**6. HDL lipoproteomics for drug discovery**

Target discovery, which is an important step in the drug development process, includes discovering and validating targets associated with the diseases. It is increasingly recognized that, in many instances, metabolomics is used to identify novel biomarkers, which can help in the discovery of therapeutic strategies for many diseases [89].

Until now, lipoproteomics has proved to be an effective method for identifying candidate cardiovascular disease markers. Studying the profiles of protein expression in drug-treated patients contributes to the discovery of multiple drug-specific targets. Traditionally, statin therapy has proven efficacy in reducing cardiovascular events, but as aforementioned, the identification of HDL-associated proteins is variable. The statin therapy has a notorious effect on the increment of A1AT associated to the large fraction of HDL particles enhancing its anti-inflammatory functionality, which may interfere with the statins outcome on reducing cholesterol levels [37]. In addition, a relationship between the CAD treatment and the HDL proteome was demonstrated using statin and niacin therapy, observing that ApoE and ApoC-II levels are enriched in the HDL3 fraction, which contains less ApoJ levels [90].

The increment in the HDL levels by CETP inhibitors is another biomarker that has continued to be disappointing in clinical research. In fact, in patients with deficiency of CETP (CETP-D), the HDL particles are enriched with ApoE, angiopoietin-like3 protein, and complement regulatory proteins such as C3, C4a, C4b, and C9 that could be associated to the increased atherogenic profile in CETP-D patients [91].

Thus, it is important to consider that among the diverse HDL populations not all possess a cardioprotective effect [92]. Therefore, we need a better knowledge of the protein cargo of the HDL populations with anti-atherogenic actions. A comprehensive understanding of the HDL proteomics can lead to the design of more effective

*Lipoproteomics: Methodologies and Analysis of Lipoprotein-Associated Proteins… DOI: http://dx.doi.org/10.5772/intechopen.93634*

anti-atherogenic drugs based on the activity of HDL-associated proteins that will provide new therapeutic strategies at the molecular level.

In the dynamic drug discovery process, the different proteomic methods, which include MS-proteomics, expand beyond the general aim of target drug discovery. It must consider the drug-protein interactions as well as elucidate the mode of action of candidate drug molecules [93]. Thus, novel HDL-based therapeutic agents, besides the traditional statins, will need consider to the functional HDL lipoproteomics to characterize the interaction of the drug with the HDL-associated proteins. This is necessary as an attempt either to elucidate the mechanism of action by direct drug-protein interaction or as a biomarker for drug validation by monitoring the pharmacological effect through an increase of HDL populations with an anti-atherogenic protein cargo.

### **7. Conclusion**

Concerning other diseases, the proteome of HDL particles has been used to identify protein markers. In nonalcoholic fatty liver disease, including individuals with nonalcoholic steatohepatitis, changes in the abundance of HDL-associated proteins such as antithrombin III and plasminogen have been identified [82]. Although not directly to HDL particles, proteomic analysis of some HDL-related apolipoproteins has been associated with viral diseases. For example, a change in the expression level of ApoA-I was suggested as a specific and appropriate alternative to conventional HIV diagnosis and progression measurements in clinical research settings [83]. Increased concentration of ApoM in sera patients with HBV infection have been detected [84]. Recently, a downregulation of ApoA-I and ApoM

*Drug Design - Novel Advances in the Omics Field and Applications*

levels have been associated with the severity of COVID-19 infection [85].

complement C3 [88].

many diseases [89].

levels [90].

patients [91].

**42**

**6. HDL lipoproteomics for drug discovery**

to discover changes in lipoproteins-associated proteins in diverse pathologies. Proteomic studies of LDL have reported that carry apolipoproteins AI, A-II, CI, C-II, C-III, C-IV, D, E, and F, in addition to apoB, as well as clusterin, C3, C4a, and C4b, and PON1 that are also associated to this particles [86]. Serum amyloid A levels were found to increase in all lipoprotein fractions, especially in LDL from atherosclerotic patients [24]. An enriched content of all the apoC-III isoforms and a lower content of apoA-I, apoC-I, and apoE were detected in the sdLDL from subjects with metabolic syndrome and subclinical peripheral atherosclerosis [87]. VLDL, IDL, and LDL fractions from Alzheimer patients exhibit low levels of

In addition to HDL, only other few lipoproteomic studies have been developed

Target discovery, which is an important step in the drug development process,

Until now, lipoproteomics has proved to be an effective method for identifying candidate cardiovascular disease markers. Studying the profiles of protein expression in drug-treated patients contributes to the discovery of multiple drug-specific targets. Traditionally, statin therapy has proven efficacy in reducing cardiovascular events, but as aforementioned, the identification of HDL-associated proteins is variable. The statin therapy has a notorious effect on the increment of A1AT associated to the large fraction of HDL particles enhancing its anti-inflammatory functionality, which may interfere with the statins outcome on reducing cholesterol levels [37]. In addition, a relationship between the CAD treatment and the HDL proteome was demonstrated using statin and niacin therapy, observing that ApoE and ApoC-II levels are enriched in the HDL3 fraction, which contains less ApoJ

The increment in the HDL levels by CETP inhibitors is another biomarker that has continued to be disappointing in clinical research. In fact, in patients with deficiency of CETP (CETP-D), the HDL particles are enriched with ApoE, angiopoietin-like3 protein, and complement regulatory proteins such as C3, C4a, C4b, and C9 that could be associated to the increased atherogenic profile in CETP-D

Thus, it is important to consider that among the diverse HDL populations not all possess a cardioprotective effect [92]. Therefore, we need a better knowledge of the protein cargo of the HDL populations with anti-atherogenic actions. A comprehensive understanding of the HDL proteomics can lead to the design of more effective

includes discovering and validating targets associated with the diseases. It is increasingly recognized that, in many instances, metabolomics is used to identify novel biomarkers, which can help in the discovery of therapeutic strategies for

The lipoproteins can be involved in different pathologies related to lipid metabolism such as atherosclerosis, cardiovascular risk, obesity, metabolic síndrome, and diabetes, among others. However, the protein cargo of these particles has been associated with several functions, which differ from the amply recognized as structural composition and receptors recognition during their function as lipid transporters. For this reason, the identification of variants of apolipoproteins and lipoprotein-associated proteins has been an important referent to detect new biomarkers. In fact, as we described here, several methodologies have been developed to improve the lipoproteomic profile.

Despite these studies, the majority concord that both biological source and lipoprotein purification are important steps to avoid protein contamination, principally from samples that are used directly as serum or plasma. Also, the most used method to identify the lipoprotein-associated proteins is the mass spectrometry, but some limits are presented that depend on the platforms to apply this methodology. Also, it is important to highlight that not everyone has the facility to use this methodology and it is necessary to develop new methodologies to apply in clinical fields to ensure discoveries about these proteins both in new lipoproteins' fractions and new diseases.

Also, the lipoproteomic analyses could be a new clinical area to evaluate the therapy of the pathologies described here as prognostic analytes. In this sense, the HDL lipoproteomics is, perhaps, the more advanced field considering the evaluations of populations with statins' treatment. However, novel HDL therapeutic agents must consider the functional lipoproteomics of these particles. Finally, these lipoproteomes can help us to describe the molecular mechanism to understand the interaction of apolipoproteins as well as the lipoprotein-carried proteins to support the other omics such as lipidomics and metabolomics.

### **Acknowledgements**

This work was supported by the Autonomous University of Mexico City (UACM) awarded to MEAS.

#### **Conflict of interest**

The authors declare no conflict of interest.
