Analytical methods for obtaining binding parameters of drug–protein interactions: A review

Wang, Limin; Zhang, Wenmei; Shao, Yunlong; Zhang, Dongtang; Guo, Guangsheng; Wang, Xiayan

doi:10.1016/j.aca.2022.340012

Cited by 25 publications

(10 citation statements)

References 202 publications

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“…Equilibrium dialysis, high-performance affinity chromatography, capillary electrophoresis, spectroscopy, etc. were commonly used for the study of drug–protein interactions (DPIs) . In our previous study, SOF has been confirmed to have specific interactions with liver-related proteins through qualitative analysis .…”

Section: Introductionmentioning

confidence: 86%

Novel Strategy for Screening Target Proteins by the Common Drugs─Sofosbuvir-Specific Profiling of HCV Patient Serum

Pan,

Wang,

Yan

et al. 2024

Anal. Chem.

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It is the scientific basis of precision medicine to study all of the targets of drugs based on the interaction between drugs and proteins. It is worth paying attention to unknown proteins that interact with drugs to find new targets for the design of new drugs. Herein, we developed a protein profiling strategy based on drug−protein interactions and drug-modified magnetic nanoparticles and took hepatitis C virus (HCV) and its corresponding drug sofosbuvir (SOF) as an example. A SOFmodified magnetic separation medium (Fe 3 O 4 @POSS@SOF) was prepared, and a gradient elution strategy was employed and optimized to profile specific proteins interacted with SOF. A series of proteomic analyses were performed to profile proteins based on SOF−protein interactions (SPIs) in the serum of HCV patients to evaluate the specificity of the profiling strategy. As a result, five proteins were profiled with strong SPIs and exhibited high relevance with liver tissue, which were potentially new drug targets. Among them, HSP60 was used to confirm the highly specific interactions between the SOF and its binding proteins by Western blotting analysis. Besides, 124 and 29 differential proteins were profiled by SOF material from three HCV patient serum and pooled 20 HCV patient serum, respectively, by comparing with healthy human serum. In comparison with those profiled by the polyhedral oligomeric silsesquioxane (POSS) material, differential proteins profiled by the SOF material were highly associated with liver diseases through GO analysis and pathway analysis. Furthermore, four common differential proteins profiled by SOF material but not by POSS material were found to be identical and expressed consistently in both pooled serum samples and independent serum samples, which might potentially be biomarkers of HCV infection. Taken together, our study proposes a highly specific protein profiling strategy to display distinctive proteomic profiles, providing a novel idea for drug design and development.

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Section: Introductionmentioning

confidence: 86%

Novel Strategy for Screening Target Proteins by the Common Drugs─Sofosbuvir-Specific Profiling of HCV Patient Serum

Pan,

Wang,

Yan

et al. 2024

Anal. Chem.

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“…This technique has emerged as a valuable resource in recent years, facilitating a comprehensive analysis of the microenvironment and conformational alterations within the structure of serum proteins induced by the presence of molecules. Its application provides a three-dimensional perspective, enhancing insights into complex molecular dynamics (MD) simulations involved in the interaction between serum proteins and molecules [34,35].…”

Section: Basic Information About Analytical Methodsmentioning

confidence: 99%

Current analytical methods and applications used in the insight of serum proteins interactions with various food additives, pesticides, and contaminants

Erkmen,

Kabir

2024

Explor Foods Foodomics

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In recent years, many societies have expressed increasing apprehension regarding the potential negative impacts of food additives, pesticides, and environmental contaminants on human health. Environmental or occupational exposure to these compounds can cause significant adverse effects on human health by causing temporary or permanent changes in the immune system. There is supporting evidence linking pesticides/food ingredients/contaminants-induced immune alterations to the prevalence of diseases associated with changes in immune responses. Hence, it is essential to comprehensively understand the key mechanisms contributing to immune dysregulation induced by these substances, including direct immunotoxicity, endocrine disruption, and antigenicity. The impact of pesticides/food ingredients and contaminants on the human body ranges from mild to severe, depending on their affinity for blood components. These compounds form complexes with blood serum proteins, influencing their metabolism, transport, absorption, and overall toxicity. Numerous studies in the literature have explored the interactions between serum proteins and various molecules, including pesticides, drugs, and food dyes. These investigations employed a range of techniques, including spectroscopy, electrochemical and chromatographic methods as well as molecular modeling and molecular dynamics simulations analyses. This recent review, spanning from 2020 to the present, has been employed to investigate the binding characteristics, mechanisms, and attributes of different food additives, pesticides, and contaminants with serum proteins by using various techniques such as steady-state fluorescence, circular dichroism and ultra-violet spectroscopies, and computational docking methods. The review provides insights into these compounds’ positions and affinities to proteins and possible effects on human health through detailed research studies.

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“…Equilibrium dialysis and ultrafiltration , are recommended as reference methods for pursuing a drug–protein binding mechanism. , Nevertheless, they suffer from errors generated by nonspecific adsorption between the drugs or proteins and components of filtration membranes. Diverse assays based on distinct principles have also been reported for studying drug–protein interactions, including fluorescence spectroscopy, absorption spectroscopy, surface plasmon resonance (SPR), and nuclear magnetic resonance spectroscopy (NMR) .…”

Section: Introductionmentioning

confidence: 99%

Affinity Chromatographic Method for Determining Drug–Protein Interaction with Enhanced Speed Than Typical Frontal Analysis

Ou,

Qiao,

et al. 2023

Langmuir

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Revealing drug−protein interaction is highly important to select a drug candidate with improved drug-like properties in the early stages of drug discovery. This highlights the urgent need to develop assays that enable the analysis of drug−protein interaction with high speed. Herein, this purpose was realized by the development of an affinity chromatographic method with a two-fold higher speed than typical assays like frontal analysis and zonal elution. The method involved synthesis of a stationary phase by immobilizing poly(ADPribose) polymerase-1 (PARP 1 ) onto macroporous silica gel through a one-step bioorthogonal reaction, characterization of mutual displacement interaction of two canonical drugs to the immobilized PARP 1 , determination of the interaction between three (iniparib, rucaparib, and olaparib) drugs and the protein, and validation of these parameters by typical frontal analysis. The numbers of binding sites on the column were (2.85 ± 0.05) × 10 −7 , (1.89 ± 0.71) × 10 −6 , and (1.49 ± 0.06) × 10 −7 M for iniparib, rucaparib, and olaparib, respectively. On these sites, the association constants of the three drugs to the protein were (9.85 ± 0.56) × 10 4 , (2.85 ± 0.34) × 10 4 , and (1.07 ± 0.35) × 10 5 M −1 . The determined parameters presented a good agreement with the calculation by typical frontal analyses, which indicated that the current continuous competitive frontal analysis method was reliable for determining drug−protein interaction. Application of the methods was achieved by screening tubeimosides I and II as the bioactive compounds against breast cancer in Bolbostemma paniculatum. Their mechanism may be the interference of DNA repair via down-regulating PARP 1 and meiotic recombination 11 expressions, thus leading to oncogene mutations and death of cancer cells. The method was high speed since it allowed simultaneous determination of binding parameters between two drugs and a protein with a smaller number of experiments to be performed. Such a feature made the method an attractive alternative for high-speed analysis of drug−protein interaction or the other bindings in a binary system.

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Analytical methods for obtaining binding parameters of drug–protein interactions: A review

Cited by 25 publications

References 202 publications

Novel Strategy for Screening Target Proteins by the Common Drugs─Sofosbuvir-Specific Profiling of HCV Patient Serum

Novel Strategy for Screening Target Proteins by the Common Drugs─Sofosbuvir-Specific Profiling of HCV Patient Serum

Current analytical methods and applications used in the insight of serum proteins interactions with various food additives, pesticides, and contaminants

Affinity Chromatographic Method for Determining Drug–Protein Interaction with Enhanced Speed Than Typical Frontal Analysis

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