1
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Sun D, Storek KM, Tegunov D, Yang Y, Arthur CP, Johnson M, Quinn JG, Liu W, Han G, Girgis HS, Alexander MK, Murchison AK, Shriver S, Tam C, Ijiri H, Inaba H, Sano T, Yanagida H, Nishikawa J, Heise CE, Fairbrother WJ, Tan MW, Skelton N, Sandoval W, Sellers BD, Ciferri C, Smith PA, Reid PC, Cunningham CN, Rutherford ST, Payandeh J. The discovery and structural basis of two distinct state-dependent inhibitors of BamA. Nat Commun 2024; 15:8718. [PMID: 39379361 PMCID: PMC11461620 DOI: 10.1038/s41467-024-52512-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/09/2024] [Indexed: 10/10/2024] Open
Abstract
BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of Gram-negative bacteria. Despite recent advances in our mechanistic and structural understanding of BamA, there are few potent and selective tool molecules that can bind to and modulate BamA activity. Here, we explored in vitro selection methods and different BamA/BAM protein formulations to discover peptide macrocycles that kill Escherichia coli by targeting extreme conformational states of BamA. Our studies show that Peptide Targeting BamA-1 (PTB1) targets an extracellular divalent cation-dependent binding site and locks BamA into a closed lateral gate conformation. By contrast, PTB2 targets a luminal binding site and traps BamA into an open lateral gate conformation. Our results will inform future antibiotic discovery efforts targeting BamA and provide a template to prospectively discover modulators of other dynamic integral membrane proteins.
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Affiliation(s)
- Dawei Sun
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Dimitry Tegunov
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Ying Yang
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Christopher P Arthur
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Matthew Johnson
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - John G Quinn
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Weijing Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Guanghui Han
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
- PTM Bio, Alameda, CA, USA
| | - Hany S Girgis
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Mary Kate Alexander
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Austin K Murchison
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Stephanie Shriver
- Department of BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Christine Tam
- Department of BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | | | - Christopher E Heise
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
- Septerna, South San Francisco, CA, USA
| | - Wayne J Fairbrother
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas Skelton
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin D Sellers
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
- Vilya, South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Peter A Smith
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
- Revagenix, San Mateo, CA, USA
| | | | - Christian N Cunningham
- Department of Peptide Therapeutics, Genentech Inc., South San Francisco, CA, USA.
- PeptiDream, Kawasaki, Japan.
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA.
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
- Exelixis, Alameda, CA, USA.
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2
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Cui Z, Ayva CE, Liew YJ, Guo Z, Mutschler R, Dreier B, Fiorito MM, Walden P, Howard CB, Ely F, Plückthun A, Pretorius C, Ungerer JPJ, Buckle AM, Alexandrov K. mRNA Display Pipeline for Protein Biosensor Construction. ACS Sens 2024; 9:2846-2857. [PMID: 38807313 PMCID: PMC11218749 DOI: 10.1021/acssensors.3c02471] [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: 11/20/2023] [Revised: 05/01/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Despite the significant potential of protein biosensors, their construction remains a trial-and-error process. The most obvious approach for addressing this is to utilize modular biosensor architectures where specificity-conferring modalities can be readily generated to recognize new targets. Toward this goal, we established a workflow that uses mRNA display-based selection of hyper-stable monobody domains for the target of choice or ribosome display to select equally stable DARPins. These binders were integrated into a two-component allosteric biosensor architecture based on a calmodulin-reporter chimera. This workflow was tested by developing biosensors for liver toxicity markers such as cytosolic aspartate aminotransferase, mitochondrial aspartate aminotransferase, and alanine aminotransferase 1. We demonstrate that our pipeline consistently produced >103 unique binders for each target within a week. Our analysis revealed that the affinity of the binders for their targets was not a direct predictor of the binder's performance in a biosensor context. The interactions between the binding domains and the reporter module affect the biosensor activity and the dynamic range. We conclude that following binding domain selection, the multiplexed biosensor assembly and prototyping appear to be the most promising approach for identifying biosensors with the desired properties.
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Affiliation(s)
- Zhenling Cui
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Cagla Ergun Ayva
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Yi Jin Liew
- CSIRO
Health & Biosecurity, Westmead, New South Wales 2145,Australia
| | - Zhong Guo
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Roxane Mutschler
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Birgit Dreier
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Maria M Fiorito
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Patricia Walden
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Christopher B Howard
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Andreas Plückthun
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Carel Pretorius
- Department
of Chemical Pathology, Pathology Queensland, Brisbane, Queensland 4006, Australia
- Faculty
of Health and Behavioural Sciences, The
University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jacobus PJ Ungerer
- Department
of Chemical Pathology, Pathology Queensland, Brisbane, Queensland 4006, Australia
- Faculty
of Health and Behavioural Sciences, The
University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Kirill Alexandrov
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
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3
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Vulpetti A, Rondeau JM, Bellance MH, Blank J, Boesch R, Boettcher A, Bornancin F, Buhr S, Connor LE, Dumelin CE, Esser O, Hediger M, Hintermann S, Hommel U, Koch E, Lapointe G, Leder L, Lehmann S, Lehr P, Meier P, Muller L, Ostermeier D, Ramage P, Schiebel-Haddad S, Smith AB, Stojanovic A, Velcicky J, Yamamoto R, Hurth K. Ligandability Assessment of IL-1β by Integrated Hit Identification Approaches. J Med Chem 2024; 67:8141-8160. [PMID: 38728572 DOI: 10.1021/acs.jmedchem.4c00240] [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: 05/12/2024]
Abstract
Human interleukin-1β (IL-1β) is a pro-inflammatory cytokine that plays a critical role in the regulation of the immune response and the development of various inflammatory diseases. In this publication, we disclose our efforts toward the discovery of IL-1β binders that interfere with IL-1β signaling. To this end, several technologies were used in parallel, including fragment-based screening (FBS), DNA-encoded library (DEL) technology, peptide discovery platform (PDP), and virtual screening. The utilization of distinct technologies resulted in the identification of new chemical entities exploiting three different sites on IL-1β, all of them also inhibiting the interaction with the IL-1R1 receptor. Moreover, we identified lysine 103 of IL-1β as a target residue suitable for the development of covalent, low-molecular-weight IL-1β antagonists.
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Affiliation(s)
- Anna Vulpetti
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | | | | | - Jutta Blank
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | - Ralf Boesch
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | | | | | - Sylvia Buhr
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | | | | | - Oliver Esser
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | | | | | - Ulrich Hommel
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | - Elke Koch
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | | | - Lukas Leder
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | - Sylvie Lehmann
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | - Philipp Lehr
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | - Peter Meier
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | - Lionel Muller
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | | | - Paul Ramage
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | | | | | | | - Juraj Velcicky
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
| | - Rina Yamamoto
- Biomedical Research, Novartis, CH-4002 Basel, Switzerland
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4
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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5
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Cremosnik G, Mesrouze Y, Zueger P, Furkert D, Grandjean F, Argoti D, Mermet-Meillon F, Bauer MR, Brittain S, Rogemoser P, Yang W, Giovannoni J, McGregor L, Tang J, Knapp M, Holzinger S, Buhr S, Muller L, Leder L, Xie L, Fernandez C, Nieto-Oberhuber C, Chène P, Galli GG, Sesterhenn F. mRNA Display Identifies Potent, Paralog-Selective Peptidic Ligands for ARID1B. ACS Chem Biol 2024; 19:1142-1150. [PMID: 38655884 PMCID: PMC11106749 DOI: 10.1021/acschembio.4c00083] [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: 02/02/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The ARID1A and ARID1B subunits are mutually exclusive components of the BAF variant of SWI/SNF chromatin remodeling complexes. Loss of function mutations in ARID1A are frequently observed in various cancers, resulting in a dependency on the paralog ARID1B for cancer cell proliferation. However, ARID1B has never been targeted directly, and the high degree of sequence similarity to ARID1A poses a challenge for the development of selective binders. In this study, we used mRNA display to identify peptidic ligands that bind with nanomolar affinities to ARID1B and showed high selectivity over ARID1A. Using orthogonal biochemical, biophysical, and chemical biology tools, we demonstrate that the peptides engage two different binding pockets, one of which directly involves an ARID1B-exclusive cysteine that could allow covalent targeting by small molecules. Our findings impart the first evidence of the ligandability of ARID1B, provide valuable tools for drug discovery, and suggest opportunities for the development of selective molecules to exploit the synthetic lethal relationship between ARID1A and ARID1B in cancer.
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Affiliation(s)
- Gregor
S. Cremosnik
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - Yannick Mesrouze
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Patrik Zueger
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - David Furkert
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Frédéric Grandjean
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Dayana Argoti
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | | | - Matthias R. Bauer
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - Scott Brittain
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Phuong Rogemoser
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Winnie Yang
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jerome Giovannoni
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lynn McGregor
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jenny Tang
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | - Mark Knapp
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | - Sandra Holzinger
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Sylvia Buhr
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lionel Muller
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lukas Leder
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lili Xie
- Discovery
Sciences, Novartis Biomedical Research, Emeryville, California 94608, United States
| | - Cesar Fernandez
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | | | - Patrick Chène
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Giorgio G. Galli
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Fabian Sesterhenn
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
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6
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Lin F, Clift R, Ehara T, Yanagida H, Horton S, Noncovich A, Guest M, Kim D, Salvador K, Richardson S, Miller T, Han G, Bhat A, Song K, Li G. Peptide Binder to Glypican-3 as a Theranostic Agent for Hepatocellular Carcinoma. J Nucl Med 2024; 65:586-592. [PMID: 38423788 DOI: 10.2967/jnumed.123.266766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Glypican-3 (GPC3) is a membrane-associated glycoprotein that is significantly upregulated in hepatocellular carcinomas (HCC) with minimal to no expression in normal tissues. The differential expression of GPC3 between tumor and normal tissues provides an opportunity for targeted radiopharmaceutical therapy to treat HCC, a leading cause of cancer-related deaths worldwide. Methods: DOTA-RYZ-GPC3 (RAYZ-8009) comprises a novel macrocyclic peptide binder to GPC3, a linker, and a chelator that can be complexed with different radioisotopes. The binding affinity was determined by surface plasma resonance and radioligand binding assays. Target-mediated cellular internalization was radiometrically measured at multiple time points. In vivo biodistribution, monotherapy, and combination treatments with 177Lu or 225Ac were performed on HCC xenografts. Results: RAYZ-8009 showed high binding affinity to GPC3 protein of human, mouse, canine, and cynomolgus monkey origins and no binding to other glypican family members. Potent cellular binding was confirmed in GPC3-positive HepG2 cells and was not affected by isotope switching. RAYZ-8009 achieved efficient internalization on binding to HepG2 cells. Biodistribution study of 177Lu-RAYZ-8009 showed sustained tumor uptake and fast renal clearance, with minimal or no uptake in other normal tissues. Tumor-specific uptake was also demonstrated in orthotopic HCC tumors, with no uptake in surrounding liver tissue. Therapeutically, significant and durable tumor regression and survival benefit were achieved with 177Lu- and 225Ac-labeled RAYZ-8009, as single agents and in combination with lenvatinib, in GPC3-positive HCC xenografts. Conclusion: Preclinical in vitro and in vivo data demonstrate the potential of RAYZ-8009 as a theranostic agent for the treatment of patients with GPC3-positive HCC.
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Affiliation(s)
| | | | | | | | | | | | - Matt Guest
- RayzeBio, Inc., San Diego, California; and
| | - Daniel Kim
- RayzeBio, Inc., San Diego, California; and
| | | | | | | | | | | | | | - Gary Li
- RayzeBio, Inc., San Diego, California; and
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7
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Qiao JX, Witmer MR, Lee V, Wang TC, Reid PC, Arioka Y, Farr G, Hill-Drzewi M, Schweizer L, Yamniuk A, Cheng L, Abramczyk B, Corbett M, Calambur D, Szapiel N, Ryseck R, Ponath P, Poss MA, Carter P. Exploration of macrocyclic peptide binders to the extracellular CRD domain of human receptor tyrosine kinase-like orphan receptor 1 (ROR1). Bioorg Med Chem Lett 2024; 98:129589. [PMID: 38097140 DOI: 10.1016/j.bmcl.2023.129589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/03/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Elevated levels of receptor tyrosine kinase-like orphan receptor 1 (RORl) expression are observed in multiple hematological and solid tumors, but not in most of the healthy adult tissues, identifying ROR1 as an attractive target for tumor-specific therapy. Herein we will describe the discovery of macrocyclic peptides as binders of the extracellular Cysteine-Rich Domain (CRD) of human ROR1 via mRNA in vitro selection technology using the PDPS platform, followed by exploration of sidechain SAR of parent macrocycle peptides, fluorescently labeled analogs, and a Peptide Drug Conjugate (PDC). The parent macrocyclic peptides represented by Compound 1 and Compound 14 displayed nanomolar cell-based binding to ROR1 and relatively good internalization in 786-O and MDA-MB-231 tumor cell lines. However, these peptides were not observed to induce apoptosis in Mia PaCa-2 cells, a model pancreatic tumor cell line with a relatively low level of cell surface expression of ROR1.
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Affiliation(s)
| | - Mark R Witmer
- Molecular Discovery Technology, Princeton, NJ 08543, United States
| | - Ving Lee
- Discovery Chemistry, Princeton, NJ 08543, United States
| | - Tammy C Wang
- Discovery Chemistry, Princeton, NJ 08543, United States
| | - Patrick C Reid
- PeptiDream 3-25-23 Tonomachi, Kawasaki-Ku, Kawasaki-Shi, Kanagawa 210-0821, Japan
| | - Yuki Arioka
- PeptiDream 3-25-23 Tonomachi, Kawasaki-Ku, Kawasaki-Shi, Kanagawa 210-0821, Japan
| | - Glen Farr
- Leads Discovery & Optimization, Princeton, NJ 08543, United States
| | | | - Liang Schweizer
- Leads Discovery & Optimization, Princeton, NJ 08543, United States
| | - Aaron Yamniuk
- Molecular Discovery Technology, Princeton, NJ 08543, United States
| | - Lin Cheng
- Molecular Discovery Technology, Princeton, NJ 08543, United States
| | - Bozena Abramczyk
- Molecular Discovery Technology, Princeton, NJ 08543, United States
| | - Martin Corbett
- Molecular Discovery Technology, Princeton, NJ 08543, United States
| | - Deepa Calambur
- Molecular Discovery Technology, Princeton, NJ 08543, United States
| | - Nicolas Szapiel
- Molecular Discovery Technology, Princeton, NJ 08543, United States
| | - Rolf Ryseck
- Molecular Discovery Technology, Princeton, NJ 08543, United States
| | - Paul Ponath
- Discovery Biology, Bristol-Myers Squibb, Princeton, NJ 08543, United States
| | | | - Percy Carter
- Discovery Chemistry, Princeton, NJ 08543, United States
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8
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Thomas B, Chockalingam K, Chen Z. Methods for Engineering Binders to Multi-Pass Membrane Proteins. Bioengineering (Basel) 2023; 10:1351. [PMID: 38135942 PMCID: PMC10741020 DOI: 10.3390/bioengineering10121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Numerous potential drug targets, including G-protein-coupled receptors and ion channel proteins, reside on the cell surface as multi-pass membrane proteins. Unfortunately, despite advances in engineering technologies, engineering biologics against multi-pass membrane proteins remains a formidable task. In this review, we focus on the different methods used to prepare/present multi-pass transmembrane proteins for engineering target-specific biologics such as antibodies, nanobodies and synthetic scaffold proteins. The engineered biologics exhibit high specificity and affinity, and have broad applications as therapeutics, probes for cell staining and chaperones for promoting protein crystallization. We primarily cover publications on this topic from the past 10 years, with a focus on the different formats of multi-pass transmembrane proteins. Finally, the remaining challenges facing this field and new technologies developed to overcome a number of obstacles are discussed.
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Affiliation(s)
- Benjamin Thomas
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77845, USA;
| | - Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA;
| | - Zhilei Chen
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77845, USA;
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA;
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9
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Yoshida S, Sako Y, Nikaido E, Ueda T, Kozono I, Ichihashi Y, Nakahashi A, Onishi M, Yamatsu Y, Kato T, Nishikawa J, Tachibana Y. Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of β-Herpesvirus Proteases. ACS Med Chem Lett 2023; 14:1558-1566. [PMID: 37974946 PMCID: PMC10641906 DOI: 10.1021/acsmedchemlett.3c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
Viral proteases, the key enzymes that regulate viral replication and assembly, are promising targets for antiviral drug discovery. Herpesvirus proteases are enzymes with no crystallographically confirmed noncovalent active-site binders, owing to their shallow and polar substrate-binding pockets. Here, we applied our previously reported "Peptide-to-Small Molecule" strategy to generate novel inhibitors of β-herpesvirus proteases. Rapid selection with a display technology was used to identify macrocyclic peptide 1 bound to the active site of human cytomegalovirus protease (HCMVPro) with high affinity, and pharmacophore queries were defined based on the results of subsequent intermolecular interaction analyses. Membrane-permeable small molecule 19, designed de novo according to this hypothesis, exhibited enzyme inhibitory activity (IC50 = 10-6 to 10-7 M) against β-herpesvirus proteases, and the design concept was proved by X-ray cocrystal analysis.
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Affiliation(s)
- Shuhei Yoshida
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Sako
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Eiji Nikaido
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Taichi Ueda
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Iori Kozono
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Ichihashi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsufumi Nakahashi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Motoyasu Onishi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yukiko Yamatsu
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Teruhisa Kato
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Junichi Nishikawa
- PeptiDream
Inc., 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Yuki Tachibana
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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10
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Liu M, Morewood R, Yoshisada R, Pascha MN, Hopstaken AJP, Tarcoveanu E, Poole DA, de Haan CAM, Nitsche C, Jongkees SAK. Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis. Chem Sci 2023; 14:10561-10569. [PMID: 37799990 PMCID: PMC10548512 DOI: 10.1039/d3sc03117a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023] Open
Abstract
Peptide display technologies are a powerful method for discovery of new bioactive sequences, but linear sequences are often very unstable in a biological setting. Macrocyclisation of such peptides is beneficial for target affinity, selectivity, stability, and cell permeability. However, macrocyclisation of a linear hit is unreliable and requires extensive structural knowledge. Genetically encoding macrocyclisation during the discovery process is a better approach, and so there is a need for diverse cyclisation options that can be deployed in the context of peptide display techniques such as mRNA display. In this work we show that meta-cyanopyridylalanine (mCNP) can be ribosomally incorporated into peptides, forming a macrocycle in a spontaneous and selective reaction with an N-terminal cysteine generated from bypassing the initiation codon in translation. This reactive amino acid can also be easily incorporated into peptides during standard Fmoc solid phase peptide synthesis, which can otherwise be a bottleneck in transferring from peptide discovery to peptide testing and application. We demonstrate the potential of this new method by discovery of macrocyclic peptides targeting influenza haemagglutinin, and molecular dynamics simulation indicates the mCNP cross-link stabilises a beta sheet structure in a representative of the most abundant cluster of active hits. Cyclisation by mCNP is also shown to be compatible with thioether macrocyclisation at a second cysteine to form bicycles of different architectures, provided that cysteine placement reinforces selectivity, with this bicyclisation happening spontaneously and in a controlled manner during peptide translation. Our new approach generates macrocycles with a more rigid cross-link and with better control of regiochemistry when additional cysteines are present, opening these up for further exploitation in chemical modification of in vitro translated peptides, and so is a valuable addition to the peptide discovery toolbox.
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Affiliation(s)
- Minglong Liu
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Richard Morewood
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Mirte N Pascha
- Section Virology, Division Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University Yalelaan 1 3584 CL Utrecht The Netherlands
| | - Antonius J P Hopstaken
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Eliza Tarcoveanu
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - David A Poole
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University Yalelaan 1 3584 CL Utrecht The Netherlands
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Seino A K Jongkees
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
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11
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Zeng Y, Woolley M, Chockalingam K, Thomas B, Arora S, Hook M, Chen Z. Click display: a rapid and efficient in vitro protein display method for directed evolution. Nucleic Acids Res 2023; 51:e89. [PMID: 37548398 PMCID: PMC10484664 DOI: 10.1093/nar/gkad643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023] Open
Abstract
We describe a novel method for in vitro protein display-click display-that does not depend on maintaining RNA integrity during biopanning and yields covalently linked protein-cDNA complexes from double-stranded input DNA within 2 h. The display is achieved in a one-pot format encompassing transcription, translation and reverse transcription reactions in series. Stable linkage between proteins and the encoding cDNA is mediated by a modified DNA linker-ML-generated via a click chemistry reaction between a puromycin-containing oligo and a cDNA synthesis primer. Biopanning of a click-displayed mock library coupled with next-generation sequencing analysis revealed >600-fold enrichment of target binders within a single round of panning. A synthetic library of Designed Ankyrin Repeat Proteins (DARPins) with ∼1012 individual members was generated using click display in a 25-μl reaction and six rounds of library panning against a model protein yielded a panel of nanomolar binders. This study establishes click display as a powerful tool for protein binder discovery/engineering and provides a convenient platform for in vitro biopanning selection even in RNase-rich environments such as on whole cells.
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Affiliation(s)
- Yu Zeng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Michael Woolley
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Benjamin Thomas
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, Houston, TX 77030, USA
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, Houston, TX 77030, USA
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12
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Umemoto S, Kondo T, Fujino T, Hayashi G, Murakami H. Large-scale analysis of mRNA sequences localized near the start and amber codons and their impact on the diversity of mRNA display libraries. Nucleic Acids Res 2023; 51:7465-7479. [PMID: 37395404 PMCID: PMC10415131 DOI: 10.1093/nar/gkad555] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 06/14/2023] [Accepted: 06/18/2023] [Indexed: 07/04/2023] Open
Abstract
Extremely diverse libraries are essential for effectively selecting functional peptides or proteins, and mRNA display technology is a powerful tool for generating such libraries with over 1012-1013 diversity. Particularly, the protein-puromycin linker (PuL)/mRNA complex formation yield is determining for preparing the libraries. However, how mRNA sequences affect the complex formation yield remains unclear. To study the effects of N-terminal and C-terminal coding sequences on the complex formation yield, puromycin-attached mRNAs containing three random codons after the start codon (32768 sequences) or seven random bases next to the amber codon (6480 sequences) were translated. Enrichment scores were calculated by dividing the appearance rate of every sequence in protein-PuL/mRNA complexes by that in total mRNAs. The wide range of enrichment scores (0.09-2.10 for N-terminal and 0.30-4.23 for C-terminal coding sequences) indicated that the N-terminal and C-terminal coding sequences strongly affected the complex formation yield. Using C-terminal GGC-CGA-UAG-U sequences, which resulted in the highest enrichment scores, we constructed highly diverse libraries of monobodies and macrocyclic peptides. The present study provides insights into how mRNA sequences affect the protein/mRNA complex formation yield and will accelerate the identification of functional peptides and proteins involved in various biological processes and having therapeutic applications.
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Affiliation(s)
- Shun Umemoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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13
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Targeted degradation via direct 26S proteasome recruitment. Nat Chem Biol 2023; 19:55-63. [PMID: 36577875 PMCID: PMC9797404 DOI: 10.1038/s41589-022-01218-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/25/2022] [Indexed: 12/29/2022]
Abstract
Engineered destruction of target proteins by recruitment to the cell's degradation machinery has emerged as a promising strategy in drug discovery. The majority of molecules that facilitate targeted degradation do so via a select number of ubiquitin ligases, restricting this therapeutic approach to tissue types that express the requisite ligase. Here, we describe a new strategy of targeted protein degradation through direct substrate recruitment to the 26S proteasome. The proteolytic complex is essential and abundantly expressed in all cells; however, proteasomal ligands remain scarce. We identify potent peptidic macrocycles that bind directly to the 26S proteasome subunit PSMD2, with a 2.5-Å-resolution cryo-electron microscopy complex structure revealing a binding site near the 26S pore. Conjugation of this macrocycle to a potent BRD4 ligand enabled generation of chimeric molecules that effectively degrade BRD4 in cells, thus demonstrating that degradation via direct proteasomal recruitment is a viable strategy for targeted protein degradation.
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14
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Yoshida S, Uehara S, Kondo N, Takahashi Y, Yamamoto S, Kameda A, Kawagoe S, Inoue N, Yamada M, Yoshimura N, Tachibana Y. Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides. J Med Chem 2022; 65:10655-10673. [PMID: 35904556 DOI: 10.1021/acs.jmedchem.2c00919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent technological innovations have led to the development of methods for the rapid identification of high-affinity macrocyclic peptides for a wide range of targets; however, it is still challenging to achieve the desired activity and membrane permeability at the same time. Here, we propose a novel small molecule lead discovery strategy, ″Peptide-to-Small Molecule″, which is a combination of rapid identification of high-affinity macrocyclic peptides via peptide display screening followed by pharmacophore-guided de novo design of small molecules, and demonstrate the applicability using nicotinamide N-methyltransferase (NNMT) as a target. Affinity selection by peptide display technology identified macrocyclic peptide 1 that exhibited good enzymatic inhibitory activity but no cell-based activity. Thereafter, a peptide pharmacophore-guided de novo design and further structure-based optimization resulted in highly potent and cell-active small molecule 14 (cell-free IC50 = 0.0011 μM, cell-based IC50 = 0.40 μM), indicating that this strategy could be a new option for drug discovery.
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Affiliation(s)
- Shuhei Yoshida
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shota Uehara
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Noriyasu Kondo
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yu Takahashi
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shiho Yamamoto
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsushi Kameda
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Soichiro Kawagoe
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Naoko Inoue
- PeptiDream Inc. 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Masami Yamada
- PeptiDream Inc. 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Norito Yoshimura
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yuki Tachibana
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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15
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for Expanding Encoded Chemical Diversification and Improving Hit Enrichment in mRNA-Displayed Peptide Libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA-encoded small-molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide-tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the 'drug-likeness' of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA-encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA-encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA-displayed peptide library to allow a more diversity-oriented approach to library modification. Finally, we outline alternate approaches for enriching target-binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA-display based approach could be used to discover new 'drug-like' modified small peptides.
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Affiliation(s)
- Paddy R. A. Melsen
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Seino A. K. Jongkees
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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16
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Kondo T, Matsuoka K, Umemoto S, Fujino T, Hayashi G, Iwatani Y, Murakami H. Monobodies with potent neutralizing activity against SARS-CoV-2 Delta and other variants of concern. Life Sci Alliance 2022; 5:5/6/e202101322. [PMID: 35256514 PMCID: PMC8906176 DOI: 10.26508/lsa.202101322] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/24/2022] Open
Abstract
Neutralizing antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are useful for patients' treatment of the coronavirus disease 2019 (COVID-19). We report here affinity maturation of monobodies against the SARS-CoV-2 spike protein and their neutralizing activity against SARS-CoV-2 B.1.1 (Pango v.3.1.14) as well as four variants of concern. We selected matured monobodies from libraries with multi-site saturation mutagenesis on the recognition loops through in vitro selection. One clone, the C4-AM2 monobody, showed extremely high affinity (K D < 0.01 nM) against the receptor-binding domain of the SARS-CoV-2 B.1.1, even in monomer form. Furthermore, the C4-AM2 monobody efficiently neutralized the SARS-CoV-2 B.1.1 (IC 50 = 46 pM, 0.62 ng/ml), and the Alpha (IC 50 = 77 pM, 1.0 ng/ml), Beta (IC 50 = 0.54 nM, 7.2 ng/ml), Gamma (IC 50 = 0.55 nM, 7.4 ng/ml), and Delta (IC 50 = 0.59 nM, 8.0 ng/ml) variants. The obtained monobodies would be useful as neutralizing proteins against current and potentially hazardous future SARS-CoV-2 variants.
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Affiliation(s)
- Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Kazuhiro Matsuoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Shun Umemoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Japan Science and Technology Agency (JST), PRESTO, Kawaguchi, Japan
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan .,Division of Basic Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
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17
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Schneider AFL, Kallen J, Ottl J, Reid PC, Ripoche S, Ruetz S, Stachyra TM, Hintermann S, Dumelin CE, Hackenberger CPR, Marzinzik AL. Discovery, X-ray structure and CPP-conjugation enabled uptake of p53/MDM2 macrocyclic peptide inhibitors. RSC Chem Biol 2021; 2:1661-1668. [PMID: 34977581 PMCID: PMC8637822 DOI: 10.1039/d1cb00056j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/21/2021] [Indexed: 12/16/2022] Open
Abstract
Mouse double minute 2 homolog (MDM2, Hdm2) is an important negative regulator of the tumor suppressor p53. Using a mRNA based display technique to screen a library of >1012 in vitro-translated cyclic peptides, we have identified a macrocyclic ligand that shows picomolar potency on MDM2. X-Ray crystallography reveals a novel binding mode utilizing a unique pharmacophore to occupy the Phe/Trp/Leu pockets on MDM2. Conjugation of a cyclic cell-penetrating peptide (cCPP) to the initially non cell-permeable ligand enables cellular uptake and a pharmacodynamic response in SJSA-1 cells. The demonstrated enhanced intracellular availability of cyclic peptides that are identified by a display technology exemplifies a process for the application of intracellular tools for drug discovery projects.
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Affiliation(s)
- Anselm F L Schneider
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10 Berlin 13125 Germany
| | - Joerg Kallen
- Novartis Institutes for BioMedical Research, Novartis Campus Basel CH-4056 Switzerland
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Novartis Campus Basel CH-4056 Switzerland
| | - Patrick C Reid
- PeptiDream, 3-25-23 Tonomachi Kawasaki-Ku Kanagawa 210-0821 Japan
| | - Sebastien Ripoche
- Novartis Institutes for BioMedical Research, Novartis Campus Basel CH-4056 Switzerland
| | - Stephan Ruetz
- Novartis Institutes for BioMedical Research, Novartis Campus Basel CH-4056 Switzerland
| | | | - Samuel Hintermann
- Novartis Institutes for BioMedical Research, Novartis Campus Basel CH-4056 Switzerland
| | - Christoph E Dumelin
- Novartis Institutes for BioMedical Research, Novartis Campus Basel CH-4056 Switzerland
| | - Christian P R Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10 Berlin 13125 Germany .,Humboldt Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2 Berlin 12489 Germany
| | - Andreas L Marzinzik
- Novartis Institutes for BioMedical Research, Novartis Campus Basel CH-4056 Switzerland
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18
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De novo peptide grafting to a self-assembling nanocapsule yields a hepatocyte growth factor receptor agonist. iScience 2021; 24:103302. [PMID: 34805784 PMCID: PMC8581506 DOI: 10.1016/j.isci.2021.103302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/29/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
Lasso-grafting (LG) technology is a method for generating de novo biologics (neobiologics) by genetically implanting macrocyclic peptide pharmacophores, which are selected in vitro against a protein of interest, into loops of arbitrary protein scaffolds. In this study, we have generated a neo-capsid that potently binds the hepatocyte growth factor receptor MET by LG of anti-MET peptide pharmacophores into a circularly permuted variant of Aquifex aeolicus lumazine synthase (AaLS), a self-assembling protein nanocapsule. By virtue of displaying multiple-pharmacophores on its surface, the neo-capsid can induce dimerization (or multimerization) of MET, resulting in phosphorylation and endosomal internalization of the MET-capsid complex. This work demonstrates the potential of the LG technology as a synthetic biology approach for generating capsid-based neobiologics capable of activating signaling receptors. Lasso-grafting enabled multiple display of peptide pharmacophore on protein capsid Engineered capsids induced dimerization of MET resulting in phosphorylation Engineered capsids were internalized into endosome via MET phosphorylation
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19
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Wang H, Wang Y, Yuan Z, Wang Y, Li X, Song P, Lu F, Liu Y. Insight into the cross-linking preferences and characteristics of the transglutaminase from Bacillus subtilis by in vitro RNA display. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Brousseau ME, Clairmont KB, Spraggon G, Flyer AN, Golosov AA, Grosche P, Amin J, Andre J, Burdick D, Caplan S, Chen G, Chopra R, Ames L, Dubiel D, Fan L, Gattlen R, Kelly-Sullivan D, Koch AW, Lewis I, Li J, Liu E, Lubicka D, Marzinzik A, Nakajima K, Nettleton D, Ottl J, Pan M, Patel T, Perry L, Pickett S, Poirier J, Reid PC, Pelle X, Seepersaud M, Subramanian V, Vera V, Xu M, Yang L, Yang Q, Yu J, Zhu G, Monovich LG. Identification of a PCSK9-LDLR disruptor peptide with in vivo function. Cell Chem Biol 2021; 29:249-258.e5. [PMID: 34547225 DOI: 10.1016/j.chembiol.2021.08.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/13/2021] [Accepted: 08/27/2021] [Indexed: 12/20/2022]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma low-density lipoprotein cholesterol (LDL-C) levels by promoting hepatic LDL receptor (LDLR) degradation. Therapeutic antibodies that disrupt PCSK9-LDLR binding reduce LDL-C concentrations and cardiovascular disease risk. The epidermal growth factor precursor homology domain A (EGF-A) of the LDLR serves as a primary contact with PCSK9 via a flat interface, presenting a challenge for identifying small molecule PCSK9-LDLR disruptors. We employ an affinity-based screen of 1013in vitro-translated macrocyclic peptides to identify high-affinity PCSK9 ligands that utilize a unique, induced-fit pocket and partially disrupt the PCSK9-LDLR interaction. Structure-based design led to molecules with enhanced function and pharmacokinetic properties (e.g., 13PCSK9i). In mice, 13PCSK9i reduces plasma cholesterol levels and increases hepatic LDLR density in a dose-dependent manner. 13PCSK9i functions by a unique, allosteric mechanism and is the smallest molecule identified to date with in vivo PCSK9-LDLR disruptor function.
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Affiliation(s)
- Margaret E Brousseau
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Kevin B Clairmont
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Alec N Flyer
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Andrei A Golosov
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Philipp Grosche
- Novartis Institutes for BioMedical Research, Fabrikstrasse 2, Novartis Campus, 4056 Basel, Switzerland
| | - Jakal Amin
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jerome Andre
- Novartis Institutes for BioMedical Research, Fabrikstrasse 2, Novartis Campus, 4056 Basel, Switzerland
| | - Debra Burdick
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Shari Caplan
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Guanjing Chen
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Raj Chopra
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lisa Ames
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Diana Dubiel
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Li Fan
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Raphael Gattlen
- Novartis Institutes for BioMedical Research, Fabrikstrasse 2, Novartis Campus, 4056 Basel, Switzerland
| | - Dawn Kelly-Sullivan
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Alexander W Koch
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ian Lewis
- Novartis Institutes for BioMedical Research, Fabrikstrasse 2, Novartis Campus, 4056 Basel, Switzerland
| | - Jingzhou Li
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Eugene Liu
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Danuta Lubicka
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Andreas Marzinzik
- Novartis Institutes for BioMedical Research, Fabrikstrasse 2, Novartis Campus, 4056 Basel, Switzerland
| | - Katsumasa Nakajima
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David Nettleton
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Fabrikstrasse 2, Novartis Campus, 4056 Basel, Switzerland
| | - Meihui Pan
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Tajesh Patel
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lauren Perry
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Stephanie Pickett
- Novartis Institutes for BioMedical Research, Fabrikstrasse 2, Novartis Campus, 4056 Basel, Switzerland
| | - Jennifer Poirier
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Patrick C Reid
- PeptiDream, Inc., KOL Building, Room 405, 4-6-1 Komaba, Meguro-Ku, Tokyo 153-8904, Japan
| | - Xavier Pelle
- Novartis Institutes for BioMedical Research, Fabrikstrasse 2, Novartis Campus, 4056 Basel, Switzerland
| | - Mohindra Seepersaud
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Vanitha Subramanian
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Victoria Vera
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mei Xu
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lihua Yang
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qing Yang
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jinghua Yu
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Guoming Zhu
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lauren G Monovich
- Novartis Institutes for BioMedical Research, 22 Windsor Street and 181 Massachusetts Avenue, Cambridge, MA 02139, USA
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21
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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22
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Kondo T, Eguchi M, Tsuzuki N, Murata N, Fujino T, Hayashi G, Murakami H. Construction of a Highly Diverse mRNA Library for in vitro Selection of Monobodies. Bio Protoc 2021; 11:e4125. [PMID: 34541043 DOI: 10.21769/bioprotoc.4125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/07/2021] [Accepted: 05/16/2021] [Indexed: 11/02/2022] Open
Abstract
Recently, we developed transcription/translation coupled with the association of puromycin linker (TRAP) display as a quick in vitro selection method to obtain antibody-like proteins. For the in vitro selection, it is important to prepare mRNA libraries among which the diversity is high. Here, we describe a method for the preparation of monobody mRNA libraries with greater than 1013 theoretical diversity. First, we synthesized two long single-stranded DNAs that corresponded to fragments of monobody DNA, with random codons in the BC and FG loops. These oligonucleotides were ligated by T4 DNA ligase with the support of guide oligonucleotides containing 3' ends that were protected by a modification. After amplifying the product DNAs by PCR, one end of each DNA fragment was digested with the type II restriction enzyme BsaI, and the resulting DNA fragments were ligated using T4 DNA ligase. After amplification of the DNA product, mRNAs were synthesized by T7 RNA polymerase. This method is simple and could be used for the preparation of mRNA libraries for various antibody-like proteins. Graphic abstract: Construction of a highly diverse mRNA library.
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Affiliation(s)
- Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Minori Eguchi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Nariaki Tsuzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Naoya Murata
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Japan Science and Technology Agency (JST), PRESTO, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
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23
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Hayashi K, Uehara S, Yamamoto S, Cary DR, Nishikawa J, Ueda T, Ozasa H, Mihara K, Yoshimura N, Kawai T, Ono T, Yamamoto S, Fumoto M, Mikamiyama H. Macrocyclic Peptides as a Novel Class of NNMT Inhibitors: A SAR Study Aimed at Inhibitory Activity in the Cell. ACS Med Chem Lett 2021; 12:1093-1101. [PMID: 34267879 DOI: 10.1021/acsmedchemlett.1c00134] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
Nicotinamide N-methyltransferase (NNMT), which catalyzes the methylation of nicotinamide, is a cytosolic enzyme that has attracted much attention as a therapeutic target for a variety of diseases. However, despite the considerable interest in this target, reports of NNMT inhibitors have still been limited to date. In this work, utilizing in vitro translated macrocyclic peptide libraries, we identified peptide 1 as a novel class of NNMT inhibitors. Further exploration based on the X-ray cocrystal structures of the peptides with NNMT provided a dramatic improvement in inhibitory activity (peptide 23: IC50 = 0.15 nM). Furthermore, by balance of the peptides' lipophilicity and biological activity, inhibitory activity against NNMT in cell-based assay was successfully achieved (peptide 26: cell-based IC50 = 770 nM). These findings illuminate the potential of cyclic peptides as a relatively new drug discovery modality even for intracellular targets.
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Affiliation(s)
- Kyohei Hayashi
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shota Uehara
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shiho Yamamoto
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Douglas R. Cary
- PeptiDream Inc., 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Junichi Nishikawa
- PeptiDream Inc., 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Taichi Ueda
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Hiroki Ozasa
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Kousuke Mihara
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Norito Yoshimura
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Taeko Kawai
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Takashi Ono
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Saki Yamamoto
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Masataka Fumoto
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Hidenori Mikamiyama
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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24
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Inhibition of Escherichia coli Lipoprotein Diacylglyceryl Transferase Is Insensitive to Resistance Caused by Deletion of Braun's Lipoprotein. J Bacteriol 2021; 203:e0014921. [PMID: 33875545 PMCID: PMC8316002 DOI: 10.1128/jb.00149-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Lipoprotein diacylglyceryl transferase (Lgt) catalyzes the first step in the biogenesis of Gram-negative bacterial lipoproteins which play crucial roles in bacterial growth and pathogenesis. We demonstrate that Lgt depletion in a clinical uropathogenic Escherichia coli strain leads to permeabilization of the outer membrane and increased sensitivity to serum killing and antibiotics. Importantly, we identify G2824 as the first-described Lgt inhibitor that potently inhibits Lgt biochemical activity in vitro and is bactericidal against wild-type Acinetobacter baumannii and E. coli strains. While deletion of a gene encoding a major outer membrane lipoprotein, lpp, leads to rescue of bacterial growth after genetic depletion or pharmacologic inhibition of the downstream type II signal peptidase, LspA, no such rescue of growth is detected after Lgt depletion or treatment with G2824. Inhibition of Lgt does not lead to significant accumulation of peptidoglycan-linked Lpp in the inner membrane. Our data validate Lgt as a novel antibacterial target and suggest that, unlike downstream steps in lipoprotein biosynthesis and transport, inhibition of Lgt may not be sensitive to one of the most common resistance mechanisms that invalidate inhibitors of bacterial lipoprotein biosynthesis and transport. IMPORTANCE As the emerging threat of multidrug-resistant (MDR) bacteria continues to increase, no new classes of antibiotics have been discovered in the last 50 years. While previous attempts to inhibit the lipoprotein biosynthetic (LspA) or transport (LolCDE) pathways have been made, most efforts have been hindered by the emergence of a common mechanism leading to resistance, namely, the deletion of the gene encoding a major Gram-negative outer membrane lipoprotein lpp. Our unexpected finding that inhibition of Lgt is not susceptible to lpp deletion-mediated resistance uncovers the complexity of bacterial lipoprotein biogenesis and the corresponding enzymes involved in this essential outer membrane biogenesis pathway and potentially points to new antibacterial targets in this pathway.
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25
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Kondo T, Eguchi M, Kito S, Fujino T, Hayashi G, Murakami H. cDNA TRAP display for rapid and stable in vitro selection of antibody-like proteins. Chem Commun (Camb) 2021; 57:2416-2419. [PMID: 33554979 DOI: 10.1039/d0cc07541h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We developed a cDNA TRAP display for the rapid selection of antibody-like proteins in various conditions. By modifying the original puromycin linker in the TRAP display, a monobody was covalently attached to the cDNA. As a proof-of-concept, we demonstrated a rapid model selection of an anti-EGFR1 monobody in a solution containing ribonuclease.
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Affiliation(s)
- Taishi Kondo
- Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
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26
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Zhang C, Bai X, Dedkova LM, Hecht SM. Protein synthesis with conformationally constrained cyclic dipeptides. Bioorg Med Chem 2020; 28:115780. [PMID: 33007560 DOI: 10.1016/j.bmc.2020.115780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 01/27/2023]
Abstract
We have synthesized several conformationally constrained dipeptide analogues as possible substrates for incorporation into proteins. These have included three cyclic dipeptides formed from Boc derivatives of 2,4-diaminobutyric acid, ornithine and lysine, having 5-, 6-, and 7-membered lactam rings, respectively. These dipeptides were used to activate a suppressor tRNA transcript, the latter of which had been prepared by in vitro transcription. Using modified E. coli ribosomes described previously, these activated suppressor tRNAs enabled the incorporation of the three cyclic dipeptides into dihydrofolate reductase (DHFR) at positions 18 and 49. The suppression yields increased with increasing lactam ring size and were found to proceed in suppression yields ranging from 3.4 to 8.9% at two different protein sites for the 5-, 6- and 7-membered lactam dipeptides. The greater facility of incorporation of the 7-membered lactam prompted us to prepare two 7-membered cyclic acylhydrazides (4 and 5) by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDCI)-mediated cyclization of amino acids having selectively protected hydrazine functional groups in their side chains. In common with the lactam dipeptides, acylhydrazide dipeptides 4 and 5 could be used to activate the same suppressor tRNA transcript and to incorporate the cyclic dipeptides into DHFR. They were incorporated into the same two DHFR sites in suppression yields ranging from 8.3 to 11.2%.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States.
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States.
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27
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Wang H, Song P, Li X, Wang Y, Gui S, Liu Y, Lu F. Screening of the candidate inhibitory peptides of subtilisin by in vitro RNA display technique. Int J Biol Macromol 2020; 163:1162-1167. [PMID: 32673721 DOI: 10.1016/j.ijbiomac.2020.07.115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 11/19/2022]
Abstract
The application of inhibitors facilitates the stable preservation of enzyme in liquid detergent by mitigating the proteolytic activity of subtilisin. The conventionally used subtilisin inhibitors such as boric acid pose a threat to the environment and human health. Thus, the formulation of novel subtilisin inhibitors demands immediate attention. In the current study, we have screened the peptide inhibitors for subtilisin by employing the in vitro mRNA display technique. It is a sensitive screening technique with a high library capacity. The affinity screening was performed between the biotin-modified subtilisin immobilized on the streptavidin magnetic beads and the cDNA-mRNA-peptide fusion molecular library acquired from the in vitro translation and reverse transcription. The candidate peptides with high affinity were obtained after multiple rounds of screening. Furthermore, the inhibitory effect was evaluated, showing that some candidate peptides had inhibitory effects, but the isothermal titration calorimetry and time dependent experiments ultimately proved that these candidate peptides were not stable inhibitors. However, the in vitro mRNA display method explored in this study can be used as a preliminary screening method to provide candidate peptides for the screening of subtilisin inhibitors.
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Affiliation(s)
- Hongbin Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Ping Song
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xue Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yufa Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shuqi Gui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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28
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Busby SA, Carbonneau S, Concannon J, Dumelin CE, Lee Y, Numao S, Renaud N, Smith TM, Auld DS. Advancements in Assay Technologies and Strategies to Enable Drug Discovery. ACS Chem Biol 2020; 15:2636-2648. [PMID: 32880443 DOI: 10.1021/acschembio.0c00495] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Assays drive drug discovery from the exploratory phases to the clinical testing of drug candidates. As such, numerous assay technologies and methodologies have arisen to support drug discovery efforts. Robust identification and characterization of tractable chemical matter requires biochemical, biophysical, and cellular approaches and often benefits from high-throughput methods. To increase throughput, efforts have been made to provide assays in miniaturized volumes which can be arrayed in microtiter plates to support the testing of as many as 100,000 samples/day. Alongside these efforts has been the growth of microtiter plate-free formats with encoded libraries that can support the screening of billions of compounds, a hunt for new drug modalities, as well as emphasis on more disease relevant formats using complex cell models of disease states. This review will focus on recent developments in high-throughput assay technologies applied to identify starting points for drug discovery. We also provide recommendations on strategies for implementing various assay types to select high quality leads for drug development.
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Affiliation(s)
- Scott A. Busby
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Seth Carbonneau
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - John Concannon
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | | | - YounKyoung Lee
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Shin Numao
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nicole Renaud
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Thomas M. Smith
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Douglas S. Auld
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
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29
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Kondo T, Iwatani Y, Matsuoka K, Fujino T, Umemoto S, Yokomaku Y, Ishizaki K, Kito S, Sezaki T, Hayashi G, Murakami H. Antibody-like proteins that capture and neutralize SARS-CoV-2. SCIENCE ADVANCES 2020; 6:sciadv.abd3916. [PMID: 32948512 PMCID: PMC7556756 DOI: 10.1126/sciadv.abd3916] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/28/2020] [Indexed: 05/10/2023]
Abstract
To combat severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and any unknown emerging pathogens in the future, the development of a rapid and effective method to generate high-affinity antibodies or antibody-like proteins is of critical importance. We here report high-speed in vitro selection of multiple high-affinity antibody-like proteins against various targets including the SARS-CoV-2 spike protein. The sequences of monobodies against the SARS-CoV-2 spike protein were successfully procured within only 4 days. Furthermore, the obtained monobody efficiently captured SARS-CoV-2 particles from the nasal swab samples of patients and exhibited a high neutralizing activity against SARS-CoV-2 infection (half-maximal inhibitory concentration, 0.5 nanomolar). High-speed in vitro selection of antibody-like proteins is a promising method for rapid development of a detection method for, and of a neutralizing protein against, a virus responsible for an ongoing, and possibly a future, pandemic.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Antibodies, Immobilized/chemistry
- Antibodies, Immobilized/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- Betacoronavirus/isolation & purification
- COVID-19
- Cell Surface Display Techniques/methods
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Dimerization
- Humans
- Kinetics
- Pandemics
- Peptides/chemistry
- Peptides/immunology
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/immunology
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Domains/immunology
- Protein Subunits/chemistry
- Protein Subunits/immunology
- Protein Subunits/metabolism
- RNA, Viral/metabolism
- SARS-CoV-2
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- T Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Y Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - K Matsuoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - T Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - S Umemoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Y Yokomaku
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - K Ishizaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - S Kito
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - T Sezaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - G Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
- Japan Science and Technology Agency (JST), PRESTO, Saitama, Japan
| | - H Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
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30
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Yamamoto Y, Terai T, Kumachi S, Nemoto N. In Vitro Construction of Large-scale DNA Libraries from Fragments Containing Random Regions using Deoxyinosine-containing Oligonucleotides and Endonuclease V. ACS COMBINATORIAL SCIENCE 2020; 22:165-171. [PMID: 32212679 DOI: 10.1021/acscombsci.9b00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient and precise construction of DNA libraries is a fundamental starting point for directed evolution of polypeptides. Recently, several in vitro selection methods have been reported that do not rely on cells for protein expression, where peptide libraries in the order of 1013 species are used for in vitro affinity selection. To maximize their potential, simple yet versatile construction of DNA libraries from several fragments containing random regions without bacterial transformation is essential. To address this issue, we herein propose a novel DNA construction methodology based on the use of polymerase chain reaction (PCR) primers containing a single deoxyinosine (I) residue near their 5' end. Treatment of the PCR products with endonuclease V generates 3' overhangs with customized lengths and sequences, which can be ligated accurately and efficiently with other fragments having exactly complementary overhangs. As a proof of concept, we constructed an artificial gene library of single-domain antibodies from four DNA fragments.
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Affiliation(s)
- Yasuhide Yamamoto
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama City, 338-8570, Japan
| | - Takuya Terai
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama City, 338-8570, Japan
| | - Shigefumi Kumachi
- Epsilon Molecular Engineering, Inc., 255 Shimo-okubo, Sakura-ku, Saitama City 338-8570, Saitama, Japan
| | - Naoto Nemoto
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama City, 338-8570, Japan
- Epsilon Molecular Engineering, Inc., 255 Shimo-okubo, Sakura-ku, Saitama City 338-8570, Saitama, Japan
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31
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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32
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Hirose H, Hideshima T, Katoh T, Suga H. A Case Study on the Keap1 Interaction with Peptide Sequence Epitopes Selected by the Peptidomic mRNA Display. Chembiochem 2019; 20:2089-2100. [PMID: 31169361 DOI: 10.1002/cbic.201900039] [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: 01/21/2019] [Revised: 03/12/2019] [Indexed: 11/08/2022]
Abstract
Many protein-protein and peptide-protein interactions (PPIs) play key roles in the regulation of biological functions, and therefore, the modulation of PPIs has become an attractive target of new drug development. Although a number of PPIs have already been identified, over 100 000 unknown PPIs are predicted to exist. To uncover such unknown PPIs, it is important to devise a conceptually distinct method from that of currently available methods. Herein, an mRNA display by using a total RNA library derived from various human tissues, which serves as a unique method to physically isolate peptide epitopes that potentially bind to a target protein of interest, is reported. In this study, selection was performed against Kelch-like ECH-associated protein (Keap1) as a model target protein, leading to a peptide epitope originating from astrotactin-1 (ASTN1). It turned out that this ASTN1 peptide was able to interact with Keap1 more strongly than that with a known peptide derived from Nrf2; a well-known, naturally occurring Keap1 binder. This case study demonstrates the applicability of peptidomic mRNA display for the rapid exploration of consensus binding peptide motifs and the potential for the discovery of unknown PPIs with other proteins of interest.
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Affiliation(s)
- Hisaaki Hirose
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomoki Hideshima
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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33
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Ottl J, Leder L, Schaefer JV, Dumelin CE. Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery. Molecules 2019; 24:E1629. [PMID: 31027189 PMCID: PMC6514559 DOI: 10.3390/molecules24081629] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/17/2019] [Accepted: 04/21/2019] [Indexed: 01/22/2023] Open
Abstract
The scope of targets investigated in pharmaceutical research is continuously moving into uncharted territory. Consequently, finding suitable chemical matter with current compound collections is proving increasingly difficult. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These binders facilitate drug discovery projects both as tools for target validation, structural elucidation and assay development as well as starting points for medicinal chemistry. Novartis internalized two complementing encoded library platforms to accelerate the initiation of its drug discovery programs. For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides. This review discusses how we apply these two platforms in our research and why we consider it beneficial to run both pipelines in-house.
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Affiliation(s)
- Johannes Ottl
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Lukas Leder
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Jonas V Schaefer
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
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34
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Huang Y, Wiedmann MM, Suga H. RNA Display Methods for the Discovery of Bioactive Macrocycles. Chem Rev 2018; 119:10360-10391. [PMID: 30395448 DOI: 10.1021/acs.chemrev.8b00430] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The past two decades have witnessed the emergence of macrocycles, including macrocyclic peptides, as a promising yet underexploited class of de novo drug candidates. Both rational/computational design and in vitro display systems have contributed tremendously to the development of cyclic peptide binders of either traditional targets such as cell-surface receptors and enzymes or challenging targets such as protein-protein interaction surfaces. mRNA display, a key platform technology for the discovery of cyclic peptide ligands, has become one of the leading strategies that can generate natural-product-like macrocyclic peptide binders with antibody-like affinities. On the basis of the original cell-free transcription/translation system, mRNA display is highly evolvable to realize its full potential by applying genetic reprogramming and chemical/enzymatic modifications. In addition, mRNA display also allows the follow-up hit-to-lead development using high-throughput focused affinity maturation. Finally, mRNA-displayed peptides can be readily engineered to create chemical conjugates based on known small molecules or biologics. This review covers the birth and growth of mRNA display and discusses the above features of mRNA display with success stories and future perspectives and is up to date as of August 2018.
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Affiliation(s)
- Yichao Huang
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Mareike Margarete Wiedmann
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
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35
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Exploring sequence space: harnessing chemical and biological diversity towards new peptide leads. Curr Opin Chem Biol 2017; 38:52-61. [DOI: 10.1016/j.cbpa.2017.02.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 12/29/2022]
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36
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37
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Leenheer D, ten Dijke P, Hipolito CJ. A current perspective on applications of macrocyclic-peptide-based high-affinity ligands. Biopolymers 2016; 106:889-900. [PMID: 27352774 PMCID: PMC5132055 DOI: 10.1002/bip.22900] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 05/24/2016] [Accepted: 05/31/2016] [Indexed: 01/05/2023]
Abstract
Monoclonal antibodies can bind with high affinity and high selectivity to their targets. As a tool in therapeutics or diagnostics, however, their large size (∼150 kDa) reduces penetration into tissue and prevents passive cellular uptake. To overcome these and other problems, minimized protein scaffolds have been chosen or engineered, with care taken to not compromise binding affinity or specificity. An alternate approach is to begin with a minimal non-antibody scaffold and select functional ligands from a de novo library. We will discuss the structure, production, applications, strengths, and weaknesses of several classes of antibody-derived ligands, that is, antibodies, intrabodies, and nanobodies, and nonantibody-derived ligands, that is, monobodies, affibodies, and macrocyclic peptides. In particular, this review is focussed on macrocyclic peptides produced by the Random non-standard Peptides Integrated Discovery (RaPID) system that are small in size (typically ∼2 kDa), but are able to perform tasks typically handled by larger proteinaceous ligands.
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Affiliation(s)
- Daniël Leenheer
- Ph.D. Program in Human Biology, School of Integrative and Global MajorsUniversity of TsukubaTsukubaIbarakiJapan
| | - Peter ten Dijke
- Leiden University Medical Center, Department of Molecular Cell BiologyLeidenSouth HollandThe Netherlands
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
| | - Christopher John Hipolito
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
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38
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Maini R, Umemoto S, Suga H. Ribosome-mediated synthesis of natural product-like peptides via cell-free translation. Curr Opin Chem Biol 2016; 34:44-52. [DOI: 10.1016/j.cbpa.2016.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/06/2016] [Indexed: 11/29/2022]
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39
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Naimuddin M, Kubo T. A High Performance Platform Based on cDNA Display for Efficient Synthesis of Protein Fusions and Accelerated Directed Evolution. ACS COMBINATORIAL SCIENCE 2016; 18:117-29. [PMID: 26812183 DOI: 10.1021/acscombsci.5b00139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a high performance platform based on cDNA display technology by developing a new modified puromycin linker-oligonucleotide. The linker consists of four major characteristics: a "ligation site" for hybridization and ligation of mRNA by T4 RNA ligase, a "puromycin arm" for covalent linkage of the protein, a "polyadenosine site" for a longer puromycin arm and purification of protein fusions (optional) using oligo-dT matrices, and a "reverse transcription site" for the formation of stable cDNA protein fusions whose cDNA is covalently linked to its encoded protein. The linker was synthesized by a novel branching strategy and provided >8-fold higher yield than previous linkers. This linker enables rapid and highly efficient ligation of mRNA (>90%) and synthesis of protein fusions (∼ 50-95%) in various cell-free expression systems. Overall, this new cDNA display method provides 10-200 fold higher end-usage fusions than previous methods and benefits higher diversity libraries crucial for directed protein/peptide evolution. With the increased efficiency, this system was able to reduce the time for one selection cycle to <8 h and is potentially amenable to high-throughput systems. We demonstrate the efficiency of this system for higher throughput selections of various biomolecular interactions and achieved 30-40-fold enrichment per selection cycle. Furthermore, a 4-fold higher enrichment of Flag-tag was obtained from a doped mixture compared with that of the previous cDNA display method. A three-finger protein library was evolved to isolate superior nanomolar range binding candidates for vascular endothelial growth factor. This method is expected to provide a beneficial impact to accelerated drug discovery and proteome analysis.
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Affiliation(s)
- Mohammed Naimuddin
- Biomedical
Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Janusys Corporation, #508, Saitama
Industrial Technology Center, Skip City, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
| | - Tai Kubo
- Biomedical
Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Molecular
Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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40
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Fujino T, Goto Y, Suga H, Murakami H. Ribosomal Synthesis of Peptides with Multiple β-Amino Acids. J Am Chem Soc 2016; 138:1962-9. [DOI: 10.1021/jacs.5b12482] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomoshige Fujino
- Department
of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuki Goto
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Hiroshi Murakami
- Department
of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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41
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Fujino T, Murakami H. In VitroSelection Combined with Ribosomal Translation Containing Non-proteinogenic Amino Acids. CHEM REC 2016; 16:365-77. [DOI: 10.1002/tcr.201500239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Tomoshige Fujino
- Department of Chemical and Biological Engineering, School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroshi Murakami
- Department of Chemical and Biological Engineering, School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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42
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Mochizuki Y, Suzuki T, Fujimoto K, Nemoto N. A versatile puromycin-linker using cnvK for high-throughput in vitro selection by cDNA display. J Biotechnol 2015; 212:174-80. [DOI: 10.1016/j.jbiotec.2015.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 01/04/2023]
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43
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Rogers JM, Suga H. Discovering functional, non-proteinogenic amino acid containing, peptides using genetic code reprogramming. Org Biomol Chem 2015; 13:9353-63. [PMID: 26280393 DOI: 10.1039/c5ob01336d] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The protein synthesis machinery of the cell, the ribosome and associated factors, is able to accurately follow the canonical genetic code, that which maps RNA sequence to protein sequence, to assemble functional proteins from the twenty or so proteinogenic amino acids. A number of innovative methods have arisen to take advantage of this accurate, and efficient, machinery to direct the assembly of non-proteinogenic amino acids. We review and compare these routes to 'reprogram the genetic code' including in vitro translation, engineered aminoacyl tRNA synthetases, and RNA 'flexizymes'. These studies show that the ribosome is highly tolerant of unnatural amino acids, with hundreds of unusual substrates of varying structure and chemistries being incorporated into protein chains. We also discuss how these methods have been coupled to selection techniques, such as phage display and mRNA display, opening up an exciting new avenue for the production of proteins and peptides with properties and functions beyond that which is possible using proteins composed entirely of the proteinogenic amino acids.
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Affiliation(s)
- J M Rogers
- Department of Chemistry, The University of Tokyo, Graduate School of Science, Tokyo, Japan.
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44
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Dodevski I, Markou GC, Sarkar CA. Conceptual and methodological advances in cell-free directed evolution. Curr Opin Struct Biol 2015; 33:1-7. [PMID: 26093059 DOI: 10.1016/j.sbi.2015.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/14/2015] [Accepted: 04/30/2015] [Indexed: 12/13/2022]
Abstract
Although cell-free directed evolution methods have been used to engineer proteins for nearly two decades, selections on more complex phenotypes have largely remained in the domain of cell-based engineering approaches. Here, we review recent conceptual advances that now enable in vitro display of multimeric proteins, integral membrane proteins, and proteins with an expanded amino acid repertoire. Additionally, we discuss methodological improvements that have enhanced the accessibility, efficiency, and robustness of cell-free approaches. Coupling these advances with the in vitro advantages of creating exceptionally large libraries and precisely controlling all experimental conditions, cell-free directed evolution is poised to contribute significantly to our understanding and engineering of more complex protein phenotypes.
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Affiliation(s)
- Igor Dodevski
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - George C Markou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Casim A Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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45
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Achenbach J, Jahnz M, Bethge L, Paal K, Jung M, Schuster M, Albrecht R, Jarosch F, Nierhaus KH, Klussmann S. Outwitting EF-Tu and the ribosome: translation with d-amino acids. Nucleic Acids Res 2015; 43:5687-98. [PMID: 26026160 PMCID: PMC4499158 DOI: 10.1093/nar/gkv566] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/18/2015] [Indexed: 01/09/2023] Open
Abstract
Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d-amino acids (d-aa) into polypeptides. The rare appearance of d-aa in natural polypeptides arises from post-translational modifications or non-ribosomal synthesis. We introduce an in vitro translation system that enables single incorporation of 17 out of 18 tested d-aa into a polypeptide; incorporation of two or three successive d-aa was also observed in several cases. The system consists of wild-type components and d-aa are introduced via artificially charged, unmodified tRNAGly that was selected according to the rules of ‘thermodynamic compensation’. The results reveal an unexpected plasticity of the ribosomal peptidyltransferase center and thus shed new light on the mechanism of chiral discrimination during translation. Furthermore, ribosomal incorporation of d-aa into polypeptides may greatly expand the armamentarium of in vitro translation towards the identification of peptides and proteins with new properties and functions.
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Affiliation(s)
- John Achenbach
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Michael Jahnz
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Lucas Bethge
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Krisztina Paal
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Maria Jung
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Maja Schuster
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Renate Albrecht
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Florian Jarosch
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Knud H Nierhaus
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
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46
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Terasaka N, Iwane Y, Geiermann AS, Goto Y, Suga H. Recent developments of engineered translational machineries for the incorporation of non-canonical amino acids into polypeptides. Int J Mol Sci 2015; 16:6513-31. [PMID: 25803109 PMCID: PMC4394545 DOI: 10.3390/ijms16036513] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/03/2022] Open
Abstract
Genetic code expansion and reprogramming methodologies allow us to incorporate non-canonical amino acids (ncAAs) bearing various functional groups, such as fluorescent groups, bioorthogonal functional groups, and post-translational modifications, into a desired position or multiple positions in polypeptides both in vitro and in vivo. In order to efficiently incorporate a wide range of ncAAs, several methodologies have been developed, such as orthogonal aminoacyl-tRNA-synthetase (AARS)–tRNA pairs, aminoacylation ribozymes, frame-shift suppression of quadruplet codons, and engineered ribosomes. More recently, it has been reported that an engineered translation system specifically utilizes an artificially built genetic code and functions orthogonally to naturally occurring counterpart. In this review we summarize recent advances in the field of ribosomal polypeptide synthesis containing ncAAs.
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Affiliation(s)
- Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yoshihiko Iwane
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Anna-Skrollan Geiermann
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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47
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Buhr F, Kohl-Landgraf J, tom Dieck S, Hanus C, Chatterjee D, Hegelein A, Schuman EM, Wachtveitl J, Schwalbe H. Design of Photocaged Puromycin for Nascent Polypeptide Release and Spatiotemporal Monitoring of Translation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410940] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Buhr F, Kohl-Landgraf J, tom Dieck S, Hanus C, Chatterjee D, Hegelein A, Schuman EM, Wachtveitl J, Schwalbe H. Design of photocaged puromycin for nascent polypeptide release and spatiotemporal monitoring of translation. Angew Chem Int Ed Engl 2015; 54:3717-21. [PMID: 25656536 DOI: 10.1002/anie.201410940] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 11/26/2014] [Indexed: 01/25/2023]
Abstract
The antibiotic puromycin, which inhibits protein translation, is used in a broad range of biochemical applications. The synthesis, characterization, and biological applications of NVOC-puromycin, a photocaged derivative that is activated by UV illumination, are presented. The caged compound had no effect either on prokaryotic or eukaryotic translation or on the viability of HEK 293 cells. Furthermore, no significant release of ribosome-bound polypeptide chains was detected in vitro. Upon illumination, cytotoxic activity, in vitro translation inhibition, and polypeptide release triggered by the uncaging of NVOC-puromycin were equivalent to those of the commercial compound. The quantum yield of photolysis was determined to be 1.1±0.2% and the NVOC-puromycin was applied to the detection of newly translated proteins with remarkable spatiotemporal resolution by using two-photon laser excitation, puromycin immunohistochemistry, and imaging in rat hippocampal neurons.
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Affiliation(s)
- Florian Buhr
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main (Germany)
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49
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Construction and screening of vast libraries of natural product-like macrocyclic peptides using in vitro display technologies. Curr Opin Chem Biol 2015; 24:131-8. [DOI: 10.1016/j.cbpa.2014.11.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/07/2014] [Accepted: 11/14/2014] [Indexed: 11/20/2022]
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50
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Foster AD, Ingram JD, Leitch EK, Lennard KR, Osher EL, Tavassoli A. Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery. ACTA ACUST UNITED AC 2015; 20:563-76. [DOI: 10.1177/1087057114566803] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/11/2014] [Indexed: 12/23/2022]
Abstract
The identification of initial hits is a crucial stage in the drug discovery process. Although many projects adopt high-throughput screening of small-molecule libraries at this stage, there is significant potential for screening libraries of macromolecules created using chemical biology approaches. Not only can the production of the library be directly interfaced with a cell-based assay, but these libraries also require significantly fewer resources to generate and maintain. In this context, cyclic peptides are increasingly viewed as ideal scaffolds and have proven capability against challenging targets such as protein-protein interactions. Here we discuss a range of methods used for the creation of cyclic peptide libraries and detail examples of their successful implementation.
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Affiliation(s)
| | | | | | | | | | - Ali Tavassoli
- Chemistry, University of Southampton, Southampton, UK
- Cancer Sciences, University of Southampton, Southampton, UK
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