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Cell Cycle (Georgetown, Tex.) Jan 2005Specificity of phosphorylation by protein kinases is essential to the integrity of biological signal transduction. Specificity is determined by two critical elements:... (Review)
Review
Specificity of phosphorylation by protein kinases is essential to the integrity of biological signal transduction. Specificity is determined by two critical elements: (1) peptide specificity of the kinase, i. e., preferential phosphorylation of S/T/Y residues surrounded by particular patterns of amino acids; and (2) recruitment, i. e., increasing the frequency of encounter between kinase and substrate. Historically, the importance of peptide specificity was studied first, but it has been somewhat overshadowed by emerging emphasis on the importance of recruitment. Recent studies confirm and extend understanding of the relative contribution of these two elements. Peptide specificity always constrains the range of sites that can be phosphorylated by a kinase. Only when recruitment is very strong, as in the case with autophosphorylation, can markedly suboptimal substrates be phosphorylated.
Topics: Amino Acid Sequence; Enzyme Activation; Humans; Peptide Fragments; Peptides; Phosphorylation; Protein Interaction Mapping; Protein Kinases; Signal Transduction; Substrate Specificity
PubMed: 15655379
DOI: 10.4161/cc.4.1.1353 -
International Journal of Molecular... Jun 2021Copper (Cu) has been implicated in the progression of Alzheimer's disease (AD), and aggregation of Cu and amyloid β peptide (Aβ) are considered key pathological...
Copper (Cu) has been implicated in the progression of Alzheimer's disease (AD), and aggregation of Cu and amyloid β peptide (Aβ) are considered key pathological features of AD. Metal chelators are considered to be potential therapeutic agents for AD because of their capacity to reduce metal ion-induced Aβ aggregation through the regulation of metal ion distribution. Here, we used phage display technology to screen, synthesize, and evaluate a novel Cu(II)-binding peptide that specifically blocked Cu-triggered Aβ aggregation. The Cu(II)-binding peptide (S-A-Q-I-A-P-H, PCu) identified from the phage display heptapeptide library was used to explore the mechanism of PCu inhibition of Cu-mediated Aβ aggregation and Aβ production. In vitro experiments revealed that PCu directly inhibited Cu-mediated Aβ aggregation and regulated copper levels to reduce biological toxicity. Furthermore, PCu reduced the production of Aβ by inhibiting Cu-induced BACE1 expression and improving Cu(II)-mediated cell oxidative damage. Cell culture experiments further demonstrated that PCu had relatively low toxicity. This Cu(II)-binding peptide that we have identified using phage display technology provides a potential therapeutic approach to prevent or treat AD.
Topics: Amino Acid Sequence; Amyloid beta-Peptides; Animals; Carrier Proteins; Cell Surface Display Techniques; Copper; Humans; Mice; Oxidation-Reduction; Oxidative Stress; Peptides; Protein Aggregates; Protein Aggregation, Pathological; Protein Interaction Mapping
PubMed: 34202166
DOI: 10.3390/ijms22136842 -
Journal of the American Chemical Society Nov 2021Stapled peptides with an enforced α-helical conformation have been shown to overcome major limitations in the development of short peptides targeting protein-protein...
Stapled peptides with an enforced α-helical conformation have been shown to overcome major limitations in the development of short peptides targeting protein-protein interactions (PPIs). While the growing arsenal of methodologies to staple peptides facilitates their preparation, stapling methodologies are not broadly embraced in synthetic library screening. Herein, we report a strategy leveraged on hybridization of short PNA-peptide conjugates wherein nucleobase driven assembly facilitates ligation of peptide fragments and constrains the peptide's conformation into an α-helix. Using native chemical ligation, we show that a mixture of peptide fragments can be combinatorially ligated and used directly in affinity selection against a target of interest. This approach was exemplified with a focused library targeting the p-53/MDM2 interaction. One hundred peptides were obtained in a one-pot ligation reaction, selected by affinity against MDM2 immobilized on beads, and the best binders were identified by mass spectrometry.
Topics: Humans; Nucleic Acid Hybridization; Peptide Library; Peptide Nucleic Acids; Peptides; Protein Binding; Protein Conformation, alpha-Helical; Proto-Oncogene Proteins c-mdm2; Tumor Suppressor Protein p53
PubMed: 34739233
DOI: 10.1021/jacs.1c07013 -
Protein and Peptide Letters 2008The observation in 1979 that opioid receptors interact, led to the design of bivalent ligands in an attempt to improve selectivity and affinity towards the different... (Review)
Review
The observation in 1979 that opioid receptors interact, led to the design of bivalent ligands in an attempt to improve selectivity and affinity towards the different subtypes( i.e. mu, delta, and kappa). Dimers of monovalent 'parent' opioid structures have been evaluated and include: (a) endogenous (e.g enkephalins) or exogenous (e.g dermorphin) peptide dimer analogues (b) mixed peptidic -non-peptidic bivalent ligands and (c) dual non-peptidic dimers. Chimeric structures, using an opioid pharmacophore in combination with a a non-opioid pharmacophore, have also been prepared. The common aim in all these studies is to improve the pharmacological profile of potential analgesics to minimize common opioid-induced side effects, such as physical dependence and tolerance. Here we present a brief overview efforts to develop bivalent opioid ligands for use in pain-related research.
Topics: Amino Acid Sequence; Analgesics, Opioid; Animals; Dimerization; Drug Design; Humans; Ligands; Molecular Structure; Peptides; Protein Structure, Quaternary; Receptors, Opioid
PubMed: 18782061
DOI: 10.2174/092986608785133672 -
Current Opinion in Structural Biology Aug 2016Molecules intended to antagonize protein-protein interactions or augment polypeptide-based signaling must bind tightly to large and specific surfaces on target proteins.... (Review)
Review
Molecules intended to antagonize protein-protein interactions or augment polypeptide-based signaling must bind tightly to large and specific surfaces on target proteins. Some types of unnatural oligomers with discrete folding propensities ('foldamers') have recently been shown to display this capability. This review covers important recent advances among several classes of foldamers, including α-peptides with secondary structures stabilized by covalent bonds, d-α-peptides, α/β-peptides and oligo-oxopiperazines. Recent advances in this area have involved enhancing membrane permeability to provide access to intracellular protein targets, improving pharmacokinetics and duration of action in vivo, and developing strategies appropriate for targeting large and irregularly-shaped protein surfaces.
Topics: Animals; Binding Sites; Humans; Peptides; Protein Binding; Protein Folding; Protein Structure, Secondary; Proteins
PubMed: 27390896
DOI: 10.1016/j.sbi.2016.06.014 -
Journal of the American Chemical Society Mar 2019Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein... (Review)
Review
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.
Topics: Animals; Cell Membrane Permeability; Cyclization; Drug Discovery; Humans; Peptides, Cyclic; Protein Stability
PubMed: 30768253
DOI: 10.1021/jacs.8b13178 -
Nature Chemistry Mar 2018Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of...
Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.
Topics: Biocatalysis; Molecular Structure; Peptide Biosynthesis; Peptide Synthases; Peptides; Protein Engineering; Ribosomes
PubMed: 29461527
DOI: 10.1038/nchem.2891 -
Current Opinion in Structural Biology Aug 2018This review details recent developments in the design of supramolecular materials with customizable properties that can be coordinated in space and time. We highlight... (Review)
Review
This review details recent developments in the design of supramolecular materials with customizable properties that can be coordinated in space and time. We highlight examples where both kinetic and thermodynamic considerations are incorporated in design, to address three challenges: control of order/disorder in supramolecular assembly; formation of structures with distinct functional domains; formation of out-of-equilibrium structures with controlled lifetimes. The examples that are discussed are based on self-assembling peptide and saccharide-based amphiphiles. These biomolecular amphiphiles are of low complexity and ideally suited to fundamental, systematic studies while they are also considered for applications in environmental remediation, food science, cosmetics and nanomedicine.
Topics: Bioengineering; Kinetics; Macromolecular Substances; Metabolic Networks and Pathways; Peptides; Structure-Activity Relationship; Sugars; Thermodynamics
PubMed: 29494797
DOI: 10.1016/j.sbi.2018.02.001 -
Nature Methods Feb 2020In mammalian cells, much of signal transduction is mediated by weak protein-protein interactions between globular peptide-binding domains (PBDs) and unstructured...
In mammalian cells, much of signal transduction is mediated by weak protein-protein interactions between globular peptide-binding domains (PBDs) and unstructured peptidic motifs in partner proteins. The number and diversity of these PBDs (over 1,800 are known), their low binding affinities and the sensitivity of binding properties to minor sequence variation represent a substantial challenge to experimental and computational analysis of PBD specificity and the networks PBDs create. Here, we introduce a bespoke machine-learning approach, hierarchical statistical mechanical modeling (HSM), capable of accurately predicting the affinities of PBD-peptide interactions across multiple protein families. By synthesizing biophysical priors within a modern machine-learning framework, HSM outperforms existing computational methods and high-throughput experimental assays. HSM models are interpretable in familiar biophysical terms at three spatial scales: the energetics of protein-peptide binding, the multidentate organization of protein-protein interactions and the global architecture of signaling networks.
Topics: Biophysical Phenomena; Humans; Machine Learning; Peptides; Protein Binding; Proteins; Reproducibility of Results; Signal Transduction; src Homology Domains
PubMed: 31907444
DOI: 10.1038/s41592-019-0687-1 -
Journal of Pharmaceutical and... Sep 2018Subcutaneous (SC) injection is the most common administration route for peptide therapeutics. Catabolism at the injection site can be a specific and major degradation...
Subcutaneous (SC) injection is the most common administration route for peptide therapeutics. Catabolism at the injection site can be a specific and major degradation pathway for many SC administered peptides. In some cases, it can significantly affect pharmacokinetics, particularly bioavailability, and have detrimental effects on the efficacy of the drug. This work describes a liquid chromatography-high resolution mass spectrometry based in vitro assay to assess peptide metabolism in the SC tissue (SCiMetPep assay). The SCiMetPep assay was developed using human, Sprague-Dawley rat and Göttingen minipig SC tissue homogenate supernatant, and allows for both determination of degradation rate (half-life) of the parent peptide and identification of metabolites generated from enzymatic proteolysis. The assay was developed and validated using known peptides including human insulin and four GLP-1 analogues (lixisenatide, exenatide, liraglutide and semaglutide). Different experimental parameters were evaluated in order to optimize the homogenization process of the SC tissue and the peptide incubation conditions. In vitro metabolism of these peptides was in good agreement with in vivo data reported in the literature. Finally, when SCiMetPep assay was applied on a series of structurally related peptides, a fairly good correlation was found between SC metabolic stability and bioavailability, suggesting that catabolism at the injection site can have a major role in the absorption, distribution, metabolism, and excretion (ADME) of peptide therapeutics. The SCiMetPep showed the ability to identify analogs with improved SC metabolic stability and hence higher bioavailability. The assay can be used in the early phases of drug discovery to identify peptide metabolic soft spots at the injection site and guide the peptide drug discovery process.
Topics: Animals; Biological Availability; Chromatography, Liquid; Humans; Injections, Subcutaneous; Peptides; Proteolysis; Rats; Subcutaneous Tissue; Swine; Tandem Mass Spectrometry
PubMed: 30041153
DOI: 10.1016/j.jpba.2018.07.009