A Practical Approach to Quantitatively Assessing Equilibrium-Constant Accuracy from a Single Binding Isotherm DOI Creative Commons
Tong Ye Wang, Jessica Latimer, Jean‐Luc Rukundo

et al.

Precision Chemistry, Journal Year: 2024, Volume and Issue: 3(2), P. 89 - 104

Published: Nov. 20, 2024

Equilibrium constants are essential for understanding and predicting the behavior of chemical systems across various scientific disciplines. Traditionally, these computed via nonlinear regression reaction isotherms, which show dependence unreacted fraction one reactant on total concentration another reactant. However, while equilibrium can be precise (with small random errors), they may also grossly inaccurate large systematic leading to potential misinterpretations. Although some statistical methods exist assessing accuracy regression, their limited practicality molecular scientists has resulted in neglect by this research community. The objective work is develop a practical method quantitatively that could easily understood immediately adopted researchers routinely determining constants. Our approach integrates error-propagation regression-stability analyses establish confidence interval (ACI)-a range within true value parameter lies with defined probability. In proof-of-principle study, we applied workflow ACI dissociation constant (K d) affinity complexes from single binding isotherm. We clearly explained how input parameters determined, finally, have implemented user-friendly web application (https://aci.sci.yorku.ca) facilitate its immediate adoption scientists, regardless mathematical computer proficiency. further conducted three case studies exemplifying use context simultaneous assessment precision determined K d values. By other through avoid misconceptions arise relying solely precision.

Language: Английский

Exploring Molecular Binding: A Fluorescence Anisotropy Lab for Undergraduates DOI

Maxine Forder,

Maira Rivera, Yuhao Chen

et al.

Journal of Chemical Education, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 7, 2025

Measuring interactions between macromolecules is essential for elucidating their dynamics in solution and critical the design study of potential therapeutics. Fluorescence anisotropy has been a powerful widely used tool studying binding interactions. When fluorescent partner excited with polarized light while bound to its cognate ligand, emitted partially polarized. This process dependent on concentration molecules, permitting determination affinity. Here, we outline highly modular undergraduate-level laboratory which students use fluorescence measure synthetic nucleic acid aptamer protein target. Students learn theory functional acids principles exploring relevance sequence/structure activity relationships via mutations aptamers. With this approach, can deepen knowledge about macromolecular are able develop valuable analytical biophysical skills. experiment adaptable suit range funding instructor availability, making it accessible tailorable most settings.

Language: Английский

Citations

0
Development of Novel Short Peptide Inhibitor Targeted to Immune Checkpoint PD-1 LBD DOI

Xingyan Zhu,

Yuping Wei, Man Zhang

et al.

International Journal of Peptide Research and Therapeutics, Journal Year: 2025, Volume and Issue: 31(3)

Published: March 7, 2025

Language: Английский

Citations

0
Combination of Autodisplay and Dynamic Pharmacophore Modeling Reveals New Insights into Cyclic Nucleotide Binding in Hyperpolarization-Activated and Cyclic Nucleotide-Gated Ion Channel 4 (HCN4) DOI Creative Commons

Magdalena N. Wojciechowski,

Johannes Jokiel,

Hanna Kuss

et al.

ACS Pharmacology & Translational Science, Journal Year: 2024, Volume and Issue: 7(12), P. 4010 - 4020

Published: Oct. 29, 2024

Hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels play a critical role in regulating neuronal and cardiac rhythmicity, with their function being modulated by nucleotide binding. Dysfunction of HCN leads to the genesis several diseases such as arrhythmia, bradycardia, or epilepsy. This study employs multidisciplinary approach integrating mutagenesis, ligand binding assays, molecular dynamics (MD) simulations combined dynamic pharmacophore studies investigate impact single residue mutations within nucleotide-binding domain (CNBD) HCN4 channels. Utilizing an autodisplay-based assay, surface-displayed CNBD mutants were evaluated for interaction 8-Fluo-cAMP, providing insights into properties. While some known mutational effects could be confirmed (R669, T670), we identified L652 crucial successful Surprisingly, C662, located center pocket, was discovered negligible cAMP-binding. Both E660 R710 shown substantially affect 8-Fluo-cAMP-binding, uncovering direct capability R710A mutant first time. Furthermore, MD coupled analysis offered detailed ligand–protein interactions, elucidating structural basis modulation induced mutations. Here, novel bypass mechanism R713 that interacts cAMP absence demonstrated. These findings unveil new perspectives on channels, foundation future pathogenic channel

Language: Английский

Citations

0
In Silico Discovery of Multi-Target Natural Ligands and Efficient siRNA Design for Overcoming Drug Resistance in Breast Cancer via Local Therapy DOI Open Access

Seyed Mohammad Javad Hashemi,

Ali Barzegar, Javad Akhtari

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 11, 2024

Abstract In this study, we designed an efficient siRNA for PKMYT1 gene knockdown, and evaluated the binding affinities of different natural ligands to crucial proteins involved in breast cancer. Designed showed strong affinity minimal off-target effects. Molecular docking studies identified new as antagonists with high aromatase, estrogen receptor alpha, HER2, PARP10, well agonists MT2 STING. The ligand SCHEMBL7562664 was introduced a golden due its among multiple targets lack cytotoxic mutagenic Natural small molecules research, their multi-target characteristics, provided solution overcome problem drug resistance cancer cells. Furthermore, proposed three dimensional scaffold design local therapy offers promising approach increase delivery efficacy these molecules, reduce systemic side effects, improve treatment outcomes. significant favorable pharmacokinetic properties were identified, which paves way further research targeted

Language: Английский

Citations

0
A Practical Approach to Quantitatively Assessing Equilibrium-Constant Accuracy from a Single Binding Isotherm DOI Creative Commons
Tong Ye Wang, Jessica Latimer, Jean‐Luc Rukundo

et al.

Precision Chemistry, Journal Year: 2024, Volume and Issue: 3(2), P. 89 - 104

Published: Nov. 20, 2024

Equilibrium constants are essential for understanding and predicting the behavior of chemical systems across various scientific disciplines. Traditionally, these computed via nonlinear regression reaction isotherms, which show dependence unreacted fraction one reactant on total concentration another reactant. However, while equilibrium can be precise (with small random errors), they may also grossly inaccurate large systematic leading to potential misinterpretations. Although some statistical methods exist assessing accuracy regression, their limited practicality molecular scientists has resulted in neglect by this research community. The objective work is develop a practical method quantitatively that could easily understood immediately adopted researchers routinely determining constants. Our approach integrates error-propagation regression-stability analyses establish confidence interval (ACI)-a range within true value parameter lies with defined probability. In proof-of-principle study, we applied workflow ACI dissociation constant (K d) affinity complexes from single binding isotherm. We clearly explained how input parameters determined, finally, have implemented user-friendly web application (https://aci.sci.yorku.ca) facilitate its immediate adoption scientists, regardless mathematical computer proficiency. further conducted three case studies exemplifying use context simultaneous assessment precision determined K d values. By other through avoid misconceptions arise relying solely precision.

Language: Английский

Citations

0