Professional Education


  • Bachelor of Science, Michigan State University (2011)
  • Doctor of Philosophy, University of Michigan Ann Arbor (2017)

Stanford Advisors


All Publications


  • Conformation-tunable ATP-competitive kinase inhibitors. Chemical communications (Cambridge, England) Agius, M. P., Ko, K., Johnson, T. K., Phadke, S., Soellner, M. B. 2022

    Abstract

    Small molecule kinase inhibitors have shown immense clinical utility for diverse indications. While >60 kinase inhibitors have been approved (and many more in clinical trials), it remains unclear whether the clinical efficacy of a kinase inhibitor is solely dependent on enzymatic inhibition, or whether non-catalytic functions play a role in the efficacy of some kinase inhibitors. Here, we designed and synthesized a series of pyrazolopyrimidine kinase inhibitors that modulate the global kinase conformation of c-Src kinase. Expanding upon our findings from the pyrazolopyrimidine inhibitor series, we designed, synthesized, and evaluated three pair of conformation-selective kinase inhibitors, each with a unique hinge-binding scaffold. We profiled each pair of kinase inhibitors across 468 kinases and identified 38 kinases that could be studied using these pair of conformation-selective inhibitors. We also explore the binding of conformation-selective kinase inhibitors to mutant kinases of EGFR, FLT3, and KIT. Together, these studies yield important insight into the design of conformation-tunable kinase inhibitors and provide a toolset of compounds to study the role of protein conformation on kinase signaling.

    View details for DOI 10.1039/d1cc06893h

    View details for PubMedID 35195624

  • Insights into the modular design of kinase inhibitors and application to Abl and Axl. RSC medicinal chemistry Phadke, S., Lopez-Barcons, L., Vandecan, N., Wu, Z., Johnson, T. K., Lachacz, E. J., Merajver, S. D., Soellner, M. B. 2022; 13 (1): 64-71

    Abstract

    Scaffold hopping is a common strategy for generating kinase inhibitors that bind to the DFG-out inactive conformation. Small structural differences in inhibitor scaffolds can have significant effects on potency and selectivity across the kinome, however, these effects are often not studied in detail. Herein, we outline a design strategy to generate an array of DFG-out conformation inhibitors with three different hinge-binders and two DFG-pocket groups. We studied inhibitor selectivity across a large segment of the kinome and elucidated binding preferences that can be used in scaffold hopping campaigns. Using these analyses, we identified two selective inhibitors that display low nanomolar potency against Axl or wild-type and clinically relevant mutants of Abl.

    View details for DOI 10.1039/d1md00296a

    View details for PubMedID 35224497

    View details for PubMedCentralID PMC8792823

  • Insights into the modular design of kinase inhibitors and application to Abl and Axl RSC MEDICINAL CHEMISTRY Phadke, S., Lopez-Barcons, L., Vandecan, N., Wu, Z., Johnson, T. K., Lachacz, E. J., Merajver, S. D., Soellner, M. B. 2021

    View details for DOI 10.1039/d1md00296a

    View details for Web of Science ID 000718311100001

  • Synergy and antagonism between allosteric and active-site inhibitors of Abl tyrosine kinase. Angewandte Chemie (International ed. in English) Johnson, T. K., Bochar, D. A., Vandecan, N. M., Furtado, J., Agius, M. P., Phadke, S., Soellner, M. 2021

    Abstract

    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.

    View details for DOI 10.1002/anie.202105351

    View details for PubMedID 34292655

  • Structure-activity mapping of ARHGAP36 reveals regulatory roles for its GAP homology and C-terminal domains. PloS one Nano, P. R., Johnson, T. K., Kudo, T., Mooney, N. A., Ni, J., Demeter, J., Jackson, P. K., Chen, J. K. 2021; 16 (5): e0251684

    Abstract

    ARHGAP36 is an atypical Rho GTPase-activating protein (GAP) family member that drives both spinal cord development and tumorigenesis, acting in part through an N-terminal motif that suppresses protein kinase A and activates Gli transcription factors. ARHGAP36 also contains isoform-specific N-terminal sequences, a central GAP-like module, and a unique C-terminal domain, and the functions of these regions remain unknown. Here we have mapped the ARHGAP36 structure-activity landscape using a deep sequencing-based mutagenesis screen and truncation mutant analyses. Using this approach, we have discovered several residues in the GAP homology domain that are essential for Gli activation and a role for the C-terminal domain in counteracting an N-terminal autoinhibitory motif that is present in certain ARHGAP36 isoforms. In addition, each of these sites modulates ARHGAP36 recruitment to the plasma membrane or primary cilium. Through comparative proteomics, we also have identified proteins that preferentially interact with active ARHGAP36, and we demonstrate that one binding partner, prolyl oligopeptidase-like protein, is a novel ARHGAP36 antagonist. Our work reveals multiple modes of ARHGAP36 regulation and establishes an experimental framework that can be applied towards other signaling proteins.

    View details for DOI 10.1371/journal.pone.0251684

    View details for PubMedID 33999959

  • Selective Proteolysis to Study the Global Conformation and Regulatory Mechanisms of c-Src Kinase. ACS chemical biology Agius, M. P., Ko, K. S., Johnson, T. K., Kwarcinski, F. E., Phadke, S., Lachacz, E. J., Soellner, M. B. 2019

    Abstract

    Protein kinase pathways are traditionally mapped by monitoring downstream phosphorylation. Meanwhile, the noncatalytic functions of protein kinases remain under-appreciated as critical components of kinase signaling. c-Src is a protein kinase known to have noncatalytic signaling function important in healthy and disease cell signaling. Large conformational changes in the regulatory domains regulate c-Src's noncatalytic functions. Herein, we demonstrate that changes in the global conformation of c-Src can be monitored using a selective proteolysis methodology. Further, we use this methodology to investigate changes in the global conformation of several clinical and nonclinical mutations of c-Src. Significantly, we identify a novel activating mutation observed clinically, W121R, that can escape down-regulation mechanisms. Our methodology can be expanded to monitor the global conformation of other tyrosine kinases, including c-Abl, and represents an important tool toward the elucidation of the noncatalytic functions of protein kinases.

    View details for DOI 10.1021/acschembio.9b00306

    View details for PubMedID 31287657

  • UM-9107: A selective wild-type and T315I Bcr-Abl inhibitor with in vivo activity against chronic myelogenous leukemia Phadke, S., Lopez-Barcons, L., Johnson, T. K., Lachacz, E. J., Merajver, S. D., Soellner, M. B. AMER ASSOC CANCER RESEARCH. 2019
  • Bivalent Inhibitors of c-Src Tyrosine Kinase That Bind a Regulatory Domain BIOCONJUGATE CHEMISTRY Johnson, T. K., Soellner, M. B. 2016; 27 (7): 1745-1749

    Abstract

    We have developed a general methodology to produce bivalent kinase inhibitors for c-Src that interact with the SH2 and ATP binding pockets. Our approach led to a highly selective bivalent inhibitor of c-Src. We demonstrate impressive selectivity for c-Src over homologous kinases. Exploration of the unexpected high level of selectivity yielded insight into the inherent flexibility of homologous kinases. Finally, we demonstrate that our methodology is modular and both the ATP-competitive fragment and conjugation chemistry can be swapped.

    View details for DOI 10.1021/acs.bioconjchem.6b00243

    View details for Web of Science ID 000380298900024

    View details for PubMedID 27266260

  • Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity ACS CHEMICAL BIOLOGY Kwarcinski, F. E., Brandvold, K. R., Phadke, S., Beleh, O. M., Johnson, T. K., Meagher, J. L., Seeliger, M. A., Stuckey, J. A., Soellner, M. B. 2016; 11 (5): 1296-1304

    Abstract

    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.

    View details for DOI 10.1021/acschembio.5b01018

    View details for Web of Science ID 000376473600017

    View details for PubMedID 26895387

  • Ordering a Dynamic Protein Via a Small-Molecule Stabilizer JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Wang, N., Majmudar, C. Y., Pomerantz, W. C., Gagnon, J. K., Sadowsky, J. D., Meagher, J. L., Johnson, T. K., Stuckey, J. A., Brooks, C. L., Wells, J. A., Mapp, A. K. 2013; 135 (9): 3363-3366

    Abstract

    Like many coactivators, the GACKIX domain of the master coactivator CBP/p300 recognizes transcriptional activators of diverse sequence composition via dynamic binding surfaces. The conformational dynamics of GACKIX that underlie its function also render it especially challenging for structural characterization. We have found that the ligand discovery strategy of Tethering is an effective method for identifying small-molecule fragments that stabilize the GACKIX domain, enabling for the first time the crystallographic characterization of this important motif. The 2.0 Å resolution structure of GACKIX complexed to a small molecule was further analyzed by molecular dynamics simulations, which revealed the importance of specific side-chain motions that remodel the activator binding site in order to accommodate binding partners of distinct sequence and size. More broadly, these results suggest that Tethering can be a powerful strategy for identifying small-molecule stabilizers of conformationally malleable proteins, thus facilitating their structural characterization and accelerating the discovery of small-molecule modulators.

    View details for DOI 10.1021/ja3122334

    View details for Web of Science ID 000315936700016

    View details for PubMedID 23384013

    View details for PubMedCentralID PMC3607081