N-Acryloylindole-alkyne (NAIA) enables imaging and profiling new ligandable cysteines and oxidized thiols by chemoproteomics

Protein Electrostatic Properties are Fine-Tuned Through Evolution

Protein ionization states provide electrostatic forces to modulate protein structure, stability, solubility, and function. Until now, predicting ionization states and understanding protein electrostatics have relied on structural information. Here we demonstrate that primary sequence alone enables remarkably accurate pK a predictions through KaML-ESM, a model pretrained on a synthetic pK a dataset that leverages evolutionary representations from large-scale protein language models ESMs. The KaML-ESM model achieves RMSEs approaching the experimental precision limit of ~0.5 pH units for Asp, Glu, His, and Lys residues, while reducing Cys prediction errors to 1.1 units - with further improvement expected as the training dataset expands. The state-of-the-art performance of KaML-ESM was further validated through external evaluations, including a proteome-wide analysis of protein pK a values. Our results support the notation that protein sequence encodes not only structure and function but also electrostatic properties, which may have been co-optimized through evolution. Lastly, we provide KaML, a sequence-based end-to-end ML platform that enables researchers to map protein electrostatic landscapes, facilitating applications ranging from drug design and protein engineering to molecular simulations.

Chemoproteomic profiling by bioorthogonal probes to reveal the novel targets of acrylamide in microglia

Neurotoxicity studies caused by exposure to acrylamide (AA) are of wide interest, but the methods for direct analysis of AA targets in living neuronal cells by cysteine profiling are still lacking. To address this, we developed a specific bioorthogonal probe, AAPA-P2, for chemical proteomics analysis of AA covalent binding sites. AAPA-P2 captured 754 target proteins, increasing the number of identified target proteins by 20-fold. Further screening revealed 96 proteins that are both highly sensitive and heavily modified by AAPA-P2, with validation performed on some potential key targets and binding sites. AA was found to induce neurotoxicity by binding to newly identified targets, Proteasome 26S Subunit, non ATPase 9 (PSMD9) and NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 5 (NDUFA5), interfering with the ubiquitin-proteasome system, and inducing mitochondria-dependent apoptosis. The present work provides an effective bioorthogonal probe tool for identifying covalent binding targets of acrylamide and offers new insights into the molecular mechanisms underlying acrylamide-induced neurotoxicity.

Targeted Covalent Modification Strategies for Drugging the Undruggable Targets

The term "undruggable" refers to proteins or other biological targets that have been historically challenging to target with conventional drugs or therapeutic strategies because of their structural, functional, or dynamic properties. Drugging such undruggable targets is essential to develop new therapies for diseases where current treatment options are limited or nonexistent. Thus, investigating methods to achieve such drugging is an important challenge in medicinal chemistry. Among the numerous methodologies for drug discovery, covalent modification of therapeutic targets has emerged as a transformative strategy. The covalent attachment of diverse functional molecules to targets provides a powerful platform for creating highly potent drugs and chemical tools as well the ability to provide valuable information on the structures and dynamics of undruggable targets. In this review, we summarize recent examples of chemical methods for the covalent modification of proteins and other biomolecules for the development of new therapeutics and to overcome drug discovery challenges and highlight how such methods contribute toward the drugging of undruggable targets. In particular, we focus on the use of covalent chemistry methods for the development of covalent drugs, target identification, drug screening, artificial modulation of post-translational modifications, cancer specific chemotherapies, and nucleic acid-based therapeutics.

Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins

Chemoproteomic probes (CPPs) have been widely considered as powerful molecular biological tools that enable the highly efficient discovery of both binding proteins and modes of action for the studied compounds. They have been successfully used to validate targets and identify binders. The design of CPP has been considered extremely challenging, which asks for the generalization using a large number of probe data. However, none of the existing databases gives such valuable data of CPPs. Herein, a database entitled 'Chem(Pro)2' was therefore developed to systematically describe the atlas of diverse types of CPPs labelling human protein in living cell/lysate. With the booming application of chemoproteomic technique and artificial intelligence in current chemical biology study, Chem(Pro)2 was expected to facilitate the AI-based learning of interacting pattern among molecules for discovering innovative targets and new drugs. Till now, Chem(Pro)2 has been open to all users without any login requirement at: https://idrblab.org/chemprosquare/.

Covalent Modification of Protein by Chemical Probe in Living Cells for Structural and Interaction Studies

Cellular activities are predominantly carried out by proteins that can dynamically adopt different structural conformations and differentially interact with other biomolecules according to cellular needs. Chemical probes are small molecules used to selectively interact and modulate the activities of specific proteins to study their functions such as the validation of potential drug targets. The remarkable performance of AlphaFold algorithms in the prediction of protein structures has pivoted interest toward elucidating the intracellular dynamics of protein structural conformation where covalent modification of proteins by chemical probes could be used to shed light upon. However, due to the barrier to entry by cell membrane and the general unfavorable reactive conditions of the intracellular environment, most studies using reactive chemical probes are still conducted on purified proteins and cell lysates. Nevertheless, recent progresses have been made in designing chemical probes with improved membrane permeability, stability and reactivity. This paper surveys the literature on recent advancements in membrane-permeable chemical probes and their applications with protein mass spectrometry for the intracellular studies of protein structural conformations and biomolecular interactions.

Coumarin-aurone based fluorescence probes for cysteine sensitive in-situ identification in living cells

The quantification of cysteine (Cys) levels in the organisms holds paramount significance in biological research and disease diagnosis, which can give the correlation between abnormal Cys levels and diseases. In this study, two fluorescent probes, designated as DEA-OH and DEA-AC, featuring a coumarin-aurone backbone specifically engineered for Cys detection, were meticulously designed and synthesized. The diethylamino coumarin-aurone probe DEA-OH and the acrylate-substituted probe DEA-AC demonstrated remarkable sensitivity in detecting cysteine by means of copper displacement (DEA-OH) and acrylate hydrolysis mechanisms (DEA-AC) with fluorescence detection limits of 7.25 μM and 1.65 μM, respectively. Moreover, the fluorescence peak wavelength of the two probes displayed a linear relationship with solvent polarity in the ET (30) range of 30-65 kcal•mol-1, indicating the potential for monitoring changes in environmental polarity within this ET (30) range. The outstanding attributes exhibited by DEA-AC including superior photostability, remarkable selectivity, and swift response (kinetic rate constant: 0.00747 s-1), coupled with the exceptional anti-interference ability, have significantly broadened its scope of applications, for example detecting alterations in Cys within biological systems.

Superoxide-responsive quinone methide precursors (QMP-SOs) to study superoxide biology by proximity labeling and chemoproteomics

Superoxide is a reactive oxygen species (ROS) with complex roles in biological systems. It can contribute to the development of serious diseases, from aging to cancers and neurodegenerative disorders. However, it can also serve as a signaling molecule for important life processes. Monitoring superoxide levels and identifying proteins regulated by superoxide are crucial to enhancing our understanding of this growing field of redox biology and signaling. Given the high reactivity and very short lifetime of superoxide compared to other ROS in biological systems, proteins redox-modified by superoxide should be in close proximity to where superoxide is generated endogenously, i.e. superoxide hotspots. This inspires us to develop superoxide-specific quinone methide-based precursors, QMP-SOs, for proximity labeling of proteins within/near superoxide hotspots to image superoxide and profile proteins associated with superoxide biology by chemoproteomics. QMP-SOs specifically react with superoxide to generate an electrophilic quinone methide intermediate, which subsequently reacts with nucleophilic amino acids to induce a covalent tag on proteins, as revealed by liquid chromatography-mass spectrometry (LC-MS) and shotgun MS experiments. The alkyne handle on the covalent tag enables installation of fluorophores onto the tagged proteins for fluorescence imaging of superoxide in cells under oxidative stress. By establishing a chemoproteomics platform, QMP-SO-TMT, we identify DJ-1 and DLDH as proteins associated with superoxide biology in liver cancer cells treated with menadione. This work should provide insights into the crosstalk between essential cellular events and superoxide redox biology, as well as the design principles of quinone methide-based probes to study redox biology through proximity labeling and chemoproteomics.

Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles

The evolving use of covalent ligands as chemical probes and therapeutic agents could greatly benefit from an expanded array of cysteine-reactive electrophiles for efficient and versatile proteome profiling. Herein, to expand the current repertoire of cysteine-reactive electrophiles, we developed a new class of strain-enabled electrophiles based on cyclopropanes. Proteome profiling has unveiled that C163 of lactate dehydrogenase A (LDHA) and C88 of adhesion regulating molecule 1 (ADRM1) are ligandable residues to modulate the protein functions. Moreover, fragment-based ligand discovery (FBLD) has revealed that one fragment (Y-35) shows strong reactivity toward C66 of thioredoxin domain-containing protein 12 (TXD12), and its covalent binding has been demonstrated to impact its downstream signal pathways. TXD12 plays a pivotal role in enabling Y-35 to exhibit its antisurvival and antiproliferative effects. Finally, dicarbonitrile-cyclopropane has been demonstrated to be an electrophilic warhead in the development of GSTO1-involved dual covalent inhibitors, which is promising to alleviate drug resistance.

A new era of cysteine proteomics - Technological advances in thiol biology

Cysteines are amenable to a diverse set of modifications that exhibit critical regulatory functions over the proteome and thereby control a wide range of cellular processes. Proteomic technologies have emerged as a powerful strategy to interrogate cysteine modifications across the proteome. Recent advancements in enrichment strategies, multiplexing capabilities and increased analytical sensitivity have enabled deeper quantitative cysteine profiling, capturing a substantial proportion of the cysteine proteome. This is complemented by a rapidly growing repertoire of analytical strategies illuminating the diverse landscape of cysteine modifications. Cysteine chemoproteomics technologies have evolved into a powerful strategy to facilitate the development of covalent drugs, opening unprecedented opportunities to target the extensive undrugged proteome. Herein we review recent technological and scientific advances that shape the cysteine proteomics field.

Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins

Chemoproteomic profiling of sulfhydryl-containing proteins has consistently been an attractive research hotspot. However, there remains a dearth of probes that are specifically designed for sulfhydryl-containing proteins, possessing sufficient reactivity, specificity, distinctive isotopic signature, as well as efficient labeling and evaluation capabilities for proteins implicated in the regulation of redox homeostasis. Here, the specific selenium-containing probes (Se-probes) in this work displayed high specificity and reactivity toward cysteine thiols on small molecules, peptides and purified proteins and showed very good competitive effect of proteins labeling in gel-ABPP. We identified more than 6000 candidate proteins. In TOP-ABPP, we investigated the peptide labeled by Se-probes, which revealed a distinct isotopic envelope pattern of selenium in both the primary and secondary mass spectra. This unique pattern can provide compelling evidence for identifying redox regulatory proteins and other target peptides. Furthermore, our examiation of post-translational modification (PTMs) of the cysteine site residues showed that oxidation PTMs was predominantly observed. We anticipate that Se-probes will enable broader and deeper proteome-wide profiling of sulfhydryl-containing proteins, provide an ideal tool for focusing on proteins that regulate redox homeostasis and advance the development of innovative selenium-based pharmaceuticals.

Recent advances in mass spectrometry-based methods to investigate reversible cysteine oxidation

The post-translational modification of cysteine to diverse oxidative states is understood as a critical cellular mechanism to combat oxidative stress. To study the role of cysteine oxidation, cysteine enrichments and subsequent analysis via mass spectrometry are necessary. As such, technologies and methods are rapidly developing for sensitive and efficient enrichments of cysteines to further explore its role in signaling pathways. In this review, we analyze recent developments in methods to miniaturize cysteine enrichments, analyze the underexplored disulfide bound redoxome, and quantify site-specific cysteine oxidation. We predict that further development of these methods will improve cysteine coverage across more diverse organisms than those previously studied and elicit novel roles cysteines play in stress response.

Chemoproteomic capture of RNA binding activity in living cells

Proteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more challenging due to the heterogenous nature of peptide adducts derived from the RNA-protein crosslinked site. Here, we present an orthogonal strategy that utilizes clickable electrophilic purines to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells. Our photo-activatable-competition and chemoproteomic enrichment (PACCE) method facilitated detection of >5500 cysteine sites across ~3000 proteins displaying RNA-sensitive alterations in probe binding. Importantly, PACCE enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we present a chemoproteomic platform for global quantification of protein-RNA binding activity in living cells.

Proteome-wide structural analysis identifies warhead- and coverage-specific biases in cysteine-focused chemoproteomics

Covalent drug discovery has undergone a resurgence over the past two decades and reactive cysteine profiling has emerged in parallel as a platform for ligand discovery through on- and off-target profiling; however, the scope of this approach has not been fully explored at the whole-proteome level. We combined AlphaFold2-predicted side-chain accessibilities for >95% of the human proteome with a meta-analysis of eighteen public cysteine profiling datasets, totaling 44,187 unique cysteine residues, revealing accessibility biases in sampled cysteines primarily dictated by warhead chemistry. Analysis of >3.5 million cysteine-fragment interactions further showed that hit elaboration and optimization drives increased bias against buried cysteine residues. Based on these data, we suggest that current profiling approaches cover a small proportion of potential ligandable cysteine residues and propose future directions for increasing coverage, focusing on high-priority residues and depth. All analysis and produced resources are freely available and extendable to other reactive amino acids.