9 research outputs found
Structure–Efficiency Relationship of [1,2,4]Triazol-3-ylamines as Novel Nicotinamide Isosteres that Inhibit Tankyrases
Tankyrases 1 and 2 are members of
the poly(ADP-ribose) polymerase
(PARP) family of enzymes that modulate Wnt pathway signaling. While
amide- and lactam-based nicotinamide mimetics that inhibit tankyrase
activity, such as XAV939, are well-known, herein we report the discovery
and evaluation of a novel nicotinamide isostere that demonstrates
selectivity over other PARP family members. We demonstrate the utilization
of lipophilic efficiency-based structure–efficiency relationships
(SER) to rapidly drive the evaluation of this series. These efforts
led to a series of selective, cell-active compounds with solubility,
physicochemical, and in vitro properties suitable for further optimization
Structural and Functional Consequences of Three Cancer-Associated Mutations of the Oncogenic Phosphatase SHP2
The proto-oncogene <i>PTPN11</i> encodes a cytoplasmic
protein tyrosine phosphatase, SHP2, which is required for normal development
and sustained activation of the Ras-MAPK signaling pathway. Germline
mutations in SHP2 cause developmental disorders, and somatic mutations
have been identified in childhood and adult cancers and drive leukemia
in mice. Despite our knowledge of the <i>PTPN11</i> variations
associated with pathology, the structural and functional consequences
of many disease-associated mutants remain poorly understood. Here,
we combine X-ray crystallography, small-angle X-ray scattering, and
biochemistry to elucidate structural and mechanistic features of three
cancer-associated SHP2 variants harboring single point mutations within
the N-SH2:PTP interdomain autoinhibitory interface. Our findings directly
compare the impact of each mutation on autoinhibition of the phosphatase
and advance the development of structure-guided and mutation-specific
SHP2 therapies
[1,2,4]Triazol-3-ylsulfanylmethyl)-3-phenyl-[1,2,4]oxadiazoles: Antagonists of the Wnt Pathway That Inhibit Tankyrases 1 and 2 via Novel Adenosine Pocket Binding
The Wnt signaling pathway is critical to the regulation
of key
cellular processes. When deregulated, it has been shown to play a
crucial role in the growth and progression of multiple human cancers.
The identification of small molecule modulators of Wnt signaling has
proven challenging, largely due to the relative paucity of druggable
nodes in this pathway. Several recent publications have identified
small molecule inhibitors of the Wnt pathway, and tankyrase (TNKS)
inhibition has been demonstrated to antagonize Wnt signaling via axin
stabilization. Herein, we report the early hit assessment of a series
of compounds previously reported to antagonize Wnt signaling. We report
the biophysical, computational characterization, structure–activity
relationship, and physicochemical properties of a novel series of
[1,2,4]triazol-3-ylsulfanylmethyl)-3-phenyl-[1,2,4]oxadiazole inhibitors
of TNKS1 and 2. Furthermore, a cocrystal structure of compound <b>24</b> complexed to TNKS1 demonstrates an alternate binding mode
for PARP family member proteins that does not involve interactions
with the nicotinamide binding pocket
Antibacterial and Solubility Optimization of Thiomuracin A
Synthetic
studies of the antimicrobial secondary metabolite thiomuracin
A (<b>1</b>) provided access to analogues in the Northern region
(C2–C10). Selective hydrolysis of the C10 amide of lead compound <b>2</b> and subsequent derivatization led to novel carbon- and nitrogen-linked
analogues (e.g., <b>3</b>) which improved antibacterial potency
across a panel of Gram-positive organisms. In addition, congeners
with improved physicochemical properties were identified which proved
efficacious in murine sepsis and hamster <i>C. difficile</i> models of disease. Optimal efficacy in the hamster model of <i>C. difficile</i> was achieved with compounds that possessed
both potent antibacterial activity and high aqueous solubility
Optimization of Fused Bicyclic Allosteric SHP2 Inhibitors
SHP2 is a nonreceptor protein tyrosine phosphatase within the mitogen-activated protein kinase (MAPK) pathway controlling cell growth, differentiation, and oncogenic transformation. SHP2 also participates in the programed cell death pathway (PD-1/PD-L1) governing immune surveillance. Small-molecule inhibition of SHP2 has been widely investigated, including in our previous reports describing SHP099 (2), which binds to a tunnel-like allosteric binding site. To broaden our approach to allosteric inhibition of SHP2, we conducted additional hit finding, evaluation, and structure-based scaffold morphing. These studies, reported here in the first of two papers, led to the identification of multiple 5,6-fused bicyclic scaffolds that bind to the same allosteric tunnel as 2. We demonstrate the structural diversity permitted by the tunnel pharmacophore and culminated in the identification of pyrazolopyrimidinones (e.g., SHP389, 1) that modulate MAPK signaling in vivo. These studies also served as the basis for further scaffold morphing and optimization, detailed in the following manuscript
Dual Allosteric Inhibition of SHP2 Phosphatase
SHP2 is a cytoplasmic protein tyrosine
phosphatase encoded by the <i>PTPN11</i> gene and is involved
in cell proliferation, differentiation, and survival. Recently, we
reported an allosteric mechanism of inhibition that stabilizes the
auto-inhibited conformation of SHP2. SHP099 (<b>1</b>) was identified
and characterized as a moderately potent, orally bioavailable, allosteric
small molecule inhibitor, which binds to a tunnel-like pocket formed
by the confluence of three domains of SHP2. In this report, we describe
further screening strategies that enabled the identification of a
second, distinct small molecule allosteric site. SHP244 (<b>2</b>) was identified as a weak inhibitor of SHP2 with modest thermal
stabilization of the enzyme. X-ray crystallography revealed that <b>2</b> binds and stabilizes the inactive, closed conformation of
SHP2, at a distinct, previously unexplored binding sitea cleft
formed at the interface of the <i>N</i>-terminal SH2 and
PTP domains. Derivatization of <b>2</b> using structure-based
design resulted in an increase in SHP2 thermal stabilization, biochemical
inhibition, and subsequent MAPK pathway modulation. Downregulation
of DUSP6 mRNA, a downstream MAPK pathway marker, was observed in KYSE-520
cancer cells. Remarkably, simultaneous occupation of both allosteric
sites by <b>1</b> and <b>2</b> was possible, as characterized
by cooperative biochemical inhibition experiments and X-ray crystallography.
Combining an allosteric site 1 inhibitor with an allosteric site 2
inhibitor led to enhanced pharmacological pathway inhibition in cells.
This work illustrates a rare example of dual allosteric targeted protein
inhibition, demonstrates screening methodology and tactics to identify
allosteric inhibitors, and enables further interrogation of SHP2 in
cancer and related pathologies
6-Amino-3-methylpyrimidinones as Potent, Selective, and Orally Efficacious SHP2 Inhibitors
Protein tyrosine phosphatase SHP2 is an oncoprotein associated with cancer as well as a potential immune modulator because of its role in the programmed cell death PD-L1/PD-1 pathway. In the preceding manuscript, we described the optimization of a fused, bicyclic screening hit for potency, selectivity, and physicochemical properties in order to further expand the chemical diversity of allosteric SHP2 inhibitors. In this manuscript, we describe the further expansion of our approach, morphing the fused, bicyclic system into a novel monocyclic pyrimidinone scaffold through our understanding of SAR and use of structure-based design. These studies led to the identification of SHP394 (1), an orally efficacious inhibitor of SHP2, with high lipophilic efficiency, improved potency, and enhanced pharmacokinetic properties. We also report other pyrimidinone analogues with favorable pharmacokinetic and potency profiles. Overall, this work improves upon our previously described allosteric inhibitors and exemplifies and extends the range of permissible chemical templates that inhibit SHP2 via the allosteric mechanism
Identification of NVP-TNKS656: The Use of Structure–Efficiency Relationships To Generate a Highly Potent, Selective, and Orally Active Tankyrase Inhibitor
Tankyrase
1 and 2 have been shown to be redundant, druggable nodes
in the Wnt pathway. As such, there has been intense interest in developing
agents suitable for modulating the Wnt pathway in vivo by targeting
this enzyme pair. By utilizing a combination of structure-based design
and LipE-based structure efficiency relationships, the core of XAV939
was optimized into a more stable, more efficient, but less potent
dihydropyran motif <b>7</b>. This core was combined with elements
of screening hits <b>2</b>, <b>19</b>, and <b>33</b> and resulted in highly potent, selective tankyrase inhibitors that
are novel three pocket binders. NVP-TNKS656 (<b>43</b>) was
identified as an orally active antagonist of Wnt pathway activity
in the MMTV-Wnt1 mouse xenograft model. With an enthalpy-driven thermodynamic
signature of binding, highly favorable physicochemical properties,
and high lipophilic efficiency, NVP-TNKS656 is a novel tankyrase inhibitor
that is well suited for further in vivo validation studies
Allosteric Inhibition of SHP2: Identification of a Potent, Selective, and Orally Efficacious Phosphatase Inhibitor
SHP2
is a nonreceptor protein tyrosine phosphatase (PTP) encoded by the <i>PTPN11</i> gene involved in cell growth and differentiation
via the MAPK signaling pathway. SHP2 also purportedly plays an important
role in the programmed cell death pathway (PD-1/PD-L1). Because it
is an oncoprotein associated with multiple cancer-related diseases,
as well as a potential immunomodulator, controlling SHP2 activity
is of significant therapeutic interest. Recently in our laboratories,
a small molecule inhibitor of SHP2 was identified as an allosteric
modulator that stabilizes the autoinhibited conformation of SHP2.
A high throughput screen was performed to identify progressable chemical
matter, and X-ray crystallography revealed the location of binding
in a previously undisclosed allosteric binding pocket. Structure-based
drug design was employed to optimize for SHP2 inhibition, and several
new protein–ligand interactions were characterized. These studies
culminated in the discovery of 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)pyrazin-2-amine
(SHP099, <b>1</b>), a potent, selective, orally bioavailable,
and efficacious SHP2 inhibitor