Publications
2026
72.
A scalable design of proximity-inducing molecules
E. Karaj, V. Venkatarangan, S. H. Sindi, S. Siriwongsup, C. Lee, R. Pergu, S. Vedagopuram, K. Kailass, K. Tran, P. Singh, S. Singh, J. Kawai, J. E. Fung, M. Tefera, R. Dhaliwal, S. K. Chaudhary, A. Keyes, A. Sadagopan, L. Boatner, N. H. Shah, C. Fehl, K. M. Backus, A. Choudhary
Under revision. BioRxiv. Doi: 10.64898/2026.02.20.706349
71.
Lysine targeting group-transfer chimeras for inducing proximity
S. Singh, K. Tran, E. Karaj, B. Mondal, W. Tian, S Siriwongsup, S. H. Sindi, U Dhawa, K. Pal, V. M. Shoba, S Shi, A. Liam, J. Mou, M. Han, P. Singh, N. F. Polizzi, A. Choudhary
Angewandte Chemie International Edition. 2026, e12131
69.
Proximity-induced rewiring of oncogenic kinase triggers apoptosis
M. L. Merz, V. M. Shoba, R. Pergu, Z. C. Severance, D. N. P. M. Godage, A. Deb, H. S. Kwok, P. M. Gosavi, P. Singh, S. Singh, W. Tian, E. Weisberg, N. C. Payne, R. Mazitschek, M. G. Rees, J. A. Roth, B. K. Wagner, J. D. Griffin, A. Choudhary
ACS Central Science. In press
BioRxiv. Doi: 10.1101/2025.06.13.659082
67.
haptenizing chimeras For neo-antigen generation using known drugs
S. Sindi, R. Pergu, E. Karaj, K. Pal, J. Fung, R. Dhaliwal, K. Tran, P. Kokkonda, S. K. Chaudhary, P. Singh, Y. Y. Chen, A. Choudhary
Under revision
66.
Anti-CRISPR-mediated continuos directed evolution of CRISPR-Cas9 in human cells
A. L. Sabol, A. A. Mengiste, V. Sreekanth, P. Singh, S. J. Hendel, M. T. N. Tran, A. M. Barybin, S. Chaudhary, R. M. Harris, K Liivak, Z. C. Severance, C. M. Locicerco, K. Kailass, C. Lee, L. Xu, V. L. Butty, A. Choudhary*, M. D. Shoulders*
Under review. BioRxiv. Doi: 10.64898/2025.12.11.693673
2025
62.
Ultrasmall chemogenetic tags with group-transfer ligands
S. Vedagopuram, S. Sindi, S. K. Chaudhary, R. Pergu, P. Singh, E. Karaj, J. E. Fung, A. Deb, S. J. DeCarlo, J. A. M. Mercer, K. Yamada, D. Rodriguez, D. R. Liu, A. Choudhary
Angewandte Chemie International Edition 2025, 64, e2025069997
Submitted. BioRxiv. Doi: 10.1101/2025.05.10.653252
61.
Protective antigen-mediated delivery of anti-CRISPR protein for precision genome editing
A. O. Vera, N. L. Truex, S. Vedagopuram, B. L. Pentelute, A. Choudhary*, R. T. Raines*
Proceedings of the National Academy of Sciences (USA) 2025, 122, e2426960122
BioRxiv. Doi: 10.1101/2025.02.23.639680
60.
Phosphorylation-Inducing molecules For regulating dynamic cellular processes
R. Pergu, S. Vedagopuram, P. Kokkonda, S. Lai, P. Kokkonda, P. K. Tiwari, S. Singh, J. Kawai, S. Singha, W. Tian, V. Thimradka, K. Tran, A. Choudhary
Journal of the American Chemical Society. 2025, 147, 25316.
BioRxiv. Doi: 10.1101/2025.05.10.652895
59.
A molecular glue approach to Control the Half-Life Of CRISPR-based technologies
V. Sreekanth, M. Jan, K. T. Zhao, D. Lim, J. R. Davis, M. McConkey, V. Kovalcik, S. Barkal, B. K. Law, J. Fife, R. Tian, M. E. Vinyard, B. Becerra, M. Kampmann, R. I. Sherwood, L. Pinello, D. R. Liu, B. L. Ebert, A. Choudhary
Journal of the American Chemical Society. 2025, 147, 23844.
BioRxiv. Doi: 10.1101/2023.03.12.531757
2024
58.
Continuos evolution of compact protein degradation tags regulated by selective cereblon molecular glues
J. A. M. Mercer, S. J. DeCarlo, S. S. R. Burman, V. Sreekanth, A. T. Nelson, M. Hunkeler, P. J. Chen, K. A. Donovan, P. Kokkonda, P. K. Tiwari, V. M. Shoba, A. Deb, A. Choudhary*, E. S. Fischer*, D. R. Liu*
Science. 2024, DOI: 10.1126/science.adk4422
57.
T. M. Nguyen, V. Sreekanth, A. Deb, P. Kokkonda, P. K. Tiwari, K. A. Donovan, V. M. Shoba, S. K. Chaudhary, J. A. M. Mercer, S. Lai, A. Sadagopan, M. Jan, E. S. Fischer, D. R. Liu, B. L. Ebert, A. Choudhary
Nature Chemistry. 2024. DOI: 10.1038/s41557-023-01379-8
BioRxiv DOI: 10.1101/2021.11.18.468552
2023
56.
bifunctional small molecules that induce nuclear localization and targeted transcriptional regulation
W. J. Gibson, A. Sadagopan, V. M. Shoba, A. Choudhary, M. Meyerson, S. L. Schreiber
Journal of the American Chemical Society. 2023, 145, 26028
55.
Development and application of chimera platforms for Tyrosine Phosphorylation
R. Pergu, V. M. Shoba, S.K. Chaudhary, D. N. P. M. Godage, A. Deb, S. Singha, V. Anokhina, S. A. Singh, U. Dhawa, S. U. Siriwardena, A. Choudhary
ACS Central Science. 2023, 9, 1558.
Highlighted: ACS Central Science
52.
Excess pancreatic elastase alters acinar-to-B-cell communication by impairing the mechano-signaling and PAR2 pathways
G. Basile, A. Vetere, J. Hu, O. Iljaduola, Y. Zhang, K-C. Liu, A. M. Eltony, D. F. De Jesus, F. Fukuda, G. Doherty, C. Leech, O. G. Chepurny, G. G. Holz, S-H, Yun, O. Andersson, A. Choudhary, B. K. Wagner, R. N. Kulkarni
Cell Metabolism. 2023, 35, 1242.
51.
FALCON Systematically Interrogates Free Fatty Acid Biology And Identifies Novel Mediator Of Lipotoxicity
N. Wieder, J. C. Fried, C. Kim, E-h Sidhom, M. R. Brown, J. L. Marshall, C. Arevalo, M D-Levitt, M. K-Alimova, J. Sieber, K. R. Gabriel, J. Pacheco, C. Clish, H. S. Abbasi, S. Singh, J. Rutter, M. Therrien, H. Yoon, Z. W. Lai, A. Baublis, R. Subramanian, R. Devkota, J. Small, V. Sreekanth, M. Han, D. Lim, A. E. Carpenter, J. Flannick, H. Finucance, M. C. Haigis, M. Claussntizer, E. Sheu, B. Stevens, B. K. Wagner, A. Choudhary, J. L. Shaw, J. L. Pablo, A. Greka
Cell Metabolism. 2023, 35, 887.
2022
50.
A general approach to identify cell-permeable and synthetic anti-cRISPR small molecules
D. Lim, Q. Zhou, K. J. Cox, B. K. Law, M. Lee, P. Kokkonda, V. Sreekanth, R. Pergu, S. K. Chaudhary, S. A. Gangopadhyaya, B. Maji, S. Lai, Y. Amako, D. B. Thompson, H. K. Subramanian, M. F. Mesleh, V. Dancik, P. A. Clemons, B. K. Wagner, C. M. Woo, G. M. Church, A. Choudhary
Nature Cell Biology. 2022, 24, 1766
49.
Synthetic reprogramming of Kinases expands cellular activites of proteins
V. M. Shoba, D. N. P. M. Godage, S. K. Chaudhary, A. Deb, S. U. Siriwardena, A. Choudhary
Angewandte Chemie International Edition. 2022, 61, e202202770
46.
K. Yamada, A. Deb, V. M. Shoba, D. Lim, B. Maji, A. E. Modell, A. Choudhary
Angewandte Chemie International Edition. 2022, 61, e202201698
45.
A. E. Modell, D. Lim, T. Nguyen, V. Sreekanth, A. Choudhary
Trends in Pharmacological Sciences. 2022, 43, 151.
2021
42.
S. Kahraman, D. Manna, E. Dirice, B. Maji, J. Small, B. K. Wagner, A. Choudhary*, R. N. Kulkarni*
Life Science Alliance. 2021, 4.4, e202000840.
2020
41.
K.C. Long, L. Alphey, G. J. Annas, C. S. Bloss, K. J. Campbell, J. Champer, C-H Chen, A. Choudhary, G. M. Church, J. P. Collins, K. L. Cooper, J. A. Delborne, O. R. Edwards, C. I. Emerson, K. Esvelt, S. W. Evans, R. M. Friedman, V. M. Gantz, F. Goud, S. Hartley, E. Heitman, J. Hemingway, H. Kanuka, J. Kuzma, J. V. Lavery, Y. Lee, M. Lorenzen, J. E. Lunshof, J. M. Marshall, P. W. Messer, C. Montell, K. A. Oye, M. J. Palmer, P. A. Papthanos, P. N. Paradkar, A. J. Piaggio, J. L. Rasgon, G. Rasic, L. Rudenko, J. R. Saah, M. J. Scott, J. T. Sutton, A. E. Vorsino, O. S. Akbari
Science. 2020, 370, 1417.
Highlighed in: EurekAlert, Phys.org, Science Daily
40.
A. E. Modell, S. U. Siriwardena, V. M. Shoba, X. Li, A. Choudhary.
Current Opinion in Chemical Biology. 2020, 60, 113.
39.
K. Yang, M. Lee, P. A. Jones, S. S. Liu, A. Zhou, J. Xu, V. Sreekanth, J. L. Y. Wu, L.Vo, E. A. Lee, R. Pop, Y. Lee, B. K. Wagner, D. A. Melton, A. Choudhary*, J. M. Karp*
Science Advances. 2020, 6, eabc3207.
38.
V. Sreekanth, Q. Zhou, P. Kokkonda, H. Bermudez-Cabrera, D. Lim, B. Law, B. Holmes, S. Chaudhary, R. Pergu, B. Leger, J. A. Walker, D. Gifford, R. Sherwood, A. Choudhary.
ACS Central Science. 2020, 6, 2228.
37.
D. Lim, V. Sreekanth, K. J. Cox, B. K. Law, B. K. Wagner, J. M. Karp, and A. Choudhary.
Nature Communications 2020, 11, 4043.
Highlighted in: Faculty of 1000, Nature Bioengineering Blog
36.
S. U. Siriwardena, D. N. P. M. Godage, V. M. Shoba, S. Lai, M. Shi, P. Wu, S. K. Chaudhary, S. L. Schreiber, and A. Choudhary
Journal of the American Chemical Society 2020, 142, 14052 – 14057
Highlighted in: BIOCENTURY, Faculty of 1000
35.
A. E. Modell, S.U. Siriwardena and A. Choudhary
Biochemistry 2020, 59, 1869-1870.
34.
V. L. D. Amo, B. S. Leger, K. J. Cox, S. Gill, A. L. Bishop, G. D. Scanlon, J. A. Walker, V. M. Gantz, A. Choudhary
Cell Reports 2020, 31,107841.
Highlighted in: GEN
33.
M. Lee, B. Maji, D. Manna, S. Kahraman, R. M. Elgamal, J. Small, P. Kokkonda, A. Vetere, J. M. Goldberg, S. J. Lippard, R. N. Kulkarni, B. K. Wagner and A. Choudhary
Journal of the American Chemical Society 2020, 142, 6477 – 6482.
2019
32.
A high-throughput platform to identify small-molecule inhibitors of CRISPR-Cas9
B. Maji, S. A. Gangopadhyay, M. Lee, M. Shi, P. Wu, R. Heler, B. Mok, D. Lim, S. U. Siriwardena, B. Paul, V. Dančík, A. Vetere, M. F. Mesleh, L. A. Marraffini, D. R. Liu, P. A. Clemons, B. K. Wagner and A. Choudhary
Cell 2019, 177, 1067-1079.
Highlighted in: Cell Press, Nature, Nature Methods, Nature Rev Drug Discovery, Broad Institute, Harvard Gazette, NewScientist, GEN, GenomeWeb, Phys.org, ScienceDaily, MIT Tech Review, In the Pipeline & several others.
2018
28.
Book Chapter: Kinase Inhibitor Drugs
© 2018 Wiley‐VCH Verlag GmbH & Co. KGaA.
2017
25.
Multidimensional chemogenic control of CRISPR-Cas9.
B. Maji, C. L. Moore, B. Zetsche, S. E. Volz, F. Zhang, M. D. Shoulders*, A. Choudhary*
Nature Chemical Biology 2017, 13, 9-11.
Highlighted in: Faculty of 1000, News & Views
2016
2015
23.
Kinase-Independent Small-Molecule Inhibition of JAK-STAT Signaling.
D. H-C. Chou,§ A. Vetere, § A. Choudhary, § S. S. Scully, M. Schenone, A. Tang, R. Gomez, S. M. Burns, M. Lundh, T. Vital, E. Comer, P. W. Faloon, V. Dančík, C. Ciarlo, J. Paulk, M. Dai, C. Reddy, H. Sun, M. Young, N. Donato, J. Jaffe, P. A. Clemons, M. Palmer, S. A. Carr, S. L. Schreiber and B. K. Wagner
Journal of the American Chemical Society 2015, 137, 7929 – 7934.
2014
2013
17.
Pyramidalization of a carbonyl C atom in (2S)-N-(selenoacetyl) proline methyl ester.
Acta Crystallographica Section E: Structure Reports Online 2013. 69, 805-806.
2012
15.
Synthesis of 5-Fluoro-and 5-Hydroxymethanoprolines via Lithiation of N-BOC-methanopyrrolidines. Constrained Cγ-Exo and Cγ-Endo Flp and Hyp Conformer Mimics.
G. R. Krow, M. D. Shoulders, R. Edupuganti, D. Gandla, F. Yu, P. E. Sonnet, M. Sender, A. Choudhary, C. DeBrosse, C. W. Ross III, P. Carroll and R. T. Raines
The Journal of Organic Chemistry 2012, 77, 5331 – 5344.
2011
10.
Synthesis of conformationally constrained 5-fluoro-and 5-hydroxymethanopyrrolidines. Ring-puckered mimics of gauche-and anti-3-fluoro-and 3-hydroxypyrrolidines.
G. R. Krow, R. Edupuganti, D. Gandla, F. Yu, M. Sender, P. E. Sonnet, M. J. Zdilla, C. DeBrosse, K. C. Cannon, C. W. Ross III and A. Choudhary, M. D. Shoulders and R. T. Raines.
The Journal of Organic Chemistry 2011, 76, 3626 – 3634.
2010
2009
2007
1.
Stereoselective synthesis of (−)-microcarpalide.
Tetrahedron Letters 2007, 48, 309-311.