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Current Opinion in Pharmacology Jun 2023Peptides form the largest group of ligands that modulate the activity of more than 120 different GPCRs. Among which linear disordered peptide ligands usually undergo... (Review)
Review
Peptides form the largest group of ligands that modulate the activity of more than 120 different GPCRs. Among which linear disordered peptide ligands usually undergo significant conformational changes upon binding that is essential for receptor recognition and activation. Conformational selection and induced fit are the extreme mechanisms of coupled folding and binding that can be distinguished by analysis of binding pathways by methods that include NMR. However, the large size of GPCRs in membrane-mimetic environments limits NMR applications. In this review, we highlight advances in the field that can be adopted to address coupled folding and binding of peptide ligands to their cognate receptors.
Topics: Humans; Receptors, G-Protein-Coupled; Ligands; Peptides; Protein Binding
PubMed: 37003111
DOI: 10.1016/j.coph.2023.102366 -
Protein Science : a Publication of the... Nov 2020PAINT (points accumulation for imaging in nanoscale topography) refers to methods that achieve the sparse temporal labeling required for super-resolution imaging by... (Review)
Review
PAINT (points accumulation for imaging in nanoscale topography) refers to methods that achieve the sparse temporal labeling required for super-resolution imaging by using transient interactions between a biomolecule of interest and a fluorophore. There have been a variety of different implementations of this method since it was first described in 2006. Recent papers illustrate how transient peptide-protein interactions, rather than small molecule binding or DNA oligonucleotide duplex formation, can be employed to perform PAINT-based single molecule localization microscopy (SMLM). We discuss the different approaches to PAINT using peptide and protein interactions, and their applications in vitro and in vivo. We highlight the important parameters to consider when selecting suitable peptide-protein interaction pairs for such studies. We also note the opportunities for protein scientists to apply their expertise in guiding the choice of peptide and protein pairs that are used. Finally, we discuss the potential for expanding super-resolution imaging methods based on transient peptide-protein interactions, including the development of simultaneous multicolor imaging of multiple proteins and the study of very high and very low abundance proteins in live cells.
Topics: Peptides; Protein Interaction Maps; Proteins; Single Molecule Imaging
PubMed: 32949055
DOI: 10.1002/pro.3953 -
Chembiochem : a European Journal of... Jan 2023The late-stage site-selective derivatisation of peptides has many potential applications in structure-activity relationship studies and postsynthetic modification or...
The late-stage site-selective derivatisation of peptides has many potential applications in structure-activity relationship studies and postsynthetic modification or conjugation of bioactive compounds. The development of orthogonal methods for C-H functionalisation is crucial for such peptide derivatisation. Among them, biocatalytic methods are increasingly attracting attention. Tryptophan halogenases emerged as valuable catalysts to functionalise tryptophan (Trp), while direct enzyme-catalysed halogenation of synthetic peptides is yet unprecedented. Here, it is reported that the Trp 6-halogenase Thal accepts a wide range of amides and peptides containing a Trp moiety. Increasing the sequence length and reaction optimisation made bromination of pentapeptides feasible with good turnovers and a broad sequence scope, while regioselectivity turned out to be sequence dependent. Comparison of X-ray single crystal structures of Thal in complex with d-Trp and a dipeptide revealed a significantly altered binding mode for the peptide. The viability of this bioorthogonal approach was exemplified by halogenation of a cyclic RGD peptide.
Topics: Halogenation; Tryptophan; Peptides; Structure-Activity Relationship; Catalysis
PubMed: 36259362
DOI: 10.1002/cbic.202200569 -
Natural Product Reports Sep 2019Covering: 2014 to 2019Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) have been the subject of engineering efforts for multiple decades. Their... (Review)
Review
Covering: 2014 to 2019Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) have been the subject of engineering efforts for multiple decades. Their modular assembly line architecture potentially allows unlocking vast chemical space for biosynthesis. However, attempts thus far are often met with mixed success, due to limited molecular compatibility of the parts used for engineering. Now, new engineering strategies, increases in genomic data, and improved computational tools provide more opportunities for major progress. In this review we highlight some of the challenges and progressive strategies for the re-design of NRPSs & type I PKSs and survey useful computational tools and approaches to attain the ultimate goal of semi-automated and design-based engineering of novel peptide and polyketide products.
Topics: Computer-Aided Design; Metabolic Engineering; Peptide Biosynthesis; Peptides; Polyketides
PubMed: 31259995
DOI: 10.1039/c9np00021f -
Angewandte Chemie (International Ed. in... Feb 2023AlphaFold has revolutionized structural biology by predicting highly accurate structures of proteins and their complexes with peptides and other proteins. However, for...
AlphaFold has revolutionized structural biology by predicting highly accurate structures of proteins and their complexes with peptides and other proteins. However, for protein-peptide systems, we are also interested in identifying the highest affinity binder among a set of candidate peptides. We present a novel competitive binding assay using AlphaFold to predict structures of the receptor in the presence of two peptides. For systems in which the individual structures of the peptides are well predicted, the assay captures the higher affinity binder in the bound state, and the other peptide in the unbound form with statistical significance. We test the application on six protein receptors for which we have experimental binding affinities to several peptides. We find that the assay is best suited for identifying medium to strong peptide binders that adopt stable secondary structures upon binding.
Topics: Protein Binding; Peptides; Proteins; Carrier Proteins; Protein Structure, Secondary
PubMed: 36542066
DOI: 10.1002/anie.202213362 -
ACS Chemical Biology Oct 2019Peptides constitute an important class of drugs for the treatment of multiple metabolic, oncological, and neurodegenerative diseases, and several hundred novel...
Peptides constitute an important class of drugs for the treatment of multiple metabolic, oncological, and neurodegenerative diseases, and several hundred novel therapeutic peptides are currently in the preclinical and clinical stages of development. However, many leads fail to advance clinically because of poor cellular membrane and tissue permeability. Therefore, assessment of the ability of a peptide to cross cellular membranes is critical when developing novel peptide-based therapeutics. Current methods to assess peptide cellular permeability are limited by multiple factors, such as the need to introduce rather large modifications (e.g., fluorescent dyes) that require complex chemical reactions as well as an inability to provide kinetic information on the internalization of a compound or distinguish between internalized and membrane-bound compounds. In addition, many of these methods are based on end point assays and require multiple sample manipulation steps. Herein, we report a novel "Split Luciferin Peptide" (SLP) assay that enables the real-time noninvasive imaging and quantification of peptide uptake both and using a very sensitive bioluminescence readout. This method is based on a straightforward, stable chemical modification of the peptide of interest with a d-cysteine tag that preserves the overall peptidic character of the original molecule. This method can be easily adapted for screening peptide libraries and can thus become an important tool for preclinical peptide drug development.
Topics: Animals; Biological Assay; Cell Line, Tumor; Cysteine; Female; Firefly Luciferin; Humans; Luciferases, Firefly; Luminescent Measurements; Mice; Nitriles; Peptides; Protein Transport
PubMed: 31498986
DOI: 10.1021/acschembio.9b00439 -
Organic & Biomolecular Chemistry Jan 2021DNAzymes were previously identified by in vitro selection for a variety of chemical reactions, including several biologically relevant peptide modifications. However,...
DNAzymes were previously identified by in vitro selection for a variety of chemical reactions, including several biologically relevant peptide modifications. However, finding DNAzymes for peptide lysine acylation is a substantial challenge. By using suitably reactive aryl ester acyl donors as the electrophiles, here we used in vitro selection to identify DNAzymes that acylate amines, including lysine side chains of DNA-anchored peptides. Some of the DNAzymes can transfer a small glutaryl group to an amino group. These results expand the scope of DNAzyme catalysis and suggest the future broader applicability of DNAzymes for sequence-selective lysine acylation of peptide and protein substrates.
Topics: Acylation; Amines; Biocatalysis; DNA, Catalytic; Lysine; Peptides
PubMed: 33150349
DOI: 10.1039/d0ob02015j -
Journal of Chemical Theory and... Jun 2022An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully...
An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully understood, impeding rational drug design. Computational techniques could positively impact their design, but modeling them and their interactions remains challenging due to their cyclic nature and their flexibility. This study presents a step-by-step protocol for generating cyclic peptide conformations and docking them to their protein target using HADDOCK2.4. A dataset of 30 cyclic peptide-protein complexes was used to optimize both cyclization and docking protocols. It supports peptides cyclized via an N- and C-terminus peptide bond and/or a disulfide bond. An ensemble of cyclic peptide conformations is then used in HADDOCK to dock them onto their target protein using knowledge of the binding site on the protein side to drive the modeling. The presented protocol predicts at least one acceptable model according to the critical assessment of prediction of interaction criteria for each complex of the dataset when the top 10 HADDOCK-ranked single structures are considered (100% success rate top 10) both in the bound and unbound docking scenarios. Moreover, its performance in both bound and fully unbound docking is similar to the state-of-the-art software in the field, Autodock CrankPep. The presented cyclization and docking protocol should make HADDOCK a valuable tool for rational cyclic peptide-based drug design and high-throughput screening.
Topics: Cyclization; Molecular Docking Simulation; Peptides, Cyclic; Protein Binding; Protein Conformation; Proteins; Software
PubMed: 35652781
DOI: 10.1021/acs.jctc.2c00075 -
Pflugers Archiv : European Journal of... Jan 2022Natriuretic peptides have long been known for their cardiovascular function. However, a growing body of evidence emphasizes the role of natriuretic peptides in the... (Review)
Review
Natriuretic peptides have long been known for their cardiovascular function. However, a growing body of evidence emphasizes the role of natriuretic peptides in the energy metabolism of several substrates in humans and animals, thus interrelating the heart, as an endocrine organ, with various insulin-sensitive tissues and organs such as adipose tissue, muscle skeletal, and liver. Adipose tissue dysfunction is associated with altered regulation of the natriuretic peptide system, also indicated as a natriuretic disability. Evidence points to a contribution of this natriuretic disability to the development of obesity, type 2 diabetes mellitus, and cardiometabolic complications; although the causal relationship is not fully understood at present. However, targeting the natriuretic peptide pathway may improve metabolic health in obesity and type 2 diabetes mellitus. This review will focus on the current literature on the metabolic functions of natriuretic peptides with emphasis on lipid metabolism and insulin sensitivity. Natriuretic peptide system alterations could be proposed as one of the linking mechanisms between adipose tissue dysfunction and cardiovascular disease.
Topics: Adipose Tissue; Animals; Cardiovascular Diseases; Cardiovascular System; Humans; Insulin Resistance; Lipid Metabolism; Natriuretic Peptides
PubMed: 34173888
DOI: 10.1007/s00424-021-02596-1 -
Molecules (Basel, Switzerland) May 2020The high affinity and specificity of peptides towards biological targets, in addition to their favorable pharmacological properties, has encouraged the development of... (Review)
Review
The high affinity and specificity of peptides towards biological targets, in addition to their favorable pharmacological properties, has encouraged the development of many peptide-based pharmaceuticals, including peptide-based positron emission tomography (PET) radiopharmaceuticals. However, the poor in vivo stability of unmodified peptides against proteolysis is a major challenge that must be overcome, as it can result in an impractically short in vivo biological half-life and a subsequently poor bioavailability when used in imaging and therapeutic applications. Consequently, many biologically and pharmacologically interesting peptide-based drugs may never see application. A potential way to overcome this is using peptide analogues designed to mimic the pharmacophore of a native peptide while also containing unnatural modifications that act to maintain or improve the pharmacological properties. This review explores strategies that have been developed to increase the metabolic stability of peptide-based pharmaceuticals. It includes modifications of the - and/or -termini, introduction of d- or other unnatural amino acids, backbone modification, PEGylation and alkyl chain incorporation, cyclization and peptide bond substitution, and where those strategies have been, or could be, applied to PET peptide-based radiopharmaceuticals.
Topics: Acylation; Animals; Carbon Radioisotopes; Cyclization; Fluorine Radioisotopes; Gallium Radioisotopes; Half-Life; Humans; Methylation; Peptides; Peptidomimetics; Positron-Emission Tomography; Protein Processing, Post-Translational; Protein Stability; Radiopharmaceuticals; Rodentia
PubMed: 32423178
DOI: 10.3390/molecules25102314