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Enzyme Upregulation by Computer-Aided Molecular Design
Our
research program for enzyme activation is comprised of computational
and experimental components. The computational component builds upon
publications in the Proceedings of the National Academy of Sciences
(PNAS) on biophysical modeling and optimization of enzymatic catalysis
by Dr. Raj Chakrabarti (Founder of CAT). The computational component is
further complemented with an experimental ultrahigh-throughput screening
component based on DNA-Encoded Libraries (DELs). State-of-the-art
machine learning algorithms are applied to this big data to guide the
Darwinian evolutionary process towards optimal drug leads faster and
more efficiently.
Two
primary applications are pursued: a) enzyme active site design for
catalysis on unnatural substrates; b) small molecule induced enzyme
activation. Both problems involve modeling and optimization of the
effects of design variables on protein structure and function. With
respect to application b), allosteric activation is currently the only
known means by which small molecule drugs can enhance the activity of
enzymes. However, the vast majority of potential drug targets are not
amenable to allosteric activation due to the lack of an allosteric site.
It is known that the ability to upregulate a variety of such enzymatic
targets could enable the treatment of a host of associated diseases.
Our
research program for non-allosteric activation of enzymes through the
modulation of active site structure, includes the activation of the
so-called sirtuin enzymes, which have been shown to play a central role
in age-related conditions, such as diabetes, neurodegenerative
disorders, and cardiovascular diseases. Among the 7 mammallian sirtuin
enzymes SIRT1-7, only SIRT1 has an allosteric site. In the absence of
nonallosteric activators, to date sirtuin activation has been pursued
pharmaceutically for SIRT1 (by Sirtris Pharmaceuticals, now GSK) by
allosteric activation and for SIRT3 by nutraceutical NAD supplements
which are not drugs (by Elysium Health). Using the above integrated drug
discovery platform, we have discovered novel hits for activation of
SIRT3 – the major mitochondrial sirtuin – that are more potent and
activate under a much wider range of physiologically relevant conditions
than the small number of hits that were previously identified in the
literature. The SIRT1 activators from Sirtris, for instance, only work
on a small number of substrates. Moreover, our platform may be used to
identify activators of multiple other SIRT enzymes and for much wider
variety of substrates. We experimentally characterized the mode of
action for novel sirtuin activators identified using
ultrahigh-throughput computational and experimental screening
techniques, uncovering for the first time the mechanism whereby they can
activate enzymes without allosteric sites. In particular, these
compounds were shown to increase up to two-fold the catalytic efficiency
of SIRT3 and its deacetylation rate under the essential cellular
cofactor nicotinamide adenine dinucleotide (NAD)+ depletion conditions
characteristic of old age. The compounds have the potential to
rejuvenate the activity of the major mitochondrial sirtuin to levels
observed in youth.
Selected Publications:
- Sequence optimization and designability of enzyme active sites. Raj Chakrabarti, Alexander M. Klibanov and Richard A. Friesner.
Proc. Natl. Acad. Sci. USA 102 (34) 12035-12040 (2005)
- Computational prediction of native protein ligand-binding and enzyme active site sequences.
Raj Chakrabarti, Alexander M. Klibanov and Richard A. Friesner.
Proc. Natl. Acad. Sci. USA 102 (29) 10153-10158 (2005)
- Mechanism of inhibition of the human sirtuin enzyme SIRT3 by nicotinamide: computational and experimental studies. Xiangying Guan, Ping Lin, Eric Knoll and Raj Chakrabarti.
PLOS ONE 9 (9): e107729 (2014)
- Molecular system identification for enzyme directed evolution and design. Xiangying Guan and Raj Chakrabarti.
J Chem Phys 147 124106 (2017)
- Biophysical characterization of hit compounds for mechanism-based enzyme activation. Xiangying Guan, Alok Upadhyay, Sudipto Munshi and Raj Chakrabarti.
PLOS ONE 13 (3): e0194175 (2018)
- Discovery of novel compounds as potent activators of Sirt3. Célina Reverdy, Gaetan Gitton, Xiangying Guan, Indranil Adhya, Rama Krishna Dumpati, Samir Roy, Santu Chall, Anisha Ghosh, Gauthier Errasti, Thomas Delacroix and Raj Chakrabarti.
Bioorganic and Medicinal Chemistry 73 116999 (2022)
Working Papers:
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