Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Non-Perturbative Molecular Grafting Strategy for Stable and Potent Therapeutic Peptide Ligands.

ABSTRACT: The gut-derived incretin hormone, glucagon-like peptide-1 (GLP1), plays an important physiological role in attenuating post-prandial blood glucose excursions in part by amplifying pancreatic insulin secretion. Native GLP1 is rapidly degraded by the serine protease, dipeptidyl peptidase-4 (DPP4); however, enzyme-resistant analogues of this 30-amino-acid peptide provide an effective therapy for type 2 diabetes (T2D) and can curb obesity via complementary functions in the brain. In addition to its medical relevance, the incretin system provides a fertile arena for exploring how to better separate agonist function at cognate receptors versus susceptibility of peptides to DPP4-induced degradation. We have discovered that novel chemical decorations can make GLP1 and its analogues completely DPP4 resistant while fully preserving GLP1 receptor activity. This strategy is also applicable to other therapeutic ligands, namely, glucose-dependent insulinotropic polypeptide (GIP), glucagon, and glucagon-like peptide-2 (GLP2), targeting the secretin family of receptors. The versatility of the approach offers hundreds of active compounds based on any template that target these receptors. These observations should allow for rapid optimization of pharmacological properties and because the appendages are in a position crucial to receptor stimulation, they proffer the possibility of conferring "biased" signaling and in turn minimizing side effects.

SUBMITTER: Sicinski KM

PROVIDER: S-EPMC8006168 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Molecular recognition of peptide and non-peptide ligands by the extracellular domains of neurohypophysial hormone receptors.

Project description:This study was designed to ascertain whether the extracellular loops of vasopressin/oxytocin receptors bind ligands and, if so, to locate the molecular determinants of this ligand-receptor interaction. Ligand-binding studies were employed using a rat liver V1a vasopressin receptor preparation and both peptide and non-peptide receptor ligands. Synthetic peptides corresponding to defined regions of the extracellular surface of the neurohypophysial hormone receptors recognized radioligands. These receptor mimetics inhibited the binding of radioligands to the V1a receptor with apparent affinities (pKi) ranging from 3.1 to 6.75. The same mimetics had no effects on the binding of angiotensin II to the rat AT1 receptor, indicating specificity for V1a receptor ligands. A mimetic peptide (DITYRFRGPDWL) of the first extracellular loop (ECII) of the V1a vasopressin receptor also inhibited vasopressin-stimulated, but not angiotensin II-stimulated, glycogen phosphorylase in isolated rat hepatocytes. In contrast, scrambled ECII mimetics displayed greatly reduced affinity for vasopressin. In addition, the role of peptide side-chain versus main-chain atoms in the binding of ligands by vasopressin receptors was addressed using retro-inverso peptide mimetics. Our findings indicate a precise orientation of the extracellular receptor surface (particularly the ECII domain) which facilitates the initial 'capture' of both peptide and non-peptide ligands. Moreover, the data indicate that the main-chain atoms of both a major binding-site determinant in the first extracellular loop of the receptor and the neurohypophysial hormones contribute significantly to the ligand-receptor interaction. These findings also suggest that soluble receptor-binding domains have therapeutic potential.

| S-EPMC1217525 | biostudies-other

Controlling Amyloid Beta Peptide Aggregation and Toxicity by Protease-Stable Ligands.

Project description:Polymerization of soluble amyloid beta (Aβ) peptide into protease-stable insoluble fibrillary aggregates is a critical step in the pathogenesis of Alzheimer's disease (AD). The N-terminal (NT) hydrophobic central domain fragment 16KLVFF20 plays an important role in the formation and stabilization of β-sheets by self-recognition of the parent Aβ peptide, followed by aggregation of Aβ in the AD brain. Here, we analyze the effect of the NT region inducing β-sheet formation in the Aβ peptide by a single amino acid mutation in the native Aβ peptide fragment. We designed 14 hydrophobic peptides (NT-01 to NT-14) by a single mutation at 18Val by using hydrophobic residues leucine and proline in the natural Aβ peptide fragment (KLVFFAE) and analyzed its effect on the formation of Aβ aggregates. Among all these peptides, NT-02, NT-03, and NT-13 significantly affected the Aβ aggregate formation. When the NT peptides were coincubated with the Aβ peptide, a significant reduction in β-sheet formation and increment in random coil content of Aβ was seen, confirmed by circular dichroism spectroscopy and Fourier transform infrared spectroscopy, followed by the reduction of fibril formation measured by the thioflavin-T (ThT) binding assay. The aggregation inhibition was monitored by Congo red and ThT staining and electron microscopic examination. Moreover, the NT peptides protect the PC-12 differentiated neurons from Aβ-induced toxicity and apoptosis in vitro. Thus, manipulation of the Aβ secondary structure with protease-stable ligands that promote the random coil conformation may provide a tool to control the Aβ aggregates observed in AD patients.

| S-EPMC10125337 | biostudies-literature

Stabilization of Monomeric Tau Protein by All D-Enantiomeric Peptide Ligands as Therapeutic Strategy for Alzheimer's Disease and Other Tauopathies.

Project description:Alzheimer's disease and other tauopathies are the world's leading causes of dementia and memory loss. These diseases are thought to be caused by the misfolding and aggregation of the intracellular tau protein, ultimately leading to neurodegeneration. The tau protein is involved in a multitude of different neurodegenerative diseases. During the onset of tauopathies, tau undergoes structural changes and posttranslational modifications and aggregates into amyloid fibrils that are able to spread with a prion-like behavior. Up to now, there is no therapeutic agent which effectively controls or reverses the disease. Most of the therapeutics that were developed and underwent clinical trials targeted misfolded or aggregated forms of tau. In the current manuscript, we present the selection and characterization of two all D-enantiomeric peptides that bind monomeric tau protein with a low nanomolar KD, stabilize tau in its monomeric intrinsically disordered conformation, and stop the conversion of monomers into aggregates. We show that the effect of the two all D-enantiomeric peptides is strong enough to stop ongoing tau aggregation in vitro and is able to significantly reduce tau fibril assembly in cell culture. Both compounds may serve as new lead components for the development of therapeutic agents against Alzheimer's disease and other tauopathies.

| S-EPMC9917023 | biostudies-literature

Synthesis and stabilities of peptide-based [1]rotaxanes: molecular grafting onto lasso peptide scaffolds.

Project description:The chemical synthesis of peptide-based [1]rotaxanes (lasso peptides) was achieved by [2]rotaxane formation followed by two chemoselective ligation reactions. Our approach enabled incorporation of various peptide sequences into a common rotaxane structure. The synthetic lasso peptides were characterized by NMR, chromatography, and partial degradation by proteases. A linear peptide epitope grafted onto the rotaxane scaffold showed significantly improved proteolytic stability.

| S-EPMC5427998 | biostudies-literature

Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics.

Project description:The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone circularization and molecular grafting), therefore enforcing their biologically active conformation and thus improving their solubility, stability, and functional activity. This review provides a short summary of approaches aimed at enhancing the biological activity of short functional peptides with a particular focus on the peptide grafting approach, whereby a functional peptide is inserted into a scaffold molecule. Intra-backbone insertions of short therapeutic peptides into scaffold proteins have been shown to enhance their activity and render them a more stable and biologically active conformation.

| S-EPMC10005171 | biostudies-literature

Non-perturbative effects in spin glasses.

Project description:We present a numerical study of an Ising spin glass with hierarchical interactions--the hierarchical Edwards-Anderson model with an external magnetic field (HEA). We study the model with Monte Carlo (MC) simulations in the mean-field (MF) and non-mean-field (NMF) regions corresponding to d ≥ 4 and d < 4 for the d-dimensional ferromagnetic Ising model respectively. We compare the MC results with those of a renormalization-group (RG) study where the critical fixed point is treated as a perturbation of the MF one, along the same lines as in the -expansion for the Ising model. The MC and the RG method agree in the MF region, predicting the existence of a transition and compatible values of the critical exponents. Conversely, the two approaches markedly disagree in the NMF case, where the MC data indicates a transition, while the RG analysis predicts that no perturbative critical fixed point exists. Also, the MC estimate of the critical exponent ν in the NMF region is about twice as large as its classical value, even if the analog of the system dimension is within only ~2% from its upper-critical-dimension value. Taken together, these results indicate that the transition in the NMF region is governed by strong non-perturbative effects.

| S-EPMC4346828 | biostudies-other

Molecular modeling of potent novel sulfonamide derivatives as non-peptide small molecule anti-COVID 19 agents.

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19. The Sulfonamides groups have been widely introduced in several drugs, especially for their antibacterial activities and generally prescribed for respiratory infections. On the other hand, imidazole groups have the multipotency to act as drugs, including antiviral activity. We have used a structure-based drug design approach to design some imidazole derivatives of sulfonamide, which can efficiently bind to the active site of SARS-CoV-2 main protease and thus may have the potential to inhibit its proteases activity. We conducted molecular docking and molecular dynamics simulation to observe the stability and flexibility of inhibitor complexes. We have checked ADMET (absorption, distribution, metabolism, excretion and toxicity) and drug-likeness rules to scrutinize toxicity and then designed the most potent compound based on computational chemistry. Our small predicted molecule non-peptide protease inhibitors could provide a useful model in the further search for novel compounds since it has many advantages over peptidic drugs, like lower side effects, toxicity and less chance of drug resistance. Further, we confirmed the stability of our inhibitor-complex and interaction profile through the Molecular dynamics simulation study. Our small predicted moleculeCommunicated by Ramaswamy H. Sarma.

| S-EPMC8171005 | biostudies-literature

Resolution of superluminal signalling in non-perturbative cavity quantum electrodynamics.

Project description:Recent technological developments have made it increasingly easy to access the non-perturbative regimes of cavity quantum electrodynamics known as ultrastrong or deep strong coupling, where the light-matter coupling becomes comparable to the bare modal frequencies. In this work, we address the adequacy of the broadly used single-mode cavity approximation to describe such regimes. We demonstrate that, in the non-perturbative light-matter coupling regimes, the single-mode models become unphysical, allowing for superluminal signalling. Moreover, considering the specific example of the quantum Rabi model, we show that the multi-mode description of the electromagnetic field, necessary to account for light propagation at finite speed, yields physical observables that differ radically from their single-mode counterparts already for moderate values of the coupling. Our multi-mode analysis also reveals phenomena of fundamental interest on the dynamics of the intracavity electric field, where a free photonic wavefront and a bound state of virtual photons are shown to coexist.

| S-EPMC5954151 | biostudies-literature

Therapeutic efficacy of stable analogues of vasoactive intestinal peptide against pathogens.

Project description:Vasoactive intestinal peptide (VIP) is an anti-inflammatory neuropeptide recently identified as a potential antimicrobial peptide. To overcome the metabolic limitations of VIP, we modified the native peptide sequence and generated two stable synthetic analogues (VIP51 and VIP51(6-30)) with better antimicrobial profiles. Herein we investigate the effects of both VIP analogues on cell viability, membrane integrity, and ultrastructure of various bacterial strains and Leishmania species. We found that the two VIP derivatives kill various non-pathogenic and pathogenic Gram-positive and Gram-negative bacteria as well as the parasite Leishmania major through a mechanism that depends on the interaction with certain components of the microbial surface, the formation of pores, and the disruption of the surface membrane. The cytotoxicity of the VIP derivatives is specific for pathogens, because they do not affect the viability of mammalian cells. Docking simulations indicate that the chemical changes made in the analogues are critical to increase their antimicrobial activities. Consequently, we found that the native VIP is less potent as an antibacterial and fails as a leishmanicidal. Noteworthy from a therapeutic point of view is that treatment with both derivatives increases the survival and reduces bacterial load and inflammation in mice with polymicrobial sepsis. Moreover, treatment with VIP51(6-30) is very effective at reducing lesion size and parasite burden in a model of cutaneous leishmaniasis. These results indicate that the VIP analogues emerge as attractive alternatives for treating drug-resistant infectious diseases and provide key insights into a rational design of novel agents against these pathogens.

| S-EPMC4031515 | biostudies-literature

Molecular hybridization strategy for tuning bioactive peptide function.

Project description:The physicochemical and structural properties of antimicrobial peptides (AMPs) determine their mechanism of action and biological function. However, the development of AMPs as therapeutic drugs has been traditionally limited by their toxicity for human cells. Tuning the physicochemical properties of such molecules may abolish toxicity and yield synthetic molecules displaying optimal safety profiles and enhanced antimicrobial activity. Here, natural peptides were modified to improve their activity by the hybridization of sequences from two different active peptide sequences. Hybrid AMPs (hAMPs) were generated by combining the amphipathic faces of the highly toxic peptide VmCT1, derived from scorpion venom, with parts of four other naturally occurring peptides having high antimicrobial activity and low toxicity against human cells. This strategy led to the design of seven synthetic bioactive variants, all of which preserved their structure and presented increased antimicrobial activity (3.1-128 μmol L-1). Five of the peptides (three being hAMPs) presented high antiplasmodial at 0.8 μmol L-1, and virtually no undesired toxic effects against red blood cells. In sum, we demonstrate that peptide hybridization is an effective strategy for redirecting biological activity to generate novel bioactive molecules with desired properties.

| S-EPMC10587126 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data