1
|
Rawale DG, Gupta M, Thakur K, V R, Rai V. Ordered immobilization of serine proteases enabled by a linchpin directed modification platform. Chem Commun (Camb) 2024; 60:7168-7171. [PMID: 38904189 DOI: 10.1039/d4cc02253j] [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: 06/22/2024]
Abstract
We report a chemoselective and site-selective precision engineering of lysine in proteases. The mild and physiological reaction conditions keep their auto-degradation under control. Furthermore, it enables single-site ordered immobilization, enhancing protein digestion and peptide mapping efficiency.
Collapse
Affiliation(s)
- Dattatraya Gautam Rawale
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| | - Mrityunjay Gupta
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| | - Kalyani Thakur
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| |
Collapse
|
2
|
Saletti M, Paolino M, Venditti J, Bonechi C, Giuliani G, Lamponi S, Tassone G, Boccia A, Botta C, Blancafort L, Poggialini F, Vagaggini C, Cappelli A. A Facile Access to Green Fluorescent Albumin Derivatives. Chembiochem 2024; 25:e202300862. [PMID: 38369609 DOI: 10.1002/cbic.202300862] [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: 02/24/2024] [Revised: 01/24/2024] [Accepted: 12/22/2023] [Indexed: 02/20/2024]
Abstract
A Morita-Baylis-Hillman Adduct (MBHA) derivative bearing a triphenylamine moiety was found to react with human serum albumin (HSA) shifting its emission from the blue to the green-yellow thus leading to green fluorescent albumin (GFA) derivatives and enlarging the platform of probes for aggregation-induced fluorescent-based detection techniques. A possible interaction of MBHA derivative 7 with a lipophilic pocket within the HSA structure was suggested by docking studies. DLS experiments showed that the reaction with HSA induce a conformational change of the protein contributing to the aggregation process of GFA derivatives. The results of investigations on the biological properties suggested that GFA retained the ability of binding drug molecules such as warfarin and diazepam. Finally, cytotoxicity evaluation studies suggested that, although the MBHA derivative 7 at 0.1 μg/mL affected the percentage of cell viability in comparison to the negative control, it cannot be considered cytotoxic, whereas at all the other concentrations≥0.5 μg/mL resulted cytotoxic at different extent.
Collapse
Affiliation(s)
- Mario Saletti
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Jacopo Venditti
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Claudia Bonechi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Stefania Lamponi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Giusy Tassone
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Antonella Boccia
- Istituto di Scienze e Tecnologie Chimiche "G. Natta" - SCITEC (CNR), Via A. Corti 12, 20133, Milano, Italy
| | - Chiara Botta
- Istituto di Scienze e Tecnologie Chimiche "G. Natta" - SCITEC (CNR), Via A. Corti 12, 20133, Milano, Italy
| | - Lluís Blancafort
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, C/M. A. Capmany 69, 17003, Girona, Spain
| | - Federica Poggialini
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Chiara Vagaggini
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di, Siena, Via Aldo Moro 2, 53100, Siena, Italy
| |
Collapse
|
3
|
Pometti MA, Di Natale G, Geremia G, Gauswami N, Garufi G, Ricciardi G, Sciortino M, Scopelliti F, Russo G, Ippolito M. A Kinetically Controlled Bioconjugation Method for the Synthesis of Radioimmunoconjugates and the Development of a Domain Mapping MS-Workflow for Its Characterization. Bioconjug Chem 2024; 35:324-332. [PMID: 38366964 PMCID: PMC10961728 DOI: 10.1021/acs.bioconjchem.3c00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/20/2024] [Accepted: 01/25/2024] [Indexed: 02/19/2024]
Abstract
Immunoconjugates exploit the high affinity of monoclonal antibodies for a recognized antigen to selectively deliver a cytotoxic payload, such as drugs or radioactive nuclides, at the site of disease. Despite numerous techniques have been recently developed for site-selective bioconjugations of protein structures, reaction of ε-amine group of lysine residues with electrophilic reactants, such as activated esters (NHS), is the main method reported in the literature as it maintains proteins in their native conformation. Since antibodies hold a high number of lysine residues, a heterogeneous mixture of conjugates will be generated, which can result in decreased target affinity. Here, we report an intradomain regioselective bioconjugation between the monoclonal antibody Trastuzumab and the N-hydroxysuccinimide ester of the chelator 2,2',2″,2‴-(1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl)tetraacetic acid (DOTA) by a kinetically controlled reaction adding substoichiometric quantities of the activated ester to the mAb working at slightly basic pH. Liquid chromatography-mass spectrometry (LC-MS) analyses were carried out to assess the chelator-antibody ratio (CAR) and the number of chelating moieties linked to the mAb chains. Proteolysis experiments showed four lysine residues mainly involved in bioconjugation (K188 for the light chain and K30, K293, and K417 for the heavy chain), each of which was located in a different domain. Since the displayed intradomain regioselectivity, a domain mapping MS-workflow, based on a selective domain denaturation, was developed to quantify the percentage of chelator linked to each mAb domain. The resulting immunoconjugate mixture showed an average CAR of 0.9. About a third of the heavy chains were found as monoconjugated, whereas conjugation of the chelator in the light chain was negligible. Domain mapping showed the CH3 domain bearing 13% of conjugated DOTA, followed by CH2 and VH respectively bearing 12.5 and 11% of bonded chelator. Bioconjugation was not found in the CH1 domain, whereas for the light chain, only the CL domain was conjugated (6%). Data analysis based on LC-MS quantification of different analytical levels (intact, reduced chains, and domains) provided the immunoconjugate formulation. A mixture of immunoconjugates restricted to 15 species was obtained, and the percentage of each one within the mixture was calculated. In particular, species bearing 1 DOTA with a relative abundance ranging from 4 to 20-fold, in comparison to species bearing 2DOTA, were observed. Pairing of bioconjugation under kinetic control with the developed domain mapping MS-workflow could raise the standard of chemical quality for immunoconjugates obtained with commercially available reactants.
Collapse
Affiliation(s)
- Marco A. Pometti
- Nuclear
Medicine Department, Cannizzaro Hospital, Via Messina 829, 95126 Catania, Italy
- FORA
S.p.A., Via Alfred Bernhard
Nobel 11/a, 43122 Parma, Italy
| | - Giuseppe Di Natale
- CNR-Istituto
di Cristallografia, Via
Paolo Gaifami 18, 95126 Catania, Italy
| | - Giancarlo Geremia
- Nuclear
Medicine Department, Cannizzaro Hospital, Via Messina 829, 95126 Catania, Italy
- Parco
scientifico e tecnologico della Sicilia S.C.P.A., Stradale Vincenzo Lancia 57, 95121 Catania, Italy
| | - Nileshgiri Gauswami
- Nuclear
Medicine Department, Cannizzaro Hospital, Via Messina 829, 95126 Catania, Italy
- Parco
scientifico e tecnologico della Sicilia S.C.P.A., Stradale Vincenzo Lancia 57, 95121 Catania, Italy
| | - Gianni Garufi
- Nuclear
Medicine Department, Cannizzaro Hospital, Via Messina 829, 95126 Catania, Italy
- Parco
scientifico e tecnologico della Sicilia S.C.P.A., Stradale Vincenzo Lancia 57, 95121 Catania, Italy
| | - Giuseppina Ricciardi
- Nuclear
Medicine Department, Cannizzaro Hospital, Via Messina 829, 95126 Catania, Italy
- FORA
S.p.A., Via Alfred Bernhard
Nobel 11/a, 43122 Parma, Italy
| | - Marcella Sciortino
- Nuclear
Medicine Department, Cannizzaro Hospital, Via Messina 829, 95126 Catania, Italy
- FORA
S.p.A., Via Alfred Bernhard
Nobel 11/a, 43122 Parma, Italy
| | - Fabrizio Scopelliti
- Nuclear
Medicine Department, Cannizzaro Hospital, Via Messina 829, 95126 Catania, Italy
| | - Giorgio Russo
- IBFM-CNR
Institute of Molecular Bioimaging and Physiology, Contrada Pietra Pollastra, 90015 Cefalù, Italy
| | - Massimo Ippolito
- Nuclear
Medicine Department, Cannizzaro Hospital, Via Messina 829, 95126 Catania, Italy
| |
Collapse
|
4
|
Nong K, Zhao YL, Yi S, Zhang X, Wei S, Yao ZJ. 3-Acyl-4-Pyranone as a Lysine Residue-Selective Bioconjugation Reagent for Peptide and Protein Modification. Bioconjug Chem 2024; 35:286-299. [PMID: 38451202 DOI: 10.1021/acs.bioconjchem.3c00447] [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: 03/08/2024]
Abstract
Chemoselective protein modification plays extremely important roles in various biological, medical, and pharmaceutical investigations. Mimicking the mechanism of the chemoselective reaction between natural azaphilones and primary amines, this work successfully simplified the azaphilone scaffold into much simpler 3-acyl-4-pyranones. Examinations confirmed that these slim-size mimics perfectly kept the unique reactivity for selective conjugation with the primary amines including lysine residues of peptides and proteins. The newly developed pyranone tool presents remarkably increased aqueous solubility and compatible second-order rate constant by comparison with the original azaphilone. Additional advantages also include the ease of biorthogonal combinative use with a copper-catalyzed azide-alkyne Click reaction, which was conveniently applied to decorate lysozyme with neutral-, positive- and negative-charged functionalities in parallel. Moderate-degree modification of lysozyme with positively charged quaternary ammoniums was revealed to increase the enzymatic activities.
Collapse
Affiliation(s)
- Keyi Nong
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Yi-Lu Zhao
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Shandong Yi
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Xuchun Zhang
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Siyuan Wei
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Zhu-Jun Yao
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| |
Collapse
|
5
|
Koutsopetras I, Vaur V, Benazza R, Diemer H, Sornay C, Ersoy Y, Rochet L, Longo C, Hernandez-Alba O, Erb S, Detappe A, Skerra A, Wagner A, Cianferani S, Chaubet G. Site-Selective Protein Conjugation by a Multicomponent Ugi Reaction. Chemistry 2024; 30:e202303242. [PMID: 38050774 DOI: 10.1002/chem.202303242] [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: 10/03/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
The chemical bioconjugation of proteins has seen tremendous applications in the past decades, with the booming of antibody-drug conjugates and their use in oncology. While genetic engineering has permitted to produce bespoke proteins featuring key (un-)natural amino acid residues poised for site-selective modifications, the conjugation of native proteins is riddled with selectivity issues. Chemoselective strategies are plentiful and enable the precise modification of virtually any residue with a reactive side-chain; site-selective methods are less common and usually most effective on small and medium-sized proteins. In this context, we studied the application of the Ugi multicomponent reaction for the site-selective conjugation of amine and carboxylate groups on proteins, and antibodies in particular. Through an in-depth mechanistic methodology work supported by peptide mapping studies, we managed to develop a set of conditions allowing the highly selective modification of antibodies bearing N-terminal glutamate and aspartate residues. We demonstrated that this strategy did not alter their affinity toward their target antigen and produced an antibody-drug conjugate with subnanomolar potency. Excitingly, we showed that the high site selectivity of our strategy was maintained on other protein formats, especially on anticalins, for which directed mutagenesis helped to highlight the key importance of a single lysine residue.
Collapse
Affiliation(s)
- Ilias Koutsopetras
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Yağmur Ersoy
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Léa Rochet
- Department of Chemistry, University College London, London, UK
| | - Carmen Longo
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | | | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| |
Collapse
|
6
|
Chauhan P, V R, Kumar M, Molla R, Mishra SD, Basa S, Rai V. Chemical technology principles for selective bioconjugation of proteins and antibodies. Chem Soc Rev 2024; 53:380-449. [PMID: 38095227 DOI: 10.1039/d3cs00715d] [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: 01/03/2024]
Abstract
Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.
Collapse
Affiliation(s)
- Preeti Chauhan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Rajib Molla
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Surya Dev Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Sneha Basa
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| |
Collapse
|
7
|
Ruan Q, Zhao C. A method for parallel microscale protein labeling and precise control over the average degree of labeling (aDoL). Sci Rep 2023; 13:8961. [PMID: 37268718 DOI: 10.1038/s41598-023-36163-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
A widely used approach for protein conjugation is through the lysine residues reacting with NHS- or other active esters. However, it is a challenge to precisely control the degree of labeling (DoL) due to the instability of active ester and variability of reaction efficiencies. Here, we provide a protocol for better control of aDoL using existing Copper-free Click Chemistry reagents. It is a two-step reaction with one purification in between. Briefly, proteins of interest were first activated with azide-NHS. After removing unreacted azide-NHS, the protein-N3 is then reacted with a limited amount of complementary click tag. Our studies have shown the click tag will fully react with the protein-N3 after 24 h' incubation, and therefore does not require additional purification steps. As such, the aDoL is equal to the input molar ratio of the click tag and the protein. Furthermore, this approach offers a much simpler and more economical way to perform parallel microscale labeling. Once a protein is pre-activated with N3-NHS, any fluorophore or molecule with the complementary click tag can be attached to the protein by mixing the two ingredients. Quantities of the protein used in the click reaction can be at any desired amount. In one example, we labeled an antibody in parallel with 9 different fluorophores using a total of 0.5 mg of antibody. In another example, we labeled Ab with targeted aDoL value from 2 to 8. In a stability comparison study, we have found the conjugated fluorophore using the suggested click protocol stayed attached to the protein longer than with standard NHS-fluorophore labeling.
Collapse
Affiliation(s)
- Qiaoqiao Ruan
- Applied Research and Technology, Abbott Diagnostics Division, AP-20, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL, 60064-6016, USA.
| | - Cheng Zhao
- Applied Research and Technology, Abbott Diagnostics Division, AP-20, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL, 60064-6016, USA
| |
Collapse
|
8
|
Teng S, Ng EWH, Zhang Z, Soon CN, Xu H, Li R, Hirao H, Loh TP. Alkynone β-trifluoroborates: A new class of amine-specific biocompatible click reagents. SCIENCE ADVANCES 2023; 9:eadg4924. [PMID: 37126553 PMCID: PMC10132755 DOI: 10.1126/sciadv.adg4924] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Amine-targeting reactions that work under biocompatible conditions or in water are green processes that are extremely useful for the synthesis of functional materials and biotherapeutics. Unfortunately, despite the usefulness of this reaction, there are very few good amine-specific click methods reported thus far. Here, we report an amine-specific click reagent using alkynone β-trifluoroborates as the electrophiles. These boron-containing alkynyl reagents exhibit extremely high chemoselectivity toward amines even in the presence of thiols. The resulting oxaboracycle products are bench-stable, displaying the reactivities of both organoborates and enaminones. Intrinsic advantages of this methodology include benign reaction conditions, operational simplicity, remarkable product stability, and excellent chemoselectivity, which satisfy the criteria of click chemistry and demonstrate the high potential in bioconjugation. Hence, this water-based chemical approach is also applicable to the modification of native amino acids, peptides, and proteins. Ultimately, the essential role of water during the reaction was elucidated.
Collapse
Affiliation(s)
- Shenghan Teng
- 100 Lianhua Street, Zhongyuan District, Henan University of Technology, Zhengzhou 450001, China
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering, and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Elvis Wang Hei Ng
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
| | - Zhenguo Zhang
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering, and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Chee Ning Soon
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering, and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Hailun Xu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ruifang Li
- 100 Lianhua Street, Zhongyuan District, Henan University of Technology, Zhengzhou 450001, China
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering, and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Hajime Hirao
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
| | - Teck-Peng Loh
- 100 Lianhua Street, Zhongyuan District, Henan University of Technology, Zhengzhou 450001, China
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering, and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| |
Collapse
|
9
|
Zhang MQ, He PY, Hu JJ, Li YM. A rapid and selective methionine oxidative modification strategy. J Pept Sci 2023; 29:e3454. [PMID: 36181422 DOI: 10.1002/psc.3454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/08/2022]
Abstract
Considering the fact that site-selective late-stage diversification of peptides and proteins remains a challenge for biochemistry, strategies targeting low-abundance natural amino acids need to be further developed. As an extremely oxidation-sensitive and low-abundance amino acid, methionine emerges as a promising target for chemo- and site-selective modification. Herein we report an efficient and highly selective modification on methionine residues by one-pot O- and N-transfer reaction, generating sulfoximine-modified peptides with near-perfect conversion within 10 min. Moreover, the great tolerance to other natural amino acids has been demonstrated in reactions with various peptide substrates. To demonstrate the generality of this protocol, we have modified natural peptides and obtained sulfoximination products with high conversion rates. This methodology provides a novel strategy as the expansion of the methionine-based peptide functionalization toolbox.
Collapse
Affiliation(s)
- Meng-Qian Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Pei-Yang He
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Jin-Jian Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China.,Beijing Institute for Brain Disorders, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| |
Collapse
|
10
|
Chauhan P, V. R, Kumar M, Molla R, V. B. U, Rai V. Dis integrate (DIN) Theory Enabling Precision Engineering of Proteins. ACS CENTRAL SCIENCE 2023; 9:137-150. [PMID: 36844488 PMCID: PMC9951294 DOI: 10.1021/acscentsci.2c01455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Indexed: 06/18/2023]
Abstract
The chemical toolbox for the selective modification of proteins has witnessed immense interest in the past few years. The rapid growth of biologics and the need for precision therapeutics have fuelled this growth further. However, the broad spectrum of selectivity parameters creates a roadblock to the field's growth. Additionally, bond formation and dissociation are significantly redefined during the translation from small molecules to proteins. Understanding these principles and developing theories to deconvolute the multidimensional attributes could accelerate the area. This outlook presents a disintegrate (DIN) theory for systematically disintegrating the selectivity challenges through reversible chemical reactions. An irreversible step concludes the reaction sequence to render an integrated solution for precise protein bioconjugation. In this perspective, we highlight the key advancements, unsolved challenges, and potential opportunities.
Collapse
|
11
|
Yu X, Ruan M, Wang Y, Nguyen A, Xiao W, Ajena Y, Solano LN, Liu R, Lam KS. Site-Specific Albumin-Selective Ligation to Human Serum Albumin under Physiological Conditions. Bioconjug Chem 2022; 33:2332-2340. [PMID: 36350013 PMCID: PMC9782315 DOI: 10.1021/acs.bioconjchem.2c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human serum albumin (HSA) is the most abundant protein in human blood plasma. It plays a critical role in the native transportation of numerous drugs, metabolites, nutrients, and small molecules. HSA has been successfully used clinically as a noncovalent carrier for insulin (e.g., Levemir), GLP-1 (e.g., Liraglutide), and paclitaxel (e.g., Abraxane). Site-specific bioconjugation strategies for HSA only would greatly expand its role as the biocompatible, non-toxic platform for theranostics purposes. Using the enabling one-bead one-compound (OBOC) technology, we generated combinatorial peptide libraries containing myristic acid, a well-known binder to HSA at Sudlow I and II binding pockets, and an acrylamide. We then used HSA as a probe to screen the OBOC myristylated peptide libraries for reactive affinity elements (RAEs) that can specifically and covalently ligate to the lysine residue at the proximity of these pockets. Several RAEs have been identified and confirmed to be able to conjugate to HSA covalently. The conjugation can occur at physiological pH and proceed with a high yield within 1 h at room temperature. Tryptic peptide profiling of derivatized HSA has revealed two lysine residues (K225 and K414) as the conjugation sites, which is much more specific than the conventional lysine labeling strategy with N-hydroxysuccinimide ester. The RAE-driven site-specific ligation to HSA was found to occur even in the presence of other prevalent blood proteins such as immunoglobulin or whole serum. Furthermore, these RAEs are orthogonal to the maleimide-based conjugation strategy for Cys34 of HSA. Together, these attributes make the RAEs the promising leads to further develop in vitro and in vivo HSA bioconjugation strategies for numerous biomedical applications.
Collapse
Affiliation(s)
- Xingjian Yu
- Department
of Chemistry, University of California Davis, Davis, 95616California, United States,Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States
| | - Ming Ruan
- Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States,School
of Food Science, Nanjing Xiaozhuang University, Nanjing, 211171, Jiangsu, China
| | - Yongheng Wang
- Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States,Department
of Biomedical Engineering, University of
California Davis, Davis, California95616, United States
| | - Audrey Nguyen
- Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States
| | - Wenwu Xiao
- Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States
| | - Yousif Ajena
- Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States
| | - Lucas N. Solano
- Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States
| | - Ruiwu Liu
- Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States,
| | - Kit S Lam
- Department
of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California95817, United States,
| |
Collapse
|
12
|
Thakur K, T K S, Singh SK, V R, Rawale DG, Adusumalli SR, Kalra N, Shukla S, Mishra RK, Rai V. Human Behavior-Inspired Linchpin-Directed Catalysis for Traceless Precision Labeling of Lysine in Native Proteins. Bioconjug Chem 2022; 33:2370-2380. [PMID: 36383773 DOI: 10.1021/acs.bioconjchem.2c00454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complex social ecosystem regulates the spectrum of human behavior. However, it becomes relatively easier to understand if we disintegrate the contributing factors, such as locality and interacting partners. Interestingly, it draws remarkable similarity with the behavior of a residue placed in a social setup of functional groups in a protein. Can it inspire principles for creating a unique environment for the precision engineering of proteins? We demonstrate that localization-regulated interacting partner(s) could render precise and traceless single-site modification of structurally diverse native proteins. The method targets a combination of high-frequency Lys residues through an array of reversible and irreversible reactions. However, excellent simultaneous control over chemoselectivity, site selectivity, and modularity ensures that the user-friendly protocol renders acyl group installation, including post-translational modifications (PTMs), on a single Lys. Besides, it offers a chemically orthogonal handle for the installation of probes. Also, a purification protocol integration delivers analytically pure single-site tagged protein bioconjugates. The precise labeling of a surface Lys residue ensures that the structure and enzymatic activities remain conserved post-bioconjugation. For example, the precise modification of insulin does not affect its uptake and downstream signaling pathway. Further, the method enables the synthesis of homogeneous antibody-fluorophore and antibody-drug conjugates (AFC and ADC; K183 and K249 labeling). The trastuzumab-rhodamine B conjugate displays excellent serum stability along with antigen-specific cellular imaging. Further, the trastuzumab-emtansine conjugate offers highly specific antiproliferative activity toward HER-2 positive SKBR-3 breast cancer cells. This work validates that disintegrate theory can create a comprehensive platform to enrich the chemical toolbox to meet the technological demands at the chemistry, biology, and medicine interface.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Neetu Kalra
- School of Bioengineering, VIT Bhopal, Bhopal 466114, Madhya Pradesh, India
| | | | | | | |
Collapse
|
13
|
Reddy NC, Molla R, Joshi PN, T. K. S, Basu I, Kawadkar J, Kalra N, Mishra RK, Chakrabarty S, Shukla S, Rai V. Traceless cysteine-linchpin enables precision engineering of lysine in native proteins. Nat Commun 2022; 13:6038. [PMID: 36229616 PMCID: PMC9561114 DOI: 10.1038/s41467-022-33772-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
The maintenance of machinery requires its operational understanding and a toolbox for repair. The methods for the precision engineering of native proteins meet a similar requirement in biosystems. Its success hinges on the principles regulating chemical reactions with a protein. Here, we report a technology that delivers high-level control over reactivity, chemoselectivity, site-selectivity, modularity, dual-probe installation, and protein-selectivity. It utilizes cysteine-based chemoselective Linchpin-Directed site-selective Modification of lysine residue in a protein (LDMC-K). The efficiency of the end-user-friendly protocol is evident in quantitative conversions within an hour. A chemically orthogonal C-S bond-formation and bond-dissociation are essential among multiple regulatory attributes. The method offers protein selectivity by targeting a single lysine residue of a single protein in a complex biomolecular mixture. The protocol renders analytically pure single-site probe-engineered protein bioconjugate. Also, it provides access to homogeneous antibody conjugates (AFC and ADC). The LDMC-K-ADC exhibits highly selective anti-proliferative activity towards breast cancer cells.
Collapse
Affiliation(s)
- Neelesh C. Reddy
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Rajib Molla
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Pralhad Namdev Joshi
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Sajeev T. K.
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Ipsita Basu
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Jyotsna Kawadkar
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | | | - Ram Kumar Mishra
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Suman Chakrabarty
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Sanjeev Shukla
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Vishal Rai
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| |
Collapse
|
14
|
Rezaei M, Kalhor HR. Amyloid fibril reduction through covalently modified lysine in HEWL and insulin. Arch Biochem Biophys 2022; 727:109350. [PMID: 35830943 DOI: 10.1016/j.abb.2022.109350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.
Collapse
Affiliation(s)
- Mohsen Rezaei
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Hamid Reza Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran.
| |
Collapse
|
15
|
Fryszkowska A, An C, Alvizo O, Banerjee G, Canada KA, Cao Y, DeMong D, Devine PN, Duan D, Elgart DM, Farasat I, Gauthier DR, Guidry EN, Jia X, Kong J, Kruse N, Lexa KW, Makarov AA, Mann BF, Milczek EM, Mitchell V, Nazor J, Neri C, Orr RK, Orth P, Phillips EM, Riggins JN, Schafer WA, Silverman SM, Strulson CA, Subramanian N, Voladri R, Yang H, Yang J, Yi X, Zhang X, Zhong W. A chemoenzymatic strategy for site-selective functionalization of native peptides and proteins. Science 2022; 376:1321-1327. [PMID: 35709255 DOI: 10.1126/science.abn2009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of new therapeutic modalities requires complementary tools for their efficient syntheses. Availability of methodologies for site-selective modification of biomolecules remains a long-standing challenge, given the inherent complexity and the presence of repeating residues that bear functional groups with similar reactivity profiles. We describe a bioconjugation strategy for modification of native peptides relying on high site selectivity conveyed by enzymes. We engineered penicillin G acylases to distinguish among free amino moieties of insulin (two at amino termini and an internal lysine) and manipulate cleavable phenylacetamide groups in a programmable manner to form protected insulin derivatives. This enables selective and specific chemical ligation to synthesize homogeneous bioconjugates, improving yield and purity compared to the existing methods, and generally opens avenues in the functionalization of native proteins to access biological probes or drugs.
Collapse
Affiliation(s)
- Anna Fryszkowska
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Chihui An
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Oscar Alvizo
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | | | - Keith A Canada
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Yang Cao
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Duane DeMong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Paul N Devine
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Da Duan
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - David M Elgart
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Iman Farasat
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Donald R Gauthier
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Erin N Guidry
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Xiujuan Jia
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jongrock Kong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Nikki Kruse
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Katrina W Lexa
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Alexey A Makarov
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Benjamin F Mann
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Erika M Milczek
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Vesna Mitchell
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Jovana Nazor
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Claudia Neri
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Robert K Orr
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Peter Orth
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Eric M Phillips
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - James N Riggins
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Wes A Schafer
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Steven M Silverman
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | | | - Rama Voladri
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Hao Yang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jie Yang
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Xiang Yi
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Xiyun Zhang
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Wendy Zhong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| |
Collapse
|
16
|
Cleavable Cys labeling directed Lys site-selective stapling and single-site modification. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1252-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
17
|
Boll LB, Raines RT. Context‐dependence of the Reactivity of Cysteine and Lysine Residues. Chembiochem 2022; 23:e202200258. [PMID: 35527228 PMCID: PMC9308718 DOI: 10.1002/cbic.202200258] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Indexed: 11/11/2022]
Abstract
The S‐alkylation of Cys residues with a maleimide and the Nϵ‐acylation of Lys residues with an N‐hydroxysuccinimide (NHS) ester are common methods for bioconjugation. Using Cys and Lys derivatives as proxies, we assessed differences in reactivity depending on the position of Cys or Lys in a protein sequence. We find that Cys position is exploitable to improve site‐selectivity in maleimide‐based modifications. Reactivity decreases substantially in the order N‐terminal>in‐chain>C‐terminal Cys due to modulation of sulfhydryl pKa by the α‐ammonium and carboxylate groups at the termini. A lower pKa value yields a larger fraction thiolate, which promotes selectivity while somewhat decreasing thiolate nucleophilicity in accord with βnuc
=0.41. Lowering pH and salt concentration enhances selectivity still further. In contrast, differences in the reactivity of Lys towards an NHS ester were modest due to an appreciable decrease in amino group nucleophilicity with a lower pKa of its conjugate acid. Hence, site‐selective Lys modification protocols will require electrophiles other than NHS esters.
Collapse
Affiliation(s)
- Linus B. Boll
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Avenue 02139 Cambridge UNITED STATES
| | - Ronald T. Raines
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Avenue, 18-498 02139-4307 Cambridge UNITED STATES
| |
Collapse
|
18
|
Pawloski W, Komiyama T, Kougentakis C, Majumdar A, Fushman D. Site-Specific Detection and Characterization of Ubiquitin Carbamylation. Biochemistry 2022; 61:712-721. [PMID: 35380792 PMCID: PMC9173829 DOI: 10.1021/acs.biochem.2c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The physiological consequences of varying in vivo CO2 levels point to a general mechanism for CO2 to influence cellular homeostasis beyond regulating pH. Aside from a few instances where CO2 has been observed to cause post-translational protein modification, by forming long-lived carbamates, little is known about how transitory and ubiquitous carbamylation events could induce a physiological response. Ubiquitin is a versatile protein involved in a multitude of cellular signaling pathways as polymeric chains of various lengths formed through one of the seven lysines or N-terminal amine. Unique polyubiquitin (polyUb) compositions present recognition signals for specific ubiquitin-receptors which enables this one protein to be involved in many different cellular processes. Advances in proteomic methods have allowed the capture and identification of protein carbamates in vivo, and Ub was found carbamylated at lysines K48 and K33. This was shown to negatively regulate ubiquitin-mediated signaling by inhibiting polyUb chain formation. Here, we expand upon these observations by characterizing the carbamylation susceptibility for all Ub amines simultaneously. Using NMR methods which directly probe 15N resonances, we determined carbamylation rates under various environmental conditions and related them to the intrinsic pKas. Our results show that the relatively low pKas for half of the Ub amines are correlated with enhanced susceptibility to carbamylation under physiological conditions. Two of these carbamylated amines, not observed by chemical capture, appear to be physiologically relevant post-translational modifications. These findings point to a mechanism for varying the levels of CO2 due to intracellular localization, cellular stresses, and metabolism to affect certain polyUb-mediated signaling pathways.
Collapse
Affiliation(s)
- Westley Pawloski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Teppei Komiyama
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Christos Kougentakis
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
19
|
Sahu T, Chilamari M, Rai V. Protein inspired chemically orthogonal imines for linchpin directed precise and modular labeling of lysine in proteins. Chem Commun (Camb) 2022; 58:1768-1771. [PMID: 35037678 DOI: 10.1039/d1cc05559c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a chemoselective, site-selective, and modular technology for precision engineering of high-frequency lysine residues in native proteins. It enables a unique, unexplored reactivity landscape on the protein surface to facilitate their single-site modification. Further, the method presents bond-architecture flexibility and enables orthogonal tagging with probes of interest.
Collapse
Affiliation(s)
- Tularam Sahu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 462066, MP, India.
| | - Maheshwerreddy Chilamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 462066, MP, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 462066, MP, India.
| |
Collapse
|
20
|
Tassone G, Paolino M, Pozzi C, Reale A, Salvini L, Giorgi G, Orlandini M, Galvagni F, Mangani S, Yang X, Carlotti B, Ortica F, Latterini L, Olivucci M, Cappelli A. Xanthopsin-Like Systems via Site-Specific Click-Functionalization of a Retinoic Acid Binding Protein. Chembiochem 2022; 23:e202100449. [PMID: 34647400 PMCID: PMC8934143 DOI: 10.1002/cbic.202100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/12/2021] [Indexed: 01/07/2023]
Abstract
The use of light-responsive proteins to control both living or synthetic cells, is at the core of the expanding fields of optogenetics and synthetic biology. It is thus apparent that a richer reaction toolbox for the preparation of such systems is of fundamental importance. Here, we provide a proof-of-principle demonstration that Morita-Baylis-Hillman adducts can be employed to perform a facile site-specific, irreversible and diastereoselective click-functionalization of a lysine residue buried into a lipophilic binding pocket and yielding an unnatural chromophore with an extended π-system. In doing so we effectively open the path to the in vitro preparation of a library of synthetic proteins structurally reminiscent of xanthopsin eubacterial photoreceptors. We argue that such a library, made of variable unnatural chromophores inserted in an easy-to-mutate and crystallize retinoic acid transporter, significantly expand the scope of the recently introduced rhodopsin mimics as both optogenetic and "lab-on-a-molecule" tools.
Collapse
Affiliation(s)
- Giusy Tassone
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Cecilia Pozzi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Annalisa Reale
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Laura Salvini
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Maurizio Orlandini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Federico Galvagni
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Stefano Mangani
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, OH 43403, USA
| | - Benedetta Carlotti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123, Perugia, Italy
| | - Fausto Ortica
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123, Perugia, Italy
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123, Perugia, Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, OH 43403, USA
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| |
Collapse
|
21
|
Linchpin-directed precise labeling of lysine in native proteins, purification, and analysis. Methods Enzymol 2022; 675:383-396. [DOI: 10.1016/bs.mie.2022.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
22
|
Sornay C, Vaur V, Wagner A, Chaubet G. An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211563. [PMID: 35116160 PMCID: PMC8790347 DOI: 10.1098/rsos.211563] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
Collapse
Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| |
Collapse
|
23
|
Horn JM, Obermeyer AC. Genetic and Covalent Protein Modification Strategies to Facilitate Intracellular Delivery. Biomacromolecules 2021; 22:4883-4904. [PMID: 34855385 PMCID: PMC9310055 DOI: 10.1021/acs.biomac.1c00745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-based therapeutics represent a rapidly growing segment of approved disease treatments. Successful intracellular delivery of proteins is an important precondition for expanded in vivo and in vitro applications of protein therapeutics. Direct modification of proteins and peptides for improved cytosolic translocation are a promising method of increasing delivery efficiency and expanding the viability of intracellular protein therapeutics. In this Review, we present recent advances in both synthetic and genetic protein modifications for intracellular delivery. Active endocytosis-based and passive internalization pathways are discussed, followed by a review of modification methods for improved cytosolic delivery. After establishing how proteins can be modified, general strategies for facilitating intracellular delivery, such as chemical supercharging or inclusion of cell-penetrating motifs, are covered. We then outline protein modifications that promote endosomal escape. We finally examine the delivery of two potential classes of therapeutic proteins, antibodies and associated antibody fragments, and gene editing proteins, such as cas9.
Collapse
|
24
|
Protein Modifications: From Chemoselective Probes to Novel Biocatalysts. Catalysts 2021. [DOI: 10.3390/catal11121466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chemical reactions can be performed to covalently modify specific residues in proteins. When applied to native enzymes, these chemical modifications can greatly expand the available set of building blocks for the development of biocatalysts. Nucleophilic canonical amino acid sidechains are the most readily accessible targets for such endeavors. A rich history of attempts to design enhanced or novel enzymes, from various protein scaffolds, has paved the way for a rapidly developing field with growing scientific, industrial, and biomedical applications. A major challenge is to devise reactions that are compatible with native proteins and can selectively modify specific residues. Cysteine, lysine, N-terminus, and carboxylate residues comprise the most widespread naturally occurring targets for enzyme modifications. In this review, chemical methods for selective modification of enzymes will be discussed, alongside with examples of reported applications. We aim to highlight the potential of such strategies to enhance enzyme function and create novel semisynthetic biocatalysts, as well as provide a perspective in a fast-evolving topic.
Collapse
|
25
|
Selective and predicable amine conjugation sites by kinetic characterization under excess reagents. Sci Rep 2021; 11:21222. [PMID: 34707190 PMCID: PMC8551328 DOI: 10.1038/s41598-021-00743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
The site selectivity for lysine conjugation on a native protein is difficult to control and characterize. Here, we applied mass spectrometry to examine the conjugation kinetics of Trastuzumab-IgG (Her-IgG) and α-lactalbumin under excess linker concentration ([L]0) based on the modified Michaelis–Menten equation, in which the initial rate constant per amine (kNH2 = Vmax/NH2/KM) was determined by the maximum reaction rate (Vmax/NH2) under saturated accessible sites and initial amine–linker affinity (1/KM). Reductive amination (RA) displayed 3–4 times greater Vmax/NH2 and a different panel of conjugation sites than that observed for N-hydroxysuccinimide ester (NHS) chemistry using the same length of polyethylene glycol (PEG) linkers. Moreover, faster conversion power rendered RA site selectivity among accessible amine groups and a greater tunable range of linker/protein ratio for aldehyde-linkers compared to those of the same length of NHS-linkers. Single conjugation with high yield or poly-conjugations with site homogeneity was demonstrated by controlling [L]0 or gradual addition to minimize the [L]0/KM ratio. Formaldehyde, the shortest aldehyde-linker with the greatest 1/KM, exhibited the highest selectivity and was shown to be a suitable probe to predict conjugation profile of aldehyde-linkers. Four linkers on the few probe-predicted hot spots were elucidated by kinetically controlled RA with conserved drug efficacy when conjugated with the payload. This study provides insights into controlling factors for homogenous and predictable amine bioconjugation.
Collapse
|
26
|
Kang MS, Kong TWS, Khoo JYX, Loh TP. Recent developments in chemical conjugation strategies targeting native amino acids in proteins and their applications in antibody-drug conjugates. Chem Sci 2021; 12:13613-13647. [PMID: 34760149 PMCID: PMC8549674 DOI: 10.1039/d1sc02973h] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Many fields in chemical biology and synthetic biology require effective bioconjugation methods to achieve their desired functions and activities. Among such biomolecule conjugates, antibody-drug conjugates (ADCs) need a linker that provides a stable linkage between cytotoxic drugs and antibodies, whilst conjugating in a biologically benign, fast and selective fashion. This review focuses on how the development of novel organic synthesis can solve the problems of traditional linker technology. The review shall introduce and analyse the current developments in the modification of native amino acids on peptides or proteins and their applicability to ADC linker. Thereafter, the review shall discuss in detail each endogenous amino acid's intrinsic reactivity and selectivity aspects, and address the research effort to construct an ADC using each conjugation method.
Collapse
Affiliation(s)
- Min Sun Kang
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Theresa Wai See Kong
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Joycelyn Yi Xin Khoo
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Teck-Peng Loh
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| |
Collapse
|
27
|
Haque M, Forte N, Baker JR. Site-selective lysine conjugation methods and applications towards antibody-drug conjugates. Chem Commun (Camb) 2021; 57:10689-10702. [PMID: 34570125 PMCID: PMC8516052 DOI: 10.1039/d1cc03976h] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Site-selective protein modification is of significant interest in chemical biology research, with lysine residues representing a particularly challenging target. Whilst lysines are popular for bioconjugation, due to their nucleophilicity, solvent accessibility and the stability of the resultant conjugates, their high abundance means site-selectivity is very difficult to achieve. Antibody-drug conjugates (ADCs) present a powerful therapeutic application of protein modification, and have often relied extensively upon lysine bioconjugation for their synthesis. Here we discuss advances in methodologies for achieving site-selective lysine modification, particularly within the context of antibody conjugate construction, including the cysteine-to-lysine transfer (CLT) protocol which we have recently reported.
Collapse
Affiliation(s)
- Muhammed Haque
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - Nafsika Forte
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - James R Baker
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| |
Collapse
|
28
|
Abstract
Antibodies, particularly of the immunoglobulin G (IgG) isotype, are a group of biomolecules that are extensively used as affinity reagents for many applications in research, disease diagnostics, and therapy. Most of these applications require antibodies to be modified with specific functional moieties, including fluorophores, drugs, and proteins. Thus, a variety of methodologies have been developed for the covalent labeling of antibodies. The most common methods stably attach functional molecules to lysine or cysteine residues, which unavoidably results in heterogeneous products that cannot be further purified. In an effort to prepare homogeneous antibody conjugates, bioorthogonal handles have been site-specifically introduced via enzymatic treatment, genetic code expansion, or genetically encoded tagging, followed by functionalization using bioorthogonal conjugation reactions. The resulting homogeneous products have proven superior to their heterogeneous counterparts for both in vitro and in vivo usage. Nevertheless, additional chemical treatment or protein engineering of antibodies is required for incorporation of the bioorthogonal handles, processes that often affect antibody folding, stability, and/or production yield and cost. Accordingly, concurrent with advances in the fields of bioorthogonal chemistry and protein engineering, there is growing interest in site-specifically labeling native (nonengineered) antibodies without chemical or enzymatic treatments. In this review, we highlight recent strategies for producing site-specific native antibody conjugates and provide a comprehensive summary of the merits and disadvantages of these strategies.
Collapse
Affiliation(s)
- Kuan-Lin Wu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Chenfei Yu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Catherine Lee
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Chao Zuo
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Zachary T Ball
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| |
Collapse
|
29
|
Kumar M, Reddy NC, Rai V. Chemical technologies for precise protein bioconjugation interfacing biology and medicine. Chem Commun (Camb) 2021; 57:7083-7095. [PMID: 34180471 DOI: 10.1039/d1cc02268g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins provide an excellent means to monitor and regulate biological processes. Hence, a precise chemical toolbox for their modification becomes indispensable. In this perspective, this feature article outlines our efforts to establish the core principles of chemoselectivity, site-selectivity, site-specificity, site-modularity, residue-modularity, and protein-specificity. With the knowledge to systematically regulate these parameters, the field has access to technological platforms that can address multiple challenges at the interface of chemistry, biology, and medicine.
Collapse
Affiliation(s)
- Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Neelesh C Reddy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| |
Collapse
|
30
|
Adakkattil R, Thakur K, Rai V. Reactivity and Selectivity Principles in Native Protein Bioconjugation. CHEM REC 2021; 21:1941-1956. [PMID: 34184826 DOI: 10.1002/tcr.202100108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/10/2021] [Indexed: 12/24/2022]
Abstract
Are chemical methods capable of precisely engineering the native proteins? Is it possible to develop platforms that can empower the regulation of chemoselectivity, site-selectivity, modularity, protein-specificity, and site-specificity? This account delineates our research journey in the last ten years on the developments revolving around these questions. It will range from the realization of chemoselective and site-selective labeling of reactivity hotspots to modular linchpin directed modification (LDM®) platform and site-specific Gly-tag® technology. Also, we outline a few biotechnology tools, including Maspecter®, that accelerated the detailed analysis of the bioconjugates and rendered a powerful toolbox for homogeneous antibody-drug conjugates (ADCs).
Collapse
Affiliation(s)
- Ramesh Adakkattil
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, 462 066, Bhopal, Madhya Pradesh, India
| | - Kalyani Thakur
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, 462 066, Bhopal, Madhya Pradesh, India
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, 462 066, Bhopal, Madhya Pradesh, India
| |
Collapse
|
31
|
Mallek AJ, Pentelute BL, Buchwald SL. Selective N‐Arylation of
p
‐Aminophenylalanine in Unprotected Peptides with Organometallic Palladium Reagents. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Aaron J. Mallek
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Stephen L. Buchwald
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| |
Collapse
|
32
|
Mallek AJ, Pentelute BL, Buchwald SL. Selective N-Arylation of p-Aminophenylalanine in Unprotected Peptides with Organometallic Palladium Reagents. Angew Chem Int Ed Engl 2021; 60:16928-16931. [PMID: 34015170 DOI: 10.1002/anie.202104780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/12/2021] [Indexed: 11/11/2022]
Abstract
The selective N-arylation of p-aminophenylalanine in polypeptides with pre-formed palladium oxidative addition complexes is described. The depressed pKa of the aniline NH2 group enables chemoselective C-N bond formation on peptides containing multiple other aliphatic amino groups at lysines or the N-terminus via Curtin-Hammett control under mild conditions. Using palladium complexes derived from electron-poor aryl halides, p-aminophenylalanine is fully arylated in aqueous buffer in as little as one hour at micromolar concentrations. A complementary protocol using the non-nucleophilic, organic base 1,5-diazabicyclo(4.3.0)non-5-ene (DBN), expands the substrate scope to tolerate electron-rich functional groups provides up to 97 % conversion. These procedures enable the chemoselective conjugation of functionally diverse small molecule pharmaceuticals to p-aminophenylalanine containing derivatives of cell-penetrating peptides.
Collapse
Affiliation(s)
- Aaron J Mallek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| |
Collapse
|
33
|
De Rosa L, Di Stasi R, Romanelli A, D’Andrea LD. Exploiting Protein N-Terminus for Site-Specific Bioconjugation. Molecules 2021; 26:3521. [PMID: 34207845 PMCID: PMC8228110 DOI: 10.3390/molecules26123521] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022] Open
Abstract
Although a plethora of chemistries have been developed to selectively decorate protein molecules, novel strategies continue to be reported with the final aim of improving selectivity and mildness of the reaction conditions, preserve protein integrity, and fulfill all the increasing requirements of the modern applications of protein conjugates. The targeting of the protein N-terminal alpha-amine group appears a convenient solution to the issue, emerging as a useful and unique reactive site universally present in each protein molecule. Herein, we provide an updated overview of the methodologies developed until today to afford the selective modification of proteins through the targeting of the N-terminal alpha-amine. Chemical and enzymatic strategies enabling the selective labeling of the protein N-terminal alpha-amine group are described.
Collapse
Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy;
| | - Luca Domenico D’Andrea
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR Via M. Bianco 9, 20131 Milano, Italy
| |
Collapse
|
34
|
Xing Y, Varghese B, Ling Z, Kar AS, Reinoso Jacome E, Ren X. Extracellular Matrix by Design: Native Biomaterial Fabrication and Functionalization to Boost Tissue Regeneration. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2021. [DOI: 10.1007/s40883-021-00210-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
35
|
Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
Collapse
Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| |
Collapse
|
36
|
Tang KC, Raj M. One‐Step Azolation Strategy for Site‐ and Chemo‐Selective Labeling of Proteins with Mass‐Sensitive Probes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202007608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kuei C. Tang
- Present address: Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Monika Raj
- Present address: Department of Chemistry Emory University Atlanta GA 30322 USA
| |
Collapse
|
37
|
Boto A, González CC, Hernández D, Romero-Estudillo I, Saavedra CJ. Site-selective modification of peptide backbones. Org Chem Front 2021. [DOI: 10.1039/d1qo00892g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exciting developments in the site-selective modification of peptide backbones are allowing an outstanding fine-tuning of peptide conformation, folding ability, and physico-chemical and biological properties.
Collapse
Affiliation(s)
- Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Iván Romero-Estudillo
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos. Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
- Catedrático CONACYT-CIQ-UAEM, Mexico
| | - Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain
| |
Collapse
|
38
|
Dhanjee HH, Buslov I, Windsor IW, Raines RT, Pentelute BL, Buchwald SL. Palladium-Protein Oxidative Addition Complexes by Amine-Selective Acylation. J Am Chem Soc 2020; 142:21237-21242. [PMID: 33319995 DOI: 10.1021/jacs.0c09180] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Palladium oxidative addition complexes (OACs) are traditionally accessed by treating an aryl halide-containing substrate with a palladium(0) source. Here, a new strategy to selectively prepare stable OACs from amino groups on native proteins is presented. The approach relies on an amine-selective acylation reaction that occurs without modification of a preformed palladium(II)-aryl group. Once transferred onto a protein substrate, the palladium(II)-aryl group facilitates conjugation by undergoing reaction with a second, cysteine-containing protein. This operationally simple method is applicable to native, nonengineered enzymes as well as antibodies and is carried out in an aqueous setting and open to air. The resulting Pd-protein OACs are stable, storable reagents that retain biological activity and can be used to achieve protein-protein cross-coupling at nanomolar concentrations within hours.
Collapse
Affiliation(s)
- Heemal H Dhanjee
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ivan Buslov
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ian W Windsor
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L Pentelute
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
39
|
Kim J, Li BX, Huang RYC, Qiao JX, Ewing WR, MacMillan DWC. Site-Selective Functionalization of Methionine Residues via Photoredox Catalysis. J Am Chem Soc 2020; 142:21260-21266. [PMID: 33290649 DOI: 10.1021/jacs.0c09926] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bioconjugation technologies have revolutionized the practice of biology and medicine by allowing access to novel biomolecular scaffolds. New methods for residue-selective bioconjugation are highly sought to expand the toolbox for a variety of bioconjugation applications. Herein we report a site-selective methionine bioconjugation protocol that uses photoexcited lumiflavin to generate open-shell intermediates. This reduction-potential-gated strategy enables access to residues unavailable with traditional nucleophilicity-based conjugation methods. To demonstrate the versatility and robustness of this new protocol, we have modified various proteins and further utilized this functional handle to append diverse biological payloads.
Collapse
Affiliation(s)
- Junyong Kim
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Beryl X Li
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08542, United States
| | - Jennifer X Qiao
- Discovery Chemistry, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08542, United States
| | - William R Ewing
- Discovery Chemistry, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08542, United States
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
40
|
Tang KC, Raj M. One‐Step Azolation Strategy for Site‐ and Chemo‐Selective Labeling of Proteins with Mass‐Sensitive Probes. Angew Chem Int Ed Engl 2020; 60:1797-1805. [PMID: 33047860 PMCID: PMC10111340 DOI: 10.1002/anie.202007608] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Indexed: 11/09/2022]
Abstract
The chemical modification of proteins in a site-selective manner leads to many advances in various scientific fields. The major challenges with conventional N-terminal bioconjugation techniques are the lack of universal sequence compatibility and poor mass-detection sensitivity of the resulting bioconjugates. This approach efficiently analyzes proteolytic fragments and native proteins in a complex mixture. Multiple chemical steps are usually required for the site-selective synthesis of bioconjugates with enhanced mass-detection sensitivity. We present a single-step, versatile strategy for the selective modification of protein N-termini with mass boosters. The chemical tag enhances the peptide detection by multiple orders thus leading to the unambiguous analysis of the resulting bioconjugates. We demonstrate that tagging proteolytic fragments with mass sensitivity probes in a complex mixture improves the detection of resulting bioconjugates.
Collapse
Affiliation(s)
- Kuei C. Tang
- Present address: Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Monika Raj
- Present address: Department of Chemistry Emory University Atlanta GA 30322 USA
| |
Collapse
|
41
|
Martínez DG, Hüttelmaier S, Bertoldo JB. Unveiling Druggable Pockets by Site-Specific Protein Modification: Beyond Antibody-Drug Conjugates. Front Chem 2020; 8:586942. [PMID: 33195086 PMCID: PMC7609475 DOI: 10.3389/fchem.2020.586942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
|
42
|
Alvarez Dorta D, Deniaud D, Mével M, Gouin SG. Tyrosine Conjugation Methods for Protein Labelling. Chemistry 2020; 26:14257-14269. [DOI: 10.1002/chem.202001992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/09/2020] [Indexed: 12/23/2022]
Affiliation(s)
| | - David Deniaud
- CNRS, CEISAM UMR, 6230 Université de Nantes 44000 Nantes France
| | - Mathieu Mével
- CHU de Nantes, INSERM UMR 1089 Université de Nantes 44200 Nantes France
| | | |
Collapse
|
43
|
Lim D, Wen X, Seebeck FP. Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation. Chembiochem 2020; 21:3515-3520. [DOI: 10.1002/cbic.202000557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 12/15/2022]
Affiliation(s)
- David Lim
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Xiaojin Wen
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| |
Collapse
|
44
|
Chinn AJ, Hwang J, Kim B, Parish CA, Krska SW, Miller SJ. Application of High-Throughput Competition Experiments in the Development of Aspartate-Directed Site-Selective Modification of Tyrosine Residues in Peptides. J Org Chem 2020; 85:9424-9433. [PMID: 32614587 DOI: 10.1021/acs.joc.0c01147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein we report a Cu-catalyzed, site-selective functionalization of peptides that employs an aspartic acid (Asp) as a native directing motif, which directs the site of O-arylation at a proximal tyrosine (Tyr) residue. Through a series of competition studies conducted in high-throughput reaction arrays, effective conditions were identified that gave high selectivity for the proximal Tyr in Asp-directed Tyr modification. Good levels of site-selectivity were achieved in the O-arylation at a proximal Tyr residue in a number of cases, including a peptide-small molecule hybrid.
Collapse
Affiliation(s)
- Alex J Chinn
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Jaeyeon Hwang
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Byoungmoo Kim
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Craig A Parish
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Shane W Krska
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Scott J Miller
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| |
Collapse
|
45
|
Richardson MB, Gabriel KN, Garcia JA, Ashby SN, Dyer RP, Kim JK, Lau CJ, Hong J, Le Tourneau RJ, Sen S, Narel DL, Katz BB, Ziller JW, Majumdar S, Collins PG, Weiss GA. Pyrocinchonimides Conjugate to Amine Groups on Proteins via Imide Transfer. Bioconjug Chem 2020; 31:1449-1462. [PMID: 32302483 DOI: 10.1021/acs.bioconjchem.0c00143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Advances in bioconjugation, the ability to link biomolecules to each other, small molecules, surfaces, and more, can spur the development of advanced materials and therapeutics. We have discovered that pyrocinchonimide, the dimethylated analogue of maleimide, undergoes a surprising transformation with biomolecules. The reaction targets amines and involves an imide transfer, which has not been previously reported for bioconjugation purposes. Despite their similarity to maleimides, pyrocinchonimides do not react with free thiols. Though both lysine residues and the N-termini of proteins can receive the transferred imide, the reaction also exhibits a marked preference for certain amines that cannot solely be ascribed to solvent accessibility. This property is peculiar among amine-targeting reactions and can reduce combinatorial diversity when many available reactive amines are available, such as in the formation of antibody-drug conjugates. Unlike amides, the modification undergoes very slow reversion under high pH conditions. The reaction offers a thermodynamically controlled route to single or multiple modifications of proteins for a wide range of applications.
Collapse
Affiliation(s)
- Mark B Richardson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Kristin N Gabriel
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Joseph A Garcia
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Shareen N Ashby
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Rebekah P Dyer
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Joshua K Kim
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Calvin J Lau
- Department of Physics & Astronomy, University of California, Irvine, Irvine, California 92697, United States
| | - John Hong
- School of Medicine, University of California, Irvine, Irvine, California 92697, United States
| | - Ryan J Le Tourneau
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Sanjana Sen
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - David L Narel
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Benjamin B Katz
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Joseph W Ziller
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Philip G Collins
- Department of Physics & Astronomy, University of California, Irvine, Irvine, California 92697, United States
| | - Gregory A Weiss
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.,Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| |
Collapse
|
46
|
Doti N, Caporale A, Monti A, Sandomenico A, Selis F, Ruvo M. A recent update on the use of microbial transglutaminase for the generation of biotherapeutics. World J Microbiol Biotechnol 2020; 36:53. [PMID: 32172335 DOI: 10.1007/s11274-020-02829-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/07/2020] [Indexed: 01/12/2023]
Abstract
The recent scientific progresses on the use of enzyme-mediated reactions in organic, non-aqueous and aqueous media have significantly supported the growing demand of new biotechnological and/or pharmacological products. Today, a plethora of microbial enzymes, used as biocatalysts, are available. Among these, microbial transglutaminases (MTGs) are broadly used for their ability to catalyse the formation of an isopeptide bond between the γ-amide group of glutamines and the ε-amino group of lysine. Due to their promiscuity towards primary amine-containing substrates and the more stringent specificity for glutamine-containing peptide sequences, several combined approaches can be tailored for different settings, making MTGs very attractive catalysts for generating protein-protein and protein small molecule's conjugates. The present review offers a recent update on the modifications attainable by MTG-catalysed bioreactions as reported between 2014 and 2019. In particular, we present a detailed and comparative overview on the MTG-based methods for proteins and antibodies engineering, with a particular outlook on the synthesis of homogeneous antibody-drug conjugates.
Collapse
Affiliation(s)
- N Doti
- Institute of Biostructure and Bioimaging, CNR (IBB-CNR), Via Mezzocannone, 16, 80134, Naples, Italy.
| | - A Caporale
- Institute of Crystallography, CNR (IC-CNR), c/o Area Science Park s.s. 14 Km 163.5, Basovizza, 34149, Trieste, Italy
| | - Alessandra Monti
- Institute of Biostructure and Bioimaging, CNR (IBB-CNR), Via Mezzocannone, 16, 80134, Naples, Italy.,Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABIF), University L. Vanvitelli, Via Vivaldi, 43, 80100, Caserta, Italy
| | - A Sandomenico
- Institute of Biostructure and Bioimaging, CNR (IBB-CNR), Via Mezzocannone, 16, 80134, Naples, Italy
| | - Fabio Selis
- BioVIIIx R&D, Via B. Brin, 59C, 80142, Naples, Italy
| | - M Ruvo
- Institute of Biostructure and Bioimaging, CNR (IBB-CNR), Via Mezzocannone, 16, 80134, Naples, Italy.
| |
Collapse
|
47
|
Ros E, Bellido M, Verdaguer X, Ribas de Pouplana L, Riera A. Synthesis and Application of 3-Bromo-1,2,4,5-Tetrazine for Protein Labeling to Trigger Click-to-Release Biorthogonal Reactions. Bioconjug Chem 2020; 31:933-938. [DOI: 10.1021/acs.bioconjchem.0c00052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Enric Ros
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marina Bellido
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Xavier Verdaguer
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament de Quı́mica Inorgànica i Orgànica, Secció Orgànica. Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament de Quı́mica Inorgànica i Orgànica, Secció Orgànica. Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| |
Collapse
|
48
|
Veggiani G, Giabbai B, Semrau MS, Medagli B, Riccio V, Bajc G, Storici P, de Marco A. Comparative analysis of fusion tags used to functionalize recombinant antibodies. Protein Expr Purif 2020; 166:105505. [DOI: 10.1016/j.pep.2019.105505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 02/06/2023]
|
49
|
Reddy NC, Kumar M, Molla R, Rai V. Chemical methods for modification of proteins. Org Biomol Chem 2020; 18:4669-4691. [DOI: 10.1039/d0ob00857e] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The field of protein bioconjugation draws attention from stakeholders in chemistry, biology, and medicine. This review provides an overview of the present status, challenges, and opportunities for organic chemists.
Collapse
Affiliation(s)
- Neelesh C. Reddy
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Mohan Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Rajib Molla
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Vishal Rai
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| |
Collapse
|
50
|
He X, Li R, Xie M, Duan J, Tang Q, Shang Y. Copper-catalyzed cascade three-component azide–alkyne cycloaddition/condensation/transesterification: easy access to 3-triazolylcoumarins. NEW J CHEM 2020. [DOI: 10.1039/d0nj02100h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A novel and efficient strategy has been developed for the synthesis of 3-triazolylcoumarins in a one-pot, copper-catalyzed multicomponent reaction involving a cascade reaction of salicylaldehydes, ethyl 2-azidoacetate, and arylacetylenes.
Collapse
Affiliation(s)
- Xinwei He
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Ruxue Li
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Mengqing Xie
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Jiahui Duan
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Qiang Tang
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Yongjia Shang
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- Anhui Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base)
- College of Chemistry and Materials Science
- Anhui Normal University
| |
Collapse
|