Chemical Modulation of Phospho-Signaling Pathways Involved in Cancer.

Advancements in our understanding of the molecular causes of cancer have led to the therapeutic targeting of key enzymes involved in cell growth. Kinase inhibitors have been the most successful forms of such targeted therapy for a select group of cancers. However, a comprehensive understanding of the biological roles of individual kinases is necessary for therapies to be effective in a majority of cancers. Thus, the development of selective kinase inhibitors is essential for continued improvement in cancer chemotherapy. Additionally, the exploration of non-kinase targets is indispensable in adding to the toolbox of effective anti-cancer agents. To increase the number of tools available for targeted therapy, we aimed to develop selective inhibitors for critical proteins involved in phospho-signaling pathways. Our studies include the development of an inhibitor of the fusion protein, Bcr-Abl, which is the primary driver of Chronic Myelogenous Leukemia (CML). Most current FDA-approved drugs are ineffective against a resistant form of CML bearing a T315I mutation in the kinase domain of Bcr-Abl. Through a hypothesis based on the prevailing model of selectivity, we developed an extremely selective compound with high potency for both the wild-type and mutant forms of Bcr-Abl. The adaptor protein Grb2 is an under-explored, non-kinase target for the treatment of CML and other cancers. Our efforts for targeting Grb2 centered on the hypothesis that utilizing conformational constraint for inhibitor development could lead to compounds with increased potency due to a lowered entropic cost of binding. Through the systematic development of conformationally constrained cyclic peptides, we identified a novel scaffold for the inhibition of Grb2 with in cellulo efficacy in a CML cell line. Lastly, while protein kinases have been traditionally targeted with small molecules directed to their ATP-binding site, targeting the peptide substrate-binding site of kinases offers an attractive alternative with several advantages. Our efforts attempted to circumvent the problems typically associated with substrate-competitive inhibitors by covalently inhibiting the target Akt1 kinase. As a whole, results from this dissertation should advance the development of potent and selective inhibitors and aid in the understanding of signaling pathways involved in cancer.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113580/1/sdphadke_1.pd

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Reply to Correspondence on “Synergy and Antagonism between Allosteric and Active-Site Inhibitors of Abl Tyrosine Kinase”

Manley and co-workers provide data demonstrating that, at super-pharmacological concentrations (300 μM), a ternary complex between Abl, asciminib, and ATP-competitive inhibitors is possible. The work in our manuscript concerns the interplay of asciminib (and GNF-2) with ATP-competitive inhibitors at pharmacologically relevant concentrations (Cmax=1.6–3.7 μM for asciminib). Manley and co-workers do not question any of the studies that we reported, nor do they provide explanations for how our work fits into their preferred model. Herein, we consider the data presented by Manley and co-workers. In addition, we provide new data supporting the findings in our Communication. Asciminib and ATP-competitive inhibitors do not simultaneously bind Abl at pharmacologically relevant concentrations unless the conformation selectivity for both ligands is matched.At pharmacologically relevant concentrations, asciminib and clinical adenosine triphosphate (ATP) kinase inhibitors cannot simultaneously bind to Abl kinase. Manley and co-workers correspond that at saturating concentrations (i.e., concentrations that are not achievable in a human), asciminib and dasatinib can simultaneously bind to Abl kinase.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/175174/1/ange202209518-sup-0001-misc_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/175174/2/ange202209518.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/175174/3/ange202209518_am.pd

Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase

Allosteric inhibitors of Abl kinase are being explored in the clinic, often in combination with ATP‐site inhibitors of Abl kinase. However, there are conflicting data on whether both ATP‐competitive inhibitors and myristoyl‐site allosteric inhibitors can simultaneously bind Abl kinase. Here, we determine whether there is synergy or antagonism between ATP‐competitive inhibitors and allosteric inhibitors of Abl. We observe that clinical ATP‐competitive inhibitors are not synergistic with allosteric ABL inhibitors, however, conformation‐selective ATP‐site inhibitors that modulate the global conformation of Abl can afford synergy. We demonstrate that kinase conformation is the key driver to simultaneously bind two compounds to Abl kinase. Finally, we explore the interaction of allosteric and conformation selective ATP‐competitive inhibitors in a series of biochemical and cellular assays.We describe a better understanding of the interaction between allosteric and ATP‐competitive inhibitors of Abl. Using a protease accessibility assay we developed, we determined the global conformation of Abl when bound to Abl inhibitors. We found that synergy between ATP‐competitive and allosteric inhibitors of Abl required a „matched“ kinase conformation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/169317/1/ange202105351_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/169317/2/ange202105351.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/169317/3/ange202105351-sup-0001-misc_information.pd

Reply to Correspondence on “Synergy and Antagonism between Allosteric and Active-Site Inhibitors of Abl Tyrosine Kinase”

Manley and co-workers provide data demonstrating that, at super-pharmacological concentrations (300 μM), a ternary complex between Abl, asciminib, and ATP-competitive inhibitors is possible. The work in our manuscript concerns the interplay of asciminib (and GNF-2) with ATP-competitive inhibitors at pharmacologically relevant concentrations (Cmax=1.6–3.7 μM for asciminib). Manley and co-workers do not question any of the studies that we reported, nor do they provide explanations for how our work fits into their preferred model. Herein, we consider the data presented by Manley and co-workers. In addition, we provide new data supporting the findings in our Communication. Asciminib and ATP-competitive inhibitors do not simultaneously bind Abl at pharmacologically relevant concentrations unless the conformation selectivity for both ligands is matched.At pharmacologically relevant concentrations, asciminib and clinical adenosine triphosphate (ATP) kinase inhibitors cannot simultaneously bind to Abl kinase. Manley and co-workers correspond that at saturating concentrations (i.e., concentrations that are not achievable in a human), asciminib and dasatinib can simultaneously bind to Abl kinase.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/175245/1/anie202209518_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/175245/2/anie202209518-sup-0001-misc_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/175245/3/anie202209518.pd

Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity

In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity