Predicting proteolytic sites in extracellular proteins: only halfway there

Kliger, Yossef; Gofer, Eyal; Wool, Assaf; Toporik, Amir; Apatoff, Avihay; Olshansky, Moshe

doi:10.1093/bioinformatics/btn084

Cited by 11 publications

(12 citation statements)

References 36 publications

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“…(The full cleavage prediction concept is detailed in Kliger et al (15).) The predicted signal peptide was removed, and potential cleavage sites were scored based on the outcome of the machine learning algorithm used for cleavage site prediction.…”

Section: Methodsmentioning

confidence: 99%

Discovery and Validation of Novel Peptide Agonists for G-protein-coupled Receptors

Shemesh

Toporik

Levine

et al. 2008

Journal of Biological Chemistry

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G-protein-coupled receptors (GPCRs) represent an important group of targets for pharmaceutical therapeutics. The completion of the human genome revealed a large number of putative GPCRs. However, the identification of their natural ligands, and especially peptides, suffers from low discovery rates, thus impeding development of therapeutics based on these potential drug targets. We describe the discovery of novel GPCR ligands encrypted in the human proteome. Hundreds of potential peptide ligands were predicted by machine learning algorithms. In vitro screening of selected 33 peptides on a set of 152 GPCRs, including a group of designated orphan receptors, was conducted by intracellular calcium measurements and cAMP assays. The screening revealed eight novel peptides as potential agonists that specifically activated six different receptors in a dose-dependent manner. Most of the peptides showed distinct stimulatory patterns targeted at designated and orphan GPCRs. Further analysis demonstrated a significant in vivo effect for one of the peptides in a mouse inflammation model.

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Section: Methodsmentioning

confidence: 99%

Discovery and Validation of Novel Peptide Agonists for G-protein-coupled Receptors

Shemesh

Toporik

Levine

et al. 2008

Journal of Biological Chemistry

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“…A peptide database was created using a cleavage‐predicting algorithm 13 on all the NCBI nonredundant (nr) (proteome in Fig. 1A) potentially secreted proteins (human proteins with a signal peptide prediction) and Swiss‐Prot/Uniprot signal peptide annotated proteins.…”

Section: Methodsmentioning

confidence: 99%

Activation of Relaxin‐Related Receptors by Short, Linear Peptides Derived from a Collagen‐Containing Precursor

Shemesh

Hermesh

Toporik

et al. 2009

Annals of the New York Academy of Sciences

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In a screening effort based on algorithmic predictions for novel G-protein-coupled receptor (GPCR) peptide activators, we were able to identify and examine two novel peptides (P59 and P74) which are short, linear, and derived from a natural, previously unidentified precursor protein containing a collagen-like repeat. Both peptides seemed to show an apparent cAMP-related effect on CHO-K1 cells transiently transfected with either LGR7 or LGR8, usually after treatment with cAMP-generating forskolin, compared to the same cells treated with forskolin plus relaxin. This activation was not found for the relaxin-3 receptor (GPR135). In a set of follow-up experiments, both peptides were found to stimulate cAMP production, mostly upon initial stimulation of cAMP production by 5 micro M forskolin in cells transfected with either LGR7 or LGR8. In a dye-free cell impedance GPCR activation assay, we were able to show that these peptides were also able to activate a cellular response mediated by these receptors. Although untransfected CHO-K1 cells showed some cellular activation by both relaxin and at least one of our newly discovered peptides, both LGR7- and LGR8-transfected cells showed a stronger response, indicating stimulation of a cellular pathway through activation of these receptors. In conclusion, we were able to show that these newly discovered peptides, which have no similarity to any member of the relaxin-insulin-like peptide family, are potential ligands for the relaxin-related family of receptors and as such might serve as novel candidates for relaxin-related therapeutic indications. Both peptides are linear and were found to be active after being chemically synthesized.

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“…This was achieved using a computational biology discovery platform, which we developed recently, that uses machine learning algorithms designed to predict novel G protein-coupled receptor (GPCR) peptide ligands cleaved from secreted proteins (extracted from the Swiss-Prot protein database) by convertase proteolysis, as described previously. 12,13 The ligands identified might, therefore, exist endogenously because of naturally occurring proteolysis. The predicted peptide ligands were synthesized and screened for activation of 152 GPCRs by calcium flux and cAMP assays.…”

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confidence: 99%

Vascular Relaxation, Antihypertensive Effect, and Cardioprotection of a Novel Peptide Agonist of the Mas Receptor

Savergnini

Beiman²,

Lautner³

et al. 2010

Hypertension

106

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Abstract-Mas stimulation with angiotensin (Ang)-(1-7) produces cardioprotective effects and vasorelaxation. Using a computational discovery platform for predicting novel naturally occurring peptides that may activate G protein-coupled receptors, we discovered a novel Mas agonist peptide, CGEN-856S. An endothelium-and NO-dependent vasodilating effect was observed for CGEN-856S in thoracic aorta rings of rats (maximal value for the relaxant effect: 39.99Ϯ5.034%), which was similar to that produced by Ang-(1-7) (10 Ϫ10 to 10 Ϫ6 mol/L). In addition, the vasodilator activity of this peptide depended on a functional Mas receptor, because it was abolished in aorta rings of Mas-knockout mice. CGEN-856S appears to bind the Mas receptor at the same binding domain as Ang- (1-7), as suggested by the blocking of its vasorelaxant effect with the Ang-(1-7) analogue D-Ala 7 -Ang-(1-7), and by its competitive inhibition of Ang-(1-7) binding to Mas-transfected cells. The effect of CGEN-856S on reperfusion arrhythmias and cardiac function was studied on ischemia reperfusion of isolated rat hearts. We found that picomolar concentration of CGEN-856S (0.04 nmol/L) had an antiarrhythmogenic effect, as demonstrated by a reduction in the incidence and duration of reperfusion arrhythmias. Furthermore, acute infusion of CGEN-856S produced a shallow dose-dependent decrease in mean arterial pressure of conscious spontaneously hypertensive rats. The maximum change during infusion was observed at the highest dose. Strikingly, blood pressure continued to drop in the postinfusion period. The results presented here indicate that the novel Mas agonist, CGEN-856S, might have a therapeutic value, because it induces vasorelaxing, antihypertensive, and cardioprotective effects. (Hypertension. 2010;56:112-120.)

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Predicting proteolytic sites in extracellular proteins: only halfway there

Cited by 11 publications

References 36 publications

Discovery and Validation of Novel Peptide Agonists for G-protein-coupled Receptors

Discovery and Validation of Novel Peptide Agonists for G-protein-coupled Receptors

Activation of Relaxin‐Related Receptors by Short, Linear Peptides Derived from a Collagen‐Containing Precursor

Vascular Relaxation, Antihypertensive Effect, and Cardioprotection of a Novel Peptide Agonist of the Mas Receptor

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