Structural diversity in de novo cyclic peptide ligands from genetically encoded library technologies

NOTE: This preprint has been retracted by consensus from all authors.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.

Download Full-text

Phage-Display Based Discovery and Characterization of Peptide Ligands against WDR5

Molecules ◽

10.3390/molecules26051225 ◽

2021 ◽

Vol 26 (5) ◽

pp. 1225

Author(s):

Jiawen Cao ◽

Tiantian Fan ◽

Yanlian Li ◽

Zhiyan Du ◽

Lin Chen ◽

...

Keyword(s):

Phage Display ◽

Cyclic Peptide ◽

Protein Complexes ◽

Peptide Ligands ◽

Phage Library ◽

Cancer Drug ◽

Protein Protein Interaction ◽

Phage Display Technique ◽

Peptide Mimic ◽

Human Proteins

WD40 is a ubiquitous domain presented in at least 361 human proteins and acts as scaffold to form protein complexes. Among them, WDR5 protein is an important mediator in several protein complexes to exert its functions in histone modification and chromatin remodeling. Therefore, it was considered as a promising epigenetic target involving in anti-cancer drug development. In view of the protein–protein interaction nature of WDR5, we initialized a campaign to discover new peptide-mimic inhibitors of WDR5. In current study, we utilized the phage display technique and screened with a disulfide-based cyclic peptide phage library. Five rounds of biopanning were performed and isolated clones were sequenced. By analyzing the sequences, total five peptides were synthesized for binding assay. The four peptides are shown to have the moderate binding affinity. Finally, the detailed binding interactions were revealed by solving a WDR5-peptide cocrystal structure.

Download Full-text

Design, selection, and development of cyclic peptide ligands for human erythropoietin

Journal of Chromatography A ◽

10.1016/j.chroma.2017.04.019 ◽

2017 ◽

Vol 1500 ◽

pp. 105-120 ◽

Cited By ~ 14

Author(s):

William S. Kish ◽

Hiroyuki Sachi ◽

Amith D. Naik ◽

Matthew K. Roach ◽

Benjamin G. Bobay ◽

...

Keyword(s):

Cyclic Peptide ◽

Peptide Ligands ◽

Human Erythropoietin ◽

Design Selection

Download Full-text

Alteration of Actin Organization by Jaspamide Inhibits Ruffling, but not Phagocytosis or Oxidative Burst, in HL-60 Cells and Human Monocytes

Blood ◽

10.1182/blood.v93.11.3994 ◽

1999 ◽

Vol 93 (11) ◽

pp. 3994-4005 ◽

Cited By ~ 15

Author(s):

Ina Fabian ◽

Drora Halperin ◽

Smadar Lefter ◽

Leonid Mittelman ◽

Rom T. Altstock ◽

...

Keyword(s):

Oxidative Burst ◽

Phagocytic Activity ◽

Mammalian Cells ◽

Molecular Mechanisms ◽

Cyclic Peptide ◽

De Novo ◽

Human Monocytes ◽

Actin Organization ◽

Fibrous Network ◽

Intracellular Movement

Abstract Jaspamide, a naturally occurring cyclic peptide isolated from the marine sponge Hemiastrella minor, has fungicidal and growth-inhibiting activities. Exposure of promyelocytic HL-60 cells and human monocytes to jaspamide induces a dramatic reorganization of actin from a typical fibrous network to focal aggregates. HL-60 cells exposed to 5 × 10−8 mol/L or 10−7 mol/L jaspamide exhibited a reduced proliferation rate. In addition, 10−7mol/L jaspamide induced maturation of HL-60 cells as indicated by the appearance of a lobulated nucleus in 55% ± 5% of the cells and immunophenotypic maturation of the leukemia cells (upregulation of CD16 and CD14 B antigens). Further characterization has shown that F-actin is aggregated both in HL-60 cells and in human monocytes exposed to 10−7 mol/L jaspamide. Well-spread cultured human monocytes contracted and adopted round shapes after treatment with jaspamide. Moreover, a dose-dependent increase in both total actin and de novo synthesized portions of the soluble actin was observed in jaspamide-treated HL-60 cells. Jaspamide treatment inhibits ruffling and intracellular movement in HL-60 cells and monocytes, but does not affect phagocytic activity or respiratory burst activity. The consequential effects of jaspamide-induced actin reorganization on ruffling, versus its negligible effect on phagocytosis and oxidative burst, may shed light on molecular mechanisms of actin involvement in these processes. Jaspamide disrupts the actin cytoskeleton of normal and malignant mammalian cells with no significant effect on phagocytic activity and may, therefore, be considered as a novel therapeutic agent.

Download Full-text

De novo designed cyclic-peptide heme complexes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2231273100 ◽

2003 ◽

Vol 100 (23) ◽

pp. 13140-13145 ◽

Cited By ~ 30

Author(s):

M. M. Rosenblatt ◽

J. Wang ◽

K. S. Suslick

Keyword(s):

Cyclic Peptide ◽

De Novo

Download Full-text

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

10.1101/2021.04.13.439703 ◽

2021 ◽

Author(s):

Chris Papadopoulos ◽

Isabelle Callebaut ◽

Jean-Christophe Gelly ◽

Isabelle Hatin ◽

Olivier Namy ◽

...

Keyword(s):

Protein Structure ◽

Amino Acid ◽

De Novo ◽

Protein Structures ◽

Structural Diversity ◽

Building Blocks ◽

Amino Acid Sequences ◽

Novel Genes ◽

Noncoding Sequences ◽

De Novo Gene

The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic ORFs (Open Reading Frames) of S. cerevisiae with the aim of (i) exploring whether the large structural diversity observed in proteomes is already present in noncoding sequences, and (ii) estimating the potential of the noncoding genome to produce novel protein bricks that can either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural diversity of canonical proteins with strikingly the majority predicted as foldable. Then, we investigated the early stages of de novo gene birth by identifying intergenic ORFs with a strong translation signal in ribosome profiling experiments and by reconstructing the ancestral sequences of 70 yeast de novo genes. This enabled us to highlight sequence and structural factors determining de novo gene emergence. Finally, we showed a strong correlation between the fold potential of de novo proteins and the one of their ancestral amino acid sequences, reflecting the relationship between the noncoding genome and the protein structure universe.

Download Full-text

Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha

10.1101/2020.12.22.423164 ◽

2020 ◽

Author(s):

Anna E. Syme ◽

Todd G.B. McLay ◽

Frank Udovicic ◽

David J. Cantrill ◽

Daniel J. Murphy

Keyword(s):

Mitochondrial Genome ◽

Chloroplast Genome ◽

De Novo ◽

Genomic Structure ◽

Structural Diversity ◽

Mitochondrial Genomes ◽

Long Reads ◽

Organelle Genomes ◽

Long Read ◽

Assembly Algorithms

AbstractAlthough organelle genomes are typically represented as single, static, circular molecules, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found different assemblies revealed contrasting arrangements of genomic segments; a hypothesis supported by mapped reads spanning alternate paths.

Download Full-text

Alteration of Actin Organization by Jaspamide Inhibits Ruffling, but not Phagocytosis or Oxidative Burst, in HL-60 Cells and Human Monocytes

Blood ◽

10.1182/blood.v93.11.3994.411k39_3994_4005 ◽

1999 ◽

Vol 93 (11) ◽

pp. 3994-4005

Author(s):

Ina Fabian ◽

Drora Halperin ◽

Smadar Lefter ◽

Leonid Mittelman ◽

Rom T. Altstock ◽

...

Keyword(s):

Oxidative Burst ◽

Phagocytic Activity ◽

Mammalian Cells ◽

Molecular Mechanisms ◽

Cyclic Peptide ◽

De Novo ◽

Human Monocytes ◽

Actin Organization ◽

Fibrous Network ◽

Intracellular Movement

Jaspamide, a naturally occurring cyclic peptide isolated from the marine sponge Hemiastrella minor, has fungicidal and growth-inhibiting activities. Exposure of promyelocytic HL-60 cells and human monocytes to jaspamide induces a dramatic reorganization of actin from a typical fibrous network to focal aggregates. HL-60 cells exposed to 5 × 10−8 mol/L or 10−7 mol/L jaspamide exhibited a reduced proliferation rate. In addition, 10−7mol/L jaspamide induced maturation of HL-60 cells as indicated by the appearance of a lobulated nucleus in 55% ± 5% of the cells and immunophenotypic maturation of the leukemia cells (upregulation of CD16 and CD14 B antigens). Further characterization has shown that F-actin is aggregated both in HL-60 cells and in human monocytes exposed to 10−7 mol/L jaspamide. Well-spread cultured human monocytes contracted and adopted round shapes after treatment with jaspamide. Moreover, a dose-dependent increase in both total actin and de novo synthesized portions of the soluble actin was observed in jaspamide-treated HL-60 cells. Jaspamide treatment inhibits ruffling and intracellular movement in HL-60 cells and monocytes, but does not affect phagocytic activity or respiratory burst activity. The consequential effects of jaspamide-induced actin reorganization on ruffling, versus its negligible effect on phagocytosis and oxidative burst, may shed light on molecular mechanisms of actin involvement in these processes. Jaspamide disrupts the actin cytoskeleton of normal and malignant mammalian cells with no significant effect on phagocytic activity and may, therefore, be considered as a novel therapeutic agent.

Download Full-text

A phage display-based strategy for the de novo creation of disulfide-constrained and isomer-free bicyclic peptide affinity reagents

Chemical Communications ◽

10.1039/c7cc09142g ◽

2018 ◽

Vol 54 (32) ◽

pp. 4029-4032 ◽

Cited By ~ 8

Author(s):

Mirao Zha ◽

Ping Lin ◽

Hongwei Yao ◽

Yibing Zhao ◽

Chuanliu Wu

Keyword(s):

Phage Display ◽

Genetic Code ◽

De Novo ◽

Screening Strategy ◽

Peptide Ligands ◽

Disulfide Bridges ◽

Chemical Modifications ◽

Affinity Reagents ◽

Peptide Affinity

We report a phage-screening strategy for the development of bicyclic peptide ligands constrained with two sterically different and isomerically forbidden noncanonical disulfide bridges without elaborate chemical modifications and recourses to genetic code reprogramming.

Download Full-text