11 research outputs found
The Discovery of (<i>S</i>)‑1-(6-(3-((4-(1-(Cyclopropanecarbonyl)piperidin-4-yl)-2-methylphenyl)amino)-2,3-dihydro‑1<i>H</i>‑inden-4-yl)pyridin-2-yl)-5-methyl‑1<i>H</i>‑pyrazole-4-carboxylic Acid, a Soluble Guanylate Cyclase Activator Specifically Designed for Topical Ocular Delivery as a Therapy for Glaucoma
Soluble
guanylate cyclase (sGC), the endogenous receptor for nitric
oxide (NO), has been implicated in several diseases associated with
oxidative stress. In a pathological oxidative environment, the heme
group of sGC can be oxidized becoming unresponsive to NO leading to
a loss in the ability to catalyze the production of cGMP. Recently
a dysfunctional sGC/NO/cGMP pathway has been implicated in contributing
to elevated intraocular pressure associated with glaucoma. Herein
we describe the discovery of molecules specifically designed for topical
ocular administration, which can activate oxidized sGC restoring the
ability to catalyze the production of cGMP. These efforts culminated
in the identification of compound <b>(+)-23</b>, which robustly
lowers intraocular pressure in a cynomolgus model of elevated intraocular
pressure over 24 h after a single topical ocular drop and has been
selected for clinical evaluation
FOCUS î—¸ Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists
Communication of data and ideas within
a medicinal chemistry project
on a global as well as local level is a crucial aspect in the drug
design cycle. Over a time frame of eight years, we built and optimized
FOCUS, a platform to produce, visualize, and share information on
various aspects of a drug discovery project such as cheminformatics,
data analysis, structural information, and design. FOCUS is tightly
integrated with internal services that involveî—¸among othersî—¸data
retrieval systems and <i>in-silico</i> models and provides
easy access to automated modeling procedures such as pharmacophore
searches, R-group analysis, and similarity searches. In addition,
an interactive 3D editor was developed to assist users in the generation
and docking of close analogues of a known lead. In this paper, we
will specifically concentrate on issues we faced during development,
deployment, and maintenance of the software and how we continually
adapted the software in order to improve usability. We will provide
usage examples to highlight the functionality as well as limitations
of FOCUS at the various stages of the development process. We aim
to make the discussion as independent of the software platform as
possible, so that our experiences can be of more general value to
the drug discovery community
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
Discovery of Darovasertib (NVP-LXS196), a Pan-PKC Inhibitor for the Treatment of Metastatic Uveal Melanoma
Uveal
melanoma (UM) is the most common primary intraocular malignancy
in the adult eye. Despite the aggressive local management of primary
UM, the development of metastases is common with no effective treatment
options for metastatic disease. Genetic analysis of UM samples reveals
the presence of mutually exclusive activating mutations in the Gq
alpha subunits GNAQ and GNA11. One of the key downstream targets of
the constitutively active Gq alpha subunits is the protein kinase
C (PKC) signaling pathway. Herein, we describe the discovery of darovasertib
(NVP-LXS196), a potent pan-PKC inhibitor with high whole kinome selectivity.
The lead series was optimized for kinase and off target selectivity
to afford a compound that is rapidly absorbed and well tolerated in
preclinical species. LXS196 is being investigated in the clinic as
a monotherapy and in combination with other agents for the treatment
of uveal melanoma (UM), including primary UM and metastatic uveal
melanoma (MUM)
Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models
The observed structure–activity
relationship of three distinct
ATP noncompetitive With-No-Lysine (WNK) kinase inhibitor series, together
with a crystal structure of a previously disclosed allosteric inhibitor
bound to WNK1, led to an overlay hypothesis defining core and side-chain
relationships across the different series. This in turn enabled an
efficient optimization through scaffold morphing, resulting in compounds
with a good balance of selectivity, cellular potency, and pharmacokinetic
profile, which were suitable for <i>in vivo</i> proof-of-concept
studies. When dosed orally, the optimized compound reduced blood pressure
in mice overexpressing human WNK1, and induced diuresis, natriuresis
and kaliuresis in spontaneously hypertensive rats (SHR), confirming
that this mechanism of inhibition of WNK kinase activity is effective
at regulating cardiovascular homeostasis
Discovery of Darovasertib (NVP-LXS196), a Pan-PKC Inhibitor for the Treatment of Metastatic Uveal Melanoma
Uveal
melanoma (UM) is the most common primary intraocular malignancy
in the adult eye. Despite the aggressive local management of primary
UM, the development of metastases is common with no effective treatment
options for metastatic disease. Genetic analysis of UM samples reveals
the presence of mutually exclusive activating mutations in the Gq
alpha subunits GNAQ and GNA11. One of the key downstream targets of
the constitutively active Gq alpha subunits is the protein kinase
C (PKC) signaling pathway. Herein, we describe the discovery of darovasertib
(NVP-LXS196), a potent pan-PKC inhibitor with high whole kinome selectivity.
The lead series was optimized for kinase and off target selectivity
to afford a compound that is rapidly absorbed and well tolerated in
preclinical species. LXS196 is being investigated in the clinic as
a monotherapy and in combination with other agents for the treatment
of uveal melanoma (UM), including primary UM and metastatic uveal
melanoma (MUM)
Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models
The observed structure–activity
relationship of three distinct
ATP noncompetitive With-No-Lysine (WNK) kinase inhibitor series, together
with a crystal structure of a previously disclosed allosteric inhibitor
bound to WNK1, led to an overlay hypothesis defining core and side-chain
relationships across the different series. This in turn enabled an
efficient optimization through scaffold morphing, resulting in compounds
with a good balance of selectivity, cellular potency, and pharmacokinetic
profile, which were suitable for <i>in vivo</i> proof-of-concept
studies. When dosed orally, the optimized compound reduced blood pressure
in mice overexpressing human WNK1, and induced diuresis, natriuresis
and kaliuresis in spontaneously hypertensive rats (SHR), confirming
that this mechanism of inhibition of WNK kinase activity is effective
at regulating cardiovascular homeostasis
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 siteî—¸a 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
Discovery and Characterization of Allosteric WNK Kinase Inhibitors
Protein kinases are
known for their highly conserved adenosine
triphosphate (ATP)-binding site, rendering the discovery of selective
inhibitors a major challenge. In theory, allosteric inhibitors can
achieve high selectivity by targeting less conserved regions of the
kinases, often with an added benefit of retaining efficacy under high
physiological ATP concentration. Although often overlooked in favor
of ATP-site directed approaches, performing a screen at high ATP concentration
or stringent hit triaging with high ATP concentration offers conceptually
simple methods of identifying inhibitors that bind outside the ATP
pocket. Here, we applied the latter approach to the With-No-Lysine
(K) (WNK) kinases to discover lead molecules for a next-generation
antihypertensive that requires a stringent safety profile. This strategy
yielded several ATP noncompetitive WNK1–4 kinase inhibitors,
the optimization of which enabled cocrystallization with WNK1, revealing
an allosteric binding mode consistent with the observed exquisite
specificity for WNK1–4 kinases. The optimized compound inhibited
rubidium uptake by sodium chloride cotransporter 1 (NKCC1) in HT29
cells, consistent with the reported physiology of WNK kinases in renal
electrolyte handling