold <ref>DOI: 10.1016/j.apsb.2014.12.007</ref>. (chemical name: 9-Ethyl-6, 6-dimethyl-8-[4-(morpholin-4-yl)piperidin-1-yl]-11-oxo-
 +
6, 11-dihydro-5H-benzo[b]carbazole-3carbonitrile hydrochloride)
 +
The <scene name='48/483889/Alectinib_-_secondary/1'>ALK protein kinase domain</scene> consists of a small N-terminus lobe and a large C-terminus lobe. The N-terminus lobe holds a 5-stranded antiparallel β sheet, and a αC helix. The C-terminus lobe contains a glycine rich ATP binding loop, located between the first and second β strands. This large lobe mostly contains α helices (six conserved segments), and two short β strands. <ref>DOI: 10.1016/j.phrs.2012.11.007</ref>
 +
The structure also contains four hydrophobic residues that form the regulatory spine, and eight hydrophobic residues that form the catalytic spine. {{Template:ColorKey_Hydrophobic}} and {{Template:ColorKey_Polar}}, regions of the ALK inhibitor can be seen <scene name='48/483889/Alectinib_-_hydrophobic_polar/1'>here</scene>.
 +
==Binding Interactions==
 +
The binding interaction of PF-0643922 with ROS1/ALK is what makes Alectinib a second generation drug. Patients developed resistance to the first generation drug crizotinib by developing point mutations in the ROS1 kinase. PF-0643922 is a very strong potent and selective small molecule inhibitor that targets the (ROS1) fusion kinase. Inhibition of the fusion kinase is the goal of this cancer therapy. PF-0643922 is the most potent and selective ROS1 inhibitor discovered to date according to the paper cited. PF-0643922 is the small molecule of the protein complex of ROS1 inhibitors that gets the job done on its own compared to alectinib and crizotinib. Alectinib's goal is to fight resistance to the inhibition of ROS1 kinase through selectively binding to the point mutations. However PF-0643922 has been shown to inhibit the crizotinib-refractory ROS1(G2032R) mutation and the ROS1(G2026M) gatekeeper mutation which would ultimately make crizotinib and alectinib obsolete ROS1 inhibitors. The crystal structure between the PF-0643922-ROS1 complex shows the interactions that contribute to the high affinity binding of PF-0643922. The first blue dot alone by itself is the N terminus, and the three carbon atoms next to the nitrogen and oxygen is the C terminus. The binding site of the protein complex is therefor the cluster of atoms with the green dot.
 +
 +
<scene name='48/483889/123/1'>Illustration of binding site</scene>
 +
==Additional Features==
 +
PF-06463922 is a compound with high affinity for ROS1 and ALK kinases. PF-06463922 is a small molecule that is orally available, ATP-competitive and can penetrate CNS. PF-06463922 exhibits cellular potency against oncogenic ROS1 fusions and inhibits the crizotinib-resistant mutant ROS1. When compared with crizotinib and the second-generation ROS1 inhibitors such as ceritinib and alectinib, PF-06463922 exhibits significantly improved inhibitory activity against ROS1 kinase. Recent studies have shown that when compared with other kinase inhibitors, PF-06463922 is 10-times more potent than crizotinib and foretinib and 100-fold more potent than either ceritinib or alectinib in both ROS1 cell growth and ROS1 kinase inhibition.
 +
PF-06463922 makes many favorable interactions with ROS1. Co-crystal structure analysis revealed that the high potency of PF-06463922 against ROS1 is due to the multiple interactions between the compound and the ROS1 kinase domain. The PF-06463922 has an aminopyridine core that makes two hydrogen bonds to the kinase hinge segment thus creating a stable complex.
 +
To investigate the PK/PD relationship between PF-06463922 plasma concentration and inhibition of tumor growth, recent conducted study showed that a direct-response modeling analysis in the NIH 3T3 FIG-ROS1 model. Their Hill equation analysis showed a reasonable fit of R2 = 0.79, and the estimated concentrations used, PF-06463922 were 5.8 nM for tumor stasis and 9 nM for 30% tumor regression of FIG-ROS1 s.c. tumors.
 +
Tyrosine kinase inhibitors for protein tyrosine kinase (ALK/LTK) and insulin receptor are phylogenetically related to the anaplastic lymphoma kinase/lymphocyte and suggests that they could have cross-activity against ROS1.
 +
<scene name='48/483889/Polargroups/1'>Shows the polar groups of the macromolecule</scene>
 +
==Quiz Question 1==
 +
Quiz question
 +
Using the inhibiting complex scene given below where is the binding site located?
 +
<scene name='48/483889/Binding_question/1'>Binding Question</scene>
 +
red:Oxygen
 +
blue:Nitrogen
 +
green:Florine
 +
A)At the nitrogen atom after the alpha helix
 +
B)At the nitrogen to oxygen complex
 +
C)At the oxygen/nitrogen complex that contains a florine atom
 +
D)all of the above
 +
 +
==See Also==
 +
[[http://proteopedia.org/wiki/index.php/4uxl Structure of Human ROS1 Kinase Domain in Complex]]
 +
[[http://www.proteopedia.org/wiki/index.php/Tyrosine_kinase Tyrosine kinase]]
 +
==Credits==
-
<font color='white'>spacing</font>
+
Introduction - Laura Feeley
-
===Overall Structure===
+
Overall Structure - Katie Kwan
-
<Structure load='1jvq' size='500' frame='true' align='right' caption='Overall Structure' scene='Insert optional scene name here' />
+
-
Our protein, Antithrombin III is a heterodimer. <ref> Whisstock JC, Pike RN. et al. (2000). "Conformational changes in serpins: II. The mechanism of activation of antithrombin by heparin". J. Mol. Biol. 301 (5): 1287–1305. doi:10.1006/jmbi.2000.3982. PMID 10966821.</ref> This <scene name='Sandbox_Reserved_432/Antithrombin_chains/1'>heterodimer</scene> consists of 2 chains, referred to as the L and I chains. The <font color='blue'>I chain</font> is also known as the native form of the protein monomer, while the <font color='yellow'>L chain</font> is also known as the latent form. The native form naturally degrades into the latent form over time, a process that may be sped up by heating, or heating in citrate. <ref>Wardell MR, Chang WS. et al. (1997). "Preparative induction and characterization of L-antithrombin: a structural homologue of latent plasminogen activator inhibitor-1". Biochemistry 36 (42): 13133–13142. doi:10.1021/bi970664u. PMID 9335576. </ref> Fun fact: a pre-latent form has also been isolated and shows some promise as an inhibitor of tumor growth.
+
Drug Binding Site - Luke Ruksnaitis
-
We see a great deal of similarity between the <scene name='Sandbox_Reserved_432/Serpin_monomeri/1'>native form</scene> and the <scene name='Sandbox_Reserved_432/Serpin_monomerl/1'>latent form</scene>. Most notably we still see the <font color='red'>(A) β-sheet</font> <scene name='Sandbox_Reserved_432/Antithrombin_sheeta/1'>(shown here)</scene> and the <font color='cyan'>(B) β-sheet</font> <scene name='Sandbox_Reserved_432/Antithrombin_sheetb/1'>(shown here)</scene> in both forms.
+
Additional Features - Rafiyu Ishtiaq
-
note:these sheets are shown in the latent form
+
Quiz Question 1 - Daniel Peters
-
The most significant difference between the two forms lies in the reative site loop. In the <font color='orange'>native form</font>, we can see a very nice <scene name='Sandbox_Reserved_432/Antithrombin_nativeloop/1'>reactive loop</scene>, while in the <scene name='Sandbox_Reserved_432/Antithrombin_reactiveloop/1'>latent form</scene> the reactive site loop is not a loop at all.
+
==References==
-
 
+
-
Also of note is the <font color='cyan'>blocking peptide</font> that is not a part of the protein itself, but has a great deal of significance when it comes to applications and is shown <scene name='Sandbox_Reserved_432/Blocking_peptide1/1'>here</scene>.
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
<font color='white'>spacing</font>
+
-
 
+
-
===Drug Binding Interactions===
+
-
<Structure load='4caa' size='500' frame='true' align='right' caption='Binding Interactions' scene='Insert optional scene name here' />
+
-
 
+
-
Quite a few forms of dementia arise due to serpins forming long chains with one another. Mutant serine protease inhibitors link their <span style="color:blue">'''reactive site loop'''</span> into the middle strand (s4A) position of the <span style="color:red">'''A ß-sheet'''</span> of another (<scene name='Sandbox_Reserved_432/Antichymotrypsin/3'>Antichymotrypsin</scene>)<ref>Lukacs CM, Zhong JQ, Plotnick MI, Rubin H, Cooperman BS, Christianson DW. Arginine substitutions in the hinge region of antichymotrypsin affect serpin beta-sheet rearrangement. Nat Struct Biol. 1996 Oct;3(10):888-93. PMID:8836107</ref> . They will continue hooking on to one another and create very long polymers.
+
-
 
+
-
Researchers at the University of Cambridge have found a couple of ways in order to negate these linkages, but only one way has been shown to be practical. Binding interactions for polymerisation and blocking polymerisation occur at the antithrombin at the residue locations P14-1. The reason why the serpins form chains with one another is due to their <span style="color:red">'''A sheet'''</span> "opening". This is kept open by random <span style="color:magenta">'''P14-P8/9'''</span> peptides that anneal to the upper half of the s4A position. This allows a domain exchange with the insertion of the P8-3 portion of the loop on another serpin molecule into the lower half of the s4A position (<scene name='Sandbox_Reserved_432/Open_a_sheet/2'>A ß-sheet that is open</scene>). They originally discovered that serpin polymerization could be blocked with synthetic P14-3 or P7-2 peptides. However, in terms of practicality, they were ultimately ineffective; the peptides were far too large for mimetic drug design and many tests proved that the binding of these peptides were far too unpredictable. After conducting crystallographic studies, the synthetic peptides would be found attached to other parts of the serpin.<ref>Zhou A, Stein PE, Huntington JA, Sivasothy P, Lomas DA, Carrell RW. How small peptides block and reverse serpin polymerisation. J Mol Biol. 2004 Sep 17;342(3):931-41. PMID:15342247 doi:10.1016/j.jmb.2004.07.078</ref>
+
-
 
+
-
The molecule that was effective was a tetrapeptide called WMDF (Trp-Met-Asp-Phe). Derived from cholecystokinin, this tetrapeptide blocked the polymerisation of antitrypsin and antithrombin. The structure of this peptide was observed at greater detail and the researchers at Cambridge started to test out the effectiveness of other tetra and tripeptides. What they found out is that WMDF binds to the
+
-
P14-8 peptide-antithrombin binary complex. Specifically, it occupies the <span style="color:darkorange">'''P7-P4 vacancy'''</span> and forms 8 hydrogen bonds with the adjacent residues, which prevents another serpin's reactive loop from forming bonds (<scene name='Sandbox_Reserved_432/Binding_site/7'>WMDF Binding Site</scene>). The tetrapeptide's bulky side chains are what contributes to its effectiveness as a blocker of serpin polymerisation. The P4 & P6 locations are very critical; WMDF has methionine at the P6 location and phenylalanine at the P4 location. The hydrophobicity of these regions results in a shift of the connecting loop when compared to latent antithrombin, which results in successful anithrombin polymerisation inhibition. Peptides that were homologous in the P4 & P6 regions to WMDF were also effective (FMRF & FLRF)<ref>Zhou A, Stein PE, Huntington JA, Sivasothy P, Lomas DA, Carrell RW. How small peptides block and reverse serpin polymerisation. J Mol Biol. 2004 Sep 17;342(3):931-41. PMID:15342247 doi:10.1016/j.jmb.2004.07.078</ref>
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
<font color='white'>spacing</font>
+
-
 
+
-
===Additional Features===
+
-
<Structure load='1jvq' size='500' frame='true' align='right' caption='Additional Features' scene='Insert optional scene name here' />
+
-
 
+
-
Since Alzheimer's is such a common threat there have been many attempts at finding ways to prevent and cure it. The main goal is to prevent intermolecular linkages from being formed from <scene name='Sandbox_Reserved_432/Beta_sheets_overview/1'>beta sheets</scene>. With this goal in mind they are trying develop therapies to aid in the prevention of these linkages. 10 million Europeans carry what we call the Z allele of antitrypsin.<ref>Zhou A, Stein PE, Huntington JA, Sivasothy P, Lomas DA, Carrell RW. How small peptides block and reverse serpin polymerisation. J Mol Biol. 2004 Sep 17;342(3):931-41. PMID:15342247 doi:10.1016/j.jmb.2004.07.078</ref> This doesn't directly mean you are at health risk though. The Z allele gives your body the ability to polymerize and store up to half of their antitrypsin in their liver cells. The problem arises when the formation exceeds the limits of the liver cells which can cause cell death which leads to organ failure.<ref>"Serpin." Wikipedia. Wikimedia Foundation, 25 Apr. 2012. Web. 25 Apr. 2012. <http://en.wikipedia.org/wiki/Serpin>.</ref>
+
-
 
+
-
Therapeutic techniques have been developed to help stop this over-formation of antitrypsin. Instead of trying to just stop the formation of antitrypsin, researchers have found a way on how they can actually change the direction of equilibrium so that it will favor dissociation. This can be achieved by the use of an agent to bind to the unstable protein forms to slowdown and stop the formation.
+
-
 
+
-
At first the only way they would be able to accomplish this binding was with a minimum of 6 amino acids. The problem with this is that the peptides were not going to be small enough. What they found out was that they could block this now by the use of only 3-4 amino acids.<ref>Zhou A, Stein PE, Huntington JA, Sivasothy P, Lomas DA, Carrell RW. How small peptides block and reverse serpin polymerisation. J Mol Biol. 2004 Sep 17;342(3):931-41. PMID:15342247 doi:10.1016/j.jmb.2004.07.078</ref> Now these smaller peptides are of more use because now they can be used for oral drug therapy which is the best way to target all the intercellular problems. This means that we could stop the serpin-serpin interactions with each other which originates in the <scene name='Sandbox_Reserved_432/Beta_sheet_gap/1'>beta sheet</scene> at the bottom with the <span style="color:blue">'''open hole'''</span>. This was found out by how <scene name='Sandbox_Reserved_432/Binding_of_glycerol/3'>glycerol</scene> was able to bind to the site (represented by the ball and stick figure) between the two beta strands that are responsible for the polymerisation. This showed that with enough glycerol to bind to these sites that we could effectively prevent the formation of polymers which are essential to our disease.
+
-
 
+
-
===Credits===
+
-
 
+
-
Introduction - Kevin Dillon
+
-
 
+
-
Overall Structure - Max Nowak
+
-
 
+
-
Drug Binding Site - Kyle Reed
+
-
 
+
-
Additional Features - Chris Carr
+
-
 
+
-
===References===
+
<references/>
<references/>

Current revision


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.


Protein complex with cancer drug Alecensa-Alectinib (4uxl)[1]

by Laura Feeley, Katie Kwan, Daniel Peters, Ishtiaq Rafiyu, Luke Ruksnaitis

Student Projects for UMass Chemistry 423 Spring 2016

Alectinib- an anaplastic lymphoma kinase inhibitor used to treat non-small-cell lung cancer (PDB entry 4uxl)

Drag the structure with the mouse to rotate
Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_432"
Personal tools