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López-Tena M, Farrera-Soler L, Barluenga S, Winssinger N. Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection). JACS Au 2023; 3:449-458. [PMID: 36873687 PMCID: PMC9975836 DOI: 10.1021/jacsau.2c00588] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo-complementary A:T base pair, Us:D, was important in achieving dsDNA invasion. Herein, we report pseudo-complementary analogues of the G:C base pair leveraged on steric and electrostatic repulsion between the cationic phenoxazine analogue of cytosine (G-clamp, C+) and N-7 methyl guanine (G+), which is also cationic. We show that while complementary peptide nucleic acids (PNA) form a much more stable homoduplex than the PNA:DNA heteroduplex, oligomers based on pseudo-C:G complementary PNA favor PNA:DNA hybridization. We show that this enables dsDNA invasion at physiological salt concentration and that stable invasion complexes are obtained with low equivalents of PNAs (2-4 equiv). We harnessed the high yield of dsDNA invasion for the detection of RT-RPA amplicon using a lateral flow assay (LFA) and showed that two strains of SARS-CoV-2 can be discriminated owing to single nucleotide resolution.
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2
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Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
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Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
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3
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López-Tena M, Chen SK, Winssinger N. Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits. Bioconjug Chem 2023; 34:111-123. [PMID: 35856656 DOI: 10.1021/acs.bioconjchem.2c00292] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.
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Affiliation(s)
- Miguel López-Tena
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Si-Kai Chen
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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4
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Imiołek M, Winssinger N. Two-Helix Supramolecular Proteomimetic Binders Assembled via PNA-Assisted Disulfide Crosslinking. Chembiochem 2023; 24:e202200561. [PMID: 36349499 DOI: 10.1002/cbic.202200561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/25/2022] [Revised: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Peptidic motifs folded in a defined conformation are able to inhibit protein-protein interactions (PPIs) covering large interfaces and as such they are biomedical molecules of interest. Mimicry of such natural structures with synthetically tractable constructs often requires complex scaffolding and extensive optimization to preserve the fidelity of binding to the target. Here, we present a novel proteomimetic strategy based on a 2-helix binding motif that is brought together by hybridization of peptide nucleic acids (PNA) and stabilized by a rationally positioned intermolecular disulfide crosslink. Using a solid phase synthesis approach (SPPS), the building blocks are easily accessible and such supramolecular peptide-PNA helical hybrids could be further coiled using precise templated chemistry. The elaboration of the structural design afforded high affinity SARS CoV-2 RBD (receptor binding domain) binders without interference with the underlying peptide sequence, creating a basis for a new architecture of supramolecular proteomimetics.
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Affiliation(s)
- Mateusz Imiołek
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, University of Geneva, 1211, Geneva, Switzerland
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5
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Dockerill M, Winssinger N. DNA‐Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202215542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
| | - Nicolas Winssinger
- University of Geneva Organic Chemistry 30, quai Ernest-Ansermet 1211 Geneva SWITZERLAND
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6
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Watson EE, Winssinger N. Synthesis of Protein-Oligonucleotide Conjugates. Biomolecules 2022; 12:biom12101523. [PMID: 36291732 PMCID: PMC9599799 DOI: 10.3390/biom12101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids and proteins form two of the key classes of functional biomolecules. Through the ability to access specific protein-oligonucleotide conjugates, a broader range of functional molecules becomes accessible which leverages both the programmability and recognition potential of nucleic acids and the structural, chemical and functional diversity of proteins. Herein, we summarize the available conjugation strategies to access such chimeric molecules and highlight some key case study examples within the field to showcase the power and utility of such technology.
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Affiliation(s)
- Emma E. Watson
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (E.E.W.); (N.W.)
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, CH-1205 Geneva, Switzerland
- Correspondence: (E.E.W.); (N.W.)
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7
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Patouret R, Barluenga S, Winssinger N. Withaferin A, a polyfunctional pharmacophore that includes covalent engagement of IPO5, is an inhibitor of influenza A replication. Bioorg Med Chem 2022; 69:116883. [DOI: 10.1016/j.bmc.2022.116883] [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] [Received: 04/20/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
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8
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Watson EE, Russo F, Moreau D, Winssinger N. Cover Picture: Optochemical Control of Therapeutic Agents through Photocatalyzed Isomerization (Angew. Chem. Int. Ed. 28/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202208067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Francesco Russo
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Dimitri Moreau
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
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9
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Watson EE, Russo F, Moreau D, Winssinger N. Optochemical Control of Therapeutic Agents through Photocatalyzed Isomerization. Angew Chem Int Ed Engl 2022; 61:e202203390. [PMID: 35510306 PMCID: PMC9400970 DOI: 10.1002/anie.202203390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/04/2022] [Indexed: 12/04/2022]
Abstract
A Ru(bpy)3Cl2 photocatalyst is applied to the rapid trans to cis isomerization of a range of alkene‐containing pharmacological agents, including combretastatin A‐4 (CA‐4), a clinical candidate in oncology, and resveratrol derivatives, switching their configuration from inactive substances to potent cytotoxic agents. Selective in cellulo activation of the CA‐4 analog Res‐3M is demonstrated, along with its potent cytotoxicity and inhibition of microtubule dynamics.
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Affiliation(s)
- Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Francesco Russo
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Dimitri Moreau
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
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10
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Hoogendoorn S, Winssinger N, Matile S. SCS Spring Meeting 2022 on Biosupramolecular Chemistry, University of Geneva, Auditoire Marignac, April 22, 2022. Chimia (Aarau) 2022. [DOI: 10.2533/chimia.2022.604] [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: 11/19/2022] Open
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11
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Watson EE, Russo F, Moreau D, Winssinger N. Optochemical Control of Therapeutic Agents through Photocatalyzed Isomerization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Francesco Russo
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Dimitri Moreau
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
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12
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Watson EE, Russo F, Moreau D, Winssinger N. Optochemical Control of Therapeutic Agents through Photocatalyzed Isomerization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Francesco Russo
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Dimitri Moreau
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
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13
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Vummidi BR, Farrera-Soler L, Daguer JP, Dockerill M, Barluenga S, Winssinger N. A mating mechanism to generate diversity for the Darwinian selection of DNA-encoded synthetic molecules. Nat Chem 2022; 14:141-152. [PMID: 34873299 DOI: 10.1038/s41557-021-00829-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/30/2021] [Indexed: 12/18/2022]
Abstract
DNA-encoded library technologies enable the screening of synthetic molecules but have thus far not tapped into the power of Darwinian selection with iterative cycles of selection, amplification and diversification. Here we report a simple strategy to rapidly assemble libraries of conformationally constrained peptides that are paired in a combinatorial fashion (suprabodies). We demonstrate that the pairing can be shuffled after each amplification cycle in a process similar to DNA shuffling or mating to regenerate diversity. Using simulations, we show the benefits of this recombination in yielding a more accurate correlation of selection fitness with affinity after multiple rounds of selection, particularly if the starting library is heterogeneous in the concentration of its members. The method was validated with selections against streptavidin and applied to the discovery of PD-L1 binders. We further demonstrate that the binding of self-assembled suprabodies can be recapitulated by smaller (∼7 kDa) synthetic products that maintain the conformational constraint of the peptides.
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Affiliation(s)
- Balayeshwanth R Vummidi
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
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14
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Farrera-Soler L, Gonse A, Kim KT, Barluenga S, Winssinger N. Combining recombinase polymerase amplification and DNA-templated reaction for SARS-CoV-2 sensing with dual fluorescence and lateral flow assay output. Biopolymers 2022; 113:e23485. [PMID: 35023571 PMCID: PMC9011641 DOI: 10.1002/bip.23485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/16/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/17/2022]
Abstract
The early phase of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic was exacerbated by a diagnostic challenge of unprecedented magnitude. In the absence of effective therapeutics or vaccines, breaking the chain of transmission through early disease detection and patient isolation was the only means to control the growing pandemic. While polymerase chain reaction (PCR)‐based methods and rapid‐antigen tests rose to the occasion, the analytical challenge of rapid and sequence‐specific nucleic acid‐sensing at a point‐of‐care or home setting stimulated intense developments. Herein we report a method that combines recombinase polymerase amplification and a DNA‐templated reaction to achieve a dual readout with either fluorescence (microtiter plate) or naked eye (lateral flow assay: LFA) detection. The nucleic acid templated reaction is based on an SNAr that simultaneously transfers biotin from one Peptide Nucleic Acid (PNA) strand to another PNA strand, enabling LFA detection while uncaging a coumarin for fluorescence readout. This methodology has been applied to the detection of a DNA or RNA sequence uniquely attributed to the SARS‐CoV‐2.
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Arthur Gonse
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
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15
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Assies L, García-Calvo J, Piazzolla F, Sanchez S, Kato T, Reymond L, Goujon A, Colom A, López-Andarias J, Straková K, Mahecic D, Mercier V, Riggi M, Jiménez-Rojo N, Roffay C, Licari G, Tsemperouli M, Neuhaus F, Fürstenberg A, Vauthey E, Hoogendoorn S, Gonzalez-Gaitan M, Zumbuehl A, Sugihara K, Gruenberg J, Riezman H, Loewith R, Manley S, Roux A, Winssinger N, Sakai N, Pitsch S, Matile S. Flipper Probes for the Community. Chimia (Aarau) 2021; 75:1004-1011. [PMID: 34920768 DOI: 10.2533/chimia.2021.1004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This article describes four fluorescent membrane tension probes that have been designed, synthesized, evaluated, commercialized and applied to current biology challenges in the context of the NCCR Chemical Biology. Their names are Flipper-TR®, ER Flipper-TR®, Lyso Flipper-TR®, and Mito Flipper-TR®. They are available from Spirochrome.
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Affiliation(s)
- Lea Assies
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - José García-Calvo
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Francesca Piazzolla
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Samantha Sanchez
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Takehiro Kato
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Luc Reymond
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Spirochrome AG, Chalberwiesenstrasse 4, CH-8260 Stein am Rhein, Switzerland
| | - Antoine Goujon
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Adai Colom
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva
| | - Javier López-Andarias
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Karolína Straková
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Dora Mahecic
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; École Polytechnique Fédérale de Lausanne - EPFL, SB Cubotron 427, CH-1015 Lausanne, Switzerland
| | - Vincent Mercier
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva
| | - Margot Riggi
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva; Department of Molecular Biology, University of Geneva
| | - Noemi Jiménez-Rojo
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva
| | - Chloé Roffay
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva
| | | | - Maria Tsemperouli
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Chemistry, University of Fribourg, 9 Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Frederik Neuhaus
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Chemistry, University of Fribourg, 9 Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Alexandre Fürstenberg
- Department of Physical Chemistry, University of Geneva; Department of Inorganic and Analytical Chemistry, University of Geneva
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva
| | - Sascha Hoogendoorn
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Marcos Gonzalez-Gaitan
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva
| | - Andreas Zumbuehl
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Chemistry, University of Fribourg, 9 Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Kaori Sugihara
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Physical Chemistry, University of Geneva
| | - Jean Gruenberg
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva
| | - Howard Riezman
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva
| | - Robbie Loewith
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Molecular Biology, University of Geneva
| | - Suliana Manley
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; École Polytechnique Fédérale de Lausanne - EPFL, SB Cubotron 427, CH-1015 Lausanne, Switzerland
| | - Aurelien Roux
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Biochemistry, University of Geneva
| | - Nicolas Winssinger
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Naomi Sakai
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland
| | - Stefan Pitsch
- Spirochrome AG, Chalberwiesenstrasse 4, CH-8260 Stein am Rhein, Switzerland
| | - Stefan Matile
- National Centre of Competence in Research (NCCR) Chemical Biology, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 CH-Geneva, Switzerland;,
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16
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Sabale PM, Imiołek M, Raia P, Barluenga S, Winssinger N. Suprastapled Peptides: Hybridization-Enhanced Peptide Ligation and Enforced α-Helical Conformation for Affinity Selection of Combinatorial Libraries. J Am Chem Soc 2021; 143:18932-18940. [PMID: 34739233 DOI: 10.1021/jacs.1c07013] [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: 12/17/2022]
Abstract
Stapled peptides with an enforced α-helical conformation have been shown to overcome major limitations in the development of short peptides targeting protein-protein interactions (PPIs). While the growing arsenal of methodologies to staple peptides facilitates their preparation, stapling methodologies are not broadly embraced in synthetic library screening. Herein, we report a strategy leveraged on hybridization of short PNA-peptide conjugates wherein nucleobase driven assembly facilitates ligation of peptide fragments and constrains the peptide's conformation into an α-helix. Using native chemical ligation, we show that a mixture of peptide fragments can be combinatorially ligated and used directly in affinity selection against a target of interest. This approach was exemplified with a focused library targeting the p-53/MDM2 interaction. One hundred peptides were obtained in a one-pot ligation reaction, selected by affinity against MDM2 immobilized on beads, and the best binders were identified by mass spectrometry.
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Affiliation(s)
- Pramod M Sabale
- Faculty of Science, NCCR Chemical Biology, University of Geneva, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Mateusz Imiołek
- Faculty of Science, NCCR Chemical Biology, University of Geneva, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pierre Raia
- Faculty of Science, NCCR Chemical Biology, University of Geneva, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Sofia Barluenga
- Faculty of Science, NCCR Chemical Biology, University of Geneva, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, NCCR Chemical Biology, University of Geneva, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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17
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Liu W, Watson EE, Winssinger N. Photocatalysis in Chemical Biology: Extending the Scope of Optochemical Control and Towards New Frontiers in Semisynthetic Bioconjugates and Biocatalysis. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Weilong Liu
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
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18
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Liu W, Winssinger N. Synthesis of α-exo-Methylene-γ-butyrolactones: Recent Developments and Applications in Natural Product Synthesis. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1577-6085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe α-exo-methylene-γ-butyrolactone moiety is present in a vast array of structurally diverse natural products and is often central to their biological activity. In this short review, we summarize new approaches to α-exo-methylene-γ-butyrolactones developed over the past decade as well as their applications in total synthesis.1 Introduction2 Approaches to α-exo-Methylene-γ-butyrolactones2.1 Enantioselective Synthesis via Lactonization Approaches2.2 Enantioselective Halolactonizations2.3 Enantioselective Barbier-Type Allylation2.4 C–H Insertion/Olefination Sequences2.5 Alkene Cyclization2.6 Strain-Driven Dyotropic Rearrangement3 β-(Hydroxymethylalkyl)-α-exo-methylene-γ-butyrolactones4 Applications in Total Synthesis4.1 Sesquiterpene Lactones4.2 Lignans4.3 Other Monocyclic Natural Products4.4 Choice of Methodology in Recent Total Syntheses5 Summary and Outlook
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19
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Pagano S, Yerly S, Meyer B, Juillard C, Suh N, Le Terrier C, Daguer JP, Farrera-Soler L, Barluenga S, Piumatti G, Hartley O, Lemaitre B, Eberhardt CS, Siegrist CA, Eckerle I, Stringhini S, Guessous I, Kaiser L, Pugin J, Winssinger N, Vuilleumier N. SARS-CoV-2 infection as a trigger of humoral response against apolipoprotein A-1. Eur J Clin Invest 2021; 51:e13661. [PMID: 34324704 PMCID: PMC8420318 DOI: 10.1111/eci.13661] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Unravelling autoimmune targets triggered by SARS-CoV-2 infection may provide crucial insights into the physiopathology of the disease and foster the development of potential therapeutic candidate targets and prognostic tools. We aimed at determining (a) the association between anti-SARS-CoV-2 and anti-apoA-1 humoral response and (b) the degree of linear homology between SARS-CoV-2, apoA-1 and Toll-like receptor 2 (TLR2) epitopes. DESIGN Bioinformatics modelling coupled with mimic peptides engineering and competition experiments were used to assess epitopes sequence homologies. Anti-SARS-CoV-2 and anti-apoA-1 IgG as well as cytokines were assessed by immunoassays on a case-control (n = 101), an intensive care unit (ICU; n = 126) and a general population cohort (n = 663) with available samples in the pre and post-pandemic period. RESULTS Using bioinformatics modelling, linear sequence homologies between apoA-1, TLR2 and Spike epitopes were identified but without experimental evidence of cross-reactivity. Overall, anti-apoA-1 IgG levels were higher in COVID-19 patients or anti-SARS-CoV-2 seropositive individuals than in healthy donors or anti-SARS-CoV-2 seronegative individuals (P < .0001). Significant and similar associations were noted between anti-apoA-1, anti-SARS-CoV-2 IgG, cytokines and lipid profile. In ICU patients, anti-SARS-CoV-2 and anti-apoA-1 seroconversion rates displayed similar 7-day kinetics, reaching 82% for anti-apoA-1 seropositivity. In the general population, SARS-CoV-2-exposed individuals displayed higher anti-apoA-1 IgG seropositivity rates than nonexposed ones (34% vs 16.8%; P = .004). CONCLUSION COVID-19 induces a marked humoral response against the major protein of high-density lipoproteins. As a correlate of poorer prognosis in other clinical settings, such autoimmunity signatures may relate to long-term COVID-19 prognosis assessment and warrant further scrutiny in the current COVID-19 pandemic.
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Affiliation(s)
- Sabrina Pagano
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
| | - Sabine Yerly
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Catherine Juillard
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
| | - Noémie Suh
- Division of Intensive Care, Geneva University Hospitals and the University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Christophe Le Terrier
- Division of Intensive Care, Geneva University Hospitals and the University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Lluc Farrera-Soler
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Giovanni Piumatti
- Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland.,Faculty of BioMedicine, Università della Svizzera Italiana, Lugano, Switzerland
| | - Oliver Hartley
- Faculty of Medicine, Department of Pathology and Immunology, University of Geneva, Switzerland
| | - Barbara Lemaitre
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
| | - Christiane S Eberhardt
- Faculty of Medicine, Departments of Pathology-Immunology and Pediatrics, University of Geneva, Geneva, Switzerland
| | - Claire-Anne Siegrist
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland.,Faculty of Medicine, Departments of Pathology-Immunology and Pediatrics, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Silvia Stringhini
- Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland.,Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland
| | - Idris Guessous
- Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland.,Faculty of Medicine, Departments of Pathology-Immunology and Pediatrics, University of Geneva, Geneva, Switzerland.,Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Jerome Pugin
- Division of Intensive Care, Geneva University Hospitals and the University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Department of Diagnostics and of Medical Specialties, Geneva University Hospitals and Geneva University, Geneva, Switzerland
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20
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Pagano S, Yerly S, Suh N, Le Terrier C, Farrera-Soler L, Piumatti G, Eberhardt CS, Siegrist CA, Eckerle I, Stringhini S, Guessous I, Kaiser L, Pugin J, Winssinger N, Vuilleumier N. Sars-CoV2- infection as a trigger of humoral response against apolipoprotein A-1. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.2757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Unravelling autoimmune targets triggered by SARS-CoV-2 infection may provide crucial insights in the physiopathology of the disease and foster the development of potential therapeutic candidate targets and prognostic tools. SARS-CoV-2 autoimmune-mediated inflammation have been reported, but the existence of autoantibodies against apolipoprotein A-1 (anti-apoA-1 IgG) in COVID-19 remains unexplored. Anti-apoA-1 IgGs have emerged as an independent biomarker for cardiovascular disease and mortality in humans with proinflammatory and proatherogenic functions in vivo and in vitro.
Purpose
We want to determine i) the degree of homology between SARS-CoV-2, apoA-1, and Toll-like receptor-2 (TLR2) epitopes, ii) the association between anti-SARSCoV2 and anti-apoA-1 IgGs, and iii) their relationship to prognosis.
Methods
We performed bioinformatics modelling coupled with mimetic peptides engineering, as well as functional and competition assays with antibodies to identify molecular mimicry between SARS-CoV-2, apoA-1 and TLR2 epitopes. Anti-Spike domain 1 (SD1) IgGs, anti-apoA-1 IgGs and against mimic peptides, as well as cytokines were assessed by immunoassays on a case-control (n=101), an intensive care unit (ICU; n=126) with a 28-days follow-up for overall mortality, and a general population cohort (n=663) with available samples in the pre and post-pandemic period.
Results
Linear sequence homologies and antibodies cross-reactivity between apoA-1, TLR2, and Spike epitopes were identified. Overall, anti-apoA-1 IgG levels were higher in COVID-19 patients or anti-SARS-CoV-2 seropositive individuals than in healthy donors or anti-SARS-CoV-2 seronegative individuals (p<0.0001). Significant and similar associations were noted between anti-apoA-1, anti-SARS-CoV-2 IgG, cytokines, and lipid profile. In ICU patients, anti-SARS-CoV-2 and anti-apoA-1 seroconversion rates displayed similar 7-days kinetics, reaching 82% for anti-apoA-1 seropositivity. C-statistics (CS) indicated that baseline anti-Spike/TLR2 mimic-peptide IgGs displayed a significant prognostic accuracy for overall mortality at 28 days (CS: 0.64; p=0.02). In the general population, SARS-CoV-2 exposure increased baseline anti-apoA-1 IgG levels.
Conclusions
COVID-19 induces a marked humoral response against the major protein of high-density lipoproteins. As a correlate of poorer prognosis in other clinical settings, such autoimmunity signatures may relate to long-term COVID-19 prognosis assessment and warrant further scrutiny in the current COVID-19 pandemic.
Funding Acknowledgement
Type of funding sources: Public Institution(s). Main funding source(s): This study was funded by the Swiss Federal Office of Public Health, Swiss School of Public Health (Corona Immunitas research program), the Fondation de Bienfaisance du Groupe Pictet, the Fondation Ancrage, the Fondation Privée des HUG, and the Center for Emerging Viral Diseases. The De Reuter (grant Nr 657) and the Schmidheiny Foundation.
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Affiliation(s)
- S Pagano
- Geneva University Hospitals, Geneva, Switzerland
| | - S Yerly
- Geneva University Hospitals, Geneva, Switzerland
| | - N Suh
- Geneva University Hospitals, Geneva, Switzerland
| | - C Le Terrier
- Geneva University Hospitals, Geneva, Switzerland
| | | | - G Piumatti
- Geneva University Hospitals, Geneva, Switzerland
| | | | - C A Siegrist
- Geneva University Hospitals, Geneva, Switzerland
| | - I Eckerle
- Geneva University Hospitals, Geneva, Switzerland
| | - S Stringhini
- Geneva University Hospitals, Geneva, Switzerland
| | - I Guessous
- Geneva University Hospitals, Geneva, Switzerland
| | - L Kaiser
- Geneva University Hospitals, Geneva, Switzerland
| | - J Pugin
- Geneva University Hospitals, Geneva, Switzerland
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21
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Laurent Q, Martinent R, Moreau D, Winssinger N, Sakai N, Matile S. Oligonucleotide Phosphorothioates Enter Cells by Thiol‐Mediated Uptake. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Quentin Laurent
- School of Chemistry and Biochemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Rémi Martinent
- School of Chemistry and Biochemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Dimitri Moreau
- School of Chemistry and Biochemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Naomi Sakai
- School of Chemistry and Biochemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Stefan Matile
- School of Chemistry and Biochemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
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22
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Laurent Q, Martinent R, Moreau D, Winssinger N, Sakai N, Matile S. Oligonucleotide Phosphorothioates Enter Cells by Thiol-Mediated Uptake. Angew Chem Int Ed Engl 2021; 60:19102-19106. [PMID: 34173696 PMCID: PMC8456962 DOI: 10.1002/anie.202107327] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 06/01/2021] [Indexed: 12/14/2022]
Abstract
Oligonucleotide phosphorothioates (OPS) are DNA or RNA mimics where one phosphate oxygen is replaced by a sulfur atom. They have been shown to enter mammalian cells much more efficiently than non-modified DNA. Thus, solving one of the key challenges with oligonucleotide technology, OPS became very useful in practice, with several FDA-approved drugs on the market or in late clinical trials. However, the mechanism accounting for this facile cellular uptake is unknown. Here, we show that OPS enter cells by thiol-mediated uptake. The transient adaptive network produced by dynamic covalent pseudo-disulfide exchange is characterized in action. Inhibitors with nanomolar efficiency are provided, together with activators that reduce endosomal capture for efficient delivery of OPS into the cytosol, the site of action.
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Affiliation(s)
- Quentin Laurent
- School of Chemistry and BiochemistryNational Centre of Competence in Research (NCCR) Chemical BiologyUniversity of GenevaGenevaSwitzerland
| | - Rémi Martinent
- School of Chemistry and BiochemistryNational Centre of Competence in Research (NCCR) Chemical BiologyUniversity of GenevaGenevaSwitzerland
| | - Dimitri Moreau
- School of Chemistry and BiochemistryNational Centre of Competence in Research (NCCR) Chemical BiologyUniversity of GenevaGenevaSwitzerland
| | - Nicolas Winssinger
- School of Chemistry and BiochemistryNational Centre of Competence in Research (NCCR) Chemical BiologyUniversity of GenevaGenevaSwitzerland
| | - Naomi Sakai
- School of Chemistry and BiochemistryNational Centre of Competence in Research (NCCR) Chemical BiologyUniversity of GenevaGenevaSwitzerland
| | - Stefan Matile
- School of Chemistry and BiochemistryNational Centre of Competence in Research (NCCR) Chemical BiologyUniversity of GenevaGenevaSwitzerland
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23
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Daguer JP, Gonse A, Shchukin Y, Farrera-Soler L, Barluenga S, Winssinger N. Dual Bcl-X L /Bcl-2 inhibitors discovered from DNA-encoded libraries using a fragment pairing strategy. Bioorg Med Chem 2021; 44:116282. [PMID: 34216984 DOI: 10.1016/j.bmc.2021.116282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/24/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022]
Abstract
A dual Bcl-XL / Bcl-2 inhibitor was discovered from DNA-encoded libraries using a two steps process. In the first step, DNA was used to pair PNA-encoded fragments exploring > 250 000 combinations. In the second step, a focused library combining the selected fragments with linkers of different lengths and geometries led to the identification of tight binding adducts that were further investigated for their selective target engagement in pull-down assays, for their affinity by SPR, and their selectivity in a cytotoxicity assay. The best compound showed comparable cellular activity to venetoclax, the first-in-class therapeutic targeting Bcl-2.
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Affiliation(s)
- Jean-Pierre Daguer
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Arthur Gonse
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Yevhenii Shchukin
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Lluc Farrera-Soler
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.
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24
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Liu W, Patouret R, Barluenga S, Plank M, Loewith R, Winssinger N. Identification of a Covalent Importin-5 Inhibitor, Goyazensolide, from a Collective Synthesis of Furanoheliangolides. ACS Cent Sci 2021; 7:954-962. [PMID: 34235256 PMCID: PMC8227592 DOI: 10.1021/acscentsci.1c00056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 06/13/2023]
Abstract
Sesquiterpenes are a rich source of covalent inhibitors with a long history in traditional medicine and include several important therapeutics and tool compounds. Herein, we report the total synthesis of 16 sesquiterpene lactones via a build/couple/pair strategy, including goyasensolide. Using an alkyne-tagged cellular probe and proteomics analysis, we discovered that goyazensolide selectively targets the oncoprotein importin-5 (IPO5) for covalent engagement. We further demonstrate that goyazensolide inhibits the translocation of RASAL-2, a cargo of IPO5, into the nucleus and perturbs the binding between IPO5 and two specific viral nuclear localization sequences.
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Affiliation(s)
- Weilong Liu
- Department
of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Rémi Patouret
- Department
of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department
of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Michael Plank
- Department
of Molecular Biology, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland
| | - Robbie Loewith
- Department
of Molecular Biology, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department
of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
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25
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Kim KT, Angerani S, Winssinger N. A minimal hybridization chain reaction (HCR) system using peptide nucleic acids. Chem Sci 2021; 12:8218-8223. [PMID: 34194712 PMCID: PMC8208298 DOI: 10.1039/d1sc01269j] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/06/2021] [Indexed: 12/28/2022] Open
Abstract
The HCR represents a powerful tool for amplification in DNA-based circuitry and sensing applications, yet requires the use of long DNA sequences to grant hairpin metastability. Here we describe a minimal HCR system based on peptide nucleic acids (PNAs). A system comprising a 5-mer stem and 5-mer loop/toehold hairpins was found to be suitable to achieve rapid amplification. These hairpins were shown to yield >10-fold amplification in 2 h and be suitable for the detection of a cancer biomarker on live cells. The use of γ-peg-modified PNA was found to be beneficial.
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26
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Farrera-Soler L, Daguer JP, Barluenga S, Winssinger N. Experimental Identification of Immuno- dominant B-cell Epitopes from SARS-CoV-2. Chimia (Aarau) 2021; 75:276-284. [PMID: 33902795 DOI: 10.2533/chimia.2021.276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current public health crisis with devastating consequences to our societies. This COVID-19 pandemic has become the most serious threat to global public health in recent history. Given the unprecedented economic and social impact that it is causing, identification of immunodominant epitopes from SARS-CoV-2 is of great interest, not only to gain better insight into the adaptive immune response, but also for the development of vaccines, treatments and diagnostic tools. In this review, we summarize the already published or preprinted reports on the experimental identification of B-cell linear epitopes of SARS-CoV-2 proteins. Six different epitopes leading to neutralizing antibodies have been identified. Moreover, a summary of peptide candidates to be used for diagnostic tools is also included.
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Affiliation(s)
- Lluc Farrera-Soler
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1211 Geneva 4;,
| | - Jean-Pierre Daguer
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1211 Geneva 4
| | - Sofia Barluenga
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1211 Geneva 4
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1211 Geneva 4
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27
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Abstract
Protein trafficking and protein-protein interactions (PPIs) are central to regulatory processes in cells. Induced dimerization systems have been developed to control PPIs and regulate protein trafficking (localization) or interactions. Chemically induced dimerization (CID) has proven to be a robust approach to control protein interactions and localization. The most recent embodiment of this technology relies on CID conjugates that react with a self-labeling protein on one side and a photocaged ligand on the other side to provide spatiotemporal control of the interaction with the protein of interest. Advancing this technology further is limited by the light delivery problem and the phototoxicity of intense irradiation necessary to achieve photouncaging. Herein, we designed a novel chemically induced dimerization system that was triggered by bioluminescence, instead of external light. Protein dimerization showed fast kinetics and was validated by an induced change of localization of a target protein (to and from the nucleus or plasma membrane) upon trigger. The technology was used transiently to activate the phosphatidylinositol 3-kinase (PI3K)/mTOR pathway and measure the impact on lipid synthesis/metabolism, assessed by lipidomics.
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Affiliation(s)
- Dalu Chang
- School of Chemistry and Biochemistry, Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
| | - Suihan Feng
- School of Chemistry and Biochemistry, Department of Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
| | - Vladimir Girik
- School of Chemistry and Biochemistry, Department of Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
| | - Howard Riezman
- School of Chemistry and Biochemistry, Department of Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry, Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Geneva 12004, Switzerland
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28
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Orth M, Albrecht V, Seidl K, Kinzel L, Unger K, Hess J, Kreutzer L, Sun N, Stegen B, Nieto A, Maas J, Winssinger N, Friedl AA, Walch AK, Belka C, Zitzelsberger H, Niyazi M, Lauber K. Inhibition of HSP90 as a Strategy to Radiosensitize Glioblastoma: Targeting the DNA Damage Response and Beyond. Front Oncol 2021; 11:612354. [PMID: 33816244 PMCID: PMC8011354 DOI: 10.3389/fonc.2021.612354] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Radiotherapy is an essential component of multi-modality treatment of glioblastoma (GBM). However, treatment failure and recurrence are frequent and give rise to the dismal prognosis of this aggressive type of primary brain tumor. A high level of inherent treatment resistance is considered to be the major underlying reason, stemming from constantly activated DNA damage response (DDR) mechanisms as a consequence of oncogene overexpression, persistent replicative stress, and other so far unknown reasons. The molecular chaperone heat shock protein 90 (HSP90) plays an important role in the establishment and maintenance of treatment resistance, since it crucially assists the folding and stabilization of various DDR regulators. Accordingly, inhibition of HSP90 represents a multi-target strategy to interfere with DDR function and to sensitize cancer cells to radiotherapy. Using NW457, a pochoxime-based HSP90 inhibitor with favorable brain pharmacokinetic profile, we show here that HSP90 inhibition at low concentrations with per se limited cytotoxicity leads to downregulation of various DNA damage response factors on the protein level, distinct transcriptomic alterations, impaired DNA damage repair, and reduced clonogenic survival in response to ionizing irradiation in glioblastoma cells in vitro. In vivo, HSP90 inhibition by NW457 improved the therapeutic outcome of fractionated CBCT-based irradiation in an orthotopic, syngeneic GBM mouse model, both in terms of tumor progression and survival. Nevertheless, in view of the promising in vitro results the in vivo efficacy was not as strong as expected, although apart from the radiosensitizing effects HSP90 inhibition also reduced irradiation-induced GBM cell migration and tumor invasiveness. Hence, our findings identify the combination of HSP90 inhibition and radiotherapy in principle as a promising strategy for GBM treatment whose performance needs to be further optimized by improved inhibitor substances, better formulations and/or administration routes, and fine-tuned treatment sequences.
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Affiliation(s)
- Michael Orth
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Valerie Albrecht
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Karin Seidl
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Linda Kinzel
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Lisa Kreutzer
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Benjamin Stegen
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium, Munich, Germany.,German Cancer Research Center, Heidelberg, Germany
| | - Alexander Nieto
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Jessica Maas
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Anna A Friedl
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Axel K Walch
- Research Unit Analytical Pathology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Claus Belka
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium, Munich, Germany.,Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Center Munich, Neuherberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Center Munich, Neuherberg, Germany
| | - Maximilian Niyazi
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Kirsten Lauber
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium, Munich, Germany.,Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Center Munich, Neuherberg, Germany
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Angerani S, Lindberg E, Klena N, Bleck CKE, Aumeier C, Winssinger N. Kinesin-1 activity recorded in living cells with a precipitating dye. Nat Commun 2021; 12:1463. [PMID: 33674590 PMCID: PMC7935933 DOI: 10.1038/s41467-021-21626-1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/03/2021] [Indexed: 01/15/2023] Open
Abstract
Kinesin-1 is a processive motor protein that uses ATP-derived energy to transport a variety of intracellular cargoes toward the cell periphery. The ability to visualize and monitor kinesin transport in live cells is critical to study the myriad of functions associated with cargo trafficking. Herein we report the discovery of a fluorogenic small molecule substrate (QPD-OTf) for kinesin-1 that yields a precipitating dye along its walking path on microtubules (MTs). QPD-OTf enables to monitor native kinesin-1 transport activity in cellulo without external modifications. In vitro assays show that kinesin-1 and MTs are sufficient to yield fluorescent crystals; in cells, kinesin-1 specific transport of cargo from the Golgi appears as trails of fluorescence over time. These findings are further supported by docking studies, which suggest the binding of the activity-based substrate in the nucleotide binding site of kinesin-1.
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Affiliation(s)
- Simona Angerani
- School of Chemistry and Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Eric Lindberg
- School of Chemistry and Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nikolai Klena
- Department of Cell Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Christopher K E Bleck
- Electron Microscopy Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charlotte Aumeier
- School of Chemistry and Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
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30
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Affiliation(s)
- Emma E. Watson
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Simona Angerani
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M. Sabale
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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31
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Liu W, Yu Z, Winssinger N. Total Syntheses of Paraconic Acids and 1,10- seco-Guaianolides via a Barbier Allylation/Translactonization Cascade of 3-(Bromomethyl)-2(5 H)-furanone. Org Lett 2021; 23:969-973. [PMID: 33502871 DOI: 10.1021/acs.orglett.0c04165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A palladium-catalyzed Barbier allylation/translactonization cascade reaction was established for the rapid construction of β,γ-disubstituted α-exo-methylene-γ-butyrolactone, an important motif in sesquiterpenes. Dimethyl zinc played significant roles in both steps for the umpolung of π-allylpalladium as a nucleophile and promoting a Lewis acid-mediated translactonization. This sequence showed a broad substrate scope and was further harnessed for the synthesis of two paraconic acids as well as the first protecting-group-free total synthesis of two 1,10-seco-guaianolides.
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Affiliation(s)
- Weilong Liu
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland
| | - Zhimei Yu
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland
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32
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Saarbach J, Barluenga S, Winssinger N. PNA-Encoded Synthesis (PES) and DNA Display of Small Molecule Libraries. Methods Mol Biol 2021; 2105:119-139. [PMID: 32088867 DOI: 10.1007/978-1-0716-0243-0_7] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
DNA-encoded library technologies have emerged as a powerful platform to rapidly screen for binders to a protein of interest. These technologies are underpinned by the ability to encode a rich diversity of small molecules. While large libraries are accessible by cycles of mix and split synthesis, libraries based on single chemistries tend to be redundant. Furthermore, the quality of libraries generally decreases with the number of synthetic transformations performed in its synthesis. An alternative approach is to use hybridization to program the combinatorial assembly of fragment pairs onto a library of DNA templates. A broad molecular diversity is more easily sampled since it arises from the pairing of diverse fragments. Upon identification of productive fragment pairs, a focused library covalently linking the fragments is prepared. This focused library includes linker of different length and geometry and offers the opportunity to enrich the selected fragment set with close neighbors. Herein we describe detailed protocols to covalently link diverse fragments and screen fragment-based libraries using commercially available microarray platform.
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Affiliation(s)
- Jacques Saarbach
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland.
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33
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Farrera-Soler L, Daguer JP, Barluenga S, Vadas O, Cohen P, Pagano S, Yerly S, Kaiser L, Vuilleumier N, Winssinger N. Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma. PLoS One 2020; 15:e0238089. [PMID: 32903266 PMCID: PMC7480855 DOI: 10.1371/journal.pone.0238089] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 01/09/2023] Open
Abstract
A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients (12) and heathy patients (6), we identified three immunodominant linear epitopes, two of which correspond to key proteolytic sites on the spike protein (S1/S2 and S2') known to be critical for cellular entry. We show biochemical evidence that plasma positive for the epitope adjacent to the S1/S2 cleavage site inhibits furin-mediated proteolysis of spike.
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Cohen
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabrina Pagano
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabine Yerly
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Division of Infectious Diseases¸ Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
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34
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Ernst A, Hennel R, Krombach J, Kapfhammer H, Brix N, Zuchtriegel G, Uhl B, Reichel CA, Frey B, Gaipl US, Winssinger N, Shirasawa S, Sasazuki T, Sperandio M, Belka C, Lauber K. Priming of Anti-tumor Immune Mechanisms by Radiotherapy Is Augmented by Inhibition of Heat Shock Protein 90. Front Oncol 2020; 10:1668. [PMID: 32984042 PMCID: PMC7481363 DOI: 10.3389/fonc.2020.01668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/10/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Radiotherapy is an essential part of multi-modal cancer therapy. Nevertheless, for certain cancer entities such as colorectal cancer (CRC) the indications of radiotherapy are limited due to anatomical peculiarities and high radiosensitivity of the surrounding normal tissue. The development of molecularly targeted, combined modality approaches may help to overcome these limitations. Preferably, such strategies should not only enhance radiation-induced tumor cell killing and the abrogation of tumor cell clonogenicity, but should also support the stimulation of anti-tumor immune mechanisms – a phenomenon which moved into the center of interest of preclinical and clinical research in radiation oncology within the last decade. The present study focuses on inhibition of heat shock protein 90 (HSP90) whose combination with radiotherapy has previously been reported to exhibit convincing therapeutic synergism in different preclinical cancer models. By employing in vitro and in vivo analyses, we examined if this therapeutic synergism also applies to the priming of anti-tumor immune mechanisms in model systems of CRC. Our results indicate that the combination of HSP90 inhibitor treatment and ionizing irradiation induced apoptosis in colorectal cancer cells with accelerated transit into secondary necrosis in a hyperactive Kras-dependent manner. During secondary necrosis, dying cancer cells released different classes of damage-associated molecular patterns (DAMPs) that stimulated migration and recruitment of monocytic cells in vitro and in vivo. Additionally, these dying cancer cell-derived DAMPs enforced the differentiation of a monocyte-derived antigen presenting cell (APC) phenotype which potently triggered the priming of allogeneic T cell responses in vitro. In summary, HSP90 inhibition – apart from its radiosensitizing potential – obviously enables and supports the initial steps of anti-tumor immune priming upon radiotherapy and thus represents a promising partner for combined modality approaches. The therapeutic performance of such strategies requires further in-depth analyses, especially for but not only limited to CRC.
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Affiliation(s)
- Anne Ernst
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Roman Hennel
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Julia Krombach
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Heidi Kapfhammer
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Nikko Brix
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Gabriele Zuchtriegel
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany.,Walter Brendel Center for Experimental Medicine, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Bernd Uhl
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany.,Walter Brendel Center for Experimental Medicine, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Christoph A Reichel
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany.,Walter Brendel Center for Experimental Medicine, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Benjamin Frey
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Udo S Gaipl
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine Fukuoka University, Fukuoka, Japan
| | | | - Markus Sperandio
- Walter Brendel Center for Experimental Medicine, Faculty of Medicine, LMU Munich, Munich, Germany.,Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, LMU Munich, Munich, Germany
| | - Claus Belka
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Heidelberg, Germany
| | - Kirsten Lauber
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Heidelberg, Germany
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35
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Angerani S, Winssinger N. Sense-and-Release Logic-Gated Molecular Network Responding to Dimeric Cell Surface Proteins. J Am Chem Soc 2020; 142:12333-12340. [PMID: 32539375 DOI: 10.1021/jacs.0c04469] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Dimeric proteins are prominent in biology, and receptor dimerization (homo- or heterodimerization) is central to signal transduction. Herein, we report a network that responds to a membrane-associated dimeric protein with the uncaging of a powerful cytotoxic. The network is based on two ligands functionalized with peptide nucleic acids (PNAs) (templating strand and catalyst-functionalized strand, respectively) and a substrate with the caged cytotoxic (monomethyl auristatin E: MMAE; a high-affinity tubulin ligand). In the presence of the dimeric protein, the network yields a cooperative supramolecular assembly with a hybridization architecture that enhances the templated reaction and enables the uncaging of a substrate. The network was tested on cells that express a cancer biomarker, carbonic anhydrase IX, in response to hypoxia. The output of the network correlates with the expression of carbonic anhydrase IX, and this biomarker was harnessed to uncage a potent cytotoxic agent.
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Affiliation(s)
- Simona Angerani
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1205 Geneva, Switzerland
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36
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Streuff J, Echavarren AM, González JM, Oestreich M, Gansäuer A, Barluenga S, Winssinger N. Kilian Muñiz (1970–2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jan Streuff
- Albert-Ludwigs-Universität Freiburg Deutschland
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Streuff J, Echavarren AM, González JM, Oestreich M, Gansäuer A, Barluenga S, Winssinger N. Kilian Muñiz (1970-2020). Angew Chem Int Ed Engl 2020; 59:7648. [PMID: 32249993 DOI: 10.1002/anie.202004481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Kilian Muñiz passed away unexpectedly on March 16th, 2020, at the age of only 49. Kilian was a leading figure in the field of catalytic (di-)amination reactions. He will be remembered as one of the finest, most passionate chemists, a dear colleague, and, most of all, as a close friend.
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Affiliation(s)
- Jan Streuff
- Albert-Ludwigs-Universität Freiburg, Germany
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Plank M, Perepelkina M, Müller M, Vaga S, Zou X, Bourgoint C, Berti M, Saarbach J, Haesendonckx S, Winssinger N, Aebersold R, Loewith R. Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9. Mol Cell Proteomics 2020; 19:655-671. [PMID: 32102971 PMCID: PMC7124472 DOI: 10.1074/mcp.ra120.001955] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 01/27/2020] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take center stage in regulating this process in S. cerevisiae To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1. Sites hypo-phosphorylated upon PKA and Sch9 inhibition were preferentially located in RRxS/T-motifs suggesting that many are directly phosphorylated by these enzymes. Interestingly, when inhibiting Ypk1 we not only detected several hypo-phosphorylated sites in the previously reported RxRxxS/T-, but also in an RRxS/T-motif. Validation experiments revealed that neutral trehalase Nth1, a known PKA target, is additionally phosphorylated and activated downstream of Ypk1. Signaling through Ypk1 is therefore more closely related to PKA- and Sch9-signaling than previously appreciated and may perform functions previously only attributed to the latter kinases.
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Affiliation(s)
- Michael Plank
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland; National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland.
| | - Mariya Perepelkina
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Markus Müller
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stefania Vaga
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Xiaoming Zou
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Clélia Bourgoint
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Marina Berti
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Jacques Saarbach
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Steven Haesendonckx
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland; Faculty of Science, University of Zurich, CH-8006, Zurich, Switzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland; National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland.
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Abstract
Detection of specific oligonucleotide sequences is central to numerous applications, and technologies amenable to point-of-care diagnostics or end users are needed. Here, we report a technology making use of a bioluminescent readout and smartphone quantification. The sensor is a semisynthetic luciferase (H-Luc-PNA conjugate) that is turned on by a strand-displacement reaction. We demonstrated sensing of three different microRNAs (miRs), as representative cancer biomarkers, and demonstrate the possibility to integrate an AND gate to sense two sequences simultaneously.
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Affiliation(s)
- Dalu Chang
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
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Farrera-Soler L, Daguer JP, Raunft P, Barluenga S, Imberty A, Winssinger N. PNA-Based Dynamic Combinatorial Libraries (PDCL) and screening of lectins. Bioorg Med Chem 2020; 28:115458. [PMID: 32241620 DOI: 10.1016/j.bmc.2020.115458] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 11/16/2022]
Abstract
Selections from dynamic combinatorial libraries (DCL) benefit from the dynamic nature of the library that can change constitution upon addition of a selection pressure, such as ligands binding to a protein. This technology has been predominantly used with small molecules interacting with each other through reversible covalent interaction. However, application of this technology in biomedical research and drug discovery has been limited by the reversibility of covalent exchange and the analytical deconvolution of small molecule fragments. Here we report a supramolecular approach based on the use of a constant short PNA tag to direct the combinatorial pairing of fragment. This PNA tag yields fast exchange kinetics, while still delivering the benefits of cooperativity, and provides favourable properties for analytical deconvolution by MALDI. A selection from >6,000 assemblies of glycans (mono-, di-, tri-saccharides) targeting AFL, a lectin from pathogenic fungus, yielded a 95 nM assembly, nearly three orders of magnitude better in affinity than the corresponding glycan alone (41 µM).
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Patrick Raunft
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Nicolas Winssinger
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
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Kim KT, Winssinger N. Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS). Chem Sci 2020; 11:4150-4157. [PMID: 34122878 PMCID: PMC8152519 DOI: 10.1039/d0sc00741b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/24/2020] [Indexed: 12/11/2022] Open
Abstract
DNA or RNA templated reactions are attractive for nucleic acid sensing and imaging. As for any hybridization-based sensing, there is a tradeoff between sensitivity (detection threshold) and resolution (single nucleotide discrimination). Longer probes afford better sensitivity but compromise single nucleotide resolution due to the small thermodynamic penalty of a single mismatch. Herein we report a design that overcomes this tradeoff. The reaction is leveraged on the hybridization of a minimal substrate (covering 4 nucleotides) which is confined by two guide DNAs functionalized respectively with a ruthenium photocatalyst. The use of a catalytic reaction is essential to bypass the exchange of guide DNAs while achieving signal amplification through substrate turnover. The guide DNAs restrain the reaction to a unique site and enhance the hybridization of short substrates by providing two π-stacking interactions. The reaction was shown to enable the detection of SNPs and SNVs down to 50 pM with a discrimination factor ranging from 24 to 309 (median 82, 27 examples from 3 oncogenes). The clinical diagnostic potential of the technology was demonstrated with the analysis of RAS amplicons obtained directly from cell culture.
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Affiliation(s)
- Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva 30 quai Ernest Ansermet 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva 30 quai Ernest Ansermet 1211 Geneva Switzerland
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42
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López-Andarias J, Saarbach J, Moreau D, Cheng Y, Derivery E, Laurent Q, González-Gaitán M, Winssinger N, Sakai N, Matile S. Cell-Penetrating Streptavidin: A General Tool for Bifunctional Delivery with Spatiotemporal Control, Mediated by Transport Systems Such as Adaptive Benzopolysulfane Networks. J Am Chem Soc 2020; 142:4784-4792. [PMID: 32109058 PMCID: PMC7307903 DOI: 10.1021/jacs.9b13621] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/17/2022]
Abstract
In this report, cell-penetrating streptavidin (CPS) is introduced to exploit the full power of streptavidin-biotin biotechnology in cellular uptake. For this purpose, transporters, here cyclic oligochalcogenides (COCs), are covalently attached to lysines of wild-type streptavidin. This leaves all four biotin binding sites free for at least bifunctional delivery. To maximize the standards of the quantitative evaluation of cytosolic delivery, the recent chloroalkane penetration assay (CAPA) is coupled with automated high content (HC) imaging, a technique that combines the advantages of fluorescence microscopy and flow cytometry. According to the resulting HC-CAPA, cytosolic delivery of CPS equipped with four benzopolysulfanes was the best among all tested CPSs, also better than the much smaller TAT peptide, the original cell-penetrating peptide from HIV. HaloTag-GFP fusion proteins expressed on mitochondria were successfully targeted using CPS carrying two different biotinylated ligands, HaloTag substrates or anti-GFP nanobodies, interfaced with peptide nucleic acids, flipper force probes, or fluorescent substrates. The delivered substrates could be released from CPS into the cytosol through desthiobiotin-biotin exchange. These results validate CPS as a general tool which enables unrestricted use of streptavidin-biotin biotechnology in cellular uptake.
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Affiliation(s)
- Javier López-Andarias
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Jacques Saarbach
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Dimitri Moreau
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Yangyang Cheng
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Emmanuel Derivery
- MRC
Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Quentin Laurent
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Marcos González-Gaitán
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Nicolas Winssinger
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Naomi Sakai
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Stefan Matile
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
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Figuerola-Conchas A, Saarbach J, Daguer JP, Cieren A, Barluenga S, Winssinger N, Gotta M. Small-Molecule Modulators of the ATPase VCP/p97 Affect Specific p97 Cellular Functions. ACS Chem Biol 2020; 15:243-253. [PMID: 31790201 DOI: 10.1021/acschembio.9b00832] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
VCP/p97 belongs to the AAA+ ATPase family and has an essential role in several cellular processes ranging from cell division to protein homeostasis. Compounds targeting p97 inhibit the main ATPase domain and cause cell death. Here, using PNA-encoded chemical libraries, we have identified two small molecules that target the regulatory domain of p97, comprising the N-terminal and the D1 ATPase domains, and do not cause cell death. One molecule, NW1028, inhibits the degradation of a p97-dependent reporter, whereas the other, NW1030, increases it. ATPase assays show that NW1028 and NW1030 do not affect the main catalytic domain of p97. Mapping of the binding site using a photoaffinity conjugate points to a cleft at the interface of the N-terminal and the D1 ATPase domains. We have therefore discovered two new compounds that bind to the regulatory domain of p97 and modulate specific p97 cellular functions. Using these compounds, we have revealed a role for p97 in the regulation of mitotic spindle orientation in HeLa cells.
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Affiliation(s)
- Ainoa Figuerola-Conchas
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Jacques Saarbach
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Adeline Cieren
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Monica Gotta
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
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44
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Laurent Q, Berthet M, Cheng Y, Sakai N, Barluenga S, Winssinger N, Matile S. Probing for Thiol-Mediated Uptake into Bacteria. Chembiochem 2020; 21:69-73. [PMID: 31603284 DOI: 10.1002/cbic.201900378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 06/07/2019] [Indexed: 01/02/2023]
Abstract
Cellular uptake mediated by cyclic oligochalcogenides (COCs) is emerging as a conceptually innovative method to penetrate mammalian cells. Their mode of action is based on dynamic covalent oligochalcogenide exchange with cellular thiols. To test thiol-mediated uptake in bacteria, five antibiotics have been equipped with up to three different COCs: One diselenolane and two dithiolanes. We found that the COCs do not activate antibiotics in Gram-negative bacteria. In Gram-positive bacteria, the COCs inactivate antibiotics that act in the cytoplasm and reduce the activity of antibiotics that act on the cell surface. These results indicate that thiol-mediated uptake operates in neither of the membranes of bacteria. COCs are likely to exchange with thiols on the inner, maybe also on the outer membrane, but do not move on. Concerning mammalian cells, the absence of a COC-mediated uptake into bacteria observed in this study disfavors trivial mechanisms, such as passive diffusion, and supports the existence of more sophisticated, so far poorly understood uptake pathways.
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Affiliation(s)
- Quentin Laurent
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Mathéo Berthet
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Yangyang Cheng
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Naomi Sakai
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Sofia Barluenga
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Stefan Matile
- National Centre of Competence in Research (NCCR), Chemical Biology, School of Chemistry and Biochemistry, University of Geneva, 1211, Geneva, Switzerland
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Galli V, Sadhu KK, Masi D, Saarbach J, Roux A, Winssinger N. Caprin‐1 Promotes Cellular Uptake of Nucleic Acids with Backbone and Sequence Discrimination. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Valentina Galli
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Kalyan K. Sadhu
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Daniela Masi
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Jacques Saarbach
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Aurélien Roux
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
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46
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Kim KT, Angerani S, Chang D, Winssinger N. Coupling of DNA Circuit and Templated Reactions for Quadratic Amplification and Release of Functional Molecules. J Am Chem Soc 2019; 141:16288-16295. [DOI: 10.1021/jacs.9b05688] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1205 Geneva, Switzerland
| | - Simona Angerani
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1205 Geneva, Switzerland
| | - Dalu Chang
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1205 Geneva, Switzerland
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47
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Chang D, Lindberg E, Feng S, Angerani S, Riezman H, Winssinger N. Luciferase‐Induced Photouncaging: Bioluminolysis. Angew Chem Int Ed Engl 2019; 58:16033-16037. [DOI: 10.1002/anie.201907734] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/06/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Dalu Chang
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Eric Lindberg
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
- Present address: National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD 20892 USA
| | - Suihan Feng
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Simona Angerani
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Howard Riezman
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
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48
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Affiliation(s)
- Dalu Chang
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Eric Lindberg
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
- Present address: National Heart, Lung, and Blood InstituteNational Institutes of Health Bethesda MD 20892 USA
| | - Suihan Feng
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Simona Angerani
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Howard Riezman
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
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49
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Saarbach J, Sabale PM, Winssinger N. Peptide nucleic acid (PNA) and its applications in chemical biology, diagnostics, and therapeutics. Curr Opin Chem Biol 2019; 52:112-124. [PMID: 31541865 DOI: 10.1016/j.cbpa.2019.06.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/07/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid (PNA) stands as one of the most successful artificial oligonucleotide mimetics. Salient features include the stability of hybridization complexes (either as duplexes or triplexes), metabolic stability, and ease of chemical modifications. These features have enabled important applications such as antisense agents, gene editing, nucleic acid sensing and as a platform to program the assembly of PNA-tagged molecules. Here, we review recent advances in these areas.
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Affiliation(s)
- Jacques Saarbach
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M Sabale
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.
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50
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Angerani S, Winssinger N. Frontispiece: Visible Light Photoredox Catalysis Using Ruthenium Complexes in Chemical Biology. Chemistry 2019. [DOI: 10.1002/chem.201982762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Simona Angerani
- Department of Organic Chemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 Quai Ernest-Ansermet 1205 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 Quai Ernest-Ansermet 1205 Geneva Switzerland
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