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共溶剂二甲基亚砜通过溶剂黏度效应影响蛋白-配体结合动力学:揭示扩散性蛋白-配体结合后复合物形成的成功率。

Cosolvent Dimethyl Sulfoxide Influences Protein-Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein-Ligand Encounter.

机构信息

Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden.

出版信息

Biochemistry. 2023 Jan 3;62(1):44-52. doi: 10.1021/acs.biochem.2c00507. Epub 2022 Dec 21.


DOI:10.1021/acs.biochem.2c00507
PMID:36542811
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9813907/
Abstract

Protein-ligand-exchange kinetics determines the duration of biochemical signals and consequently plays an important role in drug design. Binding studies commonly require solubilization of designed ligands in solvents such as dimethyl sulfoxide (DMSO), resulting in residual amounts of DMSO following titration of solubilized ligands into aqueous protein samples. Therefore, it is critical to establish whether DMSO influences protein-ligand binding. Here, we address the general and indirect effect of DMSO on protein-ligand binding caused by solvent viscosity, which is strongly dependent on the relative concentrations of DMSO and water. As a model system, we studied the binding of a drug-like ligand to the carbohydrate recognition domain of galectin-3 in the presence of variable amounts of DMSO. We used isothermal titration calorimetry to characterize binding thermodynamics and N NMR relaxation to monitor kinetics. The binding enthalpy is not affected, but we observe a subtle trend of increasingly unfavorable entropy of binding, and consequently decreased affinity, with increasing DMSO concentration. The increasing concentration of DMSO results in a reduced association rate of binding, while the dissociation rate is less affected. The observed association rate is inversely proportional to the viscosity of the DMSO-water mixture, as expected from theory, but significantly reduced from the diffusion-controlled limit. By comparing the viscosity dependence of the observed association rate with that of the theoretical diffusion-controlled association rate, we estimate the success rate of productive complex formation following an initial encounter of proteins and ligands, showing that only one out of several hundred binding "attempts" are successful.

摘要

蛋白-配体交换动力学决定了生化信号的持续时间,因此在药物设计中起着重要作用。结合研究通常需要将设计的配体溶解在二甲基亚砜(DMSO)等溶剂中,因此在将溶解的配体滴定到水性蛋白质样品中后,会残留少量 DMSO。因此,确定 DMSO 是否影响蛋白-配体结合至关重要。在这里,我们研究了溶剂粘度对蛋白-配体结合的一般和间接影响,这强烈依赖于 DMSO 和水的相对浓度。作为模型系统,我们研究了在可变 DMSO 浓度存在下,一种类似药物的配体与半乳糖凝集素-3 的碳水化合物识别结构域的结合。我们使用等温滴定量热法来描述结合热力学,使用 N 核磁共振弛豫来监测动力学。结合焓不受影响,但我们观察到结合熵逐渐不利的微妙趋势,因此结合亲和力降低。随着 DMSO 浓度的增加,结合的缔合速率降低,而解离速率的影响较小。观察到的缔合速率与 DMSO-水混合物的粘度成反比,这与理论预期一致,但与扩散控制极限相比显著降低。通过比较观察到的缔合速率与理论扩散控制缔合速率的粘度依赖性,我们估计了蛋白质和配体初始相遇后产生有效复合物形成的成功率,表明只有数百次结合“尝试”中的一次是成功的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d290/9813907/7cc6bb2ed897/bi2c00507_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d290/9813907/5a6d70465b73/bi2c00507_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d290/9813907/3ba1606427db/bi2c00507_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d290/9813907/7cc6bb2ed897/bi2c00507_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d290/9813907/5a6d70465b73/bi2c00507_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d290/9813907/3ba1606427db/bi2c00507_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d290/9813907/7cc6bb2ed897/bi2c00507_0004.jpg

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引用本文的文献

[1]
Unveiling the Solvent Effect: DMSO Interaction with Human Nerve Growth Factor and Its Implications for Drug Discovery.

Molecules. 2025-7-19

[2]
Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit.

Proc Natl Acad Sci U S A. 2024-4-2

[3]
Solubility and Thermodynamics Data of Cabozantinib Malate in Various Aqueous Solutions of Dimethyl Sulfoxide at Different Temperatures.

Molecules. 2023-11-27

[4]
Solubility and Thermodynamic Analysis of Isotretinoin in Different (DMSO + Water) Mixtures.

Molecules. 2023-10-16

本文引用的文献

[1]
Role of galectin 3 binding protein in cancer progression: a potential novel therapeutic target.

J Transl Med. 2021-9-26

[2]
Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C.

JACS Au. 2021-4-1

[3]
Mapping the energy landscape of protein-ligand binding linear free energy relationships determined by protein NMR relaxation dispersion.

RSC Chem Biol. 2020-12-23

[4]
Recent progress in molecular simulation methods for drug binding kinetics.

Curr Opin Struct Biol. 2020-10

[5]
Galectin-3 as a Next-Generation Biomarker for Detecting Early Stage of Various Diseases.

Biomolecules. 2020-3-3

[6]
Kinetics of Drug Binding and Residence Time.

Annu Rev Phys Chem. 2019-6-14

[7]
Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity.

Chemphyschem. 2019-1-21

[8]
Kinetic Solvent Viscosity Effects as Probes for Studying the Mechanisms of Enzyme Action.

Biochemistry. 2018-6-26

[9]
Systematic Tuning of Fluoro-galectin-3 Interactions Provides Thiodigalactoside Derivatives with Single-Digit nM Affinity and High Selectivity.

J Med Chem. 2018-1-11

[10]
Monosaccharide Derivatives with Low-Nanomolar Lectin Affinity and High Selectivity Based on Combined Fluorine-Amide, Phenyl-Arginine, Sulfur-π, and Halogen Bond Interactions.

ChemMedChem. 2018-1-15

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