1
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Pepanian A, Binbay FA, Pei D, Imhof D. Design, synthesis, and analysis of macrobicyclic peptides for targeting the Gαi protein. J Pept Sci 2024; 30:e3565. [PMID: 38232955 PMCID: PMC11065574 DOI: 10.1002/psc.3565] [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: 11/06/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Bicyclic peptides are important chemical tools that can function, for example, as bioactive ligands switching on/off signaling pathways mediated by guanine nucleotide-binding proteins as bicycles are more broadly applicable. Despite their relevance in medicinal chemistry, the synthesis of such peptides is challenging, and the final yield is highly dependent on the chemical composition and physicochemical properties of the scaffold. We recently discovered novel, state-specific peptide modulators targeting the Gαi protein, namely, GPM-2/GPM-3, by screening a one-bead-two-compound combinatorial library. A more detailed analysis, including sequence alignments and computer-assisted conformational studies based on the hit compounds, revealed the new peptide 10 as a potential macrobicyclic Gαi ligand sharing high sequence similarity to the known Gαi modulators. The Gαs protein was included in this study for comparison and to unravel the criteria for the specificity of modulator binding to Gαi versus Gαs. This work provides in-depth computer-assisted experimental studies for the analysis of novel macrobicyclic, library-derived Gαi protein ligands. The sequence and structural comparison of 10 with the lead compounds GPM-2 and GPM-3 reveals the importance of the size and amino acid composition of one ring of the bicyclic system and suggests features enhancing the binding affinity of the peptides to the Gαi protein.
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Affiliation(s)
- Anna Pepanian
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - F. Ayberk Binbay
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
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2
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Miyamoto E, Sato T, Matsubara T. Cyclization of Peptides Enhances the Inhibitory Activity against Ganglioside-Induced Aβ Fibril Formation. ACS Chem Neurosci 2023; 14:4199-4207. [PMID: 37971427 DOI: 10.1021/acschemneuro.3c00589] [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] [Indexed: 11/19/2023] Open
Abstract
Alzheimer's disease is a progressive neurodegenerative disease and is the most common cause of dementia. It has been reported that the assembly of amyloid β-protein (Aβ) on the cell membrane is induced by the interaction of the Aβ monomer with gangliosides such as GM1. The ganglioside-bound Aβ (GAβ) complex acts as a seed to promote the toxic assembly of the Aβ fibrils. In a previous study, we found that a GM1 cluster-binding peptide (GCBP) specifically recognizes Aβ-sensitive ganglioside nanoclusters and inhibits the assembly of Aβ on a GM1-containing lipid membrane. In this study, cysteine-substituted double mutants of GCBP were designed and cyclized by intramolecular disulfide bond formation. Affinity assays indicated that one of the cyclic peptides had a higher affinity to a GM1-containing membrane compared to that of GCBP. Furthermore, surface topography analysis indicated that this peptide recognizes GM1 nanoclusters on the lipid membrane. An evaluation of the inhibitory kinetics indicated that the cyclic peptide could inhibit the formation of Aβ fibrils with an IC50 value of 1.2 fM, which is 10,000-fold higher than that of GCBP. The cyclic peptide was also shown to have a clearance effect on Aβ fibrils deposited on the lipid membrane and suppressed the formation of toxic Aβ assemblies. Our results indicate that the cyclic peptide that binds to the Aβ-sensitive ganglioside nanocluster is a potential novel inhibitor of ganglioside-induced Aβ assembly.
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Affiliation(s)
- Erika Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
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3
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Brango-Vanegas J, Leite ML, de Oliveira KBS, da Cunha NB, Franco OL. From exploring cancer and virus targets to discovering active peptides through mRNA display. Pharmacol Ther 2023; 252:108559. [PMID: 37952905 DOI: 10.1016/j.pharmthera.2023.108559] [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: 08/09/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
During carcinogenesis, neoplastic cells accumulate mutations in genes important for cellular homeostasis, producing defective proteins. Viral infections occur when viral capsid proteins bind to the host cell receptor, allowing the virus to enter the cells. In both cases, proteins play important roles in cancer development and viral infection, so these targets can be exploited to develop alternative treatments. mRNA display technology is a very powerful tool for the development of peptides capable of acting on specific targets in neoplastic cells or on viral capsid proteins. mRNA display technology allows the selection and evolution of peptides with desired functional properties from libraries of many nucleic acid variants. Among other advantages of this technology, the use of flexizymes allows the production of peptides with unnatural amino acid residues, which can enhance the activity of these molecules. From target immobilization, peptides with greater specificity for the targets of interest are generated during the selection rounds. Herein, we will explore the use of mRNA display technology for the development of active peptides after successive rounds of selection, using proteins present in neoplastic cells and viral particles as targets.
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Affiliation(s)
- José Brango-Vanegas
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Michel Lopes Leite
- Departamento de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Nicolau Brito da Cunha
- Universidade de Brasília, Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
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4
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Kasper SH, Otten S, Squadroni B, Orr‐Terry C, Kuang Y, Mussallem L, Ge L, Yan L, Kannan S, Verma CS, Brown CJ, Johannes CW, Lane DP, Chandramohan A, Partridge AW, Roberts LR, Josien H, Therien AG, Hett EC, Howell BJ, Peier A, Ai X, Cassaday J. A high-throughput microfluidic mechanoporation platform to enable intracellular delivery of cyclic peptides in cell-based assays. Bioeng Transl Med 2023; 8:e10542. [PMID: 37693049 PMCID: PMC10487316 DOI: 10.1002/btm2.10542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 09/12/2023] Open
Abstract
Cyclic peptides are poised to target historically difficult to drug intracellular protein-protein interactions, however, their general cell impermeability poses a challenge for characterizing function. Recent advances in microfluidics have enabled permeabilization of the cytoplasmic membrane by physical cell deformation (i.e., mechanoporation), resulting in intracellular delivery of impermeable macromolecules in vector- and electrophoretic-free approaches. However, the number of payloads (e.g., peptides) and/or concentrations delivered via microfluidic mechanoporation is limited by having to pre-mix cells and payloads, a manually intensive process. In this work, we show that cells are momentarily permeable (t 1/2 = 1.1-2.8 min) after microfluidic vortex shedding (μVS) and that lower molecular weight macromolecules can be cytosolically delivered upon immediate exposure after cells are processed/permeabilized. To increase the ability to screen peptides, we built a system, dispensing-microfluidic vortex shedding (DμVS), that integrates a μVS chip with inline microplate-based dispensing. To do so, we synced an electronic pressure regulator, flow sensor, on/off dispense valve, and an x-y motion platform in a software-driven feedback loop. Using this system, we were able to deliver low microliter-scale volumes of transiently mechanoporated cells to hundreds of wells on microtiter plates in just several minutes (e.g., 96-well plate filled in <2.5 min). We validated the delivery of an impermeable peptide directed at MDM2, a negative regulator of the tumor suppressor p53, using a click chemistry- and NanoBRET-based cell permeability assay in 96-well format, with robust delivery across the full plate. Furthermore, we demonstrated that DμVS could be used to identify functional, low micromolar, cellular activity of otherwise cell-inactive MDM2-binding peptides using a p53 reporter cell assay in 96- and 384-well format. Overall, DμVS can be combined with downstream cell assays to investigate intracellular target engagement in a high-throughput manner, both for improving structure-activity relationship efforts and for early proof-of-biology of non-optimized peptide (or potentially other macromolecular) tools.
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Affiliation(s)
| | | | | | | | - Yi Kuang
- Merck & Co., Inc.CambridgeMassachusettsUSA
| | | | - Lan Ge
- Merck & Co., Inc.KenilworthNew JerseyUSA
| | - Lin Yan
- Merck & Co., Inc.KenilworthNew JerseyUSA
| | | | - Chandra S. Verma
- Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | | | | | - David P. Lane
- Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | | | | | | | | | | | | | | | | | - Xi Ai
- Merck & Co., Inc.KenilworthNew JerseyUSA
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5
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Hosono Y, Uchida S, Shinkai M, Townsend CE, Kelly CN, Naylor MR, Lee HW, Kanamitsu K, Ishii M, Ueki R, Ueda T, Takeuchi K, Sugita M, Akiyama Y, Lokey SR, Morimoto J, Sando S. Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides. Nat Commun 2023; 14:1416. [PMID: 36932083 PMCID: PMC10023679 DOI: 10.1038/s41467-023-36978-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Naturally occurring peptides with high membrane permeability often have ester bonds on their backbones. However, the impact of amide-to-ester substitutions on the membrane permeability of peptides has not been directly evaluated. Here we report the effect of amide-to-ester substitutions on the membrane permeability and conformational ensemble of cyclic peptides related to membrane permeation. Amide-to-ester substitutions are shown to improve the membrane permeability of dipeptides and a model cyclic hexapeptide. NMR-based conformational analysis and enhanced sampling molecular dynamics simulations suggest that the conformational transition of the cyclic hexapeptide upon membrane permeation is differently influenced by an amide-to-ester substitution and an amide N-methylation. The effect of amide-to-ester substitution on membrane permeability of other cyclic hexapeptides, cyclic octapeptides, and a cyclic nonapeptide is also investigated to examine the scope of the substitution. Appropriate utilization of amide-to-ester substitution based on our results will facilitate the development of membrane-permeable peptides.
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Affiliation(s)
- Yuki Hosono
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoshi Uchida
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Moe Shinkai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Colin N Kelly
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Matthew R Naylor
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Kayoko Kanamitsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mayumi Ishii
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
- Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Scott R Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA.
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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6
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Linker S, Schellhaas C, Kamenik AS, Veldhuizen MM, Waibl F, Roth HJ, Fouché M, Rodde S, Riniker S. Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes. J Med Chem 2023; 66:2773-2788. [PMID: 36762908 PMCID: PMC9969412 DOI: 10.1021/acs.jmedchem.2c01837] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Indexed: 02/11/2023]
Abstract
Cyclic peptides extend the druggable target space due to their size, flexibility, and hydrogen-bonding capacity. However, these properties impact also their passive membrane permeability. As the "journey" through membranes cannot be monitored experimentally, little is known about the underlying process, which hinders rational design. Here, we use molecular simulations to uncover how cyclic peptides permeate a membrane. We show that side chains can act as "molecular anchors", establishing the first contact with the membrane and enabling insertion. Once inside, the peptides are positioned between headgroups and lipid tails─a unique polar/apolar interface. Only one of two distinct orientations at this interface allows for the formation of the permeable "closed" conformation. In the closed conformation, the peptide crosses to the lower leaflet via another "anchoring" and flipping mechanism. Our findings provide atomistic insights into the permeation process of flexible cyclic peptides and reveal design considerations for each step of the process.
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Affiliation(s)
- Stephanie
M. Linker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Christian Schellhaas
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Anna S. Kamenik
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Mac M. Veldhuizen
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Hans-Jörg Roth
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Marianne Fouché
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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7
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Pal S, 't Hart P. RNA-Binding Macrocyclic Peptides. Front Mol Biosci 2022; 9:883060. [PMID: 35517859 PMCID: PMC9062085 DOI: 10.3389/fmolb.2022.883060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/18/2022] [Indexed: 12/03/2022] Open
Abstract
Being able to effectively target RNA with potent ligands will open up a large number of potential therapeutic options. The knowledge on how to achieve this is ever expanding but an important question that remains open is what chemical matter is suitable to achieve this goal. The high flexibility of an RNA as well as its more limited chemical diversity and featureless binding sites can be difficult to target selectively but can be addressed by well-designed cyclic peptides. In this review we will provide an overview of reported cyclic peptide ligands for therapeutically relevant RNA targets and discuss the methods used to discover them. We will also provide critical insights into the properties required for potent and selective interaction and suggestions on how to assess these parameters. The use of cyclic peptides to target RNA is still in its infancy but the lessons learned from past examples can be adopted for the development of novel potent and selective ligands.
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Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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8
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Linker SM, Schellhaas C, Ries B, Roth HJ, Fouché M, Rodde S, Riniker S. Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability. RSC Adv 2022; 12:5782-5796. [PMID: 35424539 PMCID: PMC8981571 DOI: 10.1039/d1ra09025a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
Cyclic peptides have the potential to vastly extend the scope of druggable proteins and lead to new therapeutics for currently untreatable diseases. However, cyclic peptides often suffer from poor bioavailability. To uncover design principles for permeable cyclic peptides, a promising strategy is to analyze the conformational dynamics of the peptides using molecular dynamics (MD) and Markov state models (MSMs). Previous MD studies have focused on the conformational dynamics in pure aqueous or apolar environments to rationalize membrane permeability. However, during the key steps of the permeation through the membrane, cyclic peptides are exposed to interfaces between polar and apolar regions. Recent studies revealed that these interfaces constitute the free energy minima of the permeation process. Thus, a deeper understanding of the behavior of cyclic peptides at polar/apolar interfaces is desired. Here, we investigate the conformational and kinetic behavior of cyclic decapeptides at a water/chloroform interface using unbiased MD simulations and MSMs. The distinct environments at the interface alter the conformational equilibrium as well as the interconversion kinetics of cyclic peptide conformations. For peptides with low population of the permeable conformation in aqueous solution, the polar/apolar interface facilitates the interconversion to the closed conformation, which is required for membrane permeation. Comparison to unbiased MD simulations with a POPC bilayer reveals that not only the conformations but also the orientations are relevant in a membrane system. These findings allow us to propose a permeability model that includes both ‘prefolding’ and ‘non-prefolding’ cyclic peptides – an extension that can lead to new design considerations for permeable cyclic peptides. This study uses molecular dynamics and Markov state models to analyse how interfaces interact with cyclic decapeptides and modulate their dynamic and equilibrium properties.![]()
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Affiliation(s)
- Stephanie M Linker
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Christian Schellhaas
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Benjamin Ries
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Hans-Jörg Roth
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus 4056 Basel Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus 4056 Basel Switzerland
| | - Stephane Rodde
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus 4056 Basel Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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9
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Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 417] [Impact Index Per Article: 208.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
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10
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Li Y, Han Y, Zeng Z, Li W, Feng S, Cao W. Discovery and Bioactivity of the Novel Lasso Peptide Microcin Y. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8758-8767. [PMID: 34314160 DOI: 10.1021/acs.jafc.1c02659] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lasso peptides, a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) secreted by bacteria, have antimicrobial activity. Here, a novel lasso peptide, microcin Y (MccY), was discovered and characterized. The gene cluster for MccY synthesis was cloned for expression in Escherichia coli. This peptide was purified by HPLC and characterized by Q-TOF. MIC assays showed that some Bacillus, Staphylococcus, Pseudomonas, Shigella, and Salmonella strains were sensitive to MccY. Interestingly, Salmonellatyphimurium and Salmonella infantis were efficiently inhibited by MccY, while they were not affected by MccJ25, a lasso peptide that has antibacterial effects on many Salmonella strains. Furthermore, MccY-resistant strains of S. typhimurium were screened, and mutations were found in FhuA and SbmA, indicating the importance of these transporters for MccY absorption. This novel peptide can greatly broaden the antimicrobial spectrum of MccJ25 in Salmonella and is expected to be used in food preservation and animal feed additive areas.
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Affiliation(s)
- Yu Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Yu Han
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Zhiwei Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Wenjing Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Weisheng Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, People's Republic of China
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11
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Jachak GR, Athawale PR, Choudhury R, Kashinath K, Reddy DS. Access to a Stereoisomer Library of Solomonamide Macrocycles. Chem Asian J 2019; 14:4572-4576. [DOI: 10.1002/asia.201901075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/10/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Gorakhnath R. Jachak
- CSIR-National Chemical LaboratoryDivision of Organic Chemistry Dr. Homi Bhabha Road Pune 411008 India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi- 110 025 India
| | - Paresh R. Athawale
- CSIR-National Chemical LaboratoryDivision of Organic Chemistry Dr. Homi Bhabha Road Pune 411008 India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi- 110 025 India
| | - Rahul Choudhury
- CSIR-National Chemical LaboratoryDivision of Organic Chemistry Dr. Homi Bhabha Road Pune 411008 India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi- 110 025 India
| | - K. Kashinath
- CSIR-National Chemical LaboratoryDivision of Organic Chemistry Dr. Homi Bhabha Road Pune 411008 India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi- 110 025 India
| | - D. Srinivasa Reddy
- CSIR-National Chemical LaboratoryDivision of Organic Chemistry Dr. Homi Bhabha Road Pune 411008 India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi- 110 025 India
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12
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Pham MV, Bergeron-Brlek M, Heinis C. Synthesis of DNA-Encoded Disulfide- and Thioether-Cyclized Peptides. Chembiochem 2019; 21:543-549. [PMID: 31381227 DOI: 10.1002/cbic.201900390] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Indexed: 12/19/2022]
Abstract
DNA-encoded chemical library technologies enable the screening of large combinatorial libraries of chemically and structurally diverse molecules, including short cyclic peptides. A challenge in the combinatorial synthesis of cyclic peptides is the final step, the cyclization of linear peptides that typically suffers from incomplete reactions and large variability between substrates. Several efficient peptide cyclization strategies rely on the modification of thiol groups, such as the formation of disulfide or thioether bonds between cysteines. In this work, we established a strategy and reaction conditions for the efficient chemical synthesis of cyclic peptide-DNA conjugates based on linking the side chains of cysteines. We tested two different thiol-protecting groups and found that tert-butylthio (S-tBu) works best for incorporating a pair of cysteines, and we show that the DNA-linked peptides can be efficiently cyclized through disulfide and thioether bond formation. In combination with established procedures for DNA encoding, the strategy for incorporation of cysteines may be readily applied for the generation and screening of disulfide- and thioether-cyclized peptide libraries.
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Affiliation(s)
- Manh V Pham
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fedérale de Lausanne, CH A3 398, Station 6, 1015, Lausanne, Switzerland
| | - Milan Bergeron-Brlek
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fedérale de Lausanne, CH A3 398, Station 6, 1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fedérale de Lausanne, CH A3 398, Station 6, 1015, Lausanne, Switzerland
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13
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Sumida T, Dubiley S, Wilcox B, Severinov K, Tagami S. Structural Basis of Leader Peptide Recognition in Lasso Peptide Biosynthesis Pathway. ACS Chem Biol 2019; 14:1619-1627. [PMID: 31188556 DOI: 10.1021/acschembio.9b00348] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with a unique 3D-interlocked structure, in which an N-terminal macrolactam ring is threaded by a linear C-terminal part. The unique structure of lasso peptides is introduced into ribosomally translated precursor peptides by lasso peptide synthetase encompassing proteins B and C or B1, B2, and C when the B enzyme is split into two distinct proteins. The B1 protein recognizes the leader sequence of the precursor peptide, and then the B2 protein cleaves it. The C protein catalyzes the formation of the macrolactam ring. However, the detailed mechanism of lasso peptide maturation has remained elusive, due to the lack of structural information about the responsible proteins. Here we report the crystal structure of the B1 protein from the thermophilic actinobacteria, Thermobifida fusca (TfuB1), complexed with the leader peptide (TfuA-Leader), which revealed the detailed mechanism of leader peptide recognition. The structure of TfuB1 consists of an N-terminal β-sheet and three C-terminal helices. The leader peptide is docked on one edge of the N-terminal β-sheet of TfuB1, as an additional β strand. Three conserved amino acid residues of the leader peptide (TfuA Tyr-17, Pro-14, and Leu-12) fit well on the hydrophobic cleft between the β-sheet and adjacent helices. Biochemical analysis demonstrated that these conserved residues are essential for affinity between TfuB1 and the TfuA-Leader. Furthermore, we found that TfuB1 and the leader peptide jointly form a hydrophobic patch on the β-sheet, which includes the highly conserved TfuA Phe-6 and TfuB1 Tyr33. Homology modeling and mutational analysis of the B1 protein from a firmicute, Bacillus pseudomycoides (PsmB1), revealed that the hydrophobic patch is conserved in a wide range of species and involved in the cleavage activity of the B2 protein, indicating it forms the interaction surface for the B2 protein or the core part of the precursor peptide.
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Affiliation(s)
- Tomomi Sumida
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Svetlana Dubiley
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
| | - Brendan Wilcox
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Konstantin Severinov
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
- Waksman Institute for Microbiology, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
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14
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Wang XN, Su XX, Cheng SQ, Sun ZY, Huang ZS, Ou TM. MYC modulators in cancer: a patent review. Expert Opin Ther Pat 2019; 29:353-367. [PMID: 31068032 DOI: 10.1080/13543776.2019.1612878] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION The important role of MYC in tumorigenesis makes it particularly important to design MYC modulators. Over the past decade, researchers have raised a number of strategies for designing MYC modulators, some of which are already in clinical trials. This paper aims to review the patents of MYC modulators. AREAS COVERED The important biological relevance of c-MYC and the regulation pathways related to c-MYC are briefly introduced. Base on that, the MYC modulators reported in published patents and references primarily for cancer treatment are outlined, highlighting the structures and biological activities. EXPERT OPINION There has been a growing awareness of finding and designing MYC modulators as novel anticancer drugs over recent years. Patents involving the discovery, synthesis, and application of MYC modulators are particularly important for further development in this field. Although finding direct MYC inhibitors or binders is challenging, MYC cannot be simply defined as an undruggable target. There is still substantial evidence proving the concept that MYC modulators can benefit to the treatment of both human hematological malignancies and solid tumors. More efforts should be taken to improve the activity and specificity of MYC modulators.
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Affiliation(s)
- Xiao-Na Wang
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Xiao-Xuan Su
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Sui-Qi Cheng
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Zhi-Yin Sun
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Zhi-Shu Huang
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Tian-Miao Ou
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
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15
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Mayer C. Selection, Addiction and Catalysis: Emerging Trends for the Incorporation of Noncanonical Amino Acids into Peptides and Proteins in Vivo. Chembiochem 2019; 20:1357-1364. [PMID: 30618145 PMCID: PMC6563710 DOI: 10.1002/cbic.201800733] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 12/22/2022]
Abstract
Expanding the genetic code of organisms by incorporating noncanonical amino acids (ncAAs) into target proteins through the suppression of stop codons in vivo has profoundly impacted how we perform protein modification or detect proteins and their interaction partners in their native environment. Yet, with genetic code expansion strategies maturing over the past 15 years, new applications that make use—or indeed repurpose—these techniques are beginning to emerge. This Concept article highlights three of these developments: 1) The incorporation of ncAAs for the biosynthesis and selection of bioactive macrocyclic peptides with novel ring architectures, 2) synthetic biocontainment strategies based on the addiction of microorganisms to ncAAs, and 3) enzyme design strategies, in which ncAAs with unique functionalities enable the catalysis of new‐to‐nature reactions. Key advances in all three areas are presented and potential future applications discussed.
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Affiliation(s)
- Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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16
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Vinogradov AA, Yin Y, Suga H. Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J Am Chem Soc 2019; 141:4167-4181. [PMID: 30768253 DOI: 10.1021/jacs.8b13178] [Citation(s) in RCA: 389] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein surfaces traditionally considered "undruggable". Unfortunately, at the same time, other pharmacological properties of a generic peptide, such as metabolic stability and cell permeability, are quite poor, which limits the success of de novo discovered biologically active peptides as drug candidates. Here, we review how macrocyclization as well as the incorporation of nonproteogenic amino acids and various conjugation strategies may be utilized to improve on these characteristics to create better drug candidates. We analyze recent progress and remaining challenges in improving individual pharmacological properties of bioactive peptides, and offer our opinion on interfacing these, often conflicting, considerations, to create balanced drug candidates as a potential way to make further progress in this area.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Yizhen Yin
- 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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17
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Abstract
Intracellular delivery of biological agents such as peptides, proteins, and nucleic acids generally rely on the endocytic pathway as the major uptake mechanism, resulting in their entrapment inside the endosome and lysosome. The recent discovery of cell-penetrating molecules of exceptionally high endosomal escape and cytosolic delivery efficiencies and elucidation of their mechanism of action represent major breakthroughs in this field. In this Topical Review, we provide an overview of the recent progress in understanding and enhancing the endosomal escape process and the new opportunities opened up by these recent findings.
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Affiliation(s)
- Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, USA
| | - Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, USA
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18
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Abstract
Macrocyclic peptides are a unique class of molecules that display a relatively constrained peptidic backbone as compared to their linear counterparts leading to the defined 3-D orientation of the constituent amino acids (pharmacophore). Although they are attractive candidates for lead discovery owing to the unique conformational features, their peptidic backbone is susceptible to proteolytic cleavage in various biological fluids that compromise their efficacy. In this chapter we review the various classical and contemporary chemical and biological approaches that have been utilized to combat the metabolic instability of macrocyclic peptides. We note that any chemical modification that helps in providing either local or global conformational rigidity to these macrocyclic peptides aids in improving their metabolic stability typically by slowing the cleavage kinetics by the proteases.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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19
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Chávez-Riveros A, Hernández-Vázquez E, Nieto-Camacho A, Ramírez-Apan T, Miranda LD. Synthesis of diphenylamine macrocycles and their anti-inflammatory effects. Org Biomol Chem 2019; 17:1423-1435. [DOI: 10.1039/c8ob03121e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A collection of fourteen diphenylamine macrocyclic derivatives containing a peptide chain with different substituents was synthesized using a protocol of two Ugi four component reactions (Ugi-4CR) and a Buchwald–Hartwig macrocyclization.
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Affiliation(s)
| | | | - Antonio Nieto-Camacho
- Universidad Nacional Autónoma de México
- Instituto de Química
- Ciudad Universitaria
- Mexico
| | - Teresa Ramírez-Apan
- Universidad Nacional Autónoma de México
- Instituto de Química
- Ciudad Universitaria
- Mexico
| | - Luis D. Miranda
- Universidad Nacional Autónoma de México
- Instituto de Química
- Ciudad Universitaria
- Mexico
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20
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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: 128] [Impact Index Per Article: 21.3] [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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21
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Al Bakri W, Donovan MD, Cueto M, Wu Y, Orekie C, Yang Z. Overview of intranasally delivered peptides: key considerations for pharmaceutical development. Expert Opin Drug Deliv 2018; 15:991-1005. [PMID: 30173579 DOI: 10.1080/17425247.2018.1517742] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Intranasal (IN) delivery for peptides provides unique advantages compared to other invasive systemic delivery routes. However, there still lacks a clear understanding on how to evaluate the potential of the peptides for nasal delivery and key considerations for the nasal formulation development. AREAS COVERED A retrospective analysis of intranasally delivered peptides was conducted. The goals of this undertaking were 1) to build a database of the key physicochemical and pharmacokinetic properties of peptides delivered by the nasal route, 2) to evaluate formulation attributes applied to IN peptide delivery systems, and 3) to provide key considerations for IN delivery of peptides. EXPERT OPINION/COMMENTARY Extensive data mining showed that peptides with molecular weights up to 6000 Da have been delivered intranasally. The high solubility of some peptides highlighted the possibility of delivering sufficient amounts of peptide in the limited volume available for nasal sprays. Permeation enhancers and mucoadhesives have shown promise in improving the IN bioavailability of peptides. Other formulation considerations, such as the type of formulation, pH, osmolality, as well as drug deposition, are reviewed herein. Based on this retrospective analysis, key considerations for nasal peptides formulations were proposed to guide drug discovery and development for IN delivery of peptides.
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Affiliation(s)
- Wisam Al Bakri
- a Department of Pharmaceutical Sciences and Experimental Therapeutics , The University of Iowa, College of Pharmacy , Iowa City
| | - Maureen D Donovan
- a Department of Pharmaceutical Sciences and Experimental Therapeutics , The University of Iowa, College of Pharmacy , Iowa City
| | - Maria Cueto
- b Pharmaceutical Science , Exploratory Products & Technology, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Yunhui Wu
- c Pharmaceutical Science , Biopharmaceutics and Specialty Dosage Form, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Chinedu Orekie
- c Pharmaceutical Science , Biopharmaceutics and Specialty Dosage Form, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Zhen Yang
- c Pharmaceutical Science , Biopharmaceutics and Specialty Dosage Form, Merck & Co., Inc ., Kenilworth , NJ , USA
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22
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Mull RW, Harrington A, Sanchez LA, Tal-Gan Y. Cyclic Peptides that Govern Signal Transduction Pathways: From Prokaryotes to Multi-Cellular Organisms. Curr Top Med Chem 2018; 18:625-644. [PMID: 29773060 DOI: 10.2174/1568026618666180518090705] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/30/2016] [Accepted: 12/17/2017] [Indexed: 12/16/2022]
Abstract
Cyclic peptide scaffolds are key components of signal transduction pathways in both prokaryotic and eukaryotic organisms since they act as chemical messengers that activate or inhibit specific cognate receptors. In prokaryotic organisms these peptides are utilized in non-essential pathways, such as quorum sensing, that are responsible for virulence and pathogenicity. In the more evolved eukaryotic systems, cyclic peptide hormones play a key role in the regulation of the overall function of multicellular organisms, mainly through the endocrine system. This review will highlight several prokaryote and eukaryote systems that use cyclic peptides as their primary signals and the potential associated with utilizing these scaffolds for the discovery of novel therapeutics for a wide range of diseases and illnesses.
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Affiliation(s)
- Ryan W Mull
- Department of Chemistry, University of Nevada, Reno, NV 89557, United States
| | - Anthony Harrington
- Department of Chemistry, University of Nevada, Reno, NV 89557, United States
| | - Lucia A Sanchez
- Department of Chemistry, University of Nevada, Reno, NV 89557, United States
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, NV 89557, United States
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23
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Tajima K, Katoh T, Suga H. Genetic code expansion via integration of redundant amino acid assignment by finely tuning tRNA pools. Curr Opin Chem Biol 2018; 46:212-218. [PMID: 30072241 DOI: 10.1016/j.cbpa.2018.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/23/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
In all translation systems, the genetic code assigns codons to amino acids as building blocks of polypeptides, defining their chemical, structural and physiological properties. The canonical genetic code, however, utilizes only 20 proteinogenic amino acids redundantly encoded in 61 codons. In order to expand the building block repertoire, this redundancy was reduced by tuning composition of the transfer RNA (tRNA) mixture in vitro. Depletion of particular tRNAs from the total tRNA mixture or its reconstitution with in vitro-transcribed tRNASNNs (S = C or G, N = U, C, A or G) divided a codon box to encode two amino acids, expanding the repertoire to 23. The expanded genetic codes may benefit analysis of cellular regulatory pathways and drug screening.
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Affiliation(s)
- Kenya Tajima
- 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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24
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Uematsu S, Tabuchi Y, Ito Y, Taki M. Combinatorially Screened Peptide as Targeted Covalent Binder: Alteration of Bait-Conjugated Peptide to Reactive Modifier. Bioconjug Chem 2018; 29:1866-1871. [PMID: 29792678 DOI: 10.1021/acs.bioconjchem.8b00301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A peptide-type covalent binder for a target protein was obtained by combinatorial screening of fluoroprobe-conjugated peptide libraries on bacteriophage T7. The solvatochromic fluoroprobe works as a bait during the affinity selection process of phage display. To obtain the targeted covalent binder, the bait in the selected consensus peptide was altered into a reactive warhead possessing a sulfonyl fluoride. The reaction efficiency and site/position specificity of the covalent conjugation between the binder and the target protein were evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and rationalized by a protein-ligand docking simulation.
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Affiliation(s)
- Shuta Uematsu
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering , The University of Electro-Communications (UEC) , 1-5-1 Chofugaoka , Chofu , Tokyo 182-8585 , Japan
| | - Yudai Tabuchi
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering , The University of Electro-Communications (UEC) , 1-5-1 Chofugaoka , Chofu , Tokyo 182-8585 , Japan
| | - Yuji Ito
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering , Kagoshima University , 1-21-35 Korimoto , Kagoshima , Kagoshima 890-0065 , Japan
| | - Masumi Taki
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering , The University of Electro-Communications (UEC) , 1-5-1 Chofugaoka , Chofu , Tokyo 182-8585 , Japan
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25
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Wuo MG, Arora PS. Engineered protein scaffolds as leads for synthetic inhibitors of protein-protein interactions. Curr Opin Chem Biol 2018; 44:16-22. [PMID: 29803113 DOI: 10.1016/j.cbpa.2018.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/09/2018] [Indexed: 11/18/2022]
Abstract
Rationally designed protein-protein interaction inhibitors mimic interfacial binding epitopes, specifically residues that contribute significantly to binding. However, direct mimicry often does not lead to high affinity ligands because the natural complexes themselves are functionally transient and of low affinity. The mimics typically need to be optimized for potency. Engineered proteins displaying conformationally-defined epitopes may serve as attractive alternatives to natural protein partners as they can be strictly screened for tight binding. The advantage of focused screens with conformationally-defined protein scaffolds is that conservation of the geometry of the natural binding epitopes may preserve binding site specificity while allowing direct mimicry by various synthetic secondary structure scaffolds. Here we review different classes of engineered proteins for their binding epitope geometry and as leads for synthetic secondary and tertiary structure mimics.
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Affiliation(s)
- Michael G Wuo
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA.
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26
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Ohara T, Kaneda M, Saito T, Fujii N, Ohno H, Oishi S. Head-to-tail macrocyclization of cysteine-free peptides using an o -aminoanilide linker. Bioorg Med Chem Lett 2018; 28:1283-1286. [DOI: 10.1016/j.bmcl.2018.03.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/06/2018] [Accepted: 03/11/2018] [Indexed: 11/28/2022]
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27
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Yoshida M. Solid-Phase Total Synthesis of Biologically Active Cyclodepsipeptide Spiruchostatin A. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Sawyer TK, Partridge AW, Kaan HYK, Juang YC, Lim S, Johannes C, Yuen TY, Verma C, Kannan S, Aronica P, Tan YS, Sherborne B, Ha S, Hochman J, Chen S, Surdi L, Peier A, Sauvagnat B, Dandliker PJ, Brown CJ, Ng S, Ferrer F, Lane DP. Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges. Bioorg Med Chem 2018; 26:2807-2815. [PMID: 29598901 DOI: 10.1016/j.bmc.2018.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/20/2022]
Abstract
Macrocyclic α-helical peptides have emerged as a compelling new therapeutic modality to tackle targets confined to the intracellular compartment. Within the scope of hydrocarbon-stapling there has been significant progress to date, including the first stapled α-helical peptide to enter into clinical trials. The principal design concept of stapled α-helical peptides is to mimic a cognate (protein) ligand relative to binding its target via an α-helical interface. However, it was the proclivity of such stapled α-helical peptides to exhibit cell permeability and proteolytic stability that underscored their promise as unique macrocyclic peptide drugs for intracellular targets. This perspective highlights key learnings as well as challenges in basic research with respect to structure-based design, innovative chemistry, cell permeability and proteolytic stability that are essential to fulfill the promise of stapled α-helical peptide drug development.
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29
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Goto Y, Suga H. ArtificialIn VitroBiosynthesis Systems for the Development of Pseudo-Natural Products. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20170379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
- JST-PRESTO, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
- JST-CREST, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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30
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Hubert JG, Stepek IA, Noda H, Bode JW. Synthetic fermentation of β-peptide macrocycles by thiadiazole-forming ring-closing reactions. Chem Sci 2018; 9:2159-2167. [PMID: 29719689 PMCID: PMC5896468 DOI: 10.1039/c7sc05057g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/05/2018] [Indexed: 01/12/2023] Open
Abstract
A new thiadiazole-forming macrocyclization reaction enables the one-pot synthesis of cyclic β-peptide libraries from readily accessible building blocks without additional reagents.
Macrocyclic β-peptides were efficiently prepared using a thiadiazole-forming cyclization reaction between an α-ketoacid and a thiohydrazide. The linear β-peptide precursors were assembled from isoxazolidine monomers by α-ketoacid-hydroxylamine (KAHA) ligations with a bifunctional initiator – a process we have termed ‘synthetic fermentation’ due to the analogy of producing natural product-like molecules from simpler building blocks. The linear synthetic fermentation products underwent Boc-deprotection/thiadiazole-forming macrocyclization under aqueous, acidic conditions to provide the cyclic products in a one-pot process. This reaction sequence proceeds from easily accessed initiator and monomer building blocks without the need for additional catalysts or reagents, enabling facile production of macrocyclic β-peptides, a relatively underexplored structural class.
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Affiliation(s)
- Jonathan G Hubert
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
| | - Iain A Stepek
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
| | - Hidetoshi Noda
- Institute of Microbial Chemistry (Bikaken) , 3-14-23 Kamiosaki, Shinagawa-ku , Tokyo 141-0021 , Japan
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
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31
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Goto Y. Elaboration of Pseudo-natural Products Using Artificial In Vitro Biosynthesis Systems. YAKUGAKU ZASSHI 2018; 138:55-61. [DOI: 10.1248/yakushi.17-00186-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo
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32
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He R, Di Bonaventura I, Visini R, Gan BH, Fu Y, Probst D, Lüscher A, Köhler T, van Delden C, Stocker A, Hong W, Darbre T, Reymond JL. Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa. Chem Sci 2017; 8:7464-7475. [PMID: 29163899 PMCID: PMC5676089 DOI: 10.1039/c7sc01599b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/02/2017] [Indexed: 11/30/2022] Open
Abstract
A new family of cyclic antimicrobial peptides is reported targeting multidrug resistant Pseudomonas aeruginosa by membrane disruption.
Here we report a new family of cyclic antimicrobial peptides (CAMPs) targeting MDR strains of Pseudomonas aeruginosa. These CAMPs are cyclized via a xylene double thioether bridge connecting two cysteines placed at the ends of a linear amphiphilic alternating d,l-sequence composed of lysines and tryptophans. Investigations by transmission electron microscopy (TEM), dynamic light scattering and atomic force microscopy (AFM) suggest that these peptide macrocycles interact with the membrane to form lipid–peptide aggregates. Amphiphilic conformations compatible with membrane disruption are observed in high resolution X-ray crystal structures of fucosylated derivatives in complex with lectin LecB. The potential for optimization is highlighted by N-methylation of backbone amides leading to derivatives with similar antimicrobial activity but lower hemolysis.
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Affiliation(s)
- Runze He
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Ivan Di Bonaventura
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Ricardo Visini
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Bee-Ha Gan
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Yongchun Fu
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Daniel Probst
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Alexandre Lüscher
- Department of Microbiology and Molecular Medicine , University of Geneva , Service of Infectious Diseases , University Hospital of Geneva , Geneva , Switzerland
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine , University of Geneva , Service of Infectious Diseases , University Hospital of Geneva , Geneva , Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine , University of Geneva , Service of Infectious Diseases , University Hospital of Geneva , Geneva , Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Wenjing Hong
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland . .,State Key Laboratory of Physical Chemistry of Solid Surfaces , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Tamis Darbre
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
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33
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Sakurai Y, Mizumura W, Murata M, Hada T, Yamamoto S, Ito K, Iwasaki K, Katoh T, Goto Y, Takagi A, Kohara M, Suga H, Harashima H. Efficient siRNA Delivery by Lipid Nanoparticles Modified with a Nonstandard Macrocyclic Peptide for EpCAM-Targeting. Mol Pharm 2017; 14:3290-3298. [DOI: 10.1021/acs.molpharmaceut.7b00362] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yu Sakurai
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Hokkaido 060-0812, Japan
| | - Wataru Mizumura
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Hokkaido 060-0812, Japan
| | - Manami Murata
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Hokkaido 060-0812, Japan
| | - Tomoya Hada
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Hokkaido 060-0812, Japan
| | - Shoshiro Yamamoto
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Hokkaido 060-0812, Japan
| | - Kenichiro Ito
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Kazuhiro Iwasaki
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Takayuki Katoh
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Yuki Goto
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Asako Takagi
- Department of Microbiology
and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Michinori Kohara
- Department of Microbiology
and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Hideyoshi Harashima
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Hokkaido 060-0812, Japan
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34
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Henninot A, Collins JC, Nuss JM. The Current State of Peptide Drug Discovery: Back to the Future? J Med Chem 2017; 61:1382-1414. [PMID: 28737935 DOI: 10.1021/acs.jmedchem.7b00318] [Citation(s) in RCA: 633] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, peptide drug discovery has experienced a revival of interest and scientific momentum, as the pharmaceutical industry has come to appreciate the role that peptide therapeutics can play in addressing unmet medical needs and how this class of compounds can be an excellent complement or even preferable alternative to small molecule and biological therapeutics. In this Perspective, we give a concise description of the recent progress in peptide drug discovery in a holistic manner, highlighting enabling technological advances affecting nearly every aspect of this field: from lead discovery, to synthesis and optimization, to peptide drug delivery. An emphasis is placed on describing research efforts to overcome the inherent weaknesses of peptide drugs, in particular their poor pharmacokinetic properties, and how these efforts have been critical to the discovery, design, and subsequent development of novel therapeutics.
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Affiliation(s)
- Antoine Henninot
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - James C Collins
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - John M Nuss
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
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35
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Chettu SK, Konidena LNS, Korupolu RB, Kameswara Rao N, Doddipalla R, Gandham HB, Guduru R. Ring opening of benzoxazinones: An improved and efficient synthesis of clavatustides A & B. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.07.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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36
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Acylated heptapeptide binds albumin with high affinity and application as tag furnishes long-acting peptides. Nat Commun 2017; 8:16092. [PMID: 28714475 PMCID: PMC5520048 DOI: 10.1038/ncomms16092] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/24/2017] [Indexed: 12/12/2022] Open
Abstract
The rapid renal clearance of peptides in vivo limits this attractive platform for the treatment of a broad range of diseases that require prolonged drug half-lives. An intriguing approach for extending peptide circulation times works through a ‘piggy-back’ strategy in which peptides bind via a ligand to the long-lived serum protein albumin. In accordance with this strategy, we developed an easily synthesized albumin-binding ligand based on a peptide-fatty acid chimera that has a high affinity for human albumin (Kd=39 nM). This ligand prolongs the elimination half-life of cyclic peptides in rats 25-fold to over seven hours. Conjugation to a peptide factor XII inhibitor developed for anti-thrombotic therapy extends the half-life from 13 minutes to over five hours, inhibiting coagulation for eight hours in rabbits. This high-affinity albumin ligand could potentially extend the half-life of peptides in human to several days, substantially broadening the application range of peptides as therapeutics. A major challenge for the application of peptide therapeutics is their short half-life in vivo. Here, the authors design peptide-fatty acid chimeras bearing an engineered linker that promotes albumin binding and allows longer circulation times of therapeutic peptides in animal models.
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37
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Gautier A, Rodriguez R. PSL Chemical Biology Symposia First 2016 Edition: When Chemistry and Biology Share the Language of Discovery. Chembiochem 2017; 18:883-887. [PMID: 28371105 DOI: 10.1002/cbic.201700117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 01/18/2023]
Abstract
Chemical biology, the science of understanding biological processes at the molecular level, has grown exponentially with the development of chemical strategies to manipulate and quantify biology with unprecedented precision. Recent advances presented at the Université Paris Sciences et Lettres symposium are discussed.
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Affiliation(s)
- Arnaud Gautier
- Ecole Normale Supérieure, 24 rue Lhomond, 75005, Paris, France
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38
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Qian Z, Dougherty PG, Pei D. Targeting intracellular protein-protein interactions with cell-permeable cyclic peptides. Curr Opin Chem Biol 2017; 38:80-86. [PMID: 28388463 DOI: 10.1016/j.cbpa.2017.03.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for conventional drug modalities, because small molecules generally do not bind to their large, flat binding sites with high affinity, whereas monoclonal antibodies cannot cross the cell membrane to reach the targets. Cyclic peptides in the 700-2000 molecular-weight range have the sufficient size and a balanced conformational flexibility/rigidity for binding to flat PPI interfaces with antibody-like affinity and specificity. Several powerful cyclic peptide library technologies were developed over the past decade to rapidly discover potent, specific cyclic peptide ligands against proteins of interest including those involved in PPIs. Methods are also being developed to enhance the membrane permeability of cyclic peptides through both passive diffusion and active transport mechanisms. Integration of the permeability-enhancing elements into cyclic peptide design has led to an increasing number of cell-permeable and biologically active cyclic peptides against intracellular PPIs. In this account, we review the recent developments in the design and synthesis of cell-permeable cyclic peptides.
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Affiliation(s)
- Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Patrick G Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States.
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39
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Onagi J, Komatsu T, Ichihashi Y, Kuriki Y, Kamiya M, Terai T, Ueno T, Hanaoka K, Matsuzaki H, Hata K, Watanabe T, Nagano T, Urano Y. Discovery of Cell-Type-Specific and Disease-Related Enzymatic Activity Changes via Global Evaluation of Peptide Metabolism. J Am Chem Soc 2017; 139:3465-3472. [PMID: 28191944 DOI: 10.1021/jacs.6b11376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cellular homeostasis is maintained by a complex network of reactions catalyzed by enormous numbers of enzymatic activities (the enzymome), which serve to determine the phenotypes of cells. Here, we focused on the enzymomics of proteases and peptidases because these enzymes are an important class of disease-related proteins. We describe a system that (A) simultaneously evaluates metabolic activities of peptides using a series of exogenous peptide substrates and (B) identifies the enzymes that metabolize the specified peptide substrate with high throughput. We confirmed that the developed system was able to discover cell-type-specific and disease-related exo- and endopeptidase activities and identify the responsible enzymes. For example, we found that the activity of the endopeptidase neurolysin is highly elevated in human colorectal tumor tissue samples. This simple but powerful enzymomics platform should be widely applicable to uncover cell-type-specific reactions and altered enzymatic functions with potential value as biomarkers or drug targets in various disease states and to investigate the mechanisms of the underlying pathologies.
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Affiliation(s)
| | - Toru Komatsu
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Mako Kamiya
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | | | | | | | | | | | | | | | - Yasuteru Urano
- Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED) , 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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40
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Tran PT, Larsen CØ, Røndbjerg T, De Foresta M, Kunze MBA, Marek A, Løper JH, Boyhus LE, Knuhtsen A, Lindorff-Larsen K, Pedersen DS. Diversity-Oriented Peptide Stapling: A Third Generation Copper-Catalysed Azide-Alkyne Cycloaddition Stapling and Functionalisation Strategy. Chemistry 2017; 23:3490-3495. [DOI: 10.1002/chem.201700128] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Phuong Thu Tran
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Christian Ørnbøl Larsen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Tobias Røndbjerg
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Martina De Foresta
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Micha B. A. Kunze
- Structural Biology and NMR Laboratory; Department of Biology; University of Copenhagen; Ole Maaloes Vej 5 2200 Copenhagen Denmark
| | - Ales Marek
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; 16610 Prague 6 Czech Republic
| | - Jacob Hartvig Løper
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Lotte-Emilie Boyhus
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Astrid Knuhtsen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory; Department of Biology; University of Copenhagen; Ole Maaloes Vej 5 2200 Copenhagen Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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41
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Freeman MF, Helf MJ, Bhushan A, Morinaka BI, Piel J. Seven enzymes create extraordinary molecular complexity in an uncultivated bacterium. Nat Chem 2016; 9:387-395. [DOI: 10.1038/nchem.2666] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 10/02/2016] [Indexed: 12/20/2022]
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42
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Jongkees SAK, Umemoto S, Suga H. Linker-free incorporation of carbohydrates into in vitro displayed macrocyclic peptides. Chem Sci 2016; 8:1474-1481. [PMID: 28572907 PMCID: PMC5452274 DOI: 10.1039/c6sc04381j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022] Open
Abstract
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates.
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates. These reactions are selective for cysteine, and do not interfere with amplification of the nucleic acid component of an mRNA-displayed peptide. Furthermore, these reactions are shown to be compatible with two different macrocyclisation chemistries, and when applied to a peptide containing an N-terminal cysteine give a ketone that can be functionalised in an orthogonal manner. This new strategy can overcome a limitation of ribosomal translation, providing a means to incorporate untranslatable groups such as carbohydrates in amino acid side chains, and will allow for the ribosomal generation of glycopeptides, requiring only the introduction of a free thiol in the molecule to be incorporated. In combination with in vitro selection techniques, this strategy is envisaged to allow the discovery of biologically-active glycopeptides with a near-natural, but hydrolytically stable, thioglycosidic bond.
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Affiliation(s)
- S A K Jongkees
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - S Umemoto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan . .,JST CREST , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan
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43
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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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44
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Schwochert J, Lao Y, Pye CR, Naylor MR, Desai PV, Gonzalez Valcarcel IC, Barrett JA, Sawada G, Blanco MJ, Lokey RS. Stereochemistry Balances Cell Permeability and Solubility in the Naturally Derived Phepropeptin Cyclic Peptides. ACS Med Chem Lett 2016; 7:757-61. [PMID: 27563399 DOI: 10.1021/acsmedchemlett.6b00100] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022] Open
Abstract
Cyclic peptide (CP) natural products provide useful model systems for mapping "beyond-Rule-of-5" (bRo5) space. We identified the phepropeptins as natural product CPs with potential cell permeability. Synthesis of the phepropeptins and epimeric analogues revealed much more rapid cellular permeability for the natural stereochemical pattern. Despite being more cell permeable, the natural compounds exhibited similar aqueous solubility as the corresponding epimers, a phenomenon explained by solvent-dependent conformational flexibility among the natural compounds. When analyzing the polarity of the solution structures we found that neither the number of hydrogen bonds nor the total polar surface area accurately represents the solvation energies of the high and low dielectric conformations. This work adds to a growing number of natural CPs whose solvent-dependent conformational behavior allows for a balance between aqueous solubility and cell permeability, highlighting structural flexibility as an important consideration in the design of molecules in bRo5 chemical space.
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Affiliation(s)
- Joshua Schwochert
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Yongtong Lao
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Cameron R. Pye
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Matthew R. Naylor
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Prashant V. Desai
- Lilly
Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | | | - Jaclyn A. Barrett
- Lilly
Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Geri Sawada
- Lilly
Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Maria-Jesus Blanco
- Lilly
Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - R. Scott Lokey
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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45
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Affiliation(s)
- Raphael M. Franzini
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Cassie Randolph
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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46
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Chettu SK, Madhu RB, Raolji GB, Babu KR, Rao NSK, Gopalakrishnan S, Ismail A, Reddy GB, Shafi S. First total synthesis of cyclodepsipeptides clavatustide A and B and their enantiomers. RSC Adv 2016. [DOI: 10.1039/c6ra08861a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The enantiopure synthesis of clavatustides A (1) and B (3) were accomplished by a seven step synthetic protocol starting from commercially available (R)-phenyllactic acid.
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Affiliation(s)
- Suresh Kumar Chettu
- GVK Biosciences Private Limited
- Medicinal Chemistry Laboratory
- Hyderabad 500076
- India
| | | | | | - Korupolu Raghu Babu
- Andhra University
- Department of Engineering Chemistry
- Andhra University College of Engineering (A)
- Vishakhapatnam 530003
- India
| | - N. S. Kameswara Rao
- GVK Biosciences Private Limited
- Medicinal Chemistry Laboratory
- Hyderabad 500076
- India
| | | | - Ayesha Ismail
- National Institute of Nutrition
- Hyderabad-500007
- India
| | | | - Syed Shafi
- Department of Chemistry
- New Delhi-110062
- India
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47
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A Fluorescent Imaging Probe Based on a Macrocyclic Scaffold That Binds to Cellular EpCAM. J Mol Evol 2015; 81:210-7. [PMID: 26553371 DOI: 10.1007/s00239-015-9710-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/24/2015] [Indexed: 12/17/2022]
Abstract
Here, we report a fluorescent probe based on a macrocyclic peptide scaffold that specifically stains EpCAM-expressing MCF7 cells. The 14-mer macrocyclic peptide binding to the extracellular domain of EpCAM with a dissociation constant in the low nM range (1.7 nM) was discovered using the random non-standard peptide-integrated discovery system. Notably, this probe containing a fluorescence tag is less than 3000 Da in total and able to visualize nearly every live cell under high cell-density conditions, which was not achieved by the conventional mAb staining method. This suggests that the molecular probe based on the compact macrocyclic scaffold has great potentials as an imaging tool for the EpCAM biomarker as well as a delivery vehicle for drug conjugates.
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48
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Casi G, Neri D. Antibody–Drug Conjugates and Small Molecule–Drug Conjugates: Opportunities and Challenges for the Development of Selective Anticancer Cytotoxic Agents. J Med Chem 2015; 58:8751-61. [DOI: 10.1021/acs.jmedchem.5b00457] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Giulio Casi
- Philochem AG, Libernstrasse 3, CH8112 Otelfingen, Switzerland
| | - Dario Neri
- Department
of Chemistry and Applied Biosciences, Institute of Pharmaceutical
Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
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