the development of sumoylation inhibitors—a novel approach to
TRANSCRIPT
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The Development of SUMOylationInhibitors—A Novel Approach to
Combating Tumorigenesis
Mich Gehrig
Weds, May 14, 2014
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Drug Development Flowchart
Correlating an observation with an abnormality
Proof of concept (causation NOT
solely correlation) Alter the normal physiological
process (inhibitors)
Design/test inhibitors
Search for drug-like chemical scaffolds
Refine findings
Appropriate drug properties attained
(Rule of 5)
Clinical TestingDrug
Implementation
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What is SUMOylation?
Common Post – translational Modifications
• Phosphorylation/dephosph-orylation
• Acetlyation/deacetylation
• Ubiquitination/deubiquitin-ation
• Neddylation/Deneddylation
• SUMOylation/deSUMOyla-tion
SUMOylation
• Small ubiquitin-like modifier (SUMO)
• First discovered bound to RanGAP1
• Involved in:– Nuclear organization
– +/- transcriptional regulation
– +/- transcription factors
– Altered binding partners
– Protein Stability
– DNA repair
– Cell signaling 3
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• Closely parallels SUMOylation• Can serve as an introduction to the SUMOylation pathway• More studied, better understood• Cross-talk between the two
NLP*Cl Laboratory (2007). http://e3miner.biopathway.org/help_intro.html
Ubiquitination Overview
Proteasome
Target Protein is degraded
Ubiquitin recycled
~ 25 E2Enzymes
~ 9 E1Enzymes
Hundreds of E3EnzymesProblems:
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SUMO-1
(A) Ribbon diagram of the 3D structure of SUMO-1(B) Surface representation
Song J. (2004) PNAS.
ubiquitin-like-protein-processing (Ulps) enzymes
Mature SUMO-1C-terminal
N-terminal
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SUMOylation Overview
Bettermann, K. et al. (2012) Cancer Lett.
Critical Points
Start
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Why are SUMOylation Enzymes Potential Therapeutic Targets?
Edited from: Alarcon-Vargas, et al. (2002) Cancer Biol Ther.
• Only one E1 enzyme (Aos1/Uba2) and one E2 enzyme (Ubc9) are known
• Found across prokaryotes and eukaryotes
• SUMO E1, Ubc9, SUMO E3, and SENPs highly expressed in cancers
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Drug Development Flowchart
Correlating an observation with an abnormality
Proof of concept (causation NOT
solely correlation) Alter the normal physiological
process (inhibitors)
Design/test inhibitors
Search for drug-like chemical scaffolds
Refine findings
Appropriate drug properties attained
(Rule of 5)
Clinical TestingDrug
Implementation
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INTEGRAL PROBLEM
If we can inhibit SUMOylation, will it have the desired physiological
effects? (eg. Tumor supression)
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SUMOylation-Dependent Myc-driven Tumorigenesis
• c-Myc (Myc) is overexpressed in about ~25% of breast cancers
• Studies have shown that Myc is required for tumor maintenance and progression
Kessler, J.D. et al. (2011) Science
tamoxifen
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Selectively silence genes
Inducible Mycexpression
Turn Myc on (tamoxifen) or off
Death in “Myc ON” only
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SUMOylation interference synthetically lethal with hyperactivated Myc
Kessler, J.D. et al. (2011) Science11
• Inhibiton of SUMO E1 resulted in increased population doubling time
• Reinsertion of wild-type cDNA restores cells to normal cancer state
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SAE2 (E1) depletion with Mychyperactivation impairs proliferation
Kessler, J.D. et al. (2011) Science
• Increase in number of cells with aberrant DNA
• More spindle Defects
• Increased abnormal mitosis
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SAE2 (E1) depletion with Mychyperactivation impairs proliferation
Kessler, J.D. et al. (2011) Science13
• (Dox-inducible) SUMO E1 inhibition reduced tumor volume
• Low E1 levels correlated to higher survival probability in breast cancer patients
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Destruction of p53 via Mdm2 SUMOylation
• p53 = tumor suppressor protein
• Mdm2= an E3 ubiquitin ligase that targets p53
14Buschmann, T. et al. (2000) Cell.
• Self-ubiquitinated: p53 not destroyed
• SUMOylated: autoubiquitinationblocked; p53 degradated
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Drug Development Flowchart
Correlating an observation with an abnormality
Proof of concept (causation NOT
solely correlation) Alter the normal physiological
process (inhibitors)
Design/test inhibitors
Search for drug-like chemical scaffolds
Refine findings
Appropriate drug properties attained
(Rule of 5)
Clinical TestingDrug
Implementation
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SUMOylation Inhibitors:4 previously known classes (SUMO E1 Enzyme)
• Class I (2004)– Adenoviral Protein GAM1
• First ever reported E1 inhibitor
• Class II (2010)– Semi-synthetic mechanism-based proteins
• Mimic adenylate or tetrahedral bond formation during thioester bond formation
• Class III (2009)– AMP mimics
• Class IV (2009)– Natural products (ginkgolic acid, anacardic acid
kerriamycin B) 16
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Problems We Currently Face• Need to identify small molecule inhibitors
• Need to have better drug-like properties:
– Cellular entry, Solubility, Activity/Half maximal inhibitory concentration (IC50)
Kumar A. (2013) J Chem Inf Model
Chemical Name
IC50 (µM)
Class IV
Ginkgolicacid
3.0
Anacardicacid
2.2
KerriamycinB
11.7
Class III MLN4924 8.2
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Lower IC50 = greater drug potency
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The Search #1Kumar, A. et al. (2013) J Chem Inf Model
• Maybridge screening collection downloaded (77,931 compounds) and compared against downloaded crystal structure of SUMO E1– Each compound docked in
ATP binding site of SUMO E1• 5000 docked positions
generated for each ligand!
– Separated by geometrics, energetics
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SUMO activating enzyme (SUMO E1) crystal structure
Yishuzhang (2014) http://commons.wikimedia.org/wiki/File:SUMO_activating_enzyme_wi
th_Mg_and_ATP.png
ATP Binding domain
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The Search #2Kumar, A. et al. (2013) J Chem Inf Model
• Top 5% kept
• Evaluted:
– Ligand-binding free energy calculated via surface molecular mechanics analysis
• 24 compounds selected to be purchased from vendors
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The Search #3 (overview)Kumar, A. et al. (2013) J Chem Inf Model
In silico screening scheme used to identify inhibitors of SUMO E120
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SUMOylation Assay, 100µMKumar, A. et al. (2013) J Chem Inf Model
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SUMOylation Assay, 20µMKumar, A. et al. (2013) J Chem Inf Model
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IC50 of Compound 21Kumar, A. et al. (2013) J Chem Inf Model
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N,N’’-[methylene-bis(4,1-phenylene)]bis(N’’-phenylurea)scaffolding
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Binding of Compound 21 to SUMO E1Kumar, A. et al. (2013) J Chem Inf Model
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Reducing agent
Compound 21
• Disappearance of biotinylated SUMO appearance of E1-SUMO
• Reinforces that compound 21’s mode of action is achieved by targeting SUMO E1
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Results: Not So GoodKumar, A. et al. (2013) J Chem Inf Model
Chemical Name IC50 (µM)
Class IV Ginkgolic acid 3.0
Anacardic acid 2.2
Kerriamycin B 11.7
Class III MLN4924 8.2
SmallMolecule
Compound 21 14.4 ± 1.3
25
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The Search #4 (second search)Kumar, A. et al. (2013) J Chem Inf Model
• Compounds with similar structure to compound 21
– ZINC database (~18 million commercially available molecules)
• Same approach as before
– 37 compounds purchased
Compound 21
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ResultsKumar, A. et al. (2013) J Chem Inf Model
21Parent Molecule
Chemical Name IC50 (µM)
Class IV
Ginkgolic acid 3.0
Anacardic acid 2.2
Kerriamycin B 11.7
Class III MLN4924 8.2
Small Molecule
Compound 21 14.4 ± 1.3
Compound 25 11.1 ± 3.1
Compound 26 13.0 ± 0.4
Compound 30 40.3 ± 7.4
Compound 37 11.7 ± 5.327
Take Note of the Phenylurea groups
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Results: Predicted Docking of Compound 25Kumar, A. et al. (2013) J Chem Inf Model One phenylurea
protrudes into the hydrophobic
patch near Leu49 and Ile96
One phenylureais placed near
Ile384 and Thr141, the ATP binding pockets
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Results: DrugabilityKumar, A. et al. (2013) J Chem Inf Model
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The new
compounds
Discovered compounds have weaker activity, but higher drugability
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Drug Development Flowchart
Correlating an observation with an abnormality
Proof of concept (causation NOT
solely correlation) Alter the normal physiological
process (inhibitors)
Design/test inhibitors
Search for drug-like chemical scaffolds
Refine findings
Appropriate drug properties attained
(Rule of 5)
Clinical TestingDrug
Implementation
30
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Refining the Search
• Problem:
– discovered compounds barely fit within limits
– poor solubility (symmetrical)
– Active site of SUMO E1 not actually symmetric
• Methods
– Returned to Maybridge Chemical library
– Selected non-symmetrical compounds
31Kumar, A. et al. (2013) Bioorg. Med. Lett.
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A New Class of SUMO E1 InhibitorsQuinazolinyloxyl biaryl urea
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Quinazolinyloxyl biaryl urea identified as new class of SUMO E1 Inhibitors
Compound 4
Kumar, A. et al. (2013) Bioorg. Med. Lett.
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A New Class of SUMO E1 InhibitorsQuinazolinyloxyl biaryl urea
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Compound 9 the most potent version of compound 4
Compound 4
Cl binds in hydrophobic
pocket;quinazoline
N’s to Ile-96, Asp-48
This is where
adenosine in ATP binds
Kumar, A. et al. (2013) Bioorg. Med. Lett.
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Overall Results
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Chemical Name IC50 (µM)
Class IV Ginkgolic acid 3.0
Small Molecule Compound 25 11.1 ± 3.1
Quinazolinyloxyl biarylurea Compound 9 13.4
Kumar, A. et al. (2013) Bioorg. Med. Lett.
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Correlating an observation with an abnormality
Proof of concept (causation NOT
solely correlation) Alter the normal physiological
process (inhibitors)
Design/test inhibitors
Search for drug-like chemical scaffolds
Refine findings
Appropriate drug properties attained
(Rule of 5)
Clinical TestingDrug
Implementation
Drug Development Flowchart: Conclusion
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Summary
• SUMO E1, Ubc9, SUMO E3, and SENPs highly expressed in cancers
• Only one E1 enzyme (Aos1/Uba2) and one E2 (Ubc9) enzyme that are known
– Easy drug target
• SUMOylation inhibition (via E1 inhibition) prevents tumorigenesis
– Myc-dependent cancers
– Prevents ubiquitination of tumor-supressor p53
• Rapid advancement in the development of SUMO E1 inhibitors
– Establishment of Quinazolinyloxyl biaryl urea as a viable drug scaffold
• Need to:– Further refine inhibitors
– Clinical testing
– Drug implementation36
Kumar, A. et al. (2013) Bioorg. Med. Lett.
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Thank you!
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Buschmann, T.; Fuchs, S. Y.; Lee, C.; Pan, Z.; Ronai, Z. SUMO-1 Modification of Mdm2 Prevents Its Self-Ubiquitination and Increases Mdm2 Ability to
Ubiquitinate p53. Cell 2000, 101, 753-762.
Fukuda, I.; Ito, A.; Uramoto, M.; Saitoh, H.; Kawasaki, H.; Osada, H.; Yoshida, M. Kerriamycin B inhibits protein SUMOylation. J. Antibiot. (Tokyo) 2009, 62,
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