CONCEPT PAPER | doi:10.20944/preprints202205.0388.v1
Subject: Chemistry, Medicinal Chemistry Keywords: proximity labeling; spatial omics; functional proteomics; interactome mapping; electrophile signaling
Online: 30 May 2022 (06:13:07 CEST)
If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current state-of-the-art and discusses key limitations underlying these emerging approaches, in particular, the limited functional knowledge they provide in understanding local proteomes / interactomes. This limitation is directly linked to the use of non-biologically- or non-pharmaceutically-relevant reactive intermediates in the course of covalently labeling the local proteomes. As such, these methods cannot report on specific functions of localized protein players, nor can they scrutinize whether the specific functions of such proteins/interactomes can be directly manipulated by pharmacologically-relevant small-molecule ligands. The latest data hint that precision localized electrophile delivery concept ushers a means to address this limitation with high spatiotemporal resolution, and ultimately, in relevant live animals.
REVIEW | doi:10.20944/preprints202301.0209.v1
Subject: Chemistry, Medicinal Chemistry Keywords: electrophile signaling; reactive metabolites; crystal structures of protein-electrophile complexes
Online: 12 January 2023 (04:08:43 CET)
Native reactive electrophile species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RES sensing and signaling have begun to bring about improved understanding of localized RES regulatory paradigms. However, studies in purified systems—prerequisites for gaining structure/function insights—prove challenging. We here introduce emerging chemical biology tools available to probe RES signaling, and the new knowledge that these tools have brought to the field. We next discuss existing structural data of RES-sensor proteins complexed with electrophilic metabolites or small molecule drugs (limited to < 300 Da), including challenges faced in acquiring homogenous RES-bound proteins. We further offer considerations that could promote enhanced understanding of RES regulation derived from three-dimensional structures of RES-modified proteins.
REVIEW | doi:10.20944/preprints202204.0093.v1
Subject: Life Sciences, Immunology Keywords: Electrophile signaling; drug mechanism; immunology; antioxidant response; apoptosis
Online: 11 April 2022 (10:39:31 CEST)
Here we draw insights from the latest serendipitous findings made on the opposing roles of a validated drug-target protein Keap1. We weigh up how natural reactive electrophiles and electrophilic small-molecule drugs in clinical use directly impinge on seemingly conflicting, yet both Keap1-electrophile-modification-dependent, cell-survival- vs. cell-death-promoting behaviors. In the process, we convey how understanding reactive chemical-signal regulation at a single-protein-specific level is an enabling necessity in deconstructing otherwise intricate reactive-small-molecule-responsive cellular pathways. We hope this opinion piece further spurs the broader interests of basic and pharmaceutical research communities toward better understanding of molecular mechanisms underpinning reactive small-molecule-regulated signaling subsystems.
REVIEW | doi:10.20944/preprints202103.0416.v1
Online: 16 March 2021 (11:54:28 CET)
CoVID-19 is a multi-symptomatic disease which has made a global impact due to its ability to spread rapidly, and its relatively high mortality rate. Beyond the heroic efforts to develop vaccines, which we will not discuss, the response of scientists and clinicians to this complex problem has reflected the need to detect CoVID-19 rapidly, to diagnose patients likely to show adverse symptoms, and to treat severe and critical CoVID-19. Here we aim to encapsulate these varied and sometimes conflicting approaches and the resulting data in terms of chemistry and biology. In the process we highlight emerging concepts, and potential future applications that may arise out of this immense effort.
REVIEW | doi:10.20944/preprints202201.0196.v1
Online: 13 January 2022 (18:27:07 CET)
The Covid‐19 pandemic, evolving needs of students & mentors, and the drive for global educational equality are collectively shifting how courses are packaged/distributed, ushering a more holistic approach and blending of fields. We recently created interdisciplinary courses in chemical biology aimed at massive open online and small private levels. These courses cover biology, chemistry, & physics, and concepts underlying modern chemical‐biology tools. We discuss what we learned while creating/overseeing these courses: content optimization and maintaining material freshness while fostering a stimulating learning environment. We outline mechanisms that help sustain student attention throughout rapidly‐moving courses, how to integrate adaptability to students’ needs in the short & long term, and speculate how we could have improved. We believe this will be an important guide for anyone wanting to develop online learning formats ideal for nurturing interdisciplinary scientists of tomorrow.
REVIEW | doi:10.20944/preprints202105.0036.v2
Subject: Chemistry, Analytical Chemistry Keywords: Electrophile; Drug Design; Covalent Drug; Chemical Biology
Online: 19 October 2021 (10:28:15 CEST)
Of the manifold concepts in drug discovery and design, covalent drugs have re-emerged as one of the most promising over the past 20-or so years. All such drugs harness the ability of a covalent bond to drive an interaction between a target biomolecule, typically a protein, and a small molecule. Formation of a covalent bond necessarily prolongs target engagement, opening avenues to targeting shallower binding sites, protein complexes, and other difficult to drug manifolds, amongst other virtues. This opinion piece discusses frameworks around which to develop covalent drugs. Our argument, based on results from our research program on natural electrophile signaling, is that targeting specific residues innately involved in native signaling programs are ideally poised to be targeted by covalent drugs. We outline ways to identify electrophile-sensing residues, and discuss how studying ramifications of innate signaling by endogenous molecules can provide a means to predict drug mechanism and function and assess on- versus off-target behaviors.
REVIEW | doi:10.20944/preprints202103.0138.v1
Online: 3 March 2021 (14:54:03 CET)
For several years, drugs bearing reactive electrophilic appendages have been developed. These units typically confer prolonged residence time of the drugs on their protein targets, and may assist targeting shallow binding sites and/or improving drug-protein target spectrum. Studies on natural electrophilic molecules have indicated that in many instances natural electrophiles use similar mechanisms to alter signaling pathways. However, natural reactive species are also endowed with other important mechanisms to hone signaling properties that are uncommon in drug design. These include ability to be active at low occupancy and elevated inhibitor kinetics. Here we discuss how we have begun to harness these properties in inhibitor design.
REVIEW | doi:10.20944/preprints202105.0334.v1
Subject: Keywords: RES; ROS; reactive chemical species; electrophile signaling; cysteine; LDE; T-REX; G-REX; Chemical Biology
Online: 14 May 2021 (13:45:08 CEST)
In this tutorial review, we compare and contrast the chemical mechanisms of electrophile/oxidant sensing, and the molecular mechanisms of signal propagation. We critically analyze biological systems in which these different pathways are believed to be manifest and what the data really mean. Finally, we discuss applications of this knowledge to disease treatment and drug development.
ARTICLE | doi:10.20944/preprints201909.0341.v1
Subject: Life Sciences, Biochemistry Keywords: Covalent labeling; stereoselectivity; electrophile signaling; affinity; mechanism; kinetic control
Online: 30 September 2019 (07:53:42 CEST)
Significance: Electrophile signaling is coming into focus as a bona fide cell signaling mechanism. The electrophilic regulation occurs typically through a sensing event (i.e., labeling of a protein) and a signaling event (the labeling event having an effect of the proteins activity, association, etc.). Recent advances: Herein, we focus on the first step of this process, electrophile sensing. Electrophile sensing is typically a deceptively simple reaction between the thiol of a protein-cysteine, of which there are around 200,000 in the human proteome, and a Michael acceptor, of which there are numerous flavors, including enals and enones. Recent data overall paint a picture that despite being a simple chemical reaction, electrophile sensing is a discerning process, showing labeling preferences that are often not in line with reactivity of the electrophile. Critical issues: With a view to trying to decide what brings about highly electrophile-reactive protein-cysteines, and how reactive these sensors may be, we discuss aspects of the thermodynamics and kinetics of covalent/non-covalent binding. Data made available by several laboratories indicate that it is likely that specific proteins exhibit highly stereo- and chemoselective electrophile sensing, which we take as good evidence for recognition between the electrophile and the protein prior to forming a covalent bond. Future directions: We propose experiments that could help us gain a better and more quantitative understanding of the mechanisms through which sensing comes about. We further extoll the importance of performing more detailed experiments on labeling and trying to standardize the way we assess protein-specific electrophile sensing.We propose experiments that could help us gain a better and more quantitative understanding of the mechanisms through which sensing comes about. We further extoll the importance of performing more detailed experiments on labeling and trying to standardize the way we assess protein-specific electrophile sensing.
REVIEW | doi:10.20944/preprints202201.0440.v1
Subject: Life Sciences, Other Keywords: electrophiles; signaling; profiling; drug mechanism; drug discovery; T-REX
Online: 28 January 2022 (14:57:08 CET)
Our bodies produce a host of electrophilic species that can label specific endogenous proteins in cells. The signaling roles of these molecules are underactive debate. However, in our opinion it is becoming increasingly likely that electrophiles can rewire cellular signaling processes at endogenous levels. Attention is turning more to understanding how nuanced electrophile signaling in cells is. In this perspective, we describe recent work from our laboratory that has started to inform on different levels of context-specific regulation of proteins by electrophiles. We discuss the relevance of these data to the field, and to the broader application of electrophile signaling to precision medicine development, beyond the traditional views of their pleiotropic cytotoxic roles.