Journal: Biochemistry and Biophysics Reports

Article Title: Computational screening of walnut (Juglans regia) husk metabolites reveals Aesculin as a potential inhibitor of pectate lyase Pel3: Insights from molecular dynamics and τRAMD

doi: 10.1016/j.bbrep.2025.102171

Figure Lengend Snippet: RAMD-based evaluation of ligand dissociation dynamics for the Pel3–Aesculin complex. (a) Cumulative distribution function (CDF), tau (residence time) histogram, and (b) Kolmogorov–Smirnov (KS) test plot illustrates the rapid unbinding of Aesculin from the Pel3 active site, with a median dissociation time of ∼0.02 ns and a mean residence time of ∼0.015 ns. (C) The residence time histogram shows a near-normal distribution, confirmed by a Gaussian fit and KS test (p = 0.17), supporting the statistical reliability of the data. (d) The boxplot summarizes residence time dispersion across a single simulation replica, highlighting the presence of outliers that may reflect alternative dissociation pathways. (e) Distance plot showing the temporal evolution of the ligand's center-of-mass distance from the protein's active site, providing direct evidence of dissociation events and their timing during simulation Overall, the results reveal fast ligand dissociation, limited residence time, and suggest weak binding affinity between Aesculin and Pel3 under the simulated conditions.

Article Snippet: Sodium and chloride ions were added to achieve charge neutrality and an ionic concentration of 0.15 M. Among the docked compounds, Aesculin exhibited the most favorable binding free energy and was therefore selected for subsequent MD and Random Accelerated Molecular Dynamics (RAMD) simulations to further characterize its stability and unbinding kinetics within the Pel3 binding pocket.

Techniques: Dispersion, Binding Assay

Journal: British Journal of Pharmacology

Article Title: Pharmacological characterization of rat amylin receptors: implications for the identification of amylin receptor subtypes

doi: 10.1111/j.1476-5381.2011.01717.x

Figure Lengend Snippet: Distribution of pEC50 values for the agonists rCT, rAmy, rαCGRP, rβCGRP, (Cys(Et)2,7)hαCGRP, (Cys(ACM)2,7)hαCGRP, rAM and rAM2 in COS-7 cells transfected to express either (A) rCT(a) receptors, (B) rAMY1(a) receptors or (C) rAMY3(a) receptors. Data are mean ± SEM of four to 23 combined experiments. *P < 0.05, **P < 0.01, ***P < 0.001 by one-way anova followed by Tukey's test. For simplification, only comparisons against the cognate agonist for each receptor are shown (rCT for CT(a), rAmy for rAMY1(a) and rAMY3(a)); other comparisons are shown in supplementary Tables S1–3. (Cys(Et)2,7)hαCGRP and (Cys(ACM)2,7)hαCGRP were excluded from the analysis except in the rAMY3(a) receptor, where (Cys(Et)2,7)hαCGRP produced a sufficient response to be included.

Article Snippet: rAM, rCT, rαCGRP, rβCGRP, hαCGRP 8-37 and rαCGRP 8-37 were purchased from American Peptide (Sunnyvale, CA, USA). rAM2 (47 amino acids), sCT (Cys(Et) 2,7 )hαCGRP (Cys(ACM) 2,7 )hαCGRP, sCT 8-32 and AC187 were purchased from Bachem (Bubendorf, Switzerland). rAmy and rAmy 8-37 were purchased from both American Peptide and Bachem.

Techniques: Transfection, Produced

Journal: British Journal of Pharmacology

Article Title: Pharmacological characterization of rat amylin receptors: implications for the identification of amylin receptor subtypes

doi: 10.1111/j.1476-5381.2011.01717.x

Figure Lengend Snippet: Summary of p K B values for antagonism of rAmy-induced cAMP production at rCT (a) , rAMY 1(a) and rAMY 3(a) receptors

Article Snippet: rAM, rCT, rαCGRP, rβCGRP, hαCGRP 8-37 and rαCGRP 8-37 were purchased from American Peptide (Sunnyvale, CA, USA). rAM2 (47 amino acids), sCT (Cys(Et) 2,7 )hαCGRP (Cys(ACM) 2,7 )hαCGRP, sCT 8-32 and AC187 were purchased from Bachem (Bubendorf, Switzerland). rAmy and rAmy 8-37 were purchased from both American Peptide and Bachem.

Techniques:

Journal: British Journal of Pharmacology

Article Title: Pharmacological characterization of rat amylin receptors: implications for the identification of amylin receptor subtypes

doi: 10.1111/j.1476-5381.2011.01717.x

Figure Lengend Snippet: Antagonism of rAmy-induced cAMP production by the indicated concentrations of AC187 in COS-7 cells transfected to express either (A) rCT(a) receptors, (B) rAMY1(a) receptors or (C) rAMY3(a) receptors. Data are expressed as a percentage of the cAMP response generated by 50 µM forskolin. Data are mean ± SEM of three to four combined experiments, performed in triplicate or quadruplicate.

Article Snippet: rAM, rCT, rαCGRP, rβCGRP, hαCGRP 8-37 and rαCGRP 8-37 were purchased from American Peptide (Sunnyvale, CA, USA). rAM2 (47 amino acids), sCT (Cys(Et) 2,7 )hαCGRP (Cys(ACM) 2,7 )hαCGRP, sCT 8-32 and AC187 were purchased from Bachem (Bubendorf, Switzerland). rAmy and rAmy 8-37 were purchased from both American Peptide and Bachem.

Techniques: Transfection, Generated

Journal: British Journal of Pharmacology

Article Title: Pharmacological characterization of rat amylin receptors: implications for the identification of amylin receptor subtypes

doi: 10.1111/j.1476-5381.2011.01717.x

Figure Lengend Snippet: Distribution of pEC50 values for the agonists rCT, rAmy, rαCGRP, rβCGRP, (Cys(Et)2,7)hαCGRP, (Cys(ACM)2,7)hαCGRP, rAM and rAM2 in COS-7 cells transfected to express either (A) rCT(a) receptors, (B) rAMY1(a) receptors or (C) rAMY3(a) receptors. Data are mean ± SEM of four to 23 combined experiments. *P < 0.05, **P < 0.01, ***P < 0.001 by one-way anova followed by Tukey's test. For simplification, only comparisons against the cognate agonist for each receptor are shown (rCT for CT(a), rAmy for rAMY1(a) and rAMY3(a)); other comparisons are shown in supplementary Tables S1–3. (Cys(Et)2,7)hαCGRP and (Cys(ACM)2,7)hαCGRP were excluded from the analysis except in the rAMY3(a) receptor, where (Cys(Et)2,7)hαCGRP produced a sufficient response to be included.

Article Snippet: Drugs chemicals and other materials rAM, rCT, rαCGRP, rβCGRP, hαCGRP 8-37 and rαCGRP 8-37 were purchased from American Peptide (Sunnyvale, CA, USA). rAM2 (47 amino acids), sCT (Cys(Et) 2,7 )hαCGRP (Cys(ACM) 2,7 )hαCGRP, sCT 8-32 and AC187 were purchased from Bachem (Bubendorf, Switzerland). rAmy and rAmy 8-37 were purchased from both American Peptide and Bachem.

Techniques: Transfection, Produced

Journal: British Journal of Pharmacology

Article Title: Pharmacological characterization of rat amylin receptors: implications for the identification of amylin receptor subtypes

doi: 10.1111/j.1476-5381.2011.01717.x

Figure Lengend Snippet: Summary of p K B values for antagonism of rAmy-induced cAMP production at rCT (a) , rAMY 1(a) and rAMY 3(a) receptors

Article Snippet: Drugs chemicals and other materials rAM, rCT, rαCGRP, rβCGRP, hαCGRP 8-37 and rαCGRP 8-37 were purchased from American Peptide (Sunnyvale, CA, USA). rAM2 (47 amino acids), sCT (Cys(Et) 2,7 )hαCGRP (Cys(ACM) 2,7 )hαCGRP, sCT 8-32 and AC187 were purchased from Bachem (Bubendorf, Switzerland). rAmy and rAmy 8-37 were purchased from both American Peptide and Bachem.

Techniques:

Journal: British Journal of Pharmacology

Article Title: Pharmacological characterization of rat amylin receptors: implications for the identification of amylin receptor subtypes

doi: 10.1111/j.1476-5381.2011.01717.x

Figure Lengend Snippet: Antagonism of rAmy-induced cAMP production by the indicated concentrations of AC187 in COS-7 cells transfected to express either (A) rCT(a) receptors, (B) rAMY1(a) receptors or (C) rAMY3(a) receptors. Data are expressed as a percentage of the cAMP response generated by 50 µM forskolin. Data are mean ± SEM of three to four combined experiments, performed in triplicate or quadruplicate.

Article Snippet: Drugs chemicals and other materials rAM, rCT, rαCGRP, rβCGRP, hαCGRP 8-37 and rαCGRP 8-37 were purchased from American Peptide (Sunnyvale, CA, USA). rAM2 (47 amino acids), sCT (Cys(Et) 2,7 )hαCGRP (Cys(ACM) 2,7 )hαCGRP, sCT 8-32 and AC187 were purchased from Bachem (Bubendorf, Switzerland). rAmy and rAmy 8-37 were purchased from both American Peptide and Bachem.

Techniques: Transfection, Generated