Recent Publications

Graham AJ, Khoo MWL, Srivastava V, Viragova S, Kim H, Parekh K, Hennick KM, Bird M, Goldhammer N, Yu JZ, Hu G, Brinkley NT, Pardo L, Amaya JS, Morley CD, Chadha N, Lebel P, Kumar S, Rosenbluth JM, Nowakowski TJ, Chaudhuri O, Klein O, Gómez-Sjöberg R, Gartner ZJ. Stress-relaxing granular bioprinting materials enable complex and uniform organoid self-organization. Nat Mater. 2026 Jul;25(7):1239-1251. doi: 10.1038/s41563-026-02519-4. Epub 2026 Mar 10. PMID: 41807773; PMCID: PMC13178435.

Zhu Q, Jiang Z, Zuckerman B, Weinberger L, Thomson M, Gartner ZJ. Revealing a coherent cell-state landscape across single-cell datasets with CONCORD. Nat Biotechnol. 2026 Jan 5. doi: 10.1038/s41587-025-02950-z. Epub ahead of print. PMID: 41491253.

Carroll EC, Yang H, Powell WC, Charvat AF, Oehler A, Jones JG, Montgomery KM, Yung A, Millbern Z, Taylor AIP, Wilkinson M, Ranson NA, Radford SE, Vinueza NR, DeGrado WF, Mordes DA, Condello C, Gestwicki JE. High-throughput discovery of fluoroprobes that recognize amyloid fibril polymorphs. Nat Chem. 2025 Oct;17(10):1565-1575. doi: 10.1038/s41557-025-01889-7. Epub 2025 Aug 14. Erratum in: Nat Chem. 2026 Aug;18(8):1526. doi: 10.1038/s41557-026-02190-x. PMID: 40813616; PMCID: PMC12491066.

Sang R, Gestwicki JE. Radical Strategy to the Boron-to-Copper Transmetalation Problem: N-Alkylation with Alkylboronic Esters. J Am Chem Soc. 2025 Jul 2;147(26):23259-23269. doi: 10.1021/jacs.5c07856. Epub 2025 Jun 23. PMID: 40550745; PMCID: PMC12232318.

Morstein J, Borowsky J, Hu S, Sheen Y, Nisoli V, Hwang TC, Grabe M, Shokat KM. Targeting the Protein-Membrane Interface Enables Design of Long-Acting CFTR Potentiators. ACS Chem Biol. 2026 May 15;21(5):982-989. doi: 10.1021/acschembio.5c00993. Epub 2026 Apr 28. PMID: 42046515; PMCID: PMC13184935.

San Felipe CJ, Batra J, Muralidharan M, Malpotra S, Anand D, Bauer R, Verba KA, Swaney DL, Krogan NJ, Grabe M, Fraser JS. Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response. Elife. 2025 Sep 17;14:RP106484. doi: 10.7554/eLife.106484. PMID: 40960494; PMCID: PMC12443476.

Stephens CA, van Hilten N, Zheng L, Grabe M. Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove. Elife. 2025 Aug 6;14:RP105111. doi: 10.7554/eLife.105111. PMID: 40768244; PMCID: PMC12327946.

Niu Y, Lilly M, Ronayne EK, Emerman M, Chesarino NM, Gross JD. The structural mechanism of HIV-2 Vif antagonism of human APOBEC3H. Nat Commun. 2026 Jun 29. doi: 10.1038/s41467-026-75045-1. Epub ahead of print. PMID: 42373647.

Liu X, Li Y, Castro LK, Yu Z, Cheng Y, Daugherty MD, Gross JD. Structure of the E3 ligase CRL2ZYG11B with substrates reveals the molecular basis for N-degron recognition and ubiquitination. Cell Rep. 2026 Jun 23;45(6):117401. doi: 10.1016/j.celrep.2026.117401. Epub 2026 Jun 1. PMID: 42224082; PMCID: PMC13379236.

Wan Y, Liang J, Dai Y, Srinivasan K, Billesbølle C, Zhu JF, Shin JE, Paul S, Marks D, Song YS, Myers BR, Koehl A, Manglik A. Hypervariable loop profiling decodes sequence determinants of antibody stability. Nat Struct Mol Biol. 2026 Jun;33(6):998-1010. doi: 10.1038/s41594-026-01804-9. Epub 2026 Apr 30. PMID: 42062516. 

Suryawanshi RK, Jaishankar P, Correy GJ, Rachman MM, O'Leary PC, Taha TY, Matsui Y, Zapatero-Belinchón FJ, McCavitt-Malvido M, Doruk YU, Stevens MGV, Diolaiti ME, Jogalekar MP, Chen H, Richards AL, Kongpracha P, Bali S, Montano M, Rosecrans J, Matthay M, Togo T, Gonciarz RL, Gopalkrishnan S, Neitz RJ, Krogan NJ, Swaney DL, Shoichet BK, Ott M, Renslo AR, Ashworth A, Fraser JS. The Mac1 ADP-ribosylhydrolase is a therapeutic target for SARS-CoV-2. Elife. 2025 Nov 19;14:RP103484. doi: 10.7554/eLife.103484. PMID: 41258893; PMCID: PMC12629595.

Li H, Mukhtasimova N, Teng J, Cavalli ES, Gu X, Sello JK, Sine SM, Hibbs RE. Correcting congenital myasthenia-associated acetylcholine receptor defects. Nature. 2026 Jul 1:10.1038/s41586-026-10706-1. doi: 10.1038/s41586-026-10706-1. Epub ahead of print. PMID: 42386970; PMCID: PMC13430646.

Delaveris CS, Loudermilk RP, Pandey A, Remesh SG, Peters-Clarke TM, Ganjave SD, Dougherty WJN, Delavan HM, Wang C, Ling J, Camara Serrano JA, Salangsang F, Ding CC, Greenland N, Chu CE, Porten S, Steri V, Chou J, Evans MJ, Leung KK, Wells JA. Autophagolysosomal exocytosis inverts Src kinase onto the cell surface in cancer. Science. 2026 Mar 12;391(6790):eaec1778. doi: 10.1126/science.aec1778. Epub 2026 Mar 12. PMID: 41818370.

Kumru K, Yao Z, Holmes BB, Zhao F, Zhang Y, Ferrara E, Peters-Clarke TM, Leung KK, Wells JA. A cytokine receptor-targeting chimera toolbox for expanding extracellular targeted protein degradation. Proc Natl Acad Sci U S A. 2026 Jan 27;123(4):e2524129123. doi: 10.1073/pnas.2524129123. Epub 2026 Jan 21. PMID: 41564137; PMCID: PMC12846780.

Lin Z, Ngo W, Chou YT, Wu H, Susa KJ, Jun YW, Bivona TG, Doudna JA, Wells JA. Temporal photoproximity labeling of ligand-activated EGFR neighborhoods using MultiMap. Nat Chem Biol. 2026 Feb;22(2):192-204. doi: 10.1038/s41589-025-02076-y. Epub 2025 Nov 18. PMID: 41254216; PMCID: PMC12858401.

Zhao F, Wu Y, Schaefer K, Zhang Y, Miao K, Yao Z, Ganjave SD, Kumru K, Peters-Clarke TM, Inague A, Olzmann JA, Leung KK, Wells JA. Hijacking Extracellular Targeted Protein Degrader-Drug Conjugates for Enhanced Drug Delivery. J Am Chem Soc. 2025 Oct 29;147(43):39912-39925. doi: 10.1021/jacs.5c15047. Epub 2025 Oct 15. PMID: 41091621; PMCID: PMC12576823.

Bao F, Li L, Hammerlindl H, Shen SQ, Hammerlindl S, Altschuler SJ, Wu LF. Transitive prediction of small-molecule function through alignment of high-content screening resources. Nat Biotechnol. 2026 May;44(5):862-872. doi: 10.1038/s41587-025-02729-2. Epub 2025 Jul 11. PMID: 40646169; PMCID: PMC12846546.

Montaño JL, Tejus VR, Xu V, Condon AC, Ecker AK, Langen A, Leung KK, Zaro BW. An interactive resource mapping the proteome and reactive cysteine landscape across the NCI-60 reveals cell and tissue-specific profiles. Cell Chem Biol. 2026 Jan 15;33(1):117-131.e5. doi: 10.1016/j.chembiol.2025.12.003. Epub 2025 Dec 31. PMID: 41478280.

Zimanyi MA, Hulce KR, Bohn MF, Norman J, Rohweder PJ, Detomasi TC, Cheng Y, Craik CS. Antibody reveals conformational latch regulating dimerization in β- and γ-herpesvirus proteases. Nat Commun. 2026 Jul 13. doi: 10.1038/s41467-026-75438-2. Epub ahead of print. PMID: 42443199.

Kang D, Pandey A, Kumar G, Mehta AS, Detomasi TC, Anderson D, Bardine C, Asper G, Qi J, Nadig I, Cui Y, Quimby FM, Ling J, Seo Y, Cohen BE, Anwar M, Evans MJ, Craik CS. A Prodrug Strategy to Conditionally Trap Therapeutic Payloads for Improved Tumor Retention. ACS Cent Sci. 2026 May 13;12(5):719-730. doi: 10.1021/acscentsci.6c00185. PMID: 42221559; PMCID: PMC13220212.

Yang R, Yang H, Davydenko A, Mawaldi Z, Kormos R, Myerscough D, Wu Y, DeGrado WF. The emergence of novel versus known three-dimensional structures from random sequences. Proc Natl Acad Sci U S A. 2026 Jul 7;123(27):e2535076123. doi: 10.1073/pnas.2535076123. Epub 2026 Jun 29. PMID: 42372157; PMCID: PMC13342870.

Chen Y, Bhattacharya S, Bergmann L, Correy GJ, Tan SK, Hou K, Biel JT, Lu L, Bakanas I, Gestwicki JE, Volkov AN, Korendovych IV, Polizzi NF, Fraser JS, DeGrado WF. Emergence of specific binding and catalysis from a designed generalist binding protein. Nat Chem. 2026 Jul;18(7):1334-1344. doi: 10.1038/s41557-026-02125-6. Epub 2026 May 4. PMID: 42082787; PMCID: PMC13245809.

Li X, Tan SK, Chung CI, Hatstat AK, Zhao Q, Luo J, DeGrado WF, Shu X. Design of an ultrabright biosensor for dynamic imaging of kinase activity in cells. Proc Natl Acad Sci U S A. 2026 May 12;123(19):e2523631123. doi: 10.1073/pnas.2523631123. Epub 2026 May 4. PMID: 42081727; PMCID: PMC13167765.

Palla AM, Lin CC, Trnka MJ, Leao EM, Petronikolou N, Burlingame AL, McGinty RK, Fujimori DG. An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA. J Mol Biol. 2025 Oct 1;437(19):169301. doi: 10.1016/j.jmb.2025.169301. Epub 2025 Jun 20. PMID: 40545232; PMCID: PMC12443421.

Chaplot K, Zhang L, Wessman J, Rivera M, Wang Z, Wang F, Duan X, England PM, Clark IC, Ullian EM. Rapid generation of ventral A9-like dopaminergic neurons from patterned iPSCs. bioRxiv [Preprint]. 2025 Nov 2:2025.10.31.685897. doi: 10.1101/2025.10.31.685897. PMID: 41279649; PMCID: PMC12636497.

Asmerian H, Diaz AJ, Xu H, Oses-Prieto JA, Alberts J, Gnanabharathi B, Sanetra AM, Das P, Carr N, Burlingame AL, Edwards RH, Silm K. Synaptic vesicles that store monoamines and glutamate differ in protein composition. Sci Adv. 2026 Jul 24;12(30):eadz6836. doi: 10.1126/sciadv.adz6836. Epub 2026 Jul 23. PMID: 42490455; PMCID: PMC13394401.

Haddix SG, Zhang C, Liu Y, Oses-Prieto J, Burlingame AL, Rasband MN. The perijunctional zone is a molecularly distinct muscle subdomain altered in Duchenne muscular dystrophy. Nat Commun. 2026 May 21;17(1):6709. doi: 10.1038/s41467-026-73525-y. PMID: 42168231; PMCID: PMC13385842.

Guo Y, Li T, Tuomivaara ST, Teo CF, Feng S, Chalkley RJ, Zhu R, Cheng T, Li KH, Chen W, Simon A, Jin P, Younger S, Yong AJH, Li K, Li K, Burlingame AL, Jan LY, Jan YN. Identification of the peptide Vulnusin, a wound signal that mediates mechanical-injury-induced nociception in Drosophila. Neuron. 2025 Oct 15;113(20):3352-3362.e5. doi: 10.1016/j.neuron.2025.09.007. Epub 2025 Oct 3. PMID: 41045928; PMCID: PMC12774293.

Remesal L, Sucharov-Costa J, Wu Y, Pratt KJB, Bieri G, Philp A, Phan M, Aghayev T, White CW 3rd, Wheatley EG, Zou B, Desousa BR, Couthouis J, Jian IH, Xie XS, Lu Y, Maynard JC, Burlingame AL, Villeda SA. Targeting iron-associated protein Ftl1 in the brain of old mice improves age-related cognitive impairment. Nat Aging. 2025 Oct;5(10):1957-1969. doi: 10.1038/s43587-025-00940-z. Epub 2025 Aug 19. PMID: 40830655; PMCID: PMC12532579.

Virta JM, Vickery HR, Konstantinidou M, Crawford MC, Pennings MAM, Ottmann C, Brunsveld L, Arkin MR. Restoring the 14-3-3/CRAF regulatory interaction in Noonan syndrome using molecular glues. Proc Natl Acad Sci U S A. 2026 May 5;123(18):e2602101123. doi: 10.1073/pnas.2602101123. Epub 2026 Apr 28. PMID: 42048443; PMCID: PMC13142914.

Konstantinidou M, Vickery HR, Pennings MAM, Virta JM, Luo SY, Visser EJ, Bannier SD, Srikanth M, Cismoski SZ, Young LC, van den Oetelaar MCM, McCormick F, Ottmann C, Brunsveld L, Arkin MR. Modulation of the 14-3-3σ/C-RAF "Auto"inhibited Complex by Molecular Glues. J Am Chem Soc. 2026 Feb 11;148(5):4951-4965. doi: 10.1021/jacs.5c12622. Epub 2026 Jan 30. PMID: 41617210; PMCID: PMC12903857.

Sun X, Gayathri S, Kumbier K, Hammerlindl H, Ahern E, Wu LF, Altschuler SJ. ResMap: A community resource for systematic mapping of therapy-persistent residual cancer cell dependencies across contexts. Sci Adv. 2026 Jun 12;12(24):eaed7476. doi: 10.1126/sciadv.aed7476. Epub 2026 Jun 12. PMID: 42284402; PMCID: PMC13262613.

Olivier Mailhot; Katie L. Holland; Lu Paris; Dmytro S. Radchenko; Yurii S. Moroz; John J. Irwin; Brian K. Shoichet. Chemical Distance-Based Acceleration of Large Library Docking with ChemSTEP
ACS Cent. Sci. (2026).

Kang D, Pandey A, et al. Evans MJ, Craik CS. A prodrug strategy to conditionally trap therapeutic payloads for improved tumor retention. ACS Cent Sci (2026).

Niu Y, Lilly M, et al. Chesarino NM, Gross JD. The structural mechanism of HIV-2 Vif antagonism of human APOBEC3H. Nat Commun (2026).

Liu X, Li Y, et al. Daugherty MD, Gross JD. Structure of the E3 ligase CRL2ZYG11B with substrates reveals the molecular basis for N-degron recognition and ubiquitination. Cell Rep (2026).

Bao F, Li L, et al Altschuler SJ, Wu LF. Transitive prediction of small-molecule function through alignment of high-content screening resources. Nat Biotechnol (2025). 

Li L, et al & Altschuler SJ, Wu LF. A phenopushing platform to identify compounds that alleviate acute hypoxic stress by fast-tracking cellular adaptation. Nat Commun 16, 2684 (2025).

Konstantinidou M, Virta JM, Arkin MR. Stabilization of Native Protein-Protein Interactions with Molecular Glues: A 14-3-3 Case Study. Acc Chem Res. 2025 Sep 16;58(18):2840-2851. PMID: 40910885; PMCID: PMC12444995.

Konstantinidou M, et al. & Arkin MR. Scaffold-hopping for molecular glues targeting the 14-3-3/ERα complex. Nat Commun. 2025 Jul 14;16(1):6467. PMID: 40659654; PMCID: PMC12260087. 

Li F, Eriksen J, et al. Burlingame A, Grabe M, Stroud RM, Edwards RH.  Substrate recognition and allosteric regulation of synaptic vesicle glutamate transporter VGLUT2. Nat Struct Mol Biol. 2025 Aug;32(8):1479-1487.  PMID: 40461871 

Zahavi EE, et al., Burlingame AL, Fainzilber M. Repeat-element RNAs integrate a neuronal growth circuit. Cell. 2025 Aug 7;188(16):4350-4365.e22. PMID: 40381624.  

Detomasi TC, et al., Renslo AR, Craik CS. Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MPro inhibitors with potent in vivo efficacy. Sci Adv. 2025 Apr 25;11(17):eadt7836.. PMID: 40267184; PMCID: PMC12017303. 

Hou K, Huang W, Qi M, Tugwell TH, Alturaifi TM, Chen Y, Zhang X, Lu L, Mann SI, Liu P, Yang Y, DeGrado WF. De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts. Science. 2025 May 8;388(6747):665-670. PMID: 40339022; PMCID: PMC12316402. 

Grau B, Kormos R, et al., DeGrado WF, Mingarro I. Sequence-dependent scale for translocon-mediated insertion of interfacial helices in membranes. Sci Adv. 2025 Feb 21;11(8):eads6804. PMID: 39970206; PMCID: PMC11837994.

Bibel B, et al., Fraser JS, Fujimori DG. Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics. Nucleic Acids Res. 2025 Jan 24;53(3) PMID: 39907106; PMCID: PMC11795202.  

Carroll EC, et al & Gestwicki JE. High-throughput discovery of fluoroprobes that recognize amyloid fibril polymorphs. Nat Chem. 2025 Oct;17(10):1565-1575. PMID: 40813616; PMCID: PMC12491066. 

Wu T, et al. & Gestwicki JE. Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes. Nat Biotechnol. 2025 Jan;43(1):106-113. PMID: 38744946; PMCID: PMC12285679.

Meyer K, et al. & Huang B, Weiner OD. YAP charge patterning mediates signal integration through transcriptional co-condensates. Nat Commun. 2025 Aug 12;16(1):7454. PMID: 40796733; PMCID: PMC12343768. 

Howard MK, et al. & Coyote-Maestas W, Manglik A. Molecular basis of proton sensing by G protein-coupled receptors. Cell. 2025 Feb 6;188(3):671-687.e20. PMID: 39753132; PMCID: PMC11849372. 

Klope MT, et al & Renslo AR. Identifying a next-generation antimalarial trioxolane in a landscape of artemisinin partial resistance. Sci Adv. 2025 Aug 8;11(32):eads9168. PMID: 40779626; PMCID: PMC12333675.  

Correy GJ, Rachman MM, et al. & Renslo AR, Walters WP, Fraser JS. Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning. Sci Adv. 2025 May 30;11(22):eads7187. PMID: 40435250; PMCID: PMC12118597. 

Tummino TA, et al., Basbaum AI, Shoichet BK. Virtual library docking for cannabinoid-1 receptor agonists with reduced side effects. Nat Commun. 2025 Mar 6;16(1):2237. PMID: 40044644; PMCID: PMC11882969.

Liu F, Mailhot O, et al., Irwin JJ, Shoichet BK. The impact of library size and scale of testing on virtual screening. Nat Chem Biol. 2025 Jul;21(7):1039-1045. PMID: 39753705; PMCID: PMC12229919. 

Michael J Boucher et al & Zaro BW, Hiten D Madhan. Phenotypic landscape of an invasive fungal pathogen reveals its unique biology.  Cell188, 4003-4024.e24 (2025).