scholarly journals Peptide Dendrimers: From Enzyme Models to Antimicrobials and Transfection Reagents

2021 ◽  
Vol 75 (6) ◽  
pp. 535-538
Author(s):  
Jean-Louis Reymond
Keyword(s):  
Solid Phase ◽  
Chemical Space ◽  
Solid Phase Peptide Synthesis ◽  
Multidrug Resistant ◽  
Peptide Sequence ◽  
Enzyme Models ◽  
Peptide Dendrimers ◽  
Diamino Acid ◽  
Cooperativity Effects ◽  
Protein Models

Aiming at studying cooperativity effects between amino acids in easily accessible protein models, we have explored the chemistry of peptide dendrimers, which we obtain as pure products by solid-phase peptide synthesis using a branching diamino acid such as lysine at every second or third position in a peptide sequence, followed by reverse-phase HPLC purification. This article reviews discoveries driven by combinatorial library synthesis and screening, including enantioselective esterase and aldolase enzyme models, cobalamin binding and peroxidase dendrimers, glycopeptide dendrimer biofilm inhibitors and their X-ray crystal structures as complexes with lectins, antimicrobial peptide dendrimers active against multidrug resistant Gram-negative bacteria, and transfection reagents for siRNA and CRISPR-Cas9 plasmid DNA. Latest developments include cheminformatics and artificial intelligence for exploring the peptide chemical space, and the principle of stereorandomization to understand the role of peptide chirality in activity.

scholarly journals On-Resin Strategy to Label α-Conotoxins: Cy5-RgIA, a Potent α9α10 Nicotinic Acetylcholine Receptor Imaging Probe

2020 ◽  
Vol 73 (4) ◽  
pp. 327
Author(s):  
Markus Muttenthaler ◽  
Simon T. Nevin ◽  
Marco Inserra ◽  
Richard J. Lewis ◽  
David J. Adams ◽  
...  
Keyword(s):  
Acetylcholine Receptor ◽  
Nicotinic Acetylcholine Receptor ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Resonance Energy ◽  
Peptide Sequence ◽  
Hill Coefficient ◽  
Receptor Imaging ◽  
Nicotinic Acetylcholine ◽  
Site Specific

In-solution conjugation is the most commonly used strategy to label peptides and proteins with fluorophores. However, lack of site-specific control and high costs of fluorophores are recognised limitations of this approach. Here, we established facile access to grams of Cy5-COOH via a two-step synthetic route, demonstrated that Cy5 is stable to HF treatment and therefore compatible with tert-butyloxycarbonyl solid phase peptide synthesis (Boc-SPPS), and coupled Cy5 to the N-terminus of α-conotoxin RgIA while still attached to the resin. Folding of the two-disulfide containing Cy5-RgIA benefitted from the hydrophobic nature of Cy5, resulting in only the globular disulfide bond isomer. In contrast, wild-type α-RgIA folded into the inactive ribbon and bioactive globular isomer under the same conditions. Labelled α-RgIA retained its ability to inhibit acetylcholine (100µM)-evoked current reversibly with an IC50 of 5.0nM (Hill coefficient=1.7) for Cy5-RgIA and an IC50 of 1.6 (Hill coefficient=1.2) for α-RgIA at the α9α10 nicotinic acetylcholine receptor (nAChR) heterologously expressed in Xenopus oocytes. Cy5-RgIA was then used to successfully visualise nAChRs in the RAW264.7 mouse macrophage cell line. This work introduced not only a new and valuable nAChR probe, but also a new versatile synthetic strategy that facilitates production of milligram to gram quantities of fluorophore-labelled peptides at low cost, which is often required for invivo experiments. The strategy is compatible with Boc- and 9-fluorenylmethoxycarbonyl (Fmoc)-chemistry, allows site-specific labelling of free amines anywhere in the peptide sequence, and can also be used for the introduction of Cy3/Cy5 fluorescence resonance energy transfer (FRET) pairs.

scholarly journals Stereorandomization as a Method to Probe Peptide Bioactivity

2020 ◽  
Author(s):  
Thissa N. Siriwardena ◽  
Bee-Ha Gan ◽  
Thilo Köhler ◽  
Christian van Delden ◽  
Sacha Javor ◽  
...  
Keyword(s):  
Cyclic Peptide ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Therapeutic Index ◽  
Building Blocks ◽  
Polymyxin B ◽  
High Yield ◽  
Peptide Antibiotic ◽  
Disruptive Effect ◽  
Peptide Dendrimers

<p>Solid-phase peptide synthesis (SPPS) is usually performed with optically pure building blocks to prepare peptides as single enantiomers. Herein we report that SPPS using racemic amino acids provides stereorandomized (<i>sr</i>) peptides, containing up to billions of different stereoisomers,<a> </a>as well-defined single HPLC peak, single mass products with high yield, which can be used to investigate peptide bioactivity. To exemplify our method, we show that stereorandomization abolishes the membrane disruptive effect of α-helical amphiphilic antimicrobial peptides but preserves their antibiofilm effect, implying different mechanisms involving folded versus disordered conformations. For antimicrobial peptide dendrimers by contrast, stereorandomization preserves antibacterial, membrane disruptive and anti-biofilm effects but reduces hemolysis and cytotoxicity, thereby increasing their therapeutic index. Finally, we identify partially stereorandomized analogs of the last resort cyclic peptide antibiotic polymyxin B with preserved antibacterial activity but lacking membrane disruptive and lipopolysaccharide neutralizing activity, pointing to the existence of additional targets.</p>

scholarly journals Peptidomimetic Modulators of BACE1

2020 ◽  
Vol 73 (4) ◽  
pp. 366
Author(s):  
John Paul Juliano ◽  
David H. Small ◽  
Marie-Isabel Aguilar
Keyword(s):  
Amino Acids ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Amyloid Β ◽  
Amino Acid Sequences ◽  
Peptide Sequence ◽  
Fluorescent Substrate ◽  
Double Mutation ◽  
Affinity Peptide ◽  
Inhibition Potency

The β-site APP Cleaving enzyme 1 (BACE1) is a membrane-associated aspartyl protease which mediates the production of amyloid-β (Aβ), a major component of amyloid plaques in the Alzheimer’s disease brain. We have synthesised and characterised a series of peptidomimetic analogues of BACE substrates that incorporate two distinct stabilising structures. To demonstrate the potential activity of these compounds, a variety of assaying strategies were used to investigate cleavage susceptibility and inhibition potency under competitive and non-competitive conditions. β-Amino acids and scissile site N-methylation were incorporated into peptide substrate templates as transition state isostere (TSI) substitutes by positional scanning to generate series of non-TSI β-peptidomimetics. The amino acid sequences flanking the β-cleavage site within APP carrying the Swedish double mutation (APPSW), Neuregulin, the synthetic hydroxyethylene-based TSI peptide inhibitor OM99-2, and the high affinity peptide sequence SEISYEVEFR, served as the four substrate templates from which over 60 peptides were designed and synthesised by solid phase peptide synthesis. A quenched fluorescent substrate BACE1 assay in conjunction with liquid chromatography–mass spectrometry (LC-MS) analysis was established to investigate cleavage susceptibility and inhibition potency under competitive and non-competitive conditions. It was determined that β-amino acids substituted at the P1 scissile site position within known peptide substrates were resistant to proteolysis, and particular substitutions induced a concentration-dependent stimulation of BACE1, indicating a possible modulatory role of native BACE1 substrates.

Synthesis of tri-functionalized MMP2 FRET probes using a chemo-selective and late-stage modification of unprotected peptides

2017 ◽  
Vol 15 (8) ◽  
pp. 1792-1800 ◽  
Author(s):  
Sean Oriana ◽  
Ye Cai ◽  
Jeffrey W. Bode ◽  
Yoko Yamakoshi
Keyword(s):  
Peptide Synthesis ◽  
Late Stage ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Peptide Sequence ◽  
Hydroxylamine Derivative ◽  
Natural Peptide

A polymeric FRET probe for the detection of MMP2 was prepared using a new N-hydroxylamine derivative of lysine, which was successfully incorporated into the natural peptide sequence by solid phase peptide synthesis, allowing dual orthogonal ligations of the fully unprotected peptides.

scholarly journals Harnessing polarity and viscosity to identify green binary solvent mixtures as viable alternatives to DMF in solid-phase peptide synthesis

2021 ◽  
Author(s):  
Vincent Martin ◽  
Sandip Jadhav ◽  
Peter H. G. Egelund ◽  
Raphael Liffert ◽  
Henrik Johansson Castro ◽  
...  
Keyword(s):  
Pharmaceutical Industry ◽  
Peptide Synthesis ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Peptide Sequence ◽  
Binary Solvent ◽  
Solvent Mixtures ◽  
Binary Solvent Mixtures

Solid-phase peptide synthesis (SPPS) enables routine synthesis of virtually any type of peptide sequence and is the preferred method for peptide synthesis in academia and the pharmaceutical industry alike. Still,...

scholarly journals Stereorandomization as a Method to Probe Peptide Bioactivity

2020 ◽  
Author(s):  
Thissa N. Siriwardena ◽  
Bee-Ha Gan ◽  
Thilo Köhler ◽  
Christian van Delden ◽  
Sacha Javor ◽  
...  
Keyword(s):  
Cyclic Peptide ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Therapeutic Index ◽  
Building Blocks ◽  
Polymyxin B ◽  
High Yield ◽  
Peptide Antibiotic ◽  
Disruptive Effect ◽  
Peptide Dendrimers

<p>Solid-phase peptide synthesis (SPPS) is usually performed with optically pure building blocks to prepare peptides as single enantiomers. Herein we report that SPPS using racemic amino acids provides stereorandomized (<i>sr</i>) peptides, containing up to billions of different stereoisomers,<a> </a>as well-defined single HPLC peak, single mass products with high yield, which can be used to investigate peptide bioactivity. To exemplify our method, we show that stereorandomization abolishes the membrane disruptive effect of α-helical amphiphilic antimicrobial peptides but preserves their antibiofilm effect, implying different mechanisms involving folded versus disordered conformations. For antimicrobial peptide dendrimers by contrast, stereorandomization preserves antibacterial, membrane disruptive and anti-biofilm effects but reduces hemolysis and cytotoxicity, thereby increasing their therapeutic index. Finally, we identify partially stereorandomized analogs of the last resort cyclic peptide antibiotic polymyxin B with preserved antibacterial activity but lacking membrane disruptive and lipopolysaccharide neutralizing activity, pointing to the existence of additional targets.</p>

scholarly journals Solid-phase peptide synthesis: an overview focused on the preparation of biologically relevant peptides

RSC Advances ◽  
2014 ◽  
Vol 4 (62) ◽  
pp. 32658-32672 ◽  
Author(s):  
Jose M. Palomo
Keyword(s):  
Amino Acids ◽  
Posttranslational Modifications ◽  
Unnatural Amino Acids ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Peptide Sequence ◽  
Biologically Relevant ◽  
Biological Studies ◽  
Exceptional Value ◽  
Short Time

Tailor-made design preparation of complex peptide sequence including posttranslational modifications, fluorescent labels, unnatural amino acids are of exceptional value for biological studies of several important diseases. The possibility to obtain these molecules in sufficient amounts in relative short time is thanks to the solid-phase approach.

scholarly journals Synthetic Natural Product-Inspired Peptides

2021 ◽  
Author(s):  
Matthew Hostetler ◽  
Chloe Smith ◽  
Samantha Nelson ◽  
Zachary Budimir ◽  
Ramya Modi ◽  
...  
Keyword(s):  
Chemical Synthesis ◽  
Natural Product ◽  
Cyclic Peptide ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Gene Clusters ◽  
Multidrug Resistant ◽  
Bioactive Molecules ◽  
Biosynthetic Gene Clusters ◽  
Peptide Synthetases

Natural products (NPs) are a bountiful source of bioactive molecules. Unfortunately, discovery of novel bioactive NPs is challenging due to cryptic biosynthetic gene clusters (BGCs), low titers, and arduous purifications. Herein, we describe SNaPP (Synthetic Natural Product Inspired Peptides), a method for identifying NP-inspired bioactive molecules. SNaPP expedites bioactive molecule discovery by combining bioinformatics predictions of non-ribosomal peptide synthetases (NRPS) with chemical synthesis of the predicted NPs (pNPs). SNaPP utilizes a recently discovered cyclase, the penicillin binding protein (PBP)-like cyclase, as the lynchpin for the development of a library of cyclic peptide pNPs. Analysis of 500 BGCs allowed for identification of 131 novel pNPs. 51 diverse pNPs were synthesized using solid phase peptide synthesis and in-solution cyclization. Antibacterial testing revealed 14 pNPs with antibiotic activity, including activity against multidrug-resistant Gram-negative bacteria. Overall, SNaPP demonstrates the power of combining bioinformatics predictions with chemical synthesis to accelerate the discovery of bioactive molecules.

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