Maly Lab Publications:

^Zhang, J. Z.; Nguyen, W. H.; Greenwood, N.; Rose, J. C.; Ong, S. E.; ^Maly, D. J.; ^Baker, D. “Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution.” Nat. Biotech. 2024, in press . ^ = co-corresponding authors

Chakraborty, S.; Ahler, E.; Simon, J. J.; Fang, L.; Potter, Z. E.; Sitko, K. A.; Stephany, J. J.; Guttman, M.; ^Fowler, D. M.; ^Maly, D. J. “Profiling of drug resistance in Src kinase at scale uncovers a regulatory network coupling autoinhibition and catalytic domain dynamics.” Cell Chem. Biol. 2024, 31, 207. ^ = co-corresponding authors

Parsons, M.; Parsons, B.; Dean, M.; DeRocher, A. E.; Islam, Z.; Maly, D. J.; Jensen, B. C. “An essential Trypanosoma brucei protein kinase: a functional analysis of regulation and the identification of inhibitors.” Front. Parasitol. 2023, 2, 1272378.

Nguyen, V.; Ahler, E.; Sitko, K. A.; Stephany, J. J.; ^Maly. D. J.; ^Fowler, D. M. “Molecular determinants of Hsp90 dependence of Src kinase revealed by deep mutational scanning.” Protein Sci. 2023, 32, e4656. ^ = co-corresponding authors

Wei, C. T.; Popp, N. A.; Peleg, O.; Powell, R. L.; Borenstein, E.; ^Maly, D. J.; ^Fowler, D. M. “A chemically-controlled Cas9 switch enables temporal modulation of diverse effectors” Nat. Chem. Biol. 2023, 19, 981. ^ = co-corresponding authors

Tambo, C. S.; Tripathi, S. M.; Perera, B. G. K.; Maly, D. J.; Bridges, A. J.; Kiss, G.; Rubin, S. M. “Biolayer Interferometry Assay for Cyclin-Dependent Kinase-Cyclin Association Reveals Diverse Effects of Cdk2 Inhibitors on Cyclin Binding Kinetics” ACS Chem. Biol. 2023, 18, 431.

Golkowski, M.; Lius, A,; Sapre, T.; Lau, H-T; Moreno, T.; Maly, D. J.; Ong, S-E “Multiplexed kinase interactome profiling quantifies cellular network activity and plasticity” Mol. Cell, 2023, 83, 803.

Feldman, H. C.; Ghosh, R.; Auyeung, V.; Mueller, J. L.; Kim, J.; Potter, Z. E.; Perera, B. G. K.; Vidadala, V. N.; Olivier, A.; Backes, B. J.; Zikherman, J.; ^Papa, F. R.; ^Maly, D. J. “ATP-Competitive Partial Antagonists of the IRE1α RNase Segregate Outputs of the UPR” Nat. Chem. Biol. 2021, 17, 1148-56. ^ = co-corresponding authors

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Hulverson, M. A.; Choi, R.; Vidadala, R. S. R.; Whitman, G. R.; Vidadala, V. N.; Ojo, K. K.; Lynn K. Barrett, L. K.; Lynch, J. J.; Marsh, K.; Kempf, D. J.; Maly, D. J.; Van Voorhis, W. C. “Pyrrolopyrimidine Bumped Kinase Inhibitors for Treatment of Cryptosporidiosis” ACS Infect. Dis. 2021, 7, 1200.

Van Voorhis, W. C.; Hulverson, M. A.; Choi, R.; Huang, W.; Arnold, S. L. M.; Schaefer, D. A.; Betzer, D. P.; Vidadala, R. S. R.; Leef, S.; Whitman, G. R.; Barrett, L. K.; Maly, D. J.; Riggs, M. W.; Fan, E.; Kennedy, T. J.; Tzipori, S.; Doggett, J. S.; Winzer, P.; Anghel, N.; Imhof, D.; Müller, J.; Hemphill, A.; Ferre, I.; Sanchez-Sanchez, R.; Ortega-Mora, L. M.; Ojo, K. K. “One Health Therapeutics: Target-Based Drug Development for Cryptosporidiosis and Other Apicomplexa Diseases” Vet. Parasitol., 2021, 289, 109336.

Fang, L.; Maly, D. J. “The Right Tool for the Job: A Chemical and Genetic Toolkit for Interrogating DCLK1 Function” Cell Chem. Biol. 2020, 27, 1221-3.

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Potter, Z. E.; Lau, H-T; Chakraborty, S.; Fang, L.; Guttman, M.; Ong, S-E.; Fowler, D. M.; Maly, D. J. “Parallel Chemoselective Profiling for Mapping Protein Structure” Cell Chem. Biol. 2020, 27, 1084-96. (PMCID: PMC7484201)

Fang, L.; Vilas-Boas, J.; Chakraborty, S.; Potter, Z. E.; Register, A. C.; Seeliger, M. A.; Maly, D. J. “How ATP-competitive inhibitors allosterically modulate tyrosine kinases that contain a Src-like regulatory architecture” ACS Chem. Biol. 2020, 15, 2005-16.

Choi, R.; Hulverson, M. A.; Huang, W.; Vidadala, R. S. R.; Whitman, G. R.; Barrett, L. K.; Schaefer, D. A.; Betzer, D. P.; Riggs, M. W.; Doggett J. S.; Hemphill. A. Ortega-Mora, L. M.; McCloskey, M. C.; Arnold, S. L. M.; Hackman, R. C.; Marsh, K. C.; Lynch, J. J.; Freiberg, G. M.; Leroy, B. E.; Kempf, D. J.; Choy. R. K. M.; de Hostos, E. L, Maly, D. J.; Fan, E.; Ojo, K. K.; Van Voorhis, W. C. “Bumped Kinase Inhibitors as therapy for apicomplexan parasitic diseases: lessons learned.” Int. J. Parasitol. 2020, 50, 413-22. 

Anghel, N; Winzer, P. A.; Imhof, D.; Müller, J.; Langa, J.; Rieder, J.; Barrett, L. K.; Vidadala, R. S. R.; Huang, W.; Choi, R.; Hulverson, M. A.; Whitman, G. R.; Arnold, S. L.; Van Voorhis, W. C.; Ojo, K. K.; Maly, D. J.; Fan, E.; Hemphill, A. “Comparative assessment of the effects of bumped kinase inhibitors on early zebrafish embryo development and pregnancy in mice” Int. J. Antimicrob. Agents, 2020, 56, 106099.

Golkowski, M.; Lau, H-T; Chan, M.; Kenerson, H.; Vidadala, V. N.; Shoemaker, A.; Maly, D. J.; Yeung, R. S.; Gujral, T. S.; Ong, S-E “Pharmacoproteomics identifies kinase pathways that drive the epithelial-mesenchymal transition and drug resistance in hepatocellular carcinoma” Cell Syst. 2020, 11, 196-207. (PMCID: PMC7484106)

Golkowski, M.; Vidadala, V. N.; Lau, H-T; Shoemaker, A.; Shimizu-Albergine, M.; Beavo, J.; Maly, D. J.; Ong, S-E “Highly sensitive kinobead chemoproteomics enables comprehensive profiling of kinase signaling network activity” J. Prot. Res. 2020, 19, 1235-47. (PMCID: PMC7537592)

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^Rose, J. C.; Popp, N. A.; Richardson, C. D.; Stephany, J. J.; Mathieu, J.; Wei, C. T.; Corn, J. E.; ^Maly, D. J.; ^Fowler D. M. “Suppression of unwanted CRISPR/Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs” Nat. Comm. 2020, 11, 2697. ^ = co-corresponding authors

Rose, J. C.; Dieter, E. M.; Cunningham-Bryant, D.; Maly, D. J. “Examining RAS pathway rewiring with a chemically inducible activator of RAS” Small GTPases 2020, 11, 413-20. (PMCID: PMC7549627)

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Dieter, E. M.; Maly, D. J. “A chemically-controlled system for activating RAS GTPases” Methods Enzymol. 2020, 633, 103-117.

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Wei, C. T.; Maly, D. J.; Fowler, D. M. “Temporal and rheostatic control of genome editing with a chemically-inducible Cas9” Methods Enzymol. 2020, 633, 119-141.

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Fang, L.; Chakraborty, S.; Dieter, E. M.; Potter, Z. E.; Lombard, C. K.; Maly, D. J. “A Chemoproteomic Method for Profiling Inhibitor-Bound Kinase Complexes” J. Am Chem. Soc. 2019, 141, 11912-11922. (PMCID: PMC6688853)

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Foight, G. W.; Wang, Z.; Wei, C. T.; Greisen, P. J.; Warner, K.; Cunningham-Bryant, D.; Park, K.; Brunette, T. J.; Sheffler, W.; Baker, D.; Maly, D. J. “Multi-input chemical control of protein dimerization for programming graded cellular responses” Nat. Biotech. 2019, 37, 1209-16. (PMCID: PMC6776690)

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Cunningham-Bryant, D.; Dieter, E. M.; Foight, G. W.; Rose, J. C.; Maly, D. J. “A Chemically-Disrupted Proximity System for Controlling Dynamic Cellular Processes” J. Am Chem. Soc. 2019, 141, 3352-5. (PMCID: PMC6492022)

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Ahler, E.; Register, A. C.; Chakraborty, S.; Fang, L.; Dieter, E. M.; Sitko, K. A.; Vidadala, R. S. R.; Trevillian, B. M.; Golkowski, M.; Gelman, H.; Stephany, J. J.; Rubin, A. F.; Merritt, E. A.; ^Fowler, D. M.; ^Maly, D. J. “A combined approach reveals a regulatory mechanism coupling Src’s kinase activity, localization, and phosphotransferase-independent functions” Mol. Cell 2019, 74, 393-408. (PMCID: PMC6474823)

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Bucko, P. J.; Lombard, C. K.; Rathbun, L.; Garcia, I.; Bhat, A.; Wordeman, L.; Smith, F. D.; Maly, D. J.; Henly, H.; Scott, J. D. “Subcellular drug targeting illuminates local kinase action” eLife 2019, 8, pii: e52220. (PMCID: PMC6930117)

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Feldman, H. C.; Vidadala, V. N.; Potter, Z. E.; Papa, F.R.; Backes, B. J.; Maly, D. J. “Development of a chemical toolset for studying the paralog-specific function of IRE1” ACS Chem. Biol. 2019, 14, 2595-605. (PMCID: PMC6925334)

Moore, P. C.; Qi, J. Y.; Thamsen, M.; Ghosh, R.; Peng, J.; Gliedt, M.  J.; Meza-Acevedo, R.; Warren, R. E.; Hiniker, A.; Kim G. E.; Maly, D. J.; Backes, B. J.; Papa, F. R.; Oakes S. A. “Parallel signaling through IRE1α and PERK regulates pancreatic neuroendocrine tumor growth and survival” Cancer Res. 2019, 6190-203.

Arnold, S. L. M.; Ryan Choi, R.; Hulverson, M. A.; Whitman, G. R.; McCloskey, M. C.; Dorr, C. S.; Vidadala, R. S. R.; Khatod, M.; Morada, M.; Barrett, L. K.; Maly, D. J.; Yarlett, N.; Van Voorhis, W. C. “P-gp mediated efflux reduces the in vivo efficacy of a therapeutic targeting the gastrointestinal parasite Cryptosporidium” J. Infect. Dis. 2019, 220, 1188-98. (PMCID: PMC6736360)

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Chakraborty, S.; Inukai, T.; Fang, L.; Golkowski, M.; Maly, D. J. “Targeting dynamic ATP-binding site features allows discrimination between highly homologous protein kinases” ACS Chem. Biol. 2019, 14, 1249-59. (PMCID: PMC6642640)

Shrestha, A.; Ojo, K. K.; Koston, F.; Ruttkowski, B.; Vidadalac, R. S. R.; Dorr, C. S.; Navaluna, E. D.; Whitman, G. R.; Barr, K. F.; Barrett, L. K.; Hulverson, M. A.; Choi, R.; Michaels, S. A.; Maly, D. J.; Hemphill, A.; Van Voorhis, W. C.; Joachim, A.; “Bumped kinase inhibitor 1369 is effective against Cystoisospora suis in vivo and in vitro” Int. J. Parasit. Drugs Drug Resist. 2019, 10, 9-19.

Thamsen, M.; Ghosh, R.; Auyeung, V. C.; Brumwell, A.; Chapman, H. A.; Backes, B. J.; Perara, B. G. K.; Maly, D. J.; Sheppard, D.; Papa, F. R. “Small molecule inhibition of IRE1α kinase/RNase has anti-fibrotic effects in the lung” PLoS One 2019, 14, e0209824.

Hulverson, M. A.;  Bruzual, I.; McConnell, E. V.; Huang, W.;  Vidadala, R. S. R.; Choi, R.;  Arnold, S. L. M.; Whitman, G. R.; McCloskey, M. C.;  Barrett, L. K.;  Rivas, K. L.; Scheele, S.;  DeRocher, A. E.; Parsons. M.; Ojo, K. K.; Maly, D. J.; Fan, E.; Van Voorhis, W. C.; Doggett, J. S. “Pharmacokinetics and In Vivo Efficacy of Pyrazolopyrimidine, Pyrrolopyrimidine and 5-Aminopyrazole-4-Carboximide Bumped Kinase Inhibitors against Toxoplasmosis” J. Infect. Dis. 2019, 219, 1464-73.

Scheele, S.; Geiger, J. A.; DeRocher, A. E.; Choi, R.; Smith, T. R.; Hulverson, M. A.; Vidadala, R. S. R.; Barrett, L. K.; Maly, D. J.; Merritt, E. A.; Ojo, K. K.; Van Voorhis, W. C.; Parsons, M. “Toxoplasma calcium-dependent protein kinase 1 inhibitors: probing activity and resistance using cellular thermal shift assays” Antimicrob. Agents Chemother. 2018, 62, e00051-18.

Vidadala, R. S. R.; Golkowski, M.; Hulversona, M. A.; Choi, R.; McCloskey, M. C.; Whitman, G. R.; Huang, W.; Arnold, S. L. M.; Barrett, L. K.; Fan, E.; Merritt, E. A.; Van Voorhis, W. C.; Ojo, K. K.; Maly, D. J. “7H-pyrrolo[2,3-d]pyrimidin-4-amine based inhibitors of calcium dependent protein kinase 1 have distinct inhibitory and oral pharmacokinetic characteristics compared with 1Hpyrazolo[3,4-d]pyrimidin-4-amine based inhibitors.” ACS Infect. Dis. 2018, 4, 516-22.

Gimenez, F.; Hines, S. A.; Evanoff, R.; Ojo, K. K.; Van Voorhis, W. C.; Maly, D. J.; Vidadala, R. S. R.; Mealey, R. H. “In vitro growth inhibition of Theileria equi by bumped kinase inhibitors” Vet. Parasitol., 2018, 251, 90-94.

Golkowski, M.; Perera, B. G. K.; Vidadala, V. N.; Ojo, K. K.; Van Voorhis, W. C.; ^Maly D. J.; ^Ong; S-E “Kinome chemoproteomics characterization of pyrrolo[3,4-c]pyrazoles as potent and selective inhibitors of glycogen synthase kinase 3” Mol. Omics, 2018, 1, 26-36. (PMCID:  PMC5939582)

Rose, J. C.; Stephany, J. J.; Wei, C. T.; ^Fowler D. M.; ^Maly, D. J. “Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics” ACS Chem. Biol. 2018, 13, 438-442. (PMCID:  PMC5821106)

Huang W, Choi R, Hulverson MA, Zhang Z, McCloskey MC, Schaefer DA, Whitman GR, Barrett LK, Vidadala RSR, Riggs MW, Maly DJ, Van Voorhis WC, Ojo KK, Fan E. 5-Aminopyrazole-4-Carboxamide-Based Compounds Prevent the Growth of Cryptosporidium parvum. Antimicrob Agents Chemother. 2017 Jul 25;61(8). pii: e00020-17. doi: 10.1128/AAC.00020-17

Rose JC, Stephany JJ, Valente WJ, Trevillian BM, Dang HV, Bielas JH, Maly DJ, Fowler DM. Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics. Nat Methods (2017), doi:10.1038/nmeth.4368.

Morita S, Villalta SA, Feldman HC, Register AC, Rosenthal W, Hoffmann-Petersen IT, Mehdizadeh M, Ghosh R, Wang L, Colon-Negron K, Meza-Acevedo R, Backes BJ, Maly DJ, Bluestone JA, Papa FR. Targeting ABL-IRE1α Signaling Spares ER-Stressed Pancreatic β Cells to Reverse Autoimmune Diabetes. Cell Metab. 2017 May 2;25(5):1207. doi.org/10.1016/j.cmet.2017.03.018 (PMID: 28467938)

Arnold SLM, Choi R, Hulverson MA, Schaefer DA, Vinayak S, Vidadala RSR, McCloskey MC, Whitman GR, Huang W, Barrett LK, Ojo KK, Fan E, Maly DJ, Riggs MW, Striepen B, Van Voorhis WC. Bumped kinase inhibitor gastrointestinal exposure is necessary to treat Cryptosporidium infection. J Infect Dis. 2017 May 24. doi: 10.1093/infdis/jix247. (PMID: 28541457)

Rose, J. C.; Huang, P-S.; Camp, N. D.; Ye, J.; Leidal, A. M.; Goreshnik, I.; Trevillian, B. M.; Dickinson, M. S.; Cunningham-Bryant, D.; Debnath, J.; Baker, D.; Wolf-Yadlin, A.; Maly, D. J. A computationally engineered RAS rheostat reveals RAS/ERK signaling dynamics. Nat. Chem. Biol. 2017, 13, 119-26. (PMCID: PMC5161653)

Golkowski, M.; Vidadala, R. S. R.; Lombard, C. K.; Suh H. W.; Maly D. J.; Ong; S-E. Kinobead and single-shot LC-MS profiling identifies selective PKD inhibitors. J. Proteome Res. 2017 Mar 3;16(3):1216-1227. doi: 10.1021/acs.jproteome.6b00817. (PMID:28102076)

Van Voorhis, W. C.; Doggett, J. S.; Parsons, M.; Hulverson, M. A.; Choi, R.; Arnold, S.; Riggs, M. W.; Hemphill, A.; Howe, D. K.; Mealey, R. H.; Lau, A. O. T.; Merritt, E.A.; Maly, D. J.; Fan, E.; Ojo, K. K. Extended-Spectrum Antiprotozoal Bumped Kinase Inhibitors: A Review. Exp. Parasit. 2017, doi: 10.1016/j.exppara.2017.01.001

Müller, J.; Aguado-Martíneza, A.; Balmera, V.; Maly, D. J.; Fan, E.; Ortega-Morad, L-M.; Ojo, K. K.; Van Voorhis, W. C.; Hemphill, A. Two novel CDPKI-inhibitors interfere with vertical transmission in mice infected with Neospora caninum tachyzoites. Antimicrob. Agents Chemother. 2017, 61, in press.

Golkowski, M.; Maly D. J.; Ong; S-E. Proteomic profiling of protein kinase inhibitor targets by mass spectrometry. Methods Mol. Biol. 2017, in press.

Register, A. C.; Chakraborty, S.; Maly, D. J. Allosteric Modulation of Src-Family Kinases with ATP-Competitive Inhibitors. Methods Mol. Biol. 2017, in press.

Feldman, H. C.; Maly, D. J. Profiling the Dual Enzymatic Activities of the Serine/Threonine Kinase IRE1α. Methods Mol. Biol. 2017, 1513, 233-42.

Feldman, H. C.; Tong, M.; Wang, l.; Meza-Acevedo, R.; Gobillot, T. A.; Lebedev, I.; Gliedt, M. J. Hari, S. B.; Mitra, A. K.; Backes, B. J.; Papa, F. R.; Seeliger, M. A.; Maly, D. J. Structural and Functional Analysis of the Allosteric Inhibition of IRE1α with ATP-Competitive Ligands. ACS Chem. Biol. 2016, 11, 2195-205. (PMCID: PMC4992410)

Bansal, A.; Ojo, K. K.; Mu, J.; Maly, D. J.; Van Voorhis, W. C.; Miller, L. H. Reduced activity of mutant calcium dependent protein kinase 1 (CDPK1) is compensated in Plasmodium falciparum through the action of Protein Kinase G. mBio, 2016, 7, e02011-16.

Huang, W.; Hulverson, M. A.; Zhang, Z.; Choi, R.; Hart, K. J.; Kennedy, M.; Vidadala, R.S. R.; Maly, D. J.; Van Voorhis, W.C.; Lindner, S. E.; Fan, E.; Ojo, K. K. 5-Aminopyrazole-4-carboxamide analogues are selective inhibitors of Plasmodium falciparum microgametocyte exflagellation and potential malaria transmission blocking agents. Bioorg. Med. Chem. Lett. 2016, 26, 5487-91.

Schaefer, D. A.; Betzer, D. P.; Smith, K. D.; Millman, Z. G.; Michalski, H. C.; Menchaca, S. E.; Zambriski, J. A.; Ojo, K. K.; Hulverson, M. A.; Arnold, S. L. M.; Rivas, K. L.; Vidadala, R. S. R. Huang, W.; Barrett, L. K.; Maly, D. J.; Fan, E.; Van Voorhis, W. C.; Riggs, M. W. Novel Bumped Kinase Inhibitors are Safe and Effective Therapeutics in the Neonatal Calf Clinical Model for Cryprosporidiosis. J. Infect. Dis. 2016, 214, 1856-64

Ojo, K.K.; Dangoudoubiyam, S.; Verma, S. K.; Scheele, S.; DeRocher, A. E.; Yeargan, M.; Choi, R.; Smith, T. R.; Rivas, K. L.; Hulverson, M. A.; Barrett, L. K.; Fan, E.; Maly, D. J.; Parsons, M.; Dubey, J. P.; Howe, D. K.; Van Voorhis, W. C. Selective inhibition of Sarcocystis neurona calcium-dependent protein kinase 1 for equine protozoal myeloencephalitis therapy. Int. J. Parasit. 2016, 46, 871-80.

Vidadala, S. R.; Rivas, K. L.; Ojo, K. K.; Hulverson, M. A.; Zambriski, J. A.; Bruzual, I.; Schultz, T. L.; Huang, W.; Zhang, Z.; Scheele, S.; DeRocher, A. E.; Choi, R.; Barrett, L. K.; Siddaramaiah, L. K.; Hol, W. G. J.; Fan, E.; Merritt, E. A.; Parsons, M.; Freiberg, G.; Marsh, K.; Kempf, D.; Carruthers, V. B.; Isoherranen, N.; Doggett, J. S.; Van Voorhis, W. C.; Maly, D. J. Development of an Orally Available and CNS-Penetrant TgCDPK1 Inhibitor with Minimal hERG Activity for the Treatment of Toxoplasmosis. J. Med. Chem. 2016, 59, 6531-46. (PMCID: PMC5100899)

Yacoob, C.; Ojo, K. K.; Vidadala, S. R.; Zhang, Z.; Fan, E.; Maly, D. J.; Van Voorhis, W. C.; Shen, H. Partition-Optimized Single Emulsion Particles Improve Sustained Release of Amphiphilic Bumped Kinase Inhibitors to Control Malaria Transmission. IJABPT 2015, 6, 112-120.

Jensen BC, Booster N, Vidadala RS, Maly DJ, Parsons M. A novel protein kinase is essential in bloodstream Trypanosoma brucei. Int J Parasitol. 2016 Mar 23. pii: S0020-7519(16)30001-7. doi: 10.1016/j.ijpara.2016.03.001. PMID:27018127.

Crowther GJ, Hillesland HK, Keyloun KR, Reid MC, Lafuente-Monasterio MJ, Ghidelli-Disse S, Leonard SE, He P, Jones JC, Krahn MM, Mo JS, Dasari KS, Fox AM, Boesche M, El Bakkouri M, Rivas KL, Leroy D, Hui R, Drewes G, Maly DJ, Van Voorhis WC, Ojo KK. Biochemical Screening of Five Protein Kinases from Plasmodium falciparum against 14,000 Cell-Active Compounds. PLoS One. 2016 Mar 2;11(3):e0149996. doi: 10.1371/journal.pone.0149996. PMID:26790733.

Pedroni MJ, Vidadala RS, Choi R, Keyloun KR, Reid MC, Murphy RC, Barrett LK, Van Voorhis WC, Maly DJ, Ojo KK, Lau AO. Bumped kinase inhibitor prohibits egression in Babesia bovis. Vet Parasitol. 2016 Jan 15;215:22-8. doi: 10.1016/j.vetpar.2015.10.023. PMID:26790733.

Huang W, Ojo KK, Zhang Z, Rivas K, Vidadala RS, Scheele S, DeRocher AE, Choi R, Hulverson MA, Barrett LK, Bruzual I, Siddaramaiah LK, Kerchner KM, Kurnick MD, Freiberg GM, Kempf D, Hol WG, Merritt EA, Neckermann G, de Hostos EL, Isoherranen N, Maly DJ, Parsons M, Doggett JS, Van Voorhis WC, Fan E. SAR Studies of 5-Aminopyrazole-4-carboxamide Analogues as Potent and Selective Inhibitors of Toxoplasma gondii CDPK1. ACS Med Chem Lett. 2015 Oct 22;6(12):1184-1189. PMID:26693272.

Gower CM, Thomas JR, Harrington E, Murphy J, Chang ME, Cornella-Taracido I, Jain RK, Schirle M, Maly DJ. Conversion of a Single Polypharmacological Agent into Selective Bivalent Inhibitors of Intracellular Kinase Activity. ACS Chem Biol. 2016 Jan 15;11(1):121-31. doi: 10.1021/acschembio.5b00847. PubMed PMID: 26505072.

Winzer P, Müller J, Aguado-Martínez A, Rahman M, Balmer V, Manser V, Ortega-Mora LM, Ojo KK, Fan E, Maly DJ, Van Voorhis WC, Hemphill A. In Vitro and In Vivo Effects of the Bumped Kinase Inhibitor 1294 in the Related Cyst-Forming
Apicomplexans Toxoplasma gondii and Neospora caninum. Antimicrob Agents Chemother. 2015 Oct;59(10):6361-74. doi: 10.1128/AAC.01236-15.PubMed PMID: 26248379; PubMed Central PMCID: PMC4576114.

Li N, Maly DJ, Chanthery YH, Sirkis DW, Nakamura JL, Berger MS, James CD, Shokat KM, Weiss WA, Persson AI. Radiotherapy followed by aurora kinase inhibition targets tumor-propagating cells in human glioblastoma. Mol Cancer
Ther. 2015 Feb;14(2):419-28. doi: 10.1158/1535-7163.MCT-14-0526. PubMed PMID:25522764; PubMed Central PMCID: PMC4326592.

Maly DJ, Papa FR. Druggable sensors of the unfolded protein response. Nat Chem Biol. 2014 Nov;10(11):892-901. doi: 10.1038/nchembio.1664. Review. PubMed PMID:25325700.

Register AC, Leonard SE, Maly DJ. SH2-catalytic domain linker heterogeneity influences allosteric coupling across the SFK family. Biochemistry. 2014 Nov 11;53(44):6910-23. doi: 10.1021/bi5008194. Epub 2014 Oct 29. PubMed PMID:
25302671; PubMed Central PMCID: PMC4230323.

Ghosh R, Wang L, Wang ES, Perera BG, Igbaria A, Morita S, Prado K, Thamsen M, Caswell D, Macias H, Weiberth KF, Gliedt MJ, Alavi MV, Hari SB, Mitra AK, Bhhatarai B, Schürer SC, Snapp EL, Gould DB, German MS, Backes BJ, Maly DJ, Oakes SA, Papa FR. Allosteric inhibition of the IRE1α RNase preserves cell viability and function during endoplasmic reticulum stress. Cell. 2014 Jul 31;158(3):534-48. doi: 10.1016/j.cell.2014.07.002. PubMed PMID: 25018104; PubMed Central PMCID: PMC4244221.

Leonard SE, Register AC, Krishnamurty R, Brighty GJ, Maly DJ. Divergent modulation of Src-family kinase regulatory interactions with ATP-competitive inhibitors. ACS Chem Biol. 2014 Aug 15;9(8):1894-905. doi: 10.1021/cb500371g.
PubMed PMID: 24946274; PubMed Central PMCID: PMC4136698.

Keyloun KR, Reid MC, Choi R, Song Y, Fox AM, Hillesland HK, Zhang Z, Vidadala R, Merritt EA, Lau AO, Maly DJ, Fan E, Barrett LK, VAN Voorhis WC, Ojo KK. The gatekeeper residue and beyond: homologous calcium-dependent protein kinases as drug development targets for veterinarian Apicomplexa parasites. Parasitology.2014 Sep;141(11):1499-509. doi: 10.1017/S0031182014000857. PubMed PMID: 24927073; PubMed Central PMCID: PMC4390295.

Hari SB, Merritt EA, Maly DJ. Conformation-selective ATP-competitive inhibitors control regulatory interactions and noncatalytic functions of mitogen-activated protein kinases. Chem Biol. 2014 May 22;21(5):628-35. doi: 10.1016/j.chembiol.2014.02.016. PubMed PMID: 24704509; PubMed Central PMCID: PMC4123212.

Doggett JS, Ojo KK, Fan E, Maly DJ, Van Voorhis WC. Bumped kinase inhibitor 1294 treats established Toxoplasma gondii infection. Antimicrob Agents Chemother. 2014 Jun;58(6):3547-9. doi: 10.1128/AAC.01823-13. PubMed PMID:
24687502; PubMed Central PMCID: PMC4068437.

Ojo KK, Reid MC, Kallur Siddaramaiah L, Müller J, Winzer P, Zhang Z, Keyloun KR, Vidadala RS, Merritt EA, Hol WG, Maly DJ, Fan E, Van Voorhis WC, Hemphill A. Neospora caninum calcium-dependent protein kinase 1 is an effective drug target for neosporosis therapy. PLoS One. 2014 Mar 28;9(3):e92929. doi:10.1371/journal.pone.0092929. PubMed PMID: 24681759; PubMed Central PMCID: PMC3969379.

Golkowski M, Brigham JL, Perera GK, Romano GE, Maly DJ, Ong SE. Rapid profiling of protein kinase inhibitors by quantitative proteomics. Medchemcomm. 2014 Mar;5(3):363-369. PubMed PMID: 24648882; PubMed Central PMCID: PMC3955727.

Gower CM, Chang ME, Maly DJ. Bivalent inhibitors of protein kinases. Crit Rev Biochem Mol Biol. 2014 Mar-Apr;49(2):102-15. doi: 10.3109/10409238.2013.875513. Epub 2014 Feb 25. Review. PubMed PMID: 24564382; PubMed Central PMCID: PMC4627631.

Vidadala RS, Ojo KK, Johnson SM, Zhang Z, Leonard SE, Mitra A, Choi R, Reid MC, Keyloun KR, Fox AM, Kennedy M, Silver-Brace T, Hume JC, Kappe S, Verlinde CL, Fan E, Merritt EA, Van Voorhis WC, Maly DJ. Development of potent and selective Plasmodium falciparum calcium-dependent protein kinase 4 (PfCDPK4) inhibitors that block the transmission of malaria to mosquitoes. Eur J Med Chem. 2014 Mar 3;74:562-73. doi: 10.1016/j.ejmech.2013.12.048. PubMed PMID:
24531197; PubMed Central PMCID: PMC4024383.

Zhang Z, Ojo KK, Vidadala R, Huang W, Geiger JA, Scheele S, Choi R, Reid MC,Keyloun KR, Rivas K, Siddaramaiah LK, Comess KM, Robinson KP, Merta PJ, Kifle L,Hol WG, Parsons M, Merritt EA, Maly DJ, Verlinde CL, Van Voorhis WC, Fan E.
Potent and selective inhibitors of CDPK1 from T. gondii and C. parvum based on a5-aminopyrazole-4-carboxamide scaffold. ACS Med Chem Lett. 2014 Jan 9;5(1):40-44.PubMed PMID: 24494061; PubMed Central PMCID: PMC3908674.

Ojo KK, Eastman RT, Vidadala R, Zhang Z, Rivas KL, Choi R, Lutz JD, Reid MC,Fox AM, Hulverson MA, Kennedy M, Isoherranen N, Kim LM, Comess KM, Kempf DJ,Verlinde CL, Su XZ, Kappe SH, Maly DJ, Fan E, Van Voorhis WC. A specific
inhibitor of PfCDPK4 blocks malaria transmission: chemical-genetic validation. JInfect Dis. 2014 Jan 15;209(2):275-84. doi: 10.1093/infdis/jit522.PubMed PMID: 24123773; PubMed Central PMCID: PMC3873787.

Hari SB, Perera BG, Ranjitkar P, Seeliger MA, Maly DJ. Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src. ACS Chem Biol. 2013 Dec 20;8(12):2734-43. doi: 10.1021/cb400663k. PubMed PMID: 24106839; PubMed Central PMCID: PMC3880807.

Castellanos-Gonzalez A, White AC Jr, Ojo KK, Vidadala RS, Zhang Z, Reid MC, Fox AM, Keyloun KR, Rivas K, Irani A, Dann SM, Fan E, Maly DJ, Van Voorhis WC. A novel calcium-dependent protein kinase inhibitor as a lead compound for treating cryptosporidiosis. J Infect Dis. 2013 Oct 15;208(8):1342-8. doi: 10.1093/infdis/jit327. PubMed PMID: 23878324; PubMed Central PMCID: PMC3778970.

Hari SB, Merritt EA, Maly DJ. Sequence determinants of a specific inactive protein kinase conformation. Chem Biol. 2013 Jun 20;20(6):806-15. doi: 10.1016/j.chembiol.2013.05.005. PubMed PMID: 23790491; PubMed Central PMCID:
PMC3742363.

Andrews SS, Hill ZB, Perera BG, Maly DJ. Label transfer reagents to probe p38 MAPK binding partners. Chembiochem. 2013 Jan 21;14(2):209-16. doi: 10.1002/cbic.201200673. PubMed PMID: 23319368; PubMed Central PMCID: PMC3762675.

Brigham JL, Perera BG, Maly DJ. A hexylchloride-based catch-and-release system for chemical proteomic applications. ACS Chem Biol. 2013 Apr 19;8(4):691-9. doi: 10.1021/cb300623a. PubMed PMID: 23305300; PubMed Central PMCID: PMC3631427.

Krishnamurty R, Brigham JL, Leonard SE, Ranjitkar P, Larson ET, Dale EJ, Merritt EA, Maly DJ. Active site profiling reveals coupling between domains in SRC-family kinases. Nat Chem Biol. 2013 Jan;9(1):43-50. doi:10.1038/nchembio.1118. PubMed PMID: 23143416; PubMed Central PMCID: PMC3522794.

Ranjitkar P, Perera BG, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ. Affinity-based probes based on type II kinase inhibitors. J Am Chem Soc. 2012 Nov 21;134(46):19017-25. doi: 10.1021/ja306035v.
PubMed PMID: 23088519; PubMed Central PMCID: PMC3523701.

Wang L, Perera BG, Hari SB, Bhhatarai B, Backes BJ, Seeliger MA, Schürer SC, Oakes SA, Papa FR, Maly DJ. Divergent allosteric control of the IRE1α endoribonuclease using kinase inhibitors. Nat Chem Biol. 2012 Dec;8(12):982-9.
doi: 10.1038/nchembio.1094. PubMed PMID: 23086298; PubMed Central PMCID: PMC3508346.

Hari SB, Ranjitkar P, Maly DJ. Determination of the kinetics and thermodynamics of ligand binding to a specific inactive conformation in protein kinases. Methods Mol Biol. 2012;928:153-9. doi: 10.1007/978-1-62703-008-3_12.
PubMed PMID: 22956140.

Ranjitkar P, Maly DJ. Affinity purification of protein kinases that adopt a specific inactive conformation. Methods Mol Biol. 2012;928:143-51. doi: 10.1007/978-1-62703-008-3_11. PubMed PMID: 22956139.

Zhang Z, Ojo KK, Johnson SM, Larson ET, He P, Geiger JA, Castellanos-Gonzalez A, White AC Jr, Parsons M, Merritt EA, Maly DJ, Verlinde CL, Van Voorhis WC, Fan E. Benzoylbenzimidazole-based selective inhibitors targeting Cryptosporidium parvum and Toxoplasma gondii calcium-dependent protein kinase-1. Bioorg Med Chem Lett. 2012 Aug 15;22(16):5264-7. doi: 10.1016/j.bmcl.2012.06.050. PubMed PMID: 22795629;PubMed Central PMCID: PMC3420979.

Ojo KK, Pfander C, Mueller NR, Burstroem C, Larson ET, Bryan CM, Fox AM, Reid MC, Johnson SM, Murphy RC, Kennedy M, Mann H, Leibly DJ, Hewitt SN, Verlinde CL, Kappe S, Merritt EA, Maly DJ, Billker O, Van Voorhis WC. Transmission of malaria to mosquitoes blocked by bumped kinase inhibitors. J Clin Invest. 2012 Jun;122(6):2301-5. doi: 10.1172/JCI61822. PubMed PMID: 22565309; PubMed Central PMCID: PMC3366411.

Larson ET, Ojo KK, Murphy RC, Johnson SM, Zhang Z, Kim JE, Leibly DJ, Fox AM, Reid MC, Dale EJ, Perera BG, Kim J, Hewitt SN, Hol WG, Verlinde CL, Fan E, Van Voorhis WC, Maly DJ, Merritt EA. Multiple determinants for selective inhibition of apicomplexan calcium-dependent protein kinase CDPK1. J Med Chem. 2012 Mar 22;55(6):2803-10. doi: 10.1021/jm201725v. PubMed PMID: 22369268; PubMed Central PMCID: PMC3336864.

Johnson SM, Murphy RC, Geiger JA, DeRocher AE, Zhang Z, Ojo KK, Larson ET, Perera BG, Dale EJ, He P, Reid MC, Fox AM, Mueller NR, Merritt EA, Fan E, Parsons M, Van Voorhis WC, Maly DJ. Development of Toxoplasma gondii calcium-dependent protein kinase 1 (TgCDPK1) inhibitors with potent anti-toxoplasma activity. J Med Chem. 2012 Mar 8;55(5):2416-26. doi: 10.1021/jm201713h. PubMed PMID: 22320388; PubMed Central PMCID: PMC3306180.

Hill ZB, Perera BG, Andrews SS, Maly DJ. Targeting diverse signaling interaction sites allows the rapid generation of bivalent kinase inhibitors. ACS Chem Biol. 2012 Mar 16;7(3):487-95. doi: 10.1021/cb200387g. PubMed PMID: 22148755; PubMed Central PMCID: PMC3306478.

Goreshnik I, Brock AM, Maly DJ. Biochemical and pharmacological profiling of the pro-survival protein Bcl-xL. Bioorg Med Chem Lett. 2011 Sep 1;21(17):4951-5. doi: 10.1016/j.bmcl.2011.06.134. PubMed PMID: 21807512.

Krishnamurty R, Brock AM, Maly DJ. Protein kinase affinity reagents based on a 5-aminoindazole scaffold. Bioorg Med Chem Lett. 2011 Jan 1;21(1):550-4. doi: 10.1016/j.bmcl.2010.10.069. PubMed PMID: 21078554; PubMed Central PMCID: PMC4138815.

Hill ZB, Perera BG, Maly DJ. Bivalent inhibitors of the tyrosine kinases ABL and SRC: determinants of potency and selectivity. Mol Biosyst. 2011 Feb;7(2):447-56. doi: 10.1039/c0mb00108b. Epub 2010 Nov 9. PubMed PMID: 21060940;
PubMed Central PMCID: PMC3268058.

Gregersen KA, Hill ZB, Gadd JC, Fujimoto BS, Maly DJ, Chiu DT. Intracellular delivery of bioactive molecules using light-addressable nanocapsules. ACS Nano. 2010 Dec 28;4(12):7603-11. doi: 10.1021/nn102345f. PubMed PMID: 21117640; PubMed Central PMCID: PMC3075813.

Murphy RC, Ojo KK, Larson ET, Castellanos-Gonzalez A, Perera BG, Keyloun KR, Kim JE, Bhandari JG, Muller NR, Verlinde CL, White AC Jr, Merritt EA, Van Voorhis WC, Maly DJ. Discovery of Potent and Selective Inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii. ACS Med Chem Lett. 2010 Oct 14;1(7):331-335. PubMed PMID: 21116453; PubMed Central PMCID: PMC2992447.

Ojo KK, Larson ET, Keyloun KR, Castaneda LJ, Derocher AE, Inampudi KK, Kim JE, Arakaki TL, Murphy RC, Zhang L, Napuli AJ, Maly DJ, Verlinde CL, Buckner FS, Parsons M, Hol WG, Merritt EA, Van Voorhis WC. Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors. Nat Struct Mol Biol. 2010 May;17(5):602-7. doi: 10.1038/nsmb.1818. PubMed PMID: 20436472; PubMed Central PMCID: PMC2896873.

Ranjitkar P, Brock AM, Maly DJ. Affinity reagents that target a specific inactive form of protein kinases. Chem Biol. 2010 Feb 26;17(2):195-206. doi: 10.1016/j.chembiol.2010.01.008. PubMed PMID: 20189109; PubMed Central PMCID:
PMC2871157.

Krishnamurty R, Maly DJ. Biochemical mechanisms of resistance to small-molecule protein kinase inhibitors. ACS Chem Biol. 2010 Jan 15;5(1):121-38. doi: 10.1021/cb9002656. Review. PubMed PMID: 20044834; PubMed Central PMCID: PMC2879594.

Goreshnik I, Maly DJ. A small molecule-regulated guanine nucleotide exchange factor. J Am Chem Soc. 2010 Jan 27;132(3):938-40. doi: 10.1021/ja907886v. PubMed PMID: 20020680.

Hill ZB, Perera BG, Maly DJ. A chemical genetic method for generating bivalent inhibitors of protein kinases. J Am Chem Soc. 2009 May 20;131(19):6686-8. doi: 10.1021/ja900871y. PubMed PMID: 19391594.

Seeliger MA, Ranjitkar P, Kasap C, Shan Y, Shaw DE, Shah NP, Kuriyan J, Maly DJ. Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations. Cancer Res. 2009 Mar 15;69(6):2384-92. doi:
10.1158/0008-5472.CAN-08-3953. PubMed PMID: 19276351; PubMed Central PMCID: PMC2678021.

Blacken GR, Volný M, Diener M, Jackson KE, Ranjitkar P, Maly DJ, Turecek F. Reactive landing of gas-phase ions as a tool for the fabrication of metal oxide surfaces for in situ phosphopeptide enrichment. J Am Soc Mass Spectrom. 2009
Jun;20(6):915-26. doi: 10.1016/j.jasms.2009.01.006. PubMed PMID: 19251440.

Statsuk AV, Maly DJ, Seeliger MA, Fabian MA, Biggs WH 3rd, Lockhart DJ, Zarrinkar PP, Kuriyan J, Shokat KM. Tuning a three-component reaction for trapping kinase substrate complexes. J Am Chem Soc. 2008 Dec 24;130(51):17568-74.
doi: 10.1021/ja807066f. PubMed PMID: 19053485; PubMed Central PMCID: PMC2863028.

Perera BG, Maly DJ. Design, synthesis and characterization of “clickable” 4-anilinoquinazoline kinase inhibitors. Mol Biosyst. 2008 Jun;4(6):542-50. doi: 10.1039/b720014e. PubMed PMID: 18493651.

Krishnamurty R, Maly DJ. Chemical genomic and proteomic methods for determining kinase inhibitor selectivity. Comb Chem High Throughput Screen. 2007 Sep;10(8):652-66. Review. PubMed PMID: 18045078.

Maly DJ. Exploring the intermembrane space. ACS Chem Biol. 2007 Apr 24;2(4):213-6. PubMed PMID: 17455895.

Gosalia DN, Salisbury CM, Maly DJ, Ellman JA, Diamond SL. Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays. Proteomics. 2005 Apr;5(5):1292-8. PubMed PMID: 15742319.

Maly DJ, Allen JA, Shokat KM. A mechanism-based cross-linker for the identification of kinase-substrate pairs. J Am Chem Soc. 2004 Aug 4;126(30):9160-1. PubMed PMID: 15281787.

Salisbury CM, Maly DJ, Ellman JA. Peptide microarrays for the determination of protease substrate specificity. J Am Chem Soc. 2002 Dec 18;124(50):14868-70. PubMed PMID: 12475327.

Maly DJ, Leonetti F, Backes BJ, Dauber DS, Harris JL, Craik CS, Ellman JA. Expedient solid-phase synthesis of fluorogenic protease substrates using the 7-amino-4-carbamoylmethylcoumarin (ACC) fluorophore. J Org Chem. 2002 Feb
8;67(3):910-5. PubMed PMID: 11856036.

Kehoe JW, Maly DJ, Verdugo DE, Armstrong JI, Cook BN, Ouyang YB, Moore KL, Ellman JA, Bertozzi CR. Tyrosylprotein sulfotransferase inhibitors generated by combinatorial target-guided ligand assembly. Bioorg Med Chem Lett. 2002 Feb
11;12(3):329-32. PubMed PMID: 11814789.

Dauber DS, Ziermann R, Parkin N, Maly DJ, Mahrus S, Harris JL, Ellman JA, Petropoulos C, Craik CS. Altered substrate specificity of drug-resistant human immunodeficiency virus type 1 protease. J Virol. 2002 Feb;76(3):1359-68. PubMed
PMID: 11773410; PubMed Central PMCID: PMC135855.

Maly DJ, Huang L, Ellman JA. Combinatorial strategies for targeting protein families: application to the proteases. Chembiochem. 2002 Jan 4;3(1):16-37. PubMed PMID: 17590950.

Maly, D. J.; Choong, I. C.; Ellman, J. A. “Combinatorial Target-Guided Ligand Assembly: Identification of Potent Subtype-Selective c-Src Inhibitors” Proc. Natl. Acad. Sci. USA 2000, 97, 2419. PMID: 10716979

Mann, D. A.; Kanai, M.; Maly, D. J.; Kiessling, L. L. “Probing Low Affinity and Multivalent Interactions with Surface Plasmon Resonance: Ligands for Concanavalin A” J. Am. Chem. Soc. 1998, 120, 10575.