Mapping proteome-wide interactions of reactive chemicals using chemoproteomic platforms

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Highlights

  • Many pharmaceuticals and environmental chemicals act through covalent mechanisms.

  • Deciphering direct targets of reactive chemicals is important in mitigating toxicity.

  • Chemoproteomics enables selectivity assessment of irreversibly-acting chemicals.

A large number of pharmaceuticals, endogenous metabolites, and environmental chemicals act through covalent mechanisms with protein targets. Yet, their specific interactions with the proteome still remain poorly defined for most of these reactive chemicals. Deciphering direct protein targets of reactive small-molecules is critical in understanding their biological action, off-target effects, potential toxicological liabilities, and development of safer and more selective agents. Chemoproteomic technologies have arisen as a powerful strategy that enable the assessment of proteome-wide interactions of these irreversible agents directly in complex biological systems. We review here several chemoproteomic strategies that have facilitated our understanding of specific protein interactions of irreversibly-acting pharmaceuticals, endogenous metabolites, and environmental electrophiles to reveal novel pharmacological, biological, and toxicological mechanisms.

Introduction

We are exposed to a large number of chemicals that act through covalent mechanisms. These chemicals include pharmaceutical agents that irreversibly inhibit their respective protein targets to treat human diseases, such as Alzheimer's disease, obesity, pain, and cancer [1, 2, 3, 4, 5]. Also included are reactive endogenous metabolites that are formed through metabolism, such as lipid aldehydes and various forms of reactive oxygen species or nitrogen stress. Many pesticides, environmental contaminants, and household chemicals also act through covalent mechanisms [6, 7, 8, 9, 10••]. While most of these chemicals have undergone standard toxicological testing, the reactivity of these chemicals across the proteome still remains poorly defined. Understanding the selectivity of these reactive agents is of paramount importance in comprehending the mechanisms underlying their biological or therapeutic action, identifying off-target effects that may lead to ‘idiosyncratic’ toxicities, and informing the development of safer and more selective agents (Figure 1, Figure 2, Figure 3).

Over the past several years, there have been major advancements in the development and use of chemoproteomic platforms to determine the proteome-wide interactions of irreversible small-molecule tool compounds, therapeutics, endogenous electrophiles, and environmental chemicals. In this review, we will describe how chemoproteomic technologies have been used to assess both the selectivity of therapeutic agents and the toxicological mechanisms of environmental chemicals.

Section snippets

Chemoproteomic profiling to assess selectivity of therapeutic irreversible small-molecule inhibitors

Pharmaceutical companies have historically shied away from pursuing covalent inhibitors due to risks of haptenization and immunologic reactions that may occur through non-specific covalent modification of small-molecules with protein targets [11]. Nonetheless, many irreversible or pseudo-irreversible inhibitors have been successfully developed as well-tolerated drugs in the clinic. Examples include the anti-inflammatory drug aspirin, the broad class of antibacterial beta-lactam antibiotics such

Chemoproteomic profiling of reactive environmental chemicals and endogenous reactive metabolites to understand toxicological mechanisms

We are exposed to countless chemicals, many of which have been linked to adverse health effects, and most of which have not been characterized in terms of their toxicological potential or mechanisms. Of particular concern among chemicals in our environment are reactive electrophiles that we are directly exposed to or those that form through bioactivation, which have the potential to covalently and cumulatively react with nucleophilic amino acid hotspots within the proteome, leading to potential

Conclusion

We provide here several examples of chemoproteomic platforms and their applications to assess the selectivity or off-target profiles of tool compounds, therapeutics, and environmental chemicals that act through irreversible mechanisms. Historically, small-molecule agents that act through covalent mechanisms have been feared to cause non-specific adducts on proteins, which, in-turn, may lead to non-specific toxicities and potential haptenization or other types of idiosyncratic toxicities.

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

This work was supported by the Searle Scholar Award, the Center for Environmental Research on Toxics, the National Institutes of Health (P42ES004705; R01CA172667), the American Cancer Society Research Scholar Award (RSG-14-242-01-TBE), the DOD Breakthroughs Award (CDMRP W81XWH-15-1-0050), and the NSF Graduate Fellowship Program.

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