A Target-Based Method for Designing Heterochiral Cyclic Peptide Binders: De Novo Inhibitors of the PD-1/PD-L1 Interaction

NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above. ------------------------------------------------------------------------ Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-i3 and PD-i6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our de novo design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.

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Target-Templated de novo Design of Macrocyclic D-/L-Peptides: Inhibitors of the PD-1/PD-L1 Interaction

10.26434/chemrxiv.11663337 ◽

2020 ◽

Author(s):

Salvador Guardiola ◽

Monica Varese ◽

Xavier Roig ◽

Jesús Garcia ◽

Ernest Giralt

Keyword(s):

Protein Interactions ◽

Cyclic Peptides ◽

General Framework ◽

Large Scale ◽

De Novo ◽

Inhibitory Effect ◽

Original Text ◽

Protein Protein Interactions ◽

Retraction Notice ◽

Pharmaceutical Properties

NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above. ------------------------------------------------------------------------ Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-i3 and PD-i6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our de novo design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.

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A Target-Based Method for Designing Heterochiral Cyclic Peptide Binders: De Novo Inhibitors of the PD-1/PD-L1 Interaction

10.26434/chemrxiv.11663337.v1 ◽

2020 ◽

Author(s):

Salvador Guardiola ◽

Monica Varese ◽

Xavier Roig ◽

Jesús Garcia ◽

Ernest Giralt

Keyword(s):

Protein Interactions ◽

Cyclic Peptides ◽

General Framework ◽

Large Scale ◽

Cyclic Peptide ◽

De Novo ◽

Inhibitory Effect ◽

Protein Protein Interactions ◽

Macrocyclic Peptides ◽

Pharmaceutical Properties

Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-i3 and PD-i6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our de novo design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.

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The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.014781 ◽

2020 ◽

Vol 295 (42) ◽

pp. 14510-14521 ◽

Cited By ~ 1

Author(s):

Mark F. Fisher ◽

Colton D. Payne ◽

Thaveshini Chetty ◽

Darren Crayn ◽

Oliver Berkowitz ◽

...

Keyword(s):

Disulfide Bonds ◽

Cyclic Peptides ◽

Cyclic Peptide ◽

De Novo ◽

Forest Tree ◽

Whole Genome Sequencing Data ◽

The Novel ◽

Rna Seq ◽

Sequencing Data ◽

The Family

Cyclic peptides are reported to have antibacterial, antifungal, and other bioactivities. Orbitides are a class of cyclic peptides that are small, head-to-tail cyclized, composed of proteinogenic amino acids and lack disulfide bonds; they are also known in several genera of the plant family Rutaceae. Melicope xanthoxyloides is the Australian rain forest tree of the Rutaceae family in which evolidine, the first plant cyclic peptide, was discovered. Evolidine (cyclo-SFLPVNL) has subsequently been all but forgotten in the academic literature, so to redress this we used tandem MS and de novo transcriptomics to rediscover evolidine and decipher its biosynthetic origin from a short precursor just 48 residues in length. We also identified another six M. xanthoxyloides orbitides using the same techniques. These peptides have atypically diverse C termini consisting of residues not recognized by either of the known proteases plants use to macrocyclize peptides, suggesting new cyclizing enzymes await discovery. We examined the structure of two of the novel orbitides by NMR, finding one had a definable structure, whereas the other did not. Mining RNA-seq and whole genome sequencing data from other species of the Rutaceae family revealed that a large and diverse family of peptides is encoded by similar sequences across the family and demonstrates how powerful de novo transcriptomics can be at accelerating the discovery of new peptide families.

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Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057114566803 ◽

2015 ◽

Vol 20 (5) ◽

pp. 563-576 ◽

Cited By ~ 19

Author(s):

Andrew D. Foster ◽

James D. Ingram ◽

Eilidh K. Leitch ◽

Katherine R. Lennard ◽

Eliot L. Osher ◽

...

Keyword(s):

Protein Interactions ◽

High Throughput Screening ◽

Cyclic Peptides ◽

Cyclic Peptide ◽

Peptide Libraries ◽

Successful Implementation ◽

Protein Protein Interactions ◽

Lead Discovery ◽

Small Molecule Libraries ◽

The Creation

The identification of initial hits is a crucial stage in the drug discovery process. Although many projects adopt high-throughput screening of small-molecule libraries at this stage, there is significant potential for screening libraries of macromolecules created using chemical biology approaches. Not only can the production of the library be directly interfaced with a cell-based assay, but these libraries also require significantly fewer resources to generate and maintain. In this context, cyclic peptides are increasingly viewed as ideal scaffolds and have proven capability against challenging targets such as protein-protein interactions. Here we discuss a range of methods used for the creation of cyclic peptide libraries and detail examples of their successful implementation.

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Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches

Journal of The Royal Society Interface ◽

10.1098/rsif.2011.0584 ◽

2011 ◽

Vol 9 (66) ◽

pp. 20-33 ◽

Cited By ~ 58

Author(s):

Pierre Tuffery ◽

Philippe Derreumaux

Keyword(s):

Binding Affinity ◽

Protein Interactions ◽

Large Scale ◽

De Novo ◽

Three Dimensional ◽

Dimensional Structure ◽

Structure Based Drug Design ◽

Body Protein ◽

Technical Problems ◽

Multi Body

The recognition process between a protein and a partner represents a significant theoretical challenge. In silico structure-based drug design carried out with nothing more than the three-dimensional structure of the protein has led to the introduction of many compounds into clinical trials and numerous drug approvals. Central to guiding the discovery process is to recognize active among non-active compounds. While large-scale computer simulations of compounds taken from a library (virtual screening) or designed de novo are highly desirable in the post-genomic area, many technical problems remain to be adequately addressed. This article presents an overview and discusses the limits of current computational methods for predicting the correct binding pose and accurate binding affinity. It also presents the performances of the most popular algorithms for exploring binary and multi-body protein interactions.

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Target-templated de novo design of macrocyclic d-/l-peptides: discovery of drug-like inhibitors of PD-1

Chemical Science ◽

10.1039/d1sc01031j ◽

2021 ◽

Vol 12 (14) ◽

pp. 5164-5170

Author(s):

Salvador Guardiola ◽

Monica Varese ◽

Xavier Roig ◽

Macarena Sánchez-Navarro ◽

Jesús García ◽

...

Keyword(s):

Specific Surface ◽

Protein Interactions ◽

In Silico ◽

Cyclic Peptides ◽

De Novo ◽

De Novo Design ◽

Target Protein ◽

Surface Patch ◽

Protein Protein Interactions

In silico design of heterochiral cyclic peptides that bind to a specific surface patch on the target protein (PD-1, in this case) and disrupt protein–protein interactions.

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De novo prediction of RNA-protein interactions with Graph Neural Networks

10.1101/2021.09.28.462100 ◽

2021 ◽

Author(s):

Viplove Arora ◽

Guido Sanguinetti

Keyword(s):

Neural Networks ◽

Protein Interactions ◽

Large Scale ◽

Rna Binding ◽

De Novo ◽

Rna Binding Proteins ◽

Large Data ◽

Data Sets ◽

Graph Neural Networks ◽

Post Transcriptional Regulation

RNA-binding proteins (RBPs) are key co- and post-transcriptional regulators of gene expression, playing a crucial role in many biological processes. Experimental methods like CLIP-seq have enabled the identification of transcriptome-wide RNA-protein interactions for select proteins, however the time and resource intensive nature of these technologies call for the development of computational methods to complement their predictions. Here we leverage recent, large-scale CLIP-seq experiments to construct a de novo predictor of RNA-protein interactions based on graph neural networks (GNN). We show that the GNN method allows not only to predict missing links in a RNA-protein network, but to predict the entire complement of targets of previously unassayed proteins, and even to reconstruct the entire network of RNA-protein interactions in different conditions based on minimal information. Our results demonstrate the potential of machine learning methods to extract useful information on post-transcriptional regulation from large data sets.

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The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides

10.1101/2020.06.10.145326 ◽

2020 ◽

Author(s):

Mark F. Fisher ◽

Colton Payne ◽

Thaveshini Chetty ◽

Darren Crayn ◽

Oliver Berkowitz ◽

...

Keyword(s):

Disulfide Bonds ◽

Cyclic Peptides ◽

Cyclic Peptide ◽

De Novo ◽

Forest Tree ◽

Whole Genome Sequencing Data ◽

Resonance Spectroscopy ◽

The Novel ◽

Rna Seq ◽

Sequencing Data

AbstractCyclic peptides are reported to have antibacterial, antifungal and other bioactivities. Several genera of the Rutaceae family are known to produce orbitides, which are small head-to-tail cyclic peptides composed of proteinogenic amino acids and lacking disulfide bonds. Melicope xanthoxyloides is an Australian rain forest tree of the Rutaceae family in which evolidine - the first plant cyclic peptide - was discovered. Evolidine (cyclo-SFLPVNL) has subsequently been all but forgotten in the academic literature, but here we use tandem mass spectrometry to rediscover evolidine and using de novo transcriptomics we show its biosynthetic origin to be from a short precursor just 48 residues in length. In all, seven M. xanthoxyloides orbitides were found and they had atypically diverse C-termini consisting of residues not recognized by either of the known proteases plants use to macrocyclize peptides. Two of the novel orbitides were studied by nuclear magnetic resonance spectroscopy and although one had definable structure, the other did not. By mining RNA-seq and whole genome sequencing data from other species, it was apparent that a large and diverse family of peptides is encoded by sequences like these across the Rutaceae.

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Amide-to-Ester Substitution Improves Membrane Permeability of a Cyclic Peptide Without Altering Its Three-Dimensional Structure

10.26434/chemrxiv.12272861 ◽

2020 ◽

Author(s):

Yuki Hosono ◽

Jumpei Morimoto ◽

Chad Townsend ◽

Colin N. Kelly ◽

Matthew R. Naylor ◽

...

Keyword(s):

Membrane Permeability ◽

Protein Interactions ◽

Cyclic Peptides ◽

Rational Design ◽

Cyclic Peptide ◽

Three Dimensional ◽

Amide Bond ◽

Cell Membrane Permeability ◽

Dimensional Structure ◽

Molecular Mechanics Calculations

<div> <div> <div> Cyclic peptides are attractive molecules as inhibitors with high affinity and selectivity against intracellular protein-protein interactions (PPIs). On the other hand, cyclic peptides generally have low passive cell-membrane permeability, which makes it difficult to discover cyclic peptides that efficiently permeate into cells and inhibit intracellular PPIs. Here, we show that backbone amide-to-ester substitutions are useful for improving membrane permeability of peptides. Permeability in a series of model dipeptides increased upon amide-to-ester substitution. Amide-to-ester substitutions increased permeability in the same manner as amide-to-N-methyl amide substitutions, which are conventionally used for increasing permeability. Furthermore, amide-to-ester substitutions of exposed amides of a cyclic peptide successfully improved permeability. Conformational studies of the cyclic peptides using NMR and molecular mechanics calculations revealed that an amide-to-ester substitution of an exposed amide bond did not affect its low-energy conformation in CDCl3, in contrast with an N-methyl amide substitution. We envision that amide-to-ester substitution will be a potentially useful strategy for rational design of bioactive peptides with high membrane permeability. </div> </div> </div>

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