Studies of metabolite-protein interactions: a review

Abstract

The study of metabolomics can provide valuable information about biochemical pathways and processes at the molecular level. There have been many reports that have examined the structure, identity and concentrations of metabolites in biological systems. However, the binding of metabolites with proteins is also of growing interest. This review examines past reports that have looked at the binding of various types of metabolites with proteins. An overview of the techniques that have been used to characterize and study metabolite-protein binding is first provided. This is followed by examples of studies that have investigated the binding of hormones, fatty acids, drugs or other xenobiotics, and their metabolites with transport proteins and receptors. These examples include reports that have considered the structure of the resulting solute-protein complexes, the nature of the binding sites, the strength of these interactions, the variations in these interactions with solute structure, and the kinetics of these reactions. The possible effects of metabolic diseases on these processes, including the impact of alterations in the structure and function of proteins, are also considered.

Keywords: Drug–protein interactions; Fatty acid–protein interactions; Hormone–protein interactions; Metabolomics; Protein modification; Xenobiotic–protein interactions.

Figure 1

Crystal structure for the complex of human androgen receptor ligand-binding domain with testosterone (Testo). Reproduced with permission from Ref. [30].

Figure 2

Example of a competition study using high-performance affinity chromatography to examine the interactions of an injected site-selective probe with a solute that is present at a known concentration in the mobile phase. This example shows the change in the retention factor (k) that was measured for R-warfarin as a probe for Sudlow site I of human serum albumin (HSA) in the presence of various concentrations of tolbutamide as a competing agent. These results were obtained for columns that contained two clinical samples of HSA that had different levels of modification due to glycation. Adapted with permission from Ref. [39].

Figure 3

Structure of HSA, showing the regions that bind palmitic acid. This structure was generated using Protein Data Bank (PDB) file ID: 1E7H [75] and is adapted with permission from Ref. [74].

Figure 4

Chiral separation and analysis of tramadol and its major metabolites using HPLC and a column containing immobilized APG as stationary phase. The results in (a) are for a blank human plasma sample. The results in (b) are for a plasma sample taken from a volunteer 2.5 hours after receiving a 100 mg dose of racemic tramadol. Symbols: enantiomers of tramadol, +(T) and −(T); enantiomers of the metabolite O-desmethyltramadol, +(M1) and −(M1); enantiomers of the metabolite N-desmethyltramadol, +(M2) and −(M2); and internal standard (fluconazol), IS. Adapted with permission from Ref. [96].

Figure 5

Reactions involved in the early stages of glycation of a protein, using human serum albumin (HSA) as an example [145].