1
|
Kirschner T, Müller MP, Rauh D. Targeting KRAS Diversity: Covalent Modulation of G12X and Beyond in Cancer Therapy. J Med Chem 2024; 67:6044-6051. [PMID: 38621359 DOI: 10.1021/acs.jmedchem.3c02403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
The GTPase KRAS acts as a switch in cellular signaling, transitioning between inactive GDP-bound and active GTP-bound states. In about 20% of human cancers, oncogenic RAS mutations disrupt this balance, favoring the active form and promoting proliferative signaling, thus rendering KRAS an appealing target for precision medicine in oncology. In 2013, Shokat and co-workers achieved a groundbreaking feat by covalently targeting a previously undiscovered allosteric pocket (switch II pocket (SWIIP)) of KRASG12C. This breakthrough led to the development and approval of sotorasib (AMG510) and adagrasib (MRTX849), revolutionizing the treatment of KRASG12C-dependent lung cancer. Recent achievements in targeting various KRASG12X mutants, using SWIIP as a key binding pocket, are discussed. Insights from successful KRASG12C targeting informed the design of molecules addressing other mutations, often in a covalent manner. These findings offer promise for innovative approaches in addressing commonly occurring KRAS mutations such as G12D, G12V, G12A, G12S, and G12R in various cancers.
Collapse
Affiliation(s)
- Tonia Kirschner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), 44227 Dortmund, Germany
| | - Matthias P Müller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), 44227 Dortmund, Germany
| | - Daniel Rauh
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), 44227 Dortmund, Germany
| |
Collapse
|
2
|
Guo P, Chu X, Wu C, Qiao T, Guan W, Zhou C, Wang T, Tian C, He G, Chen G. Peptide Stapling by Crosslinking Two Amines with α-Ketoaldehydes through Diverse Modified Glyoxal-Lysine Dimer Linkers. Angew Chem Int Ed Engl 2024; 63:e202318893. [PMID: 38376389 DOI: 10.1002/anie.202318893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
α-Ketoaldehydes play versatile roles in the ubiquitous natural processes of protein glycation. However, leveraging the reactivity of α-ketoaldehydes for biomedical applications has been challenging. Previously, the reactivity of α-ketoaldehydes with guanidine has been harnessed to design probes for labeling Arg residues on proteins in an aqueous medium. Herein, a highly effective, broadly applicable, and operationally simple protocol for stapling native peptides by crosslinking two amino groups through diverse imidazolium linkers with various α-ketoaldehyde reagents is described. The use of hexafluoroisopropanol as a solvent facilitates rapid and clean reactions under mild conditions and enables unique selectivity for Lys over Arg. The naturally occurring GOLD/MOLD linkers have been expanded to encompass a wide range of modified glyoxal-lysine dimer (OLD) linkers. In a proof-of-concept trial, these modular stapling reactions enabled a convenient two-round strategy to streamline the structure-activity relationship (SAR) study of the wasp venom peptide anoplin, leading to enhanced biological activities.
Collapse
Affiliation(s)
- Pan Guo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chengjin Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Tianjiao Qiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Wenli Guan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Tao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
- Frontiers Science Center for New Organic Matter, Nankai University, Tianjin, 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
| |
Collapse
|
3
|
Burton NR, Backus KM. Functionalizing tandem mass tags for streamlining click-based quantitative chemoproteomics. Commun Chem 2024; 7:80. [PMID: 38600184 PMCID: PMC11006884 DOI: 10.1038/s42004-024-01162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Mapping the ligandability or potential druggability of all proteins in the human proteome is a central goal of mass spectrometry-based covalent chemoproteomics. Achieving this ambitious objective requires high throughput and high coverage sample preparation and liquid chromatography-tandem mass spectrometry analysis for hundreds to thousands of reactive compounds and chemical probes. Conducting chemoproteomic screens at this scale benefits from technical innovations that achieve increased sample throughput. Here we realize this vision by establishing the silane-based cleavable linkers for isotopically-labeled proteomics-tandem mass tag (sCIP-TMT) proteomic platform, which is distinguished by early sample pooling that increases sample preparation throughput. sCIP-TMT pairs a custom click-compatible sCIP capture reagent that is readily functionalized in high yield with commercially available TMT reagents. Synthesis and benchmarking of a 10-plex set of sCIP-TMT reveal a substantial decrease in sample preparation time together with high coverage and high accuracy quantification. By screening a focused set of four cysteine-reactive electrophiles, we demonstrate the utility of sCIP-TMT for chemoproteomic target hunting, identifying 789 total liganded cysteines. Distinguished by its compatibility with established enrichment and quantification protocols, we expect sCIP-TMT will readily translate to a wide range of covalent chemoproteomic applications.
Collapse
Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles CA, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles CA, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
| |
Collapse
|
4
|
Sadasivam P, Khanapur S, Hartimath SV, Ramasamy B, Cheng P, Feng CZ, Green D, Davis C, Goggi JL, Robins EG, Yan R. Arginine-Selective Bioconjugation Reagent for Effective 18F-labeling of Native Proteins. J Med Chem 2024; 67:5064-5074. [PMID: 38480493 PMCID: PMC10982996 DOI: 10.1021/acs.jmedchem.4c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Protein-based 18F-PET tracers offer new possibilities in early disease detection and personalized medicine. Their development relies heavily on the availability and effectiveness of 18F-prosthetic groups. We prepared and evaluated a novel arginine-selective prosthetic group, 4-[18F]fluorophenylglyoxal ([18F]FPG). [18F]FPG was radiosynthesized by a one-pot, two-step procedure with a non-decay-corrected (n.d.c.) isolated radiochemical yield (RCY) of 41 ± 8% (n = 10). [18F]FPG constitutes a generic tool for 18F-labeling of various proteins, including human serum albumin (HSA), ubiquitin, interleukin-2, and interleukin-4 in ∼30-60% n.d.c. isolated RCYs. [18F]FPG conjugation with arginine residues is highly selective, even in the presence of a large excess of lysine, cysteine, and histidine. [18F]FPG protein conjugates are able to preserve the binding affinity of the native proteins while also demonstrating excellent in vivo stability. The [18F]FPG-HSA conjugate has prolonged blood retention, which can be applied as a potential blood pool PET imaging agent. Thus, [18F]FPG is an arginine-selective bioconjugation reagent that can be effectively used for the development of 18F-labeled protein radiopharmaceuticals.
Collapse
Affiliation(s)
- Pragalath Sadasivam
- School
of Biomedical Engineering and Imaging Sciences, Department of Imaging
Chemistry and Biology, King’s College, London SE1 7EH, U.K.
- Institute
of Bioengineering and Bioimaging, Agency
for Science, Technology, and Research (A* STAR), 11 Biopolis Way, #01-02 Helios, Singapore 138667, Singapore
- Clinical
Imaging Research Centre, 14 Medical Drive, #B01-01 Centre for Translational
Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Minerva
Imaging ApS, Lyshøjvej
21, Ølstykke 3650, Denmark
| | - Shivashankar Khanapur
- Institute
of Bioengineering and Bioimaging, Agency
for Science, Technology, and Research (A* STAR), 11 Biopolis Way, #01-02 Helios, Singapore 138667, Singapore
| | - Siddesh V. Hartimath
- Institute
of Bioengineering and Bioimaging, Agency
for Science, Technology, and Research (A* STAR), 11 Biopolis Way, #01-02 Helios, Singapore 138667, Singapore
| | - Boominathan Ramasamy
- Institute
of Bioengineering and Bioimaging, Agency
for Science, Technology, and Research (A* STAR), 11 Biopolis Way, #01-02 Helios, Singapore 138667, Singapore
| | - Peter Cheng
- Institute
of Bioengineering and Bioimaging, Agency
for Science, Technology, and Research (A* STAR), 11 Biopolis Way, #01-02 Helios, Singapore 138667, Singapore
| | - Chin Zan Feng
- Institute
of Bioengineering and Bioimaging, Agency
for Science, Technology, and Research (A* STAR), 11 Biopolis Way, #01-02 Helios, Singapore 138667, Singapore
| | - David Green
- Clinical
Imaging Research Centre, 14 Medical Drive, #B01-01 Centre for Translational
Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Christopher Davis
- School
of Biomedical Engineering and Imaging Sciences, Department of Imaging
Chemistry and Biology, King’s College, London SE1 7EH, U.K.
| | - Julian L. Goggi
- Institute
of Bioengineering and Bioimaging, Agency
for Science, Technology, and Research (A* STAR), 11 Biopolis Way, #01-02 Helios, Singapore 138667, Singapore
- Minerva
Imaging ApS, Lyshøjvej
21, Ølstykke 3650, Denmark
| | - Edward G. Robins
- Institute
of Bioengineering and Bioimaging, Agency
for Science, Technology, and Research (A* STAR), 11 Biopolis Way, #01-02 Helios, Singapore 138667, Singapore
- Clinical
Imaging Research Centre, 14 Medical Drive, #B01-01 Centre for Translational
Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Molecular
Imaging and Therapy Research Unit, South Australian Health, and Medical
Research Institute (SAHMRI), North Terrace, Adelaide, SA 5000, Australia
- Adelaide
Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace & George Street, Adelaide, SA 5000, Australia
| | - Ran Yan
- School
of Biomedical Engineering and Imaging Sciences, Department of Imaging
Chemistry and Biology, King’s College, London SE1 7EH, U.K.
| |
Collapse
|
5
|
Brown T, Nguyen T, Zhou B, Zheng YG. Chemical probes and methods for the study of protein arginine methylation. RSC Chem Biol 2023; 4:647-669. [PMID: 37654509 PMCID: PMC10467615 DOI: 10.1039/d3cb00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023] Open
Abstract
Protein arginine methylation is a widespread post-translational modification (PTM) in eukaryotic cells. This chemical modification in proteins functionally modulates diverse cellular processes from signal transduction, gene expression, and DNA damage repair to RNA splicing. The chemistry of arginine methylation entails the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet, SAM) onto a guanidino nitrogen atom of an arginine residue of a target protein. This reaction is catalyzed by about 10 members of protein arginine methyltransferases (PRMTs). With impacts on a variety of cellular processes, aberrant expression and activity of PRMTs have been shown in many disease conditions. Particularly in oncology, PRMTs are commonly overexpressed in many cancerous tissues and positively correlated with tumor initiation, development and progression. As such, targeting PRMTs is increasingly recognized as an appealing therapeutic strategy for new drug discovery. In the past decade, a great deal of research efforts has been invested in illuminating PRMT functions in diseases and developing chemical probes for the mechanistic study of PRMTs in biological systems. In this review, we provide a brief developmental history of arginine methylation along with some key updates in arginine methylation research, with a particular emphasis on the chemical aspects of arginine methylation. We highlight the research endeavors for the development and application of chemical approaches and chemical tools for the study of functions of PRMTs and arginine methylation in regulating biology and disease.
Collapse
Affiliation(s)
- Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Terry Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Bo Zhou
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| |
Collapse
|
6
|
Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
Collapse
Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| |
Collapse
|
7
|
Kjærsgaard NL, Nielsen TB, Gothelf KV. Chemical Conjugation to Less Targeted Proteinogenic Amino Acids. Chembiochem 2022; 23:e202200245. [PMID: 35781760 PMCID: PMC9796363 DOI: 10.1002/cbic.202200245] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Indexed: 01/01/2023]
Abstract
Protein bioconjugates are in high demand for applications in biomedicine, diagnostics, chemical biology and bionanotechnology. Proteins are large and sensitive molecules containing multiple different functional groups and in particular nucleophilic groups. In bioconjugation reactions it can therefore be challenging to obtain a homogeneous product in high yield. Numerous strategies for protein conjugation have been developed, of which a vast majority target lysine, cysteine and to a lesser extend tyrosine. Likewise, several methods that involve recombinantly engineered protein tags have been reported. In recent years a number of methods have emerged for chemical bioconjugation to other amino acids and in this review, we present the progress in this area.
Collapse
Affiliation(s)
- Nanna L. Kjærsgaard
- Center for Multifunctional Biomolecular Drug Design Interdisciplinary Nanoscience CenterAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
- Department of ChemistryAarhus UniversityLangelandsgade 1408000Aarhus CDenmark
| | | | - Kurt V. Gothelf
- Center for Multifunctional Biomolecular Drug Design Interdisciplinary Nanoscience CenterAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
- Department of ChemistryAarhus UniversityLangelandsgade 1408000Aarhus CDenmark
| |
Collapse
|
8
|
Zhang Z, Morstein J, Ecker AK, Guiley KZ, Shokat KM. Chemoselective Covalent Modification of K-Ras(G12R) with a Small Molecule Electrophile. J Am Chem Soc 2022; 144:15916-15921. [PMID: 36001446 PMCID: PMC9460778 DOI: 10.1021/jacs.2c05377] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
KRAS mutations are one of the most common
oncogenic
drivers in human cancer. While small molecule inhibitors for the G12C
mutant have been successfully developed, allele-specific inhibition
for other KRAS hotspot mutants remains challenging.
Here we report the discovery of covalent chemical ligands for the
common oncogenic mutant K-Ras(G12R). These ligands bind in the Switch
II pocket and irreversibly react with the mutant arginine residue.
An X-ray crystal structure reveals an imidazolium condensation product
formed between the α,β-diketoamide ligand and the ε-
and η-nitrogens of arginine 12. Our results show that arginine
residues can be selectively targeted with small molecule electrophiles
despite their weak nucleophilicity and provide the basis for the development
of mutant-specific therapies for K-Ras(G12R)-driven cancer.
Collapse
Affiliation(s)
- Ziyang Zhang
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94158, United States.,Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Johannes Morstein
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Andrew K Ecker
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Keelan Z Guiley
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
9
|
Shih CT, Kuo BH, Tsai CY, Tseng MC, Shie JJ. Dibenzocyclooctendiones (DBCDOs): Arginine-Selective Chemical Labeling Reagents Obtained through Benzilic Acid Rearrangement. Org Lett 2022; 24:4694-4698. [PMID: 35727008 DOI: 10.1021/acs.orglett.2c01970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We demonstrate that dibenzocyclooctendiones (DBCDOs) are efficient chemical reagents for the site-specific labeling of arginine-containing biomolecules. Unlike the commonly used probes, DBCDOs undergo an irreversible ring-contracted rearrangement with the guanidinium group on arginine residues under mild reaction conditions. The regioselective dual-labeled arginine residues were obtained in a one-pot reaction with our tested substrates. The efficiency of DBCDOs reactions and their ease of synthesis make DBCDOs an attractive choice for the site-selective bioconjugation of arginine.
Collapse
Affiliation(s)
- Cheng-Ting Shih
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Bo-Hong Kuo
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Yi Tsai
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
10
|
Leone D, Pohl R, Hubálek M, Kadeřábková M, Krömer M, Sýkorová V, Hocek M. Glyoxal‐Linked Nucleotides and DNA for Bioconjugations and Crosslinking with Arginine‐Containing Peptides and Proteins. Chemistry 2022; 28:e202104208. [DOI: 10.1002/chem.202104208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Marta Kadeřábková
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| |
Collapse
|
11
|
Evaluation of FRET X for single-molecule protein fingerprinting. iScience 2021; 24:103239. [PMID: 34729466 PMCID: PMC8546410 DOI: 10.1016/j.isci.2021.103239] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/03/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and accumulated FRET efficiencies constitute the fingerprint for a protein. To evaluate the feasibility of this approach, we simulated fingerprints for hundreds of proteins using a coarse-grained lattice model and experimentally demonstrated FRET X fingerprinting on model peptides. Measured fingerprints are in agreement with our simulations, corroborating the validity of our modeling approach. In a simulated complex mixture of >300 human proteins of which only cysteines, lysines, and arginines were labeled, a support vector machine was able to identify constituents with 95% accuracy. We anticipate that our FRET X fingerprinting approach will form the basis of an analysis tool for targeted proteomics. We propose a FRET-based single-molecule protein identification method Peptides are experimentally distinguishable by their fingerprints Our approach can classify the constituents of complex samples with 95% accuracy
Collapse
|
12
|
Abstract
Site-selective chemical bioconjugation reactions are enabling tools for the chemical biologist. Guided by a careful study of the selenomethionine (SeM) benzylation, we have refined the reaction to meet the requirements of practical protein bioconjugation. SeM is readily introduced through auxotrophic expression and exhibits unique nucleophilic properties that allow it to be selectively modified even in the presence of cysteine. The resulting benzylselenonium adduct is stable at physiological pH, is selectively labile to glutathione, and embodies a broadly tunable cleavage profile. Specifically, a 4-bromomethylphenylacetyl (BrMePAA) linker has been applied for efficient conjugation of complex organic molecules to SeM-containing proteins. This expansion of the bioconjugation toolkit has broad potential in the development of chemically enhanced proteins.
Collapse
|
13
|
Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021; 60:17383-17387. [PMID: 34107150 PMCID: PMC8362068 DOI: 10.1002/anie.202105126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/27/2021] [Indexed: 12/28/2022]
Abstract
Linear or branched 1,3-diketone-linked thymidine 5'-O-mono- and triphosphate were synthesized through CuAAC click reaction of diketone-alkynes with 5-azidomethyl-dUMP or -dUTP. The triphosphates were good substrates for KOD XL DNA polymerase in primer extension synthesis of modified DNA. The nucleotide bearing linear 3,5-dioxohexyl group (HDO) efficiently reacted with arginine-containing peptides to form stable pyrimidine-linked conjugates, whereas the branched 2-acetyl-3-oxo-butyl (PDO) group was not reactive. Reaction with Lys or a terminal amino group formed enamine adducts that were prone to hydrolysis. This reactive HDO modification in DNA was used for bioconjugations and cross-linking with Arg-containing peptides or proteins (e.g. histones).
Collapse
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| |
Collapse
|
14
|
Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3‐Diketone‐Modified Nucleotides and DNA for Cross‐Linking with Arginine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| |
Collapse
|
15
|
Nilchan N, Alburger JM, Roush WR, Rader C. An Engineered Arginine Residue of Unusual pH-Sensitive Reactivity Facilitates Site-Selective Antibody Conjugation. Biochemistry 2021; 60:1080-1087. [PMID: 33754696 DOI: 10.1021/acs.biochem.0c00955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Monoclonal antibody h38C2 is a humanized catalytic antibody that has been used to generate various immunoconjugate species such as chemically programmed antibodies, antibody-drug conjugates, and antibody-siRNA conjugates. Highly efficient and specific conjugation of h38C2 occurs at its uniquely reactive lysine (Lys) residue buried inside the antibody's catalytic pocket. We recently reported the rational mutation of this Lys residue at position 99 in the heavy chain variable domain to an arginine (Arg) residue. The Lys99Arg mutation can be site-selectively conjugated with molecules containing a hapten-like triazolyl-phenylglyoxal (TPG) unit. Here we show that this conjugation is facilitated by the unusual pH-sensitive reactivity of the Arg99 residue, consistent with an indirectly measured pKa of 5.2. The Arg99/TPG conjugation holds promise to further expand the versatility of the h38C2 conjugation platform, such as for the generation of antibody conjugates with dual payloads.
Collapse
|
16
|
Fert-Bober J, Darrah E, Andrade F. Insights into the study and origin of the citrullinome in rheumatoid arthritis. Immunol Rev 2019; 294:133-147. [PMID: 31876028 DOI: 10.1111/imr.12834] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/08/2019] [Indexed: 12/11/2022]
Abstract
The presence of autoantibodies and autoreactive T cells to citrullinated proteins and citrullinating enzymes in patients with rheumatoid arthritis (RA), together with the accumulation of citrullinated proteins in rheumatoid joints, provides substantial evidence that dysregulated citrullination is a hallmark feature of RA. However, understanding mechanisms that dysregulate citrullination in RA has important challenges. Citrullination is a normal process in immune and non-immune cells, which is likely activated by different conditions (eg, inflammation) with no pathogenic consequences. In a complex inflammatory environment such as the RA joint, unique strategies are therefore required to dissect specific mechanisms involved in the abnormal production of citrullinated proteins. Here, we will review current models of citrullination in RA and discuss critical components that, in our view, are relevant to understanding the accumulation of citrullinated proteins in the RA joint, collectively referred to as the RA citrullinome. In particular, we will focus on potential caveats in the study of citrullination in RA and will highlight methods to precisely detect citrullinated proteins in complex biological samples, which is a confirmatory approach to mechanistically link the RA citrullinome with unique pathogenic pathways in RA.
Collapse
Affiliation(s)
- Justyna Fert-Bober
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Erika Darrah
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
17
|
Jones AX, Cao Y, Tang YL, Wang JH, Ding YH, Tan H, Chen ZL, Fang RQ, Yin J, Chen RC, Zhu X, She Y, Huang N, Shao F, Ye K, Sun RX, He SM, Lei X, Dong MQ. Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers. Nat Commun 2019; 10:3911. [PMID: 31477730 PMCID: PMC6718413 DOI: 10.1038/s41467-019-11917-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially. Cross-linking mass spectrometry can provide insights into protein structures and interactions but its scope depends on the reactivity of the cross-linker. Here, the authors develop Arg-Arg and Lys-Arg cross-linkers, which provide structural information elusive to the widely used Lys-Lys cross-linkers.
Collapse
Affiliation(s)
- Alexander X Jones
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Yong Cao
- School of Life Sciences, Peking University, 100871, Beijing, China.,National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Yu-Liang Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Yue-He Ding
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Hui Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Zhen-Lin Chen
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Run-Qian Fang
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jili Yin
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Rong-Chang Chen
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xing Zhu
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yang She
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Niu Huang
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Feng Shao
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Keqiong Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Rui-Xiang Sun
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Si-Min He
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206, Beijing, China.
| |
Collapse
|
18
|
Hwang D, Nilchan N, Nanna AR, Li X, Cameron MD, Roush WR, Park H, Rader C. Site-Selective Antibody Functionalization via Orthogonally Reactive Arginine and Lysine Residues. Cell Chem Biol 2019; 26:1229-1239.e9. [PMID: 31231031 DOI: 10.1016/j.chembiol.2019.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/23/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023]
Abstract
Homogeneous antibody-drug conjugates (ADCs) that use a highly reactive buried lysine (Lys) residue embedded in a dual variable domain (DVD)-IgG1 format can be assembled with high precision and efficiency under mild conditions. Here we show that replacing the Lys with an arginine (Arg) residue affords an orthogonal ADC assembly that is site-selective and stable. X-ray crystallography confirmed the location of the reactive Arg residue at the bottom of a deep pocket. As the Lys-to-Arg mutation is confined to a single residue in the heavy chain of the DVD-IgG1, heterodimeric assemblies that combine a buried Lys in one arm, a buried Arg in the other arm, and identical light chains, are readily assembled. Furthermore, the orthogonal conjugation chemistry enables the loading of heterodimeric DVD-IgG1s with two different cargos in a one-pot reaction and thus affords a convenient platform for dual-warhead ADCs and other multifaceted antibody conjugates.
Collapse
Affiliation(s)
- Dobeen Hwang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Napon Nilchan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Alex R Nanna
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohai Li
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Michael D Cameron
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - William R Roush
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - HaJeung Park
- X-Ray Crystallography Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.
| |
Collapse
|
19
|
Dovgan I, Erb S, Hessmann S, Ursuegui S, Michel C, Muller C, Chaubet G, Cianférani S, Wagner A. Arginine-selective bioconjugation with 4-azidophenyl glyoxal: application to the single and dual functionalisation of native antibodies. Org Biomol Chem 2018; 16:1305-1311. [DOI: 10.1039/c7ob02844j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
4-Azidophenyl glyoxal enables arginine-selective functionalisation of native antibodies. Being orthogonal to classical lysine conjugation, this method allowed straightforward generation of dual-payload antibody.
Collapse
Affiliation(s)
- Igor Dovgan
- Laboratory of Functional ChemoSystems (UMR 7199)
- LabEx Medalis
- University of Strasbourg
- France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO)
- Université de Strasbourg
- CNRS
- IPHC UMR 7178
- 67000 Strasbourg
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO)
- Université de Strasbourg
- CNRS
- IPHC UMR 7178
- 67000 Strasbourg
| | - Sylvain Ursuegui
- Laboratory of Functional ChemoSystems (UMR 7199)
- LabEx Medalis
- University of Strasbourg
- France
| | | | | | - Guilhem Chaubet
- Laboratory of Functional ChemoSystems (UMR 7199)
- LabEx Medalis
- University of Strasbourg
- France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO)
- Université de Strasbourg
- CNRS
- IPHC UMR 7178
- 67000 Strasbourg
| | - Alain Wagner
- Laboratory of Functional ChemoSystems (UMR 7199)
- LabEx Medalis
- University of Strasbourg
- France
| |
Collapse
|
20
|
Conibear AC, Farbiarz K, Mayer RL, Matveenko M, Kählig H, Becker CFW. Arginine side-chain modification that occurs during copper-catalysed azide-alkyne click reactions resembles an advanced glycation end product. Org Biomol Chem 2016; 14:6205-11. [PMID: 27282129 DOI: 10.1039/c6ob00932h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dehydroascorbate is a by-product of copper-catalysed azide-alkyne click (CuAAC) reactions and also forms advanced glycation end products (AGEs) in tissues undergoing oxidative stress. Here we isolate and characterize an arginine-dehydroascorbate adduct formed during CuAAC reactions, investigate strategies for preventing its formation, and propose its biological relevance as an AGE.
Collapse
Affiliation(s)
- Anne C Conibear
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Straße 38, 1090 Vienna, Austria.
| | | | | | | | | | | |
Collapse
|