1
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Flynn JM, Zvornicanin SN, Tsepal T, Shaqra AM, Kurt Yilmaz N, Jia W, Moquin S, Dovala D, Schiffer CA, Bolon DNA. Contributions of Hyperactive Mutations in M pro from SARS-CoV-2 to Drug Resistance. ACS Infect Dis 2024; 10:1174-1184. [PMID: 38472113 DOI: 10.1021/acsinfecdis.3c00560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The appearance and spread of mutations that cause drug resistance in rapidly evolving diseases, including infections by the SARS-CoV-2 virus, are major concerns for human health. Many drugs target enzymes, and resistance-conferring mutations impact inhibitor binding or enzyme activity. Nirmatrelvir, the most widely used inhibitor currently used to treat SARS-CoV-2 infections, targets the main protease (Mpro) preventing it from processing the viral polyprotein into active subunits. Our previous work systematically analyzed resistance mutations in Mpro that reduce binding to inhibitors; here, we investigate mutations that affect enzyme function. Hyperactive mutations that increase Mpro activity can contribute to drug resistance but have not been thoroughly studied. To explore how hyperactive mutations contribute to resistance, we comprehensively assessed how all possible individual mutations in Mpro affect enzyme function using a mutational scanning approach with a fluorescence resonance energy transfer (FRET)-based yeast readout. We identified hundreds of mutations that significantly increased the Mpro activity. Hyperactive mutations occurred both proximal and distal to the active site, consistent with protein stability and/or dynamics impacting activity. Hyperactive mutations were observed 3 times more than mutations which reduced apparent binding to nirmatrelvir in recent studies of laboratory-grown viruses selected for drug resistance. Hyperactive mutations were also about three times more prevalent than nirmatrelvir binding mutations in sequenced isolates from circulating SARS-CoV-2. Our findings indicate that hyperactive mutations are likely to contribute to the natural evolution of drug resistance in Mpro and provide a comprehensive list for future surveillance efforts.
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Affiliation(s)
- Julia M Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Sarah N Zvornicanin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Tenzin Tsepal
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Ala M Shaqra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Weiping Jia
- Novartis Biomedical Research, Emeryville, California 94608, United States
| | - Stephanie Moquin
- Novartis Biomedical Research, Emeryville, California 94608, United States
| | - Dustin Dovala
- Novartis Biomedical Research, Emeryville, California 94608, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
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2
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Ma X, Leon B, Ornelas E, Dovala D, Tandeske L, Luu C, Pardee G, Widger S, Solomon JM, Beckwith REJ, Moser H, Clifton MC, Wartchow CA. Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon. Sci Rep 2023; 13:22088. [PMID: 38086859 PMCID: PMC10716131 DOI: 10.1038/s41598-023-48606-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
The design of cereblon-binding molecular glues (MGs) that selectively recruit a desired protein while excluding teratogenic SALL4 is an area of significant interest when designing therapeutic agents. Previous studies show that SALL4 is degraded in the presence of IKZF1 degraders pomalidomide, and to a lesser extent by CC-220. To expand our understanding of the molecular basis for the interaction of SALL4 with cereblon, we performed biophysical and structural studies demonstrating that SALL4 zinc finger domains one and two (ZF1-2) interact with cereblon (CRBN) in a unique manner. ZF1 interacts with the N-terminal domain of cereblon and ZF2 binds as expected in the C-terminal IMiD-binding domain. Both ZF1 and ZF2 contribute to the potency of the interaction of ZF1-2 with CRBN:MG complexes and the affinities of SALL4 ZF1-2 for the cereblon:CC-220 complex are less potent than for the corresponding pomalidomide complex. Structural analysis provides a rationale for understanding the reduced affinity of SALL4 for cereblon in the presence of CC-220, which engages both ZF1 and ZF2. These studies further our understanding of the molecular glue-mediated interactions of zinc finger-based proteins with cereblon and may provide structural tools for the prospective design of compounds with reduced binding and degradation of SALL4.
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Affiliation(s)
- Xiaolei Ma
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Barbara Leon
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Elizabeth Ornelas
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Dustin Dovala
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Laura Tandeske
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Catherine Luu
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Gwynn Pardee
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Stephania Widger
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Jonathan M Solomon
- Discovery Sciences, Novartis Biomedical Research, Cambridge, MA, 02139, USA
| | - Rohan E J Beckwith
- Discovery Sciences, Novartis Biomedical Research, Cambridge, MA, 02139, USA
| | - Heinz Moser
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Matthew C Clifton
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Charles A Wartchow
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA.
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3
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Toriki ES, Papatzimas JW, Nishikawa K, Dovala D, Frank AO, Hesse MJ, Dankova D, Song JG, Bruce-Smythe M, Struble H, Garcia FJ, Brittain SM, Kile AC, McGregor LM, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Correction to "Rational Chemical Design of Molecular Glue Degraders". ACS Cent Sci 2023; 9:1702. [PMID: 37637749 PMCID: PMC10450871 DOI: 10.1021/acscentsci.3c00844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 08/29/2023]
Abstract
[This corrects the article DOI: 10.1021/acscentsci.2c01317.].
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4
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Flynn JM, Huang QYJ, Zvornicanin SN, Schneider-Nachum G, Shaqra AM, Yilmaz NK, Moquin SA, Dovala D, Schiffer CA, Bolon DNA. Systematic Analyses of the Resistance Potential of Drugs Targeting SARS-CoV-2 Main Protease. ACS Infect Dis 2023; 9:1372-1386. [PMID: 37390404 DOI: 10.1021/acsinfecdis.3c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Drugs that target the main protease (Mpro) of SARS-CoV-2 are effective therapeutics that have entered clinical use. Wide-scale use of these drugs will apply selection pressure for the evolution of resistance mutations. To understand resistance potential in Mpro, we performed comprehensive surveys of amino acid changes that can cause resistance to nirmatrelvir (Pfizer), and ensitrelvir (Xocova) in a yeast screen. We identified 142 resistance mutations for nirmatrelvir and 177 for ensitrelvir, many of which have not been previously reported. Ninety-nine mutations caused apparent resistance to both inhibitors, suggesting likelihood for the evolution of cross-resistance. The mutation with the strongest drug resistance score against nirmatrelvir in our study (E166V) was the most impactful resistance mutation recently reported in multiple viral passaging studies. Many mutations that exhibited inhibitor-specific resistance were consistent with the distinct interactions of each inhibitor in the substrate binding site. In addition, mutants with strong drug resistance scores tended to have reduced function. Our results indicate that strong pressure from nirmatrelvir or ensitrelvir will select for multiple distinct-resistant lineages that will include both primary resistance mutations that weaken interactions with drug while decreasing enzyme function and compensatory mutations that increase enzyme activity. The comprehensive identification of resistance mutations enables the design of inhibitors with reduced potential of developing resistance and aids in the surveillance of drug resistance in circulating viral populations.
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Affiliation(s)
- Julia M Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Qiu Yu J Huang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Sarah N Zvornicanin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Gila Schneider-Nachum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Ala M Shaqra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Stephanie A Moquin
- Novartis Institute for Biomedical Research, Emeryville, California 94608, United States
| | - Dustin Dovala
- Novartis Institute for Biomedical Research, Emeryville, California 94608, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
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5
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Toriki E, Papatzimas JW, Nishikawa K, Dovala D, Frank AO, Hesse MJ, Dankova D, Song JG, Bruce-Smythe M, Struble H, Garcia FJ, Brittain SM, Kile AC, McGregor LM, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Rational Chemical Design of Molecular Glue Degraders. ACS Cent Sci 2023; 9:915-926. [PMID: 37252349 PMCID: PMC10214506 DOI: 10.1021/acscentsci.2c01317] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Indexed: 05/31/2023]
Abstract
Targeted protein degradation with molecular glue degraders has arisen as a powerful therapeutic modality for eliminating classically undruggable disease-causing proteins through proteasome-mediated degradation. However, we currently lack rational chemical design principles for converting protein-targeting ligands into molecular glue degraders. To overcome this challenge, we sought to identify a transposable chemical handle that would convert protein-targeting ligands into molecular degraders of their corresponding targets. Using the CDK4/6 inhibitor ribociclib as a prototype, we identified a covalent handle that, when appended to the exit vector of ribociclib, induced the proteasome-mediated degradation of CDK4 in cancer cells. Further modification of our initial covalent scaffold led to an improved CDK4 degrader with the development of a but-2-ene-1,4-dione ("fumarate") handle that showed improved interactions with RNF126. Subsequent chemoproteomic profiling revealed interactions of the CDK4 degrader and the optimized fumarate handle with RNF126 as well as additional RING-family E3 ligases. We then transplanted this covalent handle onto a diverse set of protein-targeting ligands to induce the degradation of BRD4, BCR-ABL and c-ABL, PDE5, AR and AR-V7, BTK, LRRK2, HDAC1/3, and SMARCA2/4. Our study undercovers a design strategy for converting protein-targeting ligands into covalent molecular glue degraders.
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Affiliation(s)
- Ethan
S. Toriki
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - James W. Papatzimas
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Kaila Nishikawa
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Dustin Dovala
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Andreas O. Frank
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Matthew J. Hesse
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniela Dankova
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Jae-Geun Song
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Megan Bruce-Smythe
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Heidi Struble
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Francisco J. Garcia
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Scott M. Brittain
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Andrew C. Kile
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Lynn M. McGregor
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeffrey M. McKenna
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel K. Nomura
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, California 94720, United States
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6
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King EA, Cho Y, Hsu NS, Dovala D, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Chemoproteomics-enabled discovery of a covalent molecular glue degrader targeting NF-κB. Cell Chem Biol 2023; 30:394-402.e9. [PMID: 36898369 PMCID: PMC10121878 DOI: 10.1016/j.chembiol.2023.02.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 01/11/2023] [Accepted: 02/16/2023] [Indexed: 03/11/2023]
Abstract
Targeted protein degradation has arisen as a powerful therapeutic modality for degrading disease targets. While proteolysis-targeting chimera (PROTAC) design is more modular, the discovery of molecular glue degraders has been more challenging. Here, we have coupled the phenotypic screening of a covalent ligand library with chemoproteomic approaches to rapidly discover a covalent molecular glue degrader and associated mechanisms. We have identified a cysteine-reactive covalent ligand EN450 that impairs leukemia cell viability in a NEDDylation and proteasome-dependent manner. Chemoproteomic profiling revealed covalent interaction of EN450 with an allosteric C111 in the E2 ubiquitin-conjugating enzyme UBE2D. Quantitative proteomic profiling revealed the degradation of the oncogenic transcription factor NFKB1 as a putative degradation target. Our study thus puts forth the discovery of a covalent molecular glue degrader that uniquely induced the proximity of an E2 with a transcription factor to induce its degradation in cancer cells.
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Affiliation(s)
- Elizabeth A King
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Yoojin Cho
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Nathan S Hsu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Dustin Dovala
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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7
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Moon P, Zammit C, Shao Q, Boike L, Dovala D, Henning NJ, Knapp M, Spradlin JN, Ward CC, Wolleb H, Fuller D, Blake G, Murphy JP, Wang F, Lu Y, Moquin SA, Tandeske L, Hesse MJ, McKenna JM, Tallarico JA, Schirle M, Toste FD, Nomura DK. Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors. Chembiochem 2023:e202300116. [PMID: 37069799 DOI: 10.1002/cbic.202300116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/19/2023]
Abstract
Among the various genes and proteins encoded by all coronaviruses, one particularly "druggable" or relatively easy-to-drug target is the coronavirus Main Protease (3CLproor Mpro), an enzyme that is involved in cleaving a long peptide translated by the viral genome into its individual protein components that are then assembled into the virus to enable viral replication in the cell. Inhibiting Mpro with a small-molecule antiviral would effectively stop the ability of the virus to replicate, providing therapeutic benefit. In this study, we have utilized activity-based protein profiling (ABPP)-based chemoproteomic approaches to discover and further optimize cysteine-reactive pyrazoline-based covalent inhibitors for the SARS-CoV-2 Mpro. Structure-guided medicinal chemistry and modular synthesis of di- and tri-substituted pyrazolines bearing either chloroacetamide or vinyl sulfonamide cysteine-reactive warheads enabled the expedient exploration of structure-activity relationships (SAR), yielding nanomolar potency inhibitors against Mpro from not only SARS-CoV-2, but across many other coronaviruses. Our studies highlight promising chemical scaffolds that may contribute to future pan-coronavirus inhibitors.
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Affiliation(s)
- Patrick Moon
- University of California Berkeley, Chemistry, UNITED STATES
| | | | - Qian Shao
- UC Berkeley: University of California Berkeley, Chemistry, UNITED STATES
| | - Lydia Boike
- University of California Berkeley, Chemistry, UNITED STATES
| | - Dustin Dovala
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | | | - Mark Knapp
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | | | - Carl C Ward
- University of California Berkeley, Chemistry, UNITED STATES
| | - Helene Wolleb
- University of California Berkeley, Chemistry, UNITED STATES
| | - Daniel Fuller
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Gabrielle Blake
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Jason P Murphy
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Feng Wang
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Yipin Lu
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Stephanie A Moquin
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Laura Tandeske
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Matthew J Hesse
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, UNITED STATES
| | - Jeffrey M McKenna
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, UNITED STATES
| | - John A Tallarico
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Markus Schirle
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - F Dean Toste
- University of California Berkeley, Chemistry, UNITED STATES
| | - Daniel K Nomura
- University of California, Berkeley, Chemistry, 127 Morgan Hall, 94720, Berkeley, UNITED STATES
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8
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Abstract
Targeted protein degradation (TPD) with proteolysis targeting chimeras (PROTACs), heterobifunctional compounds consisting of protein targeting ligands linked to recruiters of E3 ubiquitin ligases, has arisen as a powerful therapeutic modality to induce the proximity of target proteins with E3 ligases to ubiquitinate and degrade specific proteins in cells. Thus far, PROTACs have primarily exploited the recruitment of E3 ubiquitin ligases or their substrate adapter proteins but have not exploited the recruitment of more core components of the ubiquitin-proteasome system (UPS). In this study, we used covalent chemoproteomic approaches to discover a covalent recruiter against the E2 ubiquitin conjugating enzyme UBE2D─EN67─that targets an allosteric cysteine, C111, without affecting the enzymatic activity of the protein. We demonstrated that this UBE2D recruiter could be used in heterobifunctional degraders to degrade neo-substrate targets in a UBE2D-dependent manner, including BRD4 and the androgen receptor. Overall, our data highlight the potential for the recruitment of core components of the UPS machinery, such as E2 ubiquitin conjugating enzymes, for TPD, and underscore the utility of covalent chemoproteomic strategies for identifying novel recruiters for additional components of the UPS.
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Affiliation(s)
- Nafsika Forte
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Dustin Dovala
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Matthew J Hesse
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jeffrey M McKenna
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A Tallarico
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Innovative Genomics Institute, Berkeley, California 94704, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
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9
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Zvornicanin SN, Shaqra AM, Huang QJ, Ornelas E, Moghe M, Knapp M, Moquin S, Dovala D, Schiffer CA, Kurt Yilmaz N. Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses. Viruses 2023; 15:v15030781. [PMID: 36992489 PMCID: PMC10059799 DOI: 10.3390/v15030781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
With the spread of SARS-CoV-2 throughout the globe causing the COVID-19 pandemic, the threat of zoonotic transmissions of coronaviruses (CoV) has become even more evident. As human infections have been caused by alpha- and beta-CoVs, structural characterization and inhibitor design mostly focused on these two genera. However, viruses from the delta and gamma genera also infect mammals and pose a potential zoonotic transmission threat. Here, we determined the inhibitor-bound crystal structures of the main protease (Mpro) from the delta-CoV porcine HKU15 and gamma-CoV SW1 from the beluga whale. A comparison with the apo structure of SW1 Mpro, which is also presented here, enabled the identification of structural arrangements upon inhibitor binding at the active site. The cocrystal structures reveal binding modes and interactions of two covalent inhibitors, PF-00835231 (active form of lufotrelvir) bound to HKU15, and GC376 bound to SW1 Mpro. These structures may be leveraged to target diverse coronaviruses and toward the structure-based design of pan-CoV inhibitors.
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Affiliation(s)
- Sarah N Zvornicanin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ala M Shaqra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Qiuyu J Huang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Elizabeth Ornelas
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Mallika Moghe
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Mark Knapp
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Stephanie Moquin
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Dustin Dovala
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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10
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Gowans FA, Thach DQ, Wang Y, Altamirano Poblano BE, Dovala D, Tallarico JA, McKenna JM, Schirle M, Maimone TJ, Nomura DK. Ophiobolin A Covalently Targets Complex IV Leading to Mitochondrial Metabolic Collapse in Cancer Cells. bioRxiv 2023:2023.03.09.531918. [PMID: 36945520 PMCID: PMC10029012 DOI: 10.1101/2023.03.09.531918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Ophiobolin A (OPA) is a sesterterpenoid fungal natural product with broad anti-cancer activity. While OPA possesses multiple electrophilic moieties that can covalently react with nucleophilic amino acids on proteins, the proteome-wide targets and mechanism of OPA remain poorly understood in many contexts. In this study, we used covalent chemoproteomic platforms to map the proteome-wide reactivity of OPA in a highly sensitive lung cancer cell line. Among several proteins that OPA engaged, we focused on two targets-cysteine C53 of HIG2DA and lysine K72 of COX5A-that are part of complex IV of the electron transport chain and contributed significantly to the anti-proliferative activity. OPA activated mitochondrial respiration in a HIG2DA and COX5A-dependent manner, led to an initial spike in mitochondrial ATP, but then compromised mitochondrial membrane potential leading to ATP depletion. We have used chemoproteomic strategies to discover a unique anti-cancer mechanism of OPA through activation of complex IV leading to compromised mitochondrial energetics and rapid cell death.
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Affiliation(s)
- Flor A. Gowans
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Danny Q. Thach
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Yangzhi Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Belen E. Altamirano Poblano
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Dustin Dovala
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608 USA
| | - John A. Tallarico
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Jeffrey M. McKenna
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Thomas J. Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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11
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Gonzalez-Valero A, Reeves AG, Page ACS, Moon PJ, Miller E, Coulonval K, Crossley SWM, Xie X, He D, Musacchio PZ, Christian AH, McKenna JM, Lewis RA, Fang E, Dovala D, Lu Y, McGregor LM, Schirle M, Tallarico JA, Roger PP, Toste FD, Chang CJ. An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4. J Am Chem Soc 2022; 144:22890-22901. [PMID: 36484997 PMCID: PMC10124963 DOI: 10.1021/jacs.2c04039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling (ABPP) is a versatile strategy for identifying and characterizing functional protein sites and compounds for therapeutic development. However, the vast majority of ABPP methods for covalent drug discovery target highly nucleophilic amino acids such as cysteine or lysine. Here, we report a methionine-directed ABPP platform using Redox-Activated Chemical Tagging (ReACT), which leverages a biomimetic oxidative ligation strategy for selective methionine modification. Application of ReACT to oncoprotein cyclin-dependent kinase 4 (CDK4) as a representative high-value drug target identified three new ligandable methionine sites. We then synthesized a methionine-targeting covalent ligand library bearing a diverse array of heterocyclic, heteroatom, and stereochemically rich substituents. ABPP screening of this focused library identified 1oxF11 as a covalent modifier of CDK4 at an allosteric M169 site. This compound inhibited kinase activity in a dose-dependent manner on purified protein and in breast cancer cells. Further investigation of 1oxF11 found prominent cation-π and H-bonding interactions stabilizing the binding of this fragment at the M169 site. Quantitative mass-spectrometry studies validated 1oxF11 ligation of CDK4 in breast cancer cell lysates. Further biochemical analyses revealed cross-talk between M169 oxidation and T172 phosphorylation, where M169 oxidation prevented phosphorylation of the activating T172 site on CDK4 and blocked cell cycle progression. By identifying a new mechanism for allosteric methionine redox regulation on CDK4 and developing a unique modality for its therapeutic intervention, this work showcases a generalizable platform that provides a starting point for engaging in broader chemoproteomics and protein ligand discovery efforts to find and target previously undruggable methionine sites.
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Affiliation(s)
- Angel Gonzalez-Valero
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Audrey G. Reeves
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Annika C. S. Page
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Patrick J. Moon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Edward Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Katia Coulonval
- Faculté de Médecine, Institute of Interdisciplinary Research, Université Libre de Bruxelles, Campus Erasme, Brussels 1070, Belgium
| | - Steven W. M. Crossley
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Xiao Xie
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Dan He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Patricia Z. Musacchio
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alec H. Christian
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jeffrey M. McKenna
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Richard A. Lewis
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Eric Fang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Dustin Dovala
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Yipin Lu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Lynn M. McGregor
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Pierre P. Roger
- Faculté de Médecine, Institute of Interdisciplinary Research, Université Libre de Bruxelles, Campus Erasme, Brussels 1070, Belgium
| | - F. Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
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12
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Shaqra AM, Zvornicanin SN, Huang QYJ, Lockbaum GJ, Knapp M, Tandeske L, Bakan DT, Flynn J, Bolon DNA, Moquin S, Dovala D, Kurt Yilmaz N, Schiffer CA. Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance. Nat Commun 2022; 13:3556. [PMID: 35729165 PMCID: PMC9211792 DOI: 10.1038/s41467-022-31210-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 01/01/2023] Open
Abstract
Coronaviruses can evolve and spread rapidly to cause severe disease morbidity and mortality, as exemplified by SARS-CoV-2 variants of the COVID-19 pandemic. Although currently available vaccines remain mostly effective against SARS-CoV-2 variants, additional treatment strategies are needed. Inhibitors that target essential viral enzymes, such as proteases and polymerases, represent key classes of antivirals. However, clinical use of antiviral therapies inevitably leads to emergence of drug resistance. In this study we implemented a strategy to pre-emptively address drug resistance to protease inhibitors targeting the main protease (Mpro) of SARS-CoV-2, an essential enzyme that promotes viral maturation. We solved nine high-resolution cocrystal structures of SARS-CoV-2 Mpro bound to substrate peptides and six structures with cleavage products. These structures enabled us to define the substrate envelope of Mpro, map the critical recognition elements, and identify evolutionarily vulnerable sites that may be susceptible to resistance mutations that would compromise binding of the newly developed Mpro inhibitors. Our results suggest strategies for developing robust inhibitors against SARS-CoV-2 that will retain longer-lasting efficacy against this evolving viral pathogen.
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Affiliation(s)
- Ala M Shaqra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Sarah N Zvornicanin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Qiu Yu J Huang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Mark Knapp
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Laura Tandeske
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - David T Bakan
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Julia Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Stephanie Moquin
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Dustin Dovala
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US.
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US.
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13
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Flynn JM, Samant N, Schneider-Nachum G, Bakan DT, Yilmaz NK, Schiffer CA, Moquin SA, Dovala D, Bolon DNA. Comprehensive fitness landscape of SARS-CoV-2 M pro reveals insights into viral resistance mechanisms. eLife 2022; 11:77433. [PMID: 35723575 PMCID: PMC9323007 DOI: 10.7554/elife.77433] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
With the continual evolution of new strains of SARS-CoV-2 that are more virulent, transmissible, and able to evade current vaccines, there is an urgent need for effective anti-viral drugs SARS-CoV-2 main protease (Mpro) is a leading target for drug design due to its conserved and indispensable role in the viral life cycle. Drugs targeting Mpro appear promising but will elicit selection pressure for resistance. To understand resistance potential in Mpro, we performed a comprehensive mutational scan of the protease that analyzed the function of all possible single amino acid changes. We developed three separate high-throughput assays of Mpro function in yeast, based on either the ability of Mpro variants to cleave at a defined cut-site or on the toxicity of their expression to yeast. We used deep sequencing to quantify the functional effects of each variant in each screen. The protein fitness landscapes from all three screens were strongly correlated, indicating that they captured the biophysical properties critical to Mpro function. The fitness landscapes revealed a non-active site location on the surface that is extremely sensitive to mutation making it a favorable location to target with inhibitors. In addition, we found a network of critical amino acids that physically bridge the two active sites of the Mpro dimer. The clinical variants of Mpro were predominantly functional in our screens, indicating that Mpro is under strong selection pressure in the human population. Our results provide predictions of mutations that will be readily accessible to Mpro evolution and that are likely to contribute to drug resistance. This complete mutational guide of Mpro can be used in the design of inhibitors with reduced potential of evolving viral resistance.
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Affiliation(s)
- Julia M Flynn
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Neha Samant
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Gily Schneider-Nachum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | | | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | | | | | - Daniel N A Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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14
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Henning NJ, Boike L, Spradlin JN, Ward CC, Liu G, Zhang E, Belcher BP, Brittain SM, Hesse MJ, Dovala D, McGregor LM, Valdez Misiolek R, Plasschaert LW, Rowlands DJ, Wang F, Frank AO, Fuller D, Estes AR, Randal KL, Panidapu A, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Deubiquitinase-targeting chimeras for targeted protein stabilization. Nat Chem Biol 2022; 18:412-421. [PMID: 35210618 PMCID: PMC10125259 DOI: 10.1038/s41589-022-00971-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/09/2022] [Indexed: 12/12/2022]
Abstract
Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), heterobifunctional small molecules consisting of a deubiquitinase recruiter linked to a protein-targeting ligand, to stabilize the levels of specific proteins degraded in a ubiquitin-dependent manner. Using chemoproteomic approaches, we discovered the covalent ligand EN523 that targets a non-catalytic allosteric cysteine C23 in the K48-ubiquitin-specific deubiquitinase OTUB1. We showed that a DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR), robustly stabilized ΔF508-CFTR protein levels, leading to improved chloride channel conductance in human cystic fibrosis bronchial epithelial cells. We also demonstrated stabilization of the tumor suppressor kinase WEE1 in hepatoma cells. Our study showcases covalent chemoproteomic approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS.
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Affiliation(s)
- Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gang Liu
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Bridget P Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthew J Hesse
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dustin Dovala
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Lynn M McGregor
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Feng Wang
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Andreas O Frank
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Daniel Fuller
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Abigail R Estes
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Katelyn L Randal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.
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15
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Pinch BJ, Buckley DL, Gleim S, Brittain SM, Tandeske L, D'Alessandro PL, Hauseman ZJ, Lipps J, Xu L, Harvey EP, Schirle M, Sprague ER, Forrester WC, Dovala D, McGregor LM, Thoma CR. A strategy to assess the cellular activity of E3 ligase components against neo-substrates using electrophilic probes. Cell Chem Biol 2021; 29:57-66.e6. [PMID: 34499862 DOI: 10.1016/j.chembiol.2021.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 06/17/2021] [Accepted: 08/20/2021] [Indexed: 01/12/2023]
Abstract
While there are hundreds of predicted E3 ligases, characterizing their applications for targeted protein degradation has proved challenging. Here, we report a chemical biology approach to evaluate the ability of modified recombinant E3 ligase components to support neo-substrate degradation. Bypassing the need for specific E3 ligase binders, we use maleimide-thiol chemistry for covalent functionalization followed by E3 electroporation (COFFEE) in live cells. We demonstrate that electroporated recombinant von Hippel-Lindau (VHL) protein, covalently functionalized at its ligandable cysteine with JQ1 or dasatinib, induces degradation of BRD4 or tyrosine kinases, respectively. Furthermore, by applying COFFEE to SPSB2, a Cullin-RING ligase 5 receptor, as well as to SKP1, the adaptor protein for Cullin-RING ligase 1 F box (SCF) complexes, we validate this method as a powerful approach to define the activity of previously uncharacterized ubiquitin ligase components, and provide further evidence that not only E3 ligase receptors but also adaptors can be directly hijacked for neo-substrate degradation.
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Affiliation(s)
- Benika J Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Dennis L Buckley
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott M Brittain
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Laura Tandeske
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | | | | | - Jennifer Lipps
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Lei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Edward P Harvey
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | | | - Dustin Dovala
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA.
| | - Lynn M McGregor
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
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16
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Biering SB, Van Dis E, Wehri E, Yamashiro LH, Nguyenla X, Dugast-Darzacq C, Graham TGW, Stroumza JR, Golovkine GR, Roberts AW, Fines DM, Spradlin JN, Ward CC, Bajaj T, Dovala D, Schulze-Gamen U, Bajaj R, Fox DM, Ott M, Murthy N, Nomura DK, Schaletzky J, Stanley SA. Screening a Library of FDA-Approved and Bioactive Compounds for Antiviral Activity against SARS-CoV-2. ACS Infect Dis 2021; 7:2337-2351. [PMID: 34129317 PMCID: PMC8231672 DOI: 10.1021/acsinfecdis.1c00017] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has emerged as a major global health threat. The COVID-19 pandemic has resulted in over 168 million cases and 3.4 million deaths to date, while the number of cases continues to rise. With limited therapeutic options, the identification of safe and effective therapeutics is urgently needed. The repurposing of known clinical compounds holds the potential for rapid identification of drugs effective against SARS-CoV-2. Here, we utilized a library of FDA-approved and well-studied preclinical and clinical compounds to screen for antivirals against SARS-CoV-2 in human pulmonary epithelial cells. We identified 13 compounds that exhibit potent antiviral activity across multiple orthogonal assays. Hits include known antivirals, compounds with anti-inflammatory activity, and compounds targeting host pathways such as kinases and proteases critical for SARS-CoV-2 replication. We identified seven compounds not previously reported to have activity against SARS-CoV-2, including B02, a human RAD51 inhibitor. We further demonstrated that B02 exhibits synergy with remdesivir, the only antiviral approved by the FDA to treat COVID-19, highlighting the potential for combination therapy. Taken together, our comparative compound screening strategy highlights the potential of drug repurposing screens to identify novel starting points for development of effective antiviral mono- or combination therapies to treat COVID-19.
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Affiliation(s)
- Scott B. Biering
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Eddie Wehri
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Livia H. Yamashiro
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Xammy Nguyenla
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Division of
Biochemistry, Biophysics and Structural Biology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Thomas G. W. Graham
- Department of Molecular and Cell Biology, Division of
Biochemistry, Biophysics and Structural Biology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Julien R. Stroumza
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Guillaume R. Golovkine
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Allison W. Roberts
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Daniel M. Fines
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Jessica N. Spradlin
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Carl C. Ward
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Teena Bajaj
- Department of Bioengineering, University of
California, Berkeley, Berkeley, California 94720, United
States
| | - Dustin Dovala
- Novartis Institutes for BioMedical
Research, Emeryville, California 94608, United
States
| | - Ursula Schulze-Gamen
- QBI Coronavirus Research Group Structural Biology
Consortium, University of California, San Francisco, California
94158, United States
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences,
University of California, San Francisco, San Francisco,
California 94158, United States
| | - Douglas M. Fox
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Melanie Ott
- Department of Medicine, Medical Scientist Training
Program, Biomedical Sciences Graduate Program, University of California, San
Francisco, San Francisco, California 94143, United
States
- J. David Gladstone
Institutes, San Francisco, California 94158, United
States
| | - Niren Murthy
- Department of Bioengineering, University of
California, Berkeley, Berkeley, California 94720, United
States
- Innovative Genomics Institute
(IGI), 2151 Berkeley Way, Berkeley, California 94704, United
States
| | - Daniel K. Nomura
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Julia Schaletzky
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Sarah A. Stanley
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
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17
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Vepřek NA, Peitsinis Z, Zhang Y, Trauner D, Fischer C, Rühmann KP, Yang C, Spradlin JN, Dovala D, Nomura DK. De novo Design of SARS-CoV-2 Main Protease Inhibitors. Synlett 2021; 33:458-463. [DOI: 10.1055/a-1582-0243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe COVID-19 pandemic prompted many scientists to investigate remedies against SARS-CoV-2 and related viruses that are likely to appear in the future. As the main protease of the virus, MPro, is highly conserved among coronaviruses, it has emerged as a prime target for developing inhibitors. Using a combination of virtual screening and molecular modeling, we identified small molecules that were easily accessible and could be quickly diversified. Biochemical assays confirmed a class of pyridones as low micromolar noncovalent inhibitors of the viral main protease.
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Affiliation(s)
- Nynke A. Vepřek
- Department of Chemistry, New York University
- Department of Chemistry, Ludwig-Maximilians-University Munich
| | | | | | | | | | | | - Chao Yang
- Department of Chemistry, New York University
| | | | | | - Daniel K. Nomura
- Innovative Genomics Institute, University of California Berkeley
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18
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Spangler B, Dovala D, Sawyer WS, Thompson KV, Six DA, Reck F, Feng BY. Molecular Probes for the Determination of Subcellular Compound Exposure Profiles in Gram-Negative Bacteria. ACS Infect Dis 2018; 4:1355-1367. [PMID: 29846057 DOI: 10.1021/acsinfecdis.8b00093] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Gram-negative cell envelope presents a formidable barrier to xenobiotics, and achieving sufficient compound exposure inside the cell is a key challenge for the discovery of new antibiotics. To provide insight on the molecular determinants governing compound exposure in Gram-negative bacteria, we developed a methodology leveraging a cyclooctyne-based bioorthogonal probe to assess compartment-specific compound exposure. This probe can be selectively localized to the periplasmic or cytoplasmic compartments of Gram-negative bacteria. Once localized, the probe is used to test azide-containing compounds for exposure within each compartment by quantifying the formation of click-reaction products by mass spectrometry. We demonstrate this approach is an accurate and sensitive method of determining compartment-specific compound exposure profiles. We then apply this technology to study the compartment-specific exposure profiles of a small panel of azide-bearing compounds with known permeability characteristics in Gram-negative bacteria, demonstrating the utility of the system and the insight it is able to provide regarding compound exposure within intact bacteria.
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Affiliation(s)
- Benjamin Spangler
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dustin Dovala
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - William S. Sawyer
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Katherine V. Thompson
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - David A. Six
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian Y. Feng
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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19
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Nilsson I, Grove K, Dovala D, Uehara T, Lapointe G, Six DA. Molecular characterization and verification of azido-3,8-dideoxy-d- manno-oct-2-ulosonic acid incorporation into bacterial lipopolysaccharide. J Biol Chem 2017; 292:19840-19848. [PMID: 29018092 DOI: 10.1074/jbc.m117.814962] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/05/2017] [Indexed: 11/06/2022] Open
Abstract
3-Deoxy-d-manno-oct-2-ulosonic acid (Kdo) is an essential component of LPS in the outer leaflet of the Gram-negative bacterial outer membrane. Although labeling of Escherichia coli with the chemical reporter 8-azido-3,8-dideoxy-d-manno-oct-2-ulosonic acid (Kdo-N3) has been reported, its incorporation into LPS has not been directly shown. We have now verified Kdo-N3 incorporation into E. coli LPS at the molecular level. Using microscopy and PAGE analysis, we show that Kdo-N3 is localized to the outer membrane and specifically incorporates into rough and deep-rough LPS. In an E. coli strain lacking endogenous Kdo biosynthesis, supplementation with exogenous Kdo restored full-length core-LPS, which suggests that the Kdo biosynthetic pathways might not be essential in vivo in the presence of sufficient exogenous Kdo. In contrast, exogenous Kdo-N3 only restored a small fraction of core LPS with the majority incorporated into truncated LPS. The truncated LPS were identified as Kdo-N3-lipid IVA and (Kdo-N3)2-lipid IVA by MS analysis. The low level of Kdo-N3 incorporation could be partly explained by a 6-fold reduction in the specificity constant of the CMP-Kdo synthetase KdsB with Kdo-N3 compared with Kdo. These results indicate that the azido moiety in Kdo-N3 interferes with its utilization and may limit its utility as a tracer of LPS biosynthesis and transport in E. coli We propose that our findings will be helpful for researchers using Kdo and its chemical derivatives for investigating LPS biosynthesis, transport, and assembly in Gram-negative bacteria.
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Affiliation(s)
| | - Kerri Grove
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California 94608
| | | | | | - Guillaume Lapointe
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California 94608
| | - David A Six
- From the Departments of Infectious Diseases and
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20
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Booth EA, Sterling SM, Dovala D, Nogales E, Thorner J. Effects of Bni5 Binding on Septin Filament Organization. J Mol Biol 2016; 428:4962-4980. [PMID: 27806918 DOI: 10.1016/j.jmb.2016.10.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 12/31/2022]
Abstract
Septins are a protein family found in all eukaryotes (except higher plants) that have roles in membrane remodeling and formation of diffusion barriers and as a scaffold to recruit other proteins. In budding yeast, proper execution of cytokinesis and cell division requires the formation of a collar of circumferential filaments at the bud neck. These filaments are assembled from apolar septin hetero-octamers. Currently, little is known about the mechanisms that control the arrangement and dynamics of septin structures. In this study, we utilized both Förster resonance energy transfer and electron microscopy to analyze the biophysical properties of the septin-binding protein Bni5 and how its association with septin filaments affects their organization. We found that the interaction of Bni5 with the terminal subunit (Cdc11) at the junctions between adjacent hetero-octamers in paired filaments is highly cooperative. Both the C-terminal end of Bni5 and the C-terminal extension of Cdc11 make important contributions to their interaction. Moreover, this binding may stabilize the dimerization of Bni5, which, in turn, forms cross-filament braces that significantly narrow, and impose much more uniform spacing on, the gap between paired filaments.
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Affiliation(s)
- Elizabeth A Booth
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.
| | - Sarah M Sterling
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.
| | - Dustin Dovala
- Program in Microbial Pathogenesis and Host Defense, Department of Microbiology and Immunology, University of California School of Medicine, San Francisco, CA 94143, USA.
| | - Eva Nogales
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA; Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.
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21
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Booth EA, Vane EW, Dovala D, Thorner J. A Förster Resonance Energy Transfer (FRET)-based System Provides Insight into the Ordered Assembly of Yeast Septin Hetero-octamers. J Biol Chem 2015; 290:28388-28401. [PMID: 26416886 PMCID: PMC4653696 DOI: 10.1074/jbc.m115.683128] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Indexed: 12/21/2022] Open
Abstract
Prior studies in both budding yeast (Saccharomyces cerevisiae) and in human cells have established that septin protomers assemble into linear hetero-octameric rods with 2-fold rotational symmetry. In mitotically growing yeast cells, five septin subunits are expressed (Cdc3, Cdc10, Cdc11, Cdc12, and Shs1) and assemble into two types of rods that differ only in their terminal subunit: Cdc11-Cdc12-Cdc3-Cdc10-Cdc10-Cdc3-Cdc12-Cdc11 and Shs1-Cdc12-Cdc3-Cdc10-Cdc10-Cdc3-Cdc12-Shs1. EM analysis has shown that, under low salt conditions, the Cdc11-capped rods polymerize end to end to form long paired filaments, whereas Shs1-capped rods form arcs, spirals, and rings. To develop a facile method to study septin polymerization in vitro, we exploited our previous work in which we generated septin complexes in which all endogenous cysteine (Cys) residues were eliminated by site-directed mutagenesis, except an introduced E294C mutation in Cdc11 in these experiments. Mixing samples of a preparation of such single-Cys containing Cdc11-capped rods that have been separately derivatized with organic dyes that serve as donor and acceptor, respectively, for FRET provided a spectroscopic method to monitor filament assembly mediated by Cdc11-Cdc11 interaction and to measure its affinity under specified conditions. Modifications of this same FRET scheme also allow us to assess whether Shs1-capped rods are capable of end to end association either with themselves or with Cdc11-capped rods. This FRET approach also was used to follow the binding to septin filaments of a septin-interacting protein, the type II myosin-binding protein Bni5.
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Affiliation(s)
- Elizabeth A Booth
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Eleanor W Vane
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Dustin Dovala
- Program in Microbial Pathogenesis and Host Defense, Department of Microbiology and Immunology, University of California School of Medicine, San Francisco, California 94158-2200
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202.
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22
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Dovala D, Sawyer WS, Rath CM, Metzger LE. Rapid analysis of protein expression and solubility with the SpyTag-SpyCatcher system. Protein Expr Purif 2015; 117:44-51. [PMID: 26405011 DOI: 10.1016/j.pep.2015.09.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 11/28/2022]
Abstract
Successful isolation of well-folded and active protein often first requires the creation of many constructs. These are needed to assess the effects of truncations, insertions, mutations, and the presence and position of different affinity tags. Determining which constructs yield the highest expression and solubility requires the investigator to express and partially purify each construct, and, in the case of low-expressing proteins, to follow the protein using time-consuming Western blots. Even then, many proteins form soluble aggregates, which may only be apparent after more extensive purification via size exclusion chromatography. In this work, we have utilized a covalent bond-forming tag/domain pair, known as SpyTag/SpyCatcher, to rapidly and specifically attach a fluorescent label to proteins of interest in cellular lysates. Once labeled, tagged proteins can easily be followed via SDS-PAGE and fluorescence size exclusion chromatography (F-SEC) to assess expression levels, solubility, and monodispersity without the need for purification. These techniques enable rapid and facile analysis of proteins, which may greatly facilitate optimization of protein expression constructs.
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Affiliation(s)
- Dustin Dovala
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - William S Sawyer
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Christopher M Rath
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Louis E Metzger
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States.
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23
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Rosenberg OS, Dovala D, Li X, Connolly L, Bendebury A, Finer-Moore J, Holton J, Cheng Y, Stroud RM, Cox JS. Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion. Cell 2015; 161:501-512. [PMID: 25865481 DOI: 10.1016/j.cell.2015.03.040] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/10/2014] [Accepted: 02/11/2015] [Indexed: 01/13/2023]
Abstract
Mycobacterium tuberculosis and Staphylococcus aureus secrete virulence factors via type VII protein secretion (T7S), a system that intriguingly requires all of its secretion substrates for activity. To gain insights into T7S function, we used structural approaches to guide studies of the putative translocase EccC, a unique enzyme with three ATPase domains, and its secretion substrate EsxB. The crystal structure of EccC revealed that the ATPase domains are joined by linker/pocket interactions that modulate its enzymatic activity. EsxB binds via its signal sequence to an empty pocket on the C-terminal ATPase domain, which is accompanied by an increase in ATPase activity. Surprisingly, substrate binding does not activate EccC allosterically but, rather, by stimulating its multimerization. Thus, the EsxB substrate is also an integral T7S component, illuminating a mechanism that helps to explain interdependence of substrates, and suggests a model in which binding of substrates modulates their coordinate release from the bacterium.
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Affiliation(s)
- Oren S Rosenberg
- Division of Infectious Diseases, Department of Medicine, UCSF Medical Center, University of California, San Francisco, San Francisco, CA 94143-0654, USA
| | - Dustin Dovala
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xueming Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lynn Connolly
- Division of Infectious Diseases, Department of Medicine, UCSF Medical Center, University of California, San Francisco, San Francisco, CA 94143-0654, USA; Achaogen, Inc., South San Francisco, CA 94080, USA
| | - Anastasia Bendebury
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Janet Finer-Moore
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James Holton
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA; Lawrence Berkeley National Laboratory, MS6-2100, Berkeley, CA 94720, USA
| | - Yifan Cheng
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Robert M Stroud
- Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffery S Cox
- Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA.
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24
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Dovala D, Rosenberg OS, Cox JS. Molecular Determinants of Substrate Specificity in Type VII Secretion Systems. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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