1. University of Illinois at Chicago College of PharmacyUIC
Background Oligoamines Containing 3-5-3 Linkers
Summary and Conclusions
Hypothesis
• A novel series of oligoamines containing 3-5-3 linkers has been
synthesized, characterized and tested
• Three compounds (BP-107-3, BP-107-5 and BP-107-15) display 95% or
more inhibition at 10 µM in a fluorimetric demethylation assay
• Of these three best compounds, BP-107-15 displayed a superior IC50
value in a MTS cell viability assay and exhibits competitive kinetics
• Inhibition of LSD1 by BP-107-15 significantly induces re-expression of
aberrantly silenced tumor suppressors (SFRP2, HCAD, GATA4 and p16)
• Computational docking using GOLD revealed key h-bonding and
hydrophobic interactions
• Ongoing structure-based drug discovery efforts are aimed at optimizing
the inhibitors to further improve its potency, as well as testing its efficacy in
animal models
Design, Synthesis and Biological Activities of Novel Oligoamines Containing 3-5-3 Linkers as
Epigenetic Modulators
Boobalan Pachaiyappan 1, Shannon Nowotarski 2, Melissa Sokolosky 1, Steven L. Holshouser 1,
Shiv K. Sharma 3, Robert A. Casero, Jr. 2, Patrick M. Woster 1
Contact Information:(1) Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, United States; (2) Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University,
Baltimore, MD 21231, United States; (3) Pharmaceutical Sciences, Wayne State University, Detroit, MI 48202, United States. (Email: pachaiya@musc.edu)
X = O or S; Ar = various mono and biaryl derivatives
BP-107-15
• 96% inhibition at 10 µM
• IC50 = 5.5 µM
• Cellular IC50 = 4 µM
• Competitive inhibition
Figure 6: LSD1 inhibition by BP-107-3, BP-107-5 and BP-107-15 at 10 µM
promotes re-expression of aberrantly silenced genes detected by qRT-PCR
in this Calu6 human lung adenocarcinoma cells
Figure 1: Normal mammalian cells exhibit an exquisite level of control
of chromatin architecture by maintaining a balance between histone
lysine methyl transferase and lysine-specific demethylase 1 (LSD1)
activity. In tumorigenesis, this equilibrium is disturbed due to
overexpression of LSD1, thereby resulting in decreased activating
marks and increased repressive marks resulting in aberrant silencing of
tumor suppressors
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• Synthesize
oligoamines of various
linker sizes
• Characterization using
NMR and MS
Organic
Synthesis
• In vitro and cell-
based testing
• Enzyme kinetics
• Gene re-expression
studies
Biological
Testing
• Model inhibitors and
elucidate the key
determinants for
binding to LSD1
Computational
Modeling
In Vitro Biological Testing
Figure 3: General structure of oligoamines containing 3-5-3 linkers
Figure 4: Chemical synthesis of oligoamines containing 3-5-3 linkers
Demethylated Lysine
(condensed chromatin
represses transcription)
Methylated-Lysine
(elongated chromatin
upregulates transcription)
Histone lysine methyl transferase
LSD1
Inhibitors
(?)
H3
H3
Because LSD1 catalyzes the demethylation of key chromatin marks at
histone 3 lysine 4 (H3K4me and H3K4me2), as well as H3K9, LSD1
inhibition using small molecule oligoamines will have a significant effect in
promoting transcription and re-expression of tumor suppressor genes.
Experimental Paradigm
Figure 2: Integrated strategy for LSD1 inhibitor design
References & Acknowledgements
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%LSD1ActivityRemaining
Figure 5: (Panel A): Eleven compounds were assessed for LSD1
inhibitory activity at 10 µM by combining the recombinant LSD1,
fluorogenic substrate and inhibitor, and measuring relative fluorescence of
demethylated H3K4me1; (Panel B): To determine the IC50 of BP-107-15,
inhibitory activity was measured over a range of concentrations (0.3125 to
2.5 mM); (Panel C): Kinetics of inhibition of recombinant LSD1 by BP-107-
15; (Panel D): Overall inhibitory profile of BP-107-15.
Organic Synthesis
Computational Modeling Analysis
Figure 7: (left) Computer-predicted binding mode of BP-107-15 (capped
sticks) in the LSD1 binding site (ribbon diagram); (right): molecular
interactions that govern the binding of BP-107-15 in the LSD1 pocket
- NIH 1-RO1-CA149095
(PMW)
- A generous grant from
Progen Pharmaceuticals, Ltd.
• J Med Chem (2010), 53, 5197
• Proc. Natl. Acad. Sci. USA (2007),
104, 8023
• J Med Chem (2012), 55, 7378
• Clin. Cancer. Res. (2009), 15, 7217
A
C
B
D
* p<0.1
** p<0.05
Gene Re-Expression Studies