vflip-ikk g blocker
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vFLIP-IKK g Blocker. Edith Chan WIBR. Work Study. - PowerPoint PPT PresentationTRANSCRIPT
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vFLIP-IKK Blocker
Edith Chan
WIBR
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Work Study
• The study focuses on using X-ray crystal structures, biophysical screening and structure based design to identify blockers of the vFLIP-IKK and p22-cFLIP-IKK interaction, conducting lead optimisation and identifying a development candidate.
• My immediate actions are
– Understanding of the interaction of the vFLIP-IKKcomplex using X-ray crystal structure
– Selection of compounds mimicking the IKK interaction of the complex
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X-ray crystal structure• Our collaborators at BBK have
solved the structure between vFLIP-IKK (3cl3).
• Full length IKK is 419aa long mulitdomain protein
• Both proteins are truncated– ks-vFLIP (aa1-178) [188aa]– IKKg (aa150-272) [419aa]
• The X-ray structure comprised of a dimer of two ks-vFLIP-IKKcomplex.
• The two vFLIP molecules come together solely through interactions between the two IKK chains.
A B
D
E
IKK
vFLIP
N-terminus
C-terminus
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Protein-Protein Interactions
• Each of the IKK helix is interacting with a copy of the vFLIP via two adjacent vertical clefts (Cleft1 and Cleft2)
• Cleft 1 involved more interactions between the complex, the hottest spot seems to be around Phe238 (of IKK)
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Where are the main Interactions?• SURFNET, which locates the all available clefts on a protein surface, also indentifies
Cleft1 and Cleft2. However, they are smaller than expected.
• In Cleft1, mainly F238, D242, and K246 from IKK interact with vFLIP, with F238 reaching the deepest pocket.
• In Cleft2, Q236 and E240 are pointing into the pocket. Interaction would be optimized.
Cleft1Cleft2
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Cleft1 Interactions• Residues involved in this region are
• F238 – all hydrophobic interaction, enclosed by F53, F79, L80, P54, and A57.
• D242 and K246 – enclosed by H83,T87,Y90,S89
• K246 has a H-bond with C=O of M88
• D242 has a H-bond to H83
• Mutation study showed that A57L has impaired the forming of the complex. P54G shows a reduction in affinity while Y90L retains affinity.
• D242R mutant has rendered IKK largely incapable of forming a complex.
Ala57L
Pro54G
Tyr90F
FQEYDNHIK
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-helix in Protein-Protein Interaction
• There are many other biological systems that involved the protein recognition of a a-helix, such as bacterial autotransporter NaIP, Gp41, smMLCK/CaM, HDM2/p53, Bcl-2 family, Estrogen receptor-CoA, Tachyknin receptors,…
• Many of them are studied extensively.
• Let’s us look at the HDM2/p53 system.
• HDM2 – Human double minute 2 protein/p53 is related in cancer therapy.
• The complex has protein-protein interaction, with p53 adopting helical conformation.
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p53 vs IKK• The backbone of p53 and IKKg peptides overlap well.
• 2 of the residues (F and D) that interact with protein also overlap well.
• The left picture shows an overlap between p53 and a small molecule inhibitor
P53 RFMDYWEALIKK LFQEYDNHIK
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N
N
O
OI
Cl
O
O
Cl
1t4e
N
NCl
Cl
O
O
1ttvMW = 454HA = 3HD = 1cLogP = 8.3
MW = 580HA = 4 HD = 2cLogP = 6.41
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Known Helix Mimeticsspecial groups
• Some known helix mimetic and if any similar compounds are in our 30K screening database.
R1
R2
R3
X
Y
Terphenyl1 hit, no rgroup
ONH
N O
O
R1O
O
R3
R4
R2
TerephthaiamideAbout 10 hits but without the phenol
N
NH
O
N
O
N
OR1
R2
N OH
N
COOMe
OR3
TrispyridylamideNo hits
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Known Helix MimeticSmall molecules - Common
OH
H
R4
R3
R1
R2
ChalconesPyrrole system~20 hit, 0 hitPlenty in commercial database
Aryl sulphonamides10 hits
OH
H R
N
S
S
OO
N
R
R
Isoindolinones4 hit
N R1
O
OR2
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Known Helix MimeticSmall molecules – Custom made
N
N
R
R
R
Trisubstituted imidazoles0 hit
Nutlinsno hits
N
N
R
R
NO N R2
O
R3
1,4-benzodiazepine-2,5-diones (BZD)No hit
N
N
O
O
R1
R2
R4
O
O
R3