1
|
Charalampidou A, Nehls T, Meyners C, Gandhesiri S, Pomplun S, Pentelute BL, Lermyte F, Hausch F. Automated Flow Peptide Synthesis Enables Engineering of Proteins with Stabilized Transient Binding Pockets. ACS CENTRAL SCIENCE 2024; 10:649-657. [PMID: 38559286 PMCID: PMC10979424 DOI: 10.1021/acscentsci.3c01283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 04/04/2024]
Abstract
Engineering at the amino acid level is key to enhancing the properties of existing proteins in a desired manner. So far, protein engineering has been dominated by genetic approaches, which have been extremely powerful but only allow for minimal variations beyond the canonical amino acids. Chemical peptide synthesis allows the unrestricted incorporation of a vast set of unnatural amino acids with much broader functionalities, including the incorporation of post-translational modifications or labels. Here we demonstrate the potential of chemical synthesis to generate proteins in a specific conformation, which would have been unattainable by recombinant protein expression. We use recently established rapid automated flow peptide synthesis combined with solid-phase late-stage modifications to rapidly generate a set of FK506-binding protein 51 constructs bearing defined intramolecular lactam bridges. This trapped an otherwise rarely populated transient pocket-as confirmed by crystal structures-which led to an up to 39-fold improved binding affinity for conformation-selective ligands and represents a unique system for the development of ligands for this rare conformation. Overall, our results show how rapid automated flow peptide synthesis can be applied to precision protein engineering.
Collapse
Affiliation(s)
- Anna Charalampidou
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Thomas Nehls
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Christian Meyners
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Satish Gandhesiri
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sebastian Pomplun
- Leiden
Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Frederik Lermyte
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
- Department
of Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
| | - Felix Hausch
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
- Department
of Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
2
|
Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
Collapse
Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| |
Collapse
|
3
|
Chabrol E, Stojko J, Nicolas A, Botzanowski T, Fould B, Antoine M, Cianférani S, Ferry G, Boutin JA. VHH characterization.Recombinant VHHs: Production, characterization and affinity. Anal Biochem 2019; 589:113491. [PMID: 31676284 DOI: 10.1016/j.ab.2019.113491] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/19/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
Abstract
Among the biological approaches to therapeutics, are the cells, such as CAR-T cells engineered or not, the antibodies armed or not, and the smaller protein scaffolds that can be modified to render them specific of other proteins, à la façon of antibodies. For several years, we explored ways to substitute antibodies by nanobodies (also known as VHHs), the smallest recognizing part of camelids' heavy-chain antibodies: production of those small proteins in host microorganisms, minute analyses, characterization, and qualification of their affinity towards designed targets. Here, we present three standard VHHs described in the literature: anti-albumin, anti-EGF receptor and anti-HER2, a typical cancer cell surface -associated protein. Because they differ slightly in global structure, they are good models to assess our body of analytical methodologies. The VHHs were expressed in several bacteria strains in order to identify and overcome the bottlenecks to obtain homogeneous preparations of this protein. A large panel of biophysical tools, ranging from spectroscopy to mass spectrometry, was here combined to assess VHH structural features and the impact of the disulfide bond. The routes are now ready to move to more complex VHHs raised against specific targets in numerous areas including oncology.
Collapse
Affiliation(s)
- Eric Chabrol
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Johann Stojko
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Alexandre Nicolas
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, 67000, Strasbourg, France
| | - Benjamin Fould
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Mathias Antoine
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, 67000, Strasbourg, France
| | - Gilles Ferry
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France.
| | - Jean A Boutin
- PEX Biotechnologies, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France; Institut de Recherches Internationales Servier, 50 rue Carnot, 92284, Suresnes Cedex, France.
| |
Collapse
|
4
|
Hartmann L, Botzanowski T, Galibert M, Jullian M, Chabrol E, Zeder-Lutz G, Kugler V, Stojko J, Strub JM, Ferry G, Frankiewicz L, Puget K, Wagner R, Cianférani S, Boutin JA. VHH characterization. Comparison of recombinant with chemically synthesized anti-HER2 VHH. Protein Sci 2019; 28:1865-1879. [PMID: 31423659 DOI: 10.1002/pro.3712] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 12/12/2022]
Abstract
In the continuous exploration of the VHH chemistry, biochemistry and therapeutic future use, we investigated two different production strategies of this small antibody-like protein, using an anti-HER2 VHH as a model. The total chemical synthesis of the 125 amino-acid peptide was performed with reasonable yield, even if optimization will be necessary to upgrade this kind of production. In parallel, we expressed the same sequence in two different hosts: Escherichia coli and Pichia pastoris. Both productions were successful and led to a fair amount of VHHs. The integrity and conformation of the VHH were characterized by complementary mass spectrometry approaches, while surface plasmon resonance experiments were used to assess the VHH recognition capacity and affinity toward its "antigen." Using this combination of orthogonal techniques, it was possible to show that the three VHHs-whether synthetic or recombinant ones-were properly and similarly folded and recognized the "antigen" HER2 with similar affinities, in the nanomolar range. This opens a route toward further exploration of modified VHH with unnatural amino acids and subsequently, VHH-drug conjugates.
Collapse
Affiliation(s)
- Lucie Hartmann
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
| | | | | | - Eric Chabrol
- PEX de Biotechnologie, Chimie et Biologie, Institut de REchercehs Servier, Croissy-sur-Seine, France
| | - Gabrielle Zeder-Lutz
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | - Valérie Kugler
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | - Johann Stojko
- PEX de Biotechnologie, Chimie et Biologie, Institut de REchercehs Servier, Croissy-sur-Seine, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
| | - Gilles Ferry
- PEX de Biotechnologie, Chimie et Biologie, Institut de REchercehs Servier, Croissy-sur-Seine, France
| | | | | | - Renaud Wagner
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
| | - Jean A Boutin
- Institut de Recherches Internationales Servier, Suresnes, France
| |
Collapse
|
5
|
Boutin JA, Tartar AL, van Dorsselaer A, Vaudry H. General lack of structural characterization of chemically synthesized long peptides. Protein Sci 2019; 28:857-867. [PMID: 30851143 PMCID: PMC6459998 DOI: 10.1002/pro.3601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 01/01/2023]
Abstract
Many peptide chemistry scientists have been reporting extremely interesting work on the basis of chemical peptides for which the only characterization was their purity, mass, and biological activity. It seems slightly overenthusiastic, as many of these structures should be thoroughly characterized first to demonstrate the uniqueness of the structure, as opposed to the uniqueness of the sequence. Among the peptides of identical sequences in the final chemical preparation, what amount of well-folded peptide supports the measured activity? The activity of a peptide preparation cannot prove the purity of the desired peptide. Therefore, greater care should be taken in characterizing peptides, particularly those coming from chemical synthesis. At a time when the pharmaceutical industry is changing its paradigm by moving substantially from small molecules to biologics to better serve patients' needs, it is important to understand the limitations of the descriptions of these products and to start to apply the same "good laboratory practices" to our peptide research. Here, we attempt to delineate how synthetic peptides are described and characterized and what will be needed to describe them in regards to how they are well-folded and homogeneous in their tertiary structure. Older studies were done when the tools were not yet discovered, but more recent publications are still lacking proper descriptions of these peptides. Modern tools of analysis are capable of segregating folded and unfolded peptides, even if the preparation is biologically active.
Collapse
Affiliation(s)
- Jean A. Boutin
- Institut de Recherches Internationales Servier50 rue Carnot, 92284, Suresnes‐CedexFrance
| | - André L. Tartar
- Faculté de Pharmacie 3rue du Professeur Laguesse, BP83 ‐ 59006, Lille‐CedexFrance
| | - Alain van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio‐Organique, Département des Sciences AnalytiquesInstitut Pluridisciplinaire Hubert CurienUMR 7178 (CNRS‐UdS), ECPM, 25 rue Becquerel, F67087, Strasbourg‐Cedex 2France
| | - Hubert Vaudry
- Plate‐Forme de Recherche en Imagerie Cellulaire de Normandie (PRIMACEN)Institut de Recherche et d'Innovation Biomédicales (IRIB), Université de Rouen76821, Mont‐Saint‐Aignan CedexFrance
| |
Collapse
|
6
|
Bacchi M, Fould B, Jullian M, Kreiter A, Maurras A, Nosjean O, Coursindel T, Puget K, Ferry G, Boutin JA. Screening ubiquitin specific protease activities using chemically synthesized ubiquitin and ubiquitinated peptides. Anal Biochem 2017; 519:57-70. [PMID: 27993553 DOI: 10.1016/j.ab.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022]
Abstract
Ubiquitin, a 76 amino acid protein, is a key component that contributes to cellular protein homeostasis. The specificity of this modification is due to a series of enzymes: ligases, attaching the ubiquitin to a lysine, and deubiquitinases, which remove it. More than a hundred of such proteins are implicated in the regulation of protein turnover. Their specificities are only partially understood. We chemically synthesized ubiquitin, attached it to lysines belonging to the protein sequences known to be ubiquitinated. We chose the model protein "murine double minute 2" (mdm2), a ubiquitin ligase, itself ubiquitinated and deubiquitinated. We folded the ubiquitinated peptides and checked their tridimensional conformation. We assessed the use of these substrates with a series of fifteen deubiquitinases to show the potentiality of such an enzymological technique. By manipulating the sequence of the peptide on which ubiquitin is attached, we were able to detect differences in the enzyme/substrate recognition, and to determine that these differences are deubiquitinase-dependent. This approach could be used to understand the substrate/protein relationship between the protagonists of this reaction. The methodology could be customized for a given substrate and used to advance our understanding of the key amino acids responsible for the deubiquitinase specificities.
Collapse
Affiliation(s)
- Marine Bacchi
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Benjamin Fould
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Magali Jullian
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Aude Kreiter
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Amélie Maurras
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Olivier Nosjean
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | | | - Karine Puget
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Gilles Ferry
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean A Boutin
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France.
| |
Collapse
|