Cyclization of peptides with two chemical bridges affords large scaffold diversities

Kale, Sangram S.; Villequey, Camille; Kong, Xiangxing; Zorzi, Alessandro; Deyle, Kaycie M.; Heinis, Christian

doi:10.1038/s41557-018-0042-7

Cited by 142 publications

(170 citation statements)

References 41 publications

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“…Other groups, using display-based technologies, have identified cyclic peptides with low-nanomolar affinities 21 ; these cyclic peptides, however, feature a larger ring structure (up to 14 randomized amino acid positions), and therefore benefit from a higher enthalpic contribution to binding free energy. In other instances, the peptide macrocycle is constrained via multifunctional crosslinkers to increase both the enthalpic and entropic contributions of binding free energy 22 .…”

Section: Binding Affinity Analysis Of Lysozyme Cyclic Peptidesmentioning

confidence: 99%

Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display

Bacon

Blain

Burroughs

et al. 2020

Preprint

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Cyclic peptides with engineered protein-binding activity have gained increasing attention for use in therapeutic and biotechnology applications. We describe the efficient isolation and characterization of cyclic peptide binders from genetically encoded combinatorial libraries using yeast surface display. Here, peptide cyclization is achieved by disuccinimidyl glutarate-mediated crosslinking of amine groups within a linear peptide sequence that is expressed as a yeast cell surface fusion. Using this approach, we first screened a library of cyclic heptapeptides by magnetic selection and fluorescence activated cell sorting (FACS), to isolate binders for a model target (lysozyme) with low micromolar binding affinity (K D ~ 1.2 -3.7 µM). The isolated peptides bound lysozyme selectively, and only when cyclized. Importantly, we showed that yeast surface displayed cyclic peptides could be used to efficiently obtain quantitative estimates of binding affinity, without chemical synthesis of the selected peptides. Subsequently, to demonstrate broader applicability of our approach, we isolated cyclic heptapeptides that bind human interleukin-17 (IL-17) using yeast-displayed IL-17 as a target for magnetic selection, followed by FACS using recombinant IL-17. Molecular docking simulations and follow-up experimental analyses identified a candidate cyclic peptide that binds IL-17 in its receptor binding region with moderate affinity (K D ~ 300 nM). Taken together, our results show that yeast surface display can be used to efficiently isolate and characterize cyclic peptides generated by chemical modification from combinatorial libraries.

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Section: Binding Affinity Analysis Of Lysozyme Cyclic Peptidesmentioning

confidence: 99%

Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display

Bacon

Blain

Burroughs

et al. 2020

Preprint

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“…As described in the introduction, a wide range of reagents containing two thiol‐selective electrophiles, can efficiently cyclize peptides that are terminally flanked with cysteines. Previous work with phage display peptide libraries has shown that peptides with cysteines spaced by only one amino acid (Cys‐Xaa‐Cys) can efficiently be cyclized with bis‐electrophile reagents . A potential challenge was that such reagents could theoretically also react with the DNA, in particular when the reagents had reacted with a first thiol group and the reaction with DNA would happen intramolecularly.…”

Section: Resultsmentioning

confidence: 99%

Synthesis of DNA‐Encoded Disulfide‐ and Thioether‐Cyclized Peptides

2019

Self Cite

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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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“…Another option is the introduction of chemical post-translational modifications (cPTM) that can vastly expand the diversity of peptide libraries, for example, by phosphorylation [189], conjugation to glycans [190,191], attachment of a fluorescent reporter [192], or ligation to a synthetic peptide fragment [193]. By introducing constrained topologies, cyclic [194] or bicyclic [195] variants can be generated [187]. However, cPTMs are not quantitative.…”

Section: Incorporating Unnatural Amino Acids and Constraints Into (Limentioning

confidence: 99%

Evolving a Peptide: Library Platforms and Diversification Strategies

Bozovičar

Bratkovič

2019

IJMS

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Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.

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Cyclization of peptides with two chemical bridges affords large scaffold diversities

Cited by 142 publications

References 41 publications

Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display

Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display

Synthesis of DNA‐Encoded Disulfide‐ and Thioether‐Cyclized Peptides

Evolving a Peptide: Library Platforms and Diversification Strategies

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