Amit Choudhary Lab Publications - The Amit Choudhary Lab

69.

Phosphorylation-inducing chimera Rewires oncogenic kinase to trigger 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

Submitted. BioRxiv. Doi: 10.1101/2025.06.13.659082

68.

Orthogonal resistance mechanisms of classical- and induced-proximity inhibitors

M. Merz, K. Kailass, R. Pergu, K. Tran, K. Gupta, Z. C. Severance, S. Singh, S. Vedagopuram, B. K. Law, G. Rosenblatt, R. Dhaliwal, A. Choudhary

Submitted. BioRxiv. Doi: 10.1101/2025.05.10.652755

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

Submitted

66.

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

Submitted. BioRxiv. Doi: 10.1101/2025.05.10.653252

65

a Scalable design of proximity-inducing molecules

E. Karaj, P. Singh, S. K. Chaudhary, S. H. Sindi, R. Pergu, S. Singh, S. Singha, J. E. Fung, K. Pal, M. Tefera, W. Tian, J. Kawai, M. Merz, V. M. Shoba, A. Sadagopan, L. Boatner, K. M. Backus, A. Choudhary

Submitted

64

Lysine targeting group-transfer chimeras for inducing proximity between cells

S. Singh, K. Tran, E. Karaj, B. Mondal, W. Tian, S. H. Sindi, U Dhawa, K. Pal, V. M. Shoba, A. Liam, J. Mou, M. Han, P. Singh, R. Dhaliwal, N. F. Polizzi, A. Choudhary

Submitted

63

small molecule modulators of TOX protein to re-invigorate T cell activity

B. Wu, H. J. Chang, P. Singh, A. Hostetler, Y. Xiang, S. Guo, Y. Wang, J. J. Zhong, B. S. Lefer, R. P. Sshiavoni, A. Choudhary, P. M. K. Westcott, A.N. Koehler

Submitted. BioRxiv. Doi: 10.1101/2025.03.03.641115

62

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). In press

BioRxiv. Doi: 10.1101/2025.02.23.639680

61.

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. In press

BioRxiv. Doi: 10.1101/2025.05.10.652895

60.

Photoswitchable molecular glues enable optical control of transcription factor Degradation

C. J. Arp, M. Reynders, V. Sreekanth, P. Kokkonda, M. Pagano, A. Choudhary, D. Trauner

Submitted. BioRxiv. doi: 10.1101/2023.04.09.536172

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. In press

BioRxiv. Doi: 10.1101/2023.03.12.531757

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.

PROTACs with reduced off-targets

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

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

54.

Fluorescein-based sensors to purify human alpha cells for functional and transcriptomic analyses

S. Kahraman, K. Shibue, D. F. De Jesus, J. Hu, D. Manna, B. K. Wagner, A. Choudhary, R. N. Kulkarni

eLife. 2023, 12, e85056

53.

Proximity-inducing modalities: The Past, present, and future

S. Singh, W. Tian, Z. Severance, S. Chaudhary, V. Anokhina, B. Mondal, R. Pergu, P. Singh, U. Dhawa, S. Singha, A. Choudhary

RSC Chemical Society Reviews. 2023, DOI: 10.1039/D2CS00943A

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.

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

48.

Proximity-Inducing Bifunctional Molecules Beyond PROTACs

S. C. Lai, A.E. Modell, and A. Choudhary

Protein Homeostasis in Drug Discovery: A Chemical Biology Perspective. 2022, 421

47.

Chemical Approaches For Beta-Cell Biology

A. Vetere, V. S. Parekh, A. E. Modell, V. M. Shoba, A. Choudhary, and B. K. Wagner

Nanotechnology for Diabetes Management (RSC book chapter). In press

46.

Rational Design of Silicon-based zinc ionophores

K. Yamada, A. Deb, V. M. Shoba, D. Lim, B. Maji, A. E. Modell, A. Choudhary

Angewandte Chemie International Edition. 2022, 61, e202201698

45.

CRISPR-based therapeutics: Current challenges and future applications

A. E. Modell, D. Lim, T. Nguyen, V. Sreekanth, A. Choudhary

Trends in Pharmacological Sciences. 2022, 43, 151.

44.

The use of informer sets in screening: Perspective on an efficient strategy to identify new probes

P. A. Clemons, J. Bittker, F. F. Wagner, A. Hands, J. Dahlin, V. Dancik, S. L. Schreiber, A. Choudhary, B. K. Wagner

SLAS Discovery. 2021, 26, 855.

43.

bifunctional modalities for Repurposing protein function

A. E. Modell, S. Lai, T. N. Nguyen, A. Choudhary.

Cell Chemical Biology. 2021, 28, 1081.

42.

harnessing reaction-based probes to preferentially target pancreatic beta-cells and beta-like cells

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.

41.

Core Commitments For Field Trials Of Gene Drive Organisms.

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.

Chemical And Optical Control Of CRISPR-Associated Nucleases.

A. E. Modell, S. U. Siriwardena, V. M. Shoba, X. Li, A. Choudhary.

Current Opinion in Chemical Biology. 2020, 60, 113.

39.

A 3D culture platform enables development of zinc-based prodrugs for targeted proliferation of beta cells.

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.

A chemogenetic system demonstrates that Cas9 longevity impacts genome editing outcome.

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.

Engineering designer beta cells with a CRISPR-Cas9 conjugation platform.

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.

Phosphorylation-inducing chimeric small molecules.

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 Jumbo phage forms a nucleus-like compartment to evade bacterial defense systems.

A. E. Modell, S.U. Siriwardena and A. Choudhary

Biochemistry 2020, 59, 1869-1870.

34.

A small molecule control of super-Mendelian inheritance in gene drives.

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.

Native zinc mediates selective and traceless release of small molecules in beta cells.

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.

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.

31.

Precision control of CRISPR-Cas9 using light and small molecules.

S. A. Gangopadhyay, K. J. Cox, D. Manna, D. Lim, B. Maji, Q. Zhou, A. Choudhary

Biochemistry 2019, 58, 234-244.

30.

A singular system for dose and spatiotemporal control of CRISPR-Cas9

D. Manna, B. Maji, S. A. Gangopadhyay, K. J. Cox, Q. Zhou, B. K. Law, R. Mazitschek, A. Choudhary

Angewandte Chemie International Edition 2019, 58, 6285-6289.

Highlighted in: BioSpace

29.

A universal method for sensitive and cell-free detection of CRISPR-associated nucleases.

K. J. Cox, H. K. K. Subramanian, C. C. Samaniego, E. Franco*, A. Choudhary*

Chemical Science 2019, 10, 2653 – 2662.

28.

Book Chapter: Kinase Inhibitor Drugs

P. Wu and A. Choudhary
© 2018 Wiley‐VCH Verlag GmbH & Co. KGaA.

27.

Special Issue on the Chemical Biology of CRISPR

A. G. Weidmann and A. Choudhary.

ACS Chemical Biology 2018, 13, 283–284.
Highlighted in: IGTRCN

26.

Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python.

A. L. Andrew, B, W, Perry, D. C. Card, D. R. Schield, R. P, Ruggiero, Suzanne E. McGaugh, A. Choudhary, S. M. Secor, T. A. Castoe

BMC Genomics 2017, 18, 338.

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

24.

Prolyl 4-Hydroxylase: Substrate Isosteres in Which an (E)- or (Z)-Alkene Replaces the Prolyl Peptide Bond.

J. D. Vasta, A. Choudhary, K. H. Jensen, N. A. McGrath and R. T. Raines
Biochemistry 2016, 56, 219–227.

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.

22.

4‐ketoproline: An electrophilic proline analog for bioconjugation

A. Choudhary, K. J. Kamer, M. D. Shoulders, R. T. Raines.
Peptide Science 2015, 104, 110-115.

21.

Targeting the pancreatic β-cell to treat diabetes

A. Vetere, A. Choudhary, S. M. Burns & B. K. Wagner.
Nature Reviews Drug Discovery 2014, 13, 278–289.

20.

Quantitative-Proteomic Comparison of Alpha and Beta Cells to Uncover Novel Targets for Lineage Reprogramming.

A. Choudhary, K. H. He , P. Mertins, N. D. Udeshi, V. Dančík, D. F. Yadlin, S. Kubicek, P. A. Clemons, S. L. Schreiber, S. A. Carr, B. K. Wagner.
PloS one 2014, 9, e95194.

19.

n→ π* interactions engender chirality in carbonyl groups.

A. Choudhary, R. W. Newberry and R. T. Raines
Organic Letters 2014, 16, 3421 – 3423.

18.

An n→ π* interaction reduces the electrophilicity of the acceptor carbonyl group.

A. Choudhary, C. G. Fry, K. J. Kamer, and R. T. Raines
Chemical Communications 2013, 49, 8166 – 8168.

17.

Pyramidalization of a carbonyl C atom in (2S)-N-(selenoacetyl) proline methyl ester.

I. A. Guzei, A. Choudhary, and R. T. Raines.
Acta Crystallographica Section E: Structure Reports Online 2013. 69, 805-806.

16.

Intimate interactions with carbonyl groups: dipole–dipole or n→ π*?

K. J. Kamer, A. Choudhary and R.T. Raines
The Journal of Organic Chemistry 2012, 78, 2099 – 2103.

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.

14.

A conserved interaction with the chromophore of fluorescent proteins.

A. Choudhary, K. J. Kamer and R. T Raines
Protein Science 2011, 21, 171-177.

13.

An evaluation of peptide‐bond isosteres.

A. Choudhary and R. T. Raines.
ChemBioChem 2011, 12, 1801-1807.

12.

An n→ π* interaction in aspirin: Implications for structure and reactivity.

A. Choudhary, K. J. Kamer and R. T. Raines.
The Journal of Organic Chemistry 2011, 76, 7933 – 7937.

11.

Signature of n→ π* interactions in α‐helices.

A. Choudhary and R. T. Raines.
Protein Science 2011, 20, 1077-1081.

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.

9.

Quantum mechanical origin of the conformational preferences of 4-thiaproline and its S-oxides.

A. Choudhary, K. H. Pua and R. T. Raines.
Amino Acids 2011, 41, 181-186.

8.

The aberrance of the 4S diastereomer of 4-hydroxyproline.

M. D. Shoulders, F. W. Kotch, A. Choudhary, I. A. Guzei and R. T. Raines
Journal of the American Chemical Society 2010, 132, 10857 – 10865.

7.

A Stereoelectronic Effect in Prebiotic Nucleotide Synthesis.

A. Choudhary, K. J. Kamer, M. W. Powner, J. D. Sutherland and R. T. Raines
ACS Chemical Biology 2010, 5, 655-657.

6.

n→ π* interactions in proteins.

G. J. Bartlett, A. Choudhary, R. T. Raines and D .N. Woolfson
Nature Chemical Biology 2010, 6, 615-620.

5.

n → π* Interaction and n)(π Pauli Repulsion Are Antagonistic for Protein Stability.

C. E. Jakobsche, A. Choudhary, S. J. Miller and R. T. Raines
Journal of the American Chemical Society 2010, 132, 6651 – 6653.

4.

Modulation of an n→ π* interaction with α-fluoro groups.

A. Choudhary, C. G. Fry and R. T. Raines
ARKIVOC: free online journal of organic chemistry/Arkat-USA Inc. 2010, 8, 251-262.

3.

5(6)-anti-Substituted-2-azabicyclo[2.1.1]hexanes: A Nucleophilic Displacement Route.

G. R. Krow, R. Edupuganti, D. Gandla, A. Choudhary, G. Lin, P. E. Sonnet, C. DeBrosse, C. W. Ross, K. C. Cannon and R. T. Raines
The Journal of Organic Chemistry 2009, 74, 8232 – 8242.

2.

Nature of Amide Carbonyl−Carbonyl Interactions in Proteins.

A. Choudhary, D. Gandla, G. R. Krow and R. T. Raines
Journal of the American Chemical Society 2009, 131, 7244 – 7246.

1.

Stereoselective synthesis of (−)-microcarpalide.

K. R. Prasad, K. Penchalaiah, A. Choudhary and P. Anbarasan
Tetrahedron Letters 2007, 48, 309-311.