Proteomics Experiments Research Articles

Proteomics Response of Photosynthetic Machinery to Abiotic Stresses: A Review

Abiotic stress, including drought, salinity, extreme temperatures, and light intensity, profoundly affects plant growth and development. Plants being sessile cannot escape the stress conditions, , thus have developed either evading or tolerance mechanisms during evolution. In plants several processes are affected by drought e.g. there is inhibition of growth, reduction in photosynthesis, and yield, and increased membrane damage. Plants respond to drought or tolerate stress by downregulation of growth, photosynthetic machinery and membrane fluidity, increased cuticle thickness, osmolyte accumulation, increased defense chemicals, and secondary metabolites, and stress responding proteins e.g. Late Embryogenic Abundance and Heat Shock proteins etc. The root architecture is elaborated, and leaf rolling occurs. Futher, there is an increase in the cell's antioxidant potential and antioxidant enzyme activity. Most of these mechanisms are investigated using proteomics and protein techniques. With the advent of sensitive proteomics techniques and the availability of databases for several plants, proteomics experiments have become routine in stress based studies. Current review highlights the modulation in the photosynthetic and chloroplastic proteins in higher plants that proteomics and other protein determination studies have revealed, in response to stress treatment. It specifically discusses the latest developments in terms of protein changes in leaves or other tissues from the studies using stress treatment, since several reviews have already covered the earlier findings. Moreover, it further discusses the future role of proteomics studies in elucidating stress mechanisms in plants.

PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of Proteins.

Recent improvements in methods and instruments used in mass spectrometry have greatly enhanced the detection of protein post-translational modifications (PTMs). On the computational side, the adoption of open modification search strategies now allows for the identification of a wide variety of PTMs, potentially revealing hundreds to thousands of distinct modifications in biological samples. While the observable part of the proteome is continuously growing, the visualization and interpretation of this vast amount of data in a comprehensive fashion is not yet possible. There is a clear need for methods to easily investigate the PTM landscape and to thoroughly examine modifications on proteins of interest from acquired mass spectrometry data. We present PTMVision, a web server providing an intuitive and simple way to interactively explore PTMs identified in mass spectrometry-based proteomics experiments and to analyze the modification sites of proteins within relevant context. It offers a variety of tools to visualize the PTM landscape from different angles and at different levels, such as 3D structures and contact maps, UniMod classification summaries, and site specific overviews. The web server's user-friendly interface ensures accessibility across diverse scientific backgrounds. PTMVision is available at https://ptmvision-tuevis.cs.uni-tuebingen.de/.

A Review of Protein Inference.

Protein inference is an often neglected though crucial step in most proteomic experiments. In the bottom-up proteomic approach, the actual molecules of interest, the proteins, are digested into peptides before measurement on a mass spectrometer. This approach introduces a loss of information: The actual proteins must be inferred based on the identified peptides. While this might seem trivial, there are certain problems, one of the biggest being the presence of peptides that are shared among proteins. These amino acid sequences can, based on the database used for identification, belong to more than one protein. If such peptides are identified in a sample, it cannot be said which proteins actually were in the sample, but only an estimate on the most probable proteins or protein groups can be given based on a predefined inference strategy.Here we describe the effect of the chosen database for peptide identification on the number of shared peptides. Afterward, the mainly used protein inference methods will be sketched, and the necessity of stringent false discovery rate on peptide and protein level is discussed. Finally, we explain how the tool "PIA or protein inference algorithms" can be used together with the workflow environment KNIME and OpenMS to perform protein inference in a common proteomic experiment.

Aged garlic extract enhances the production of β‑defensin 4 via activation of the Wnt/β‑catenin pathway in mouse gingiva.

Periodontal disease is recognized as a chronic multifactorial inflammatory condition initiated by dysbiosis within subgingival plaque biofilms. Antimicrobial peptides exhibit a wide spectrum of antimicrobial action, and thus, provide one of the first lines of host defense against oral pathogens. Aged garlic extract (AGE) is effective for preventing the progression of periodontal disease. The present study examined whether AGE affects the production of antimicrobial peptides in mouse gingiva. Reverse transcription-quantitative PCR analysis demonstrated that oral administration of AGE in mice increased the mRNA level of Defb4 in gingival tissue, while the levels of Defb1, Defb14 and Cramp remained unaffected. AGE also upregulated the protein levels of β-defensin 4. To explore the underlying mechanism of the increased β-defensin 4 production induced by AGE, a comprehensive phosphoproteomic analysis in gingival tissues was performed. Proteomic profiling revealed activation of the canonical Wnt/β-catenin pathway in gingiva of mice treated with AGE. Treatment of mouse gingival epithelial GE1 cells with AGE resulted in an increase of β-defensin 4 in the culture medium. In support of proteomics experiments, LF3, a specific inhibitor of Wnt/β-catenin signaling, suppressed the AGE-induced production of β-defensin 4. In addition, β-catenin protein was found to accumulate within the nucleus in cells treated with AGE. In conclusion, the present findings suggested that AGE enhanced the production of β-defensin 4 in mouse gingiva through the canonical Wnt signal transduction pathway.

Interplay between β-propeller subunits WDR26 and muskelin regulates the CTLH E3 ligase supramolecular complex

The Pro/N-degron recognizing C-terminal to LisH (CTLH) complex is an E3 ligase of emerging interest in the developmental biology field and for targeted protein degradation (TPD) modalities. The human CTLH complex forms distinct supramolecular ring-shaped structures dependent on the multimerization of WDR26 or muskelin β-propeller proteins. Here, we find that, in HeLa cells, CTLH complex E3 ligase activity is dictated by an interplay between WDR26 and muskelin in tandem with muskelin autoregulation. Proteomic experiments revealed that complex-associated muskelin protein turnover is a major ubiquitin-mediated degradation event dependent on the CTLH complex in unstimulated HeLa cells. We observed that muskelin and WDR26 binding to the scaffold of the complex is interchangeable, indicative of the formation of separate WDR26 and muskelin complexes, which correlated with distinct proteomes in WDR26 and muskelin knockout cells. We found that mTOR inhibition-induced degradation of Pro/N-degron containing protein HMGCS1 is distinctly regulated by a muskelin-specific CTLH complex. Finally, we found that mTOR inhibition also activated muskelin degradation, likely as an autoregulatory feedback mechanism to regulate CTLH complex activity. Thus, rather than swapping substrate receptors, the CTLH E3 ligase complex controls substrate selectivity through the differential association of its β-propeller oligomeric subunits WDR26 and muskelin.

Endothelial cell Ass1 inhibits arteriosclerotic calcification in diabetes mellitus

Endothelial cell (EC) dysfunction is an important pathological feature of early calcification in diabetic plaques. Argininosuccinic synthase 1 (Ass1) is important in protecting EC activity. Therefore, this study aimed to explore the effect of endothelial Ass1 on calcification in diabetic plaques and its potential regulatory mechanism. In this study, serum Ass1 levels were measured in 84 patients, and the study showed that the serum Ass1 level in patients with diabetes was significantly decreased compared with the non-diabetic group, and the serum Ass1 level in patients with coronary artery calcification was significantly decreased compared with the non-coronary artery calcification group. The ApoE-/- mouse diabetic plaque calcification model and the mouse aortic endothelial cell (MAEC) calcification model were constructed, and the influence of endothelial cell Ass1 on diabetic plaque calcification was further investigated by adeno-associated virus and plasmid intervention. Molecular biology studies have shown that endothelial Ass1 overexpression can reduce plaque calcification and inhibit MAEC osteogenic differentiation in diabetic mice, and Ass1 has protective effects on EC and blood vessels in mice. 4D-label-free proteomic sequencing, bioinformatics analysis, and IP experiments were performed on ApoE-/- mouse aorta after adeno-associated virus intervention. It was found that the differential protein Ptk2b was closely related to vascular calcification (VC) and interacted with the target protein Ass1. The above studies indicate that endothelial Ass1 affects calcification formation in diabetic plaques, and the mechanism may be related to Ptk2b. Ass1 may be a new target for the treatment of diabetic VC.

Nutritionally physiological cell culture medium and 3D culture influence breast tumour proteomics and anti-cancer drug effectiveness

Many drugs have been discontinued during phase II/III breast cancer clinical trials due to lack of clinical efficacy, indicating shortcomings in predictive value of preclinical data. Nutrient availability in the tumour cell microenvironment and the dimensionality of in vitro tumour cells likely impact on drug responsiveness. Global proteomics experiments were conducted to assess the impact of nutrient availability and dimensionality of culture. Protein set enrichment analyses identified “pathways in cancer”, “focal adhesion” and “ECM receptor in interaction” related to cell culture dimensionality in MDA-MB-231 cells. In MCF-7 cells, 4 pathways were influenced by medium composition, and 2 pathways were influenced by cell culture dimensionality (2D vs. 3D). These pathways were also identified using KEGG analyses. Eight drugs were selected for investigation according to the differential expression of their putative or known target proteins. The influence of medium composition on drug effectiveness was explored using the “Melbourne Medium” (MM), developed to have nutritionally physiological levels of metabolites as compared with conventional (hyper-nutritional) cell culture medium (CM). The influence of dimensionality on drug effectiveness was also explored, using an innovative 3D viability assessment combining automated confocal microscopy and image analysis. Dimensionality of culture appeared to have a greater influence on the proteome and drug effects than variation in nutrient levels. The number of differentially expressed proteins in the different media was greater in 2D than 3D. We conclude that the risk of qualifying inactive compounds in preclinical assessment may be mitigated using additional models incorporating physiological media and 3-dimensionality.

The rapid degradation of translated upstream regions points to an inefficient translation initiation process.

Large-scale experimental analyses find ever more abundant evidence of translation from start codons upstream of the canonical start site. This translation either generates entirely new proteins (from novel upstream open reading frames) or produces isoforms with extended N-terminals when the novel start codon is in frame Most extended N-terminals are likely to just add a disordered region to the canonical protein isoform, but some may also block the recognition of the signal peptide causing the isoform to accumulate in the incorrect cellular compartment. This analysis finds evidence that upstream translations that would interfere with signal peptides are detected in expected quantities in ribosome profiling experiments, but that the equivalent N-terminally extended protein isoforms are significantly reduced in multiple proteomics experiments. This suggests that these isoforms are likely to be degraded shortly after translation by the ubiquitination pathway, thus preventing the build up of potentially harmful proteins with hydrophobic regions in the cytoplasm. In addition, this is further evidence that most of the transcripts translated from upstream start sites are the result of an inefficient translation initiation process. This has implications for the annotation of proteins given the huge numbers of upstream translations that are being detected in large-scale experiments.

The “gut” corona at the surface of nanoparticles is dependent on exposure to bile salts and phospholipids

HypothesisThe formation of a biomolecular corona on nanoparticle surfaces significantly influences their biological behaviour, particularly in drug delivery applications. Despite the prevalence of ingestion of particles (e.g, during oral drug delivery), our understanding of corona formation within the gastrointestinal (GI) tract remains limited, especially for non-protein components. The hypothesis of this work is that the exposure of nanoparticles to bile components will form a “corona” structure and protein corona will represent proteomes different from the original bile fluid. Two major aspects of biomolecular corona formed in GI fluid (hereby termed “gut corona), which ultimately dictate the fate of particle-based carriers, include the composition and the surface structure of nanoparticle-corona complex. ExperimentsThe structure and composition of the biomolecular corona formed on model SiO2 nanoparticles within simulated and extracted bile fluids were determined using small-angle scattering, quantification assays, and liquid chromatography with tandem mass spectrometry (LC-MS/MS) techniques. FindingsThe formation of raspberry-like structures was identified, with bile micelles adopting ellipsoidal shapes around the nanoparticles, as opposed to a surface covered with a uniform corona (i.e., core–shell structure). Assay quantification and proteomics experiments revealed a notable increase in the ratio of protein to bile salt within the corona compared to the original bile fluid. The composition of the proteome differed between the bovine bile and the protein corona with only 34 proteins associated with the nanoparticles from the top 100 identified in bovine bile. Despite the differences in protein types identified between bovine bile and gut corona, the proportions of protein between different functional classes, such as enzymes and structural proteins, show little variation. This work elucidates the intricate interactions between nanoparticles and gut molecules, offering insights crucial for designing nanoparticle formulations for optimized oral drug delivery and understanding nanoparticle behaviour within the GI tract.

A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation.

The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have been proposed from large-scale RNASeq, ribosome profiling and proteomics experiments. Here we carry out an in-depth analysis of an entire proteomics database. We analysed the proteins, peptides and spectra housed in the human build of the PeptideAtlas proteomics database to identify coding regions that are not yet annotated in the GENCODE reference gene set. We find support for hundreds of missing alternative protein isoforms and unannotated upstream translations, and evidence of cross-contamination from other species. There was reliable peptide evidence for 34 novel unannotated open reading frames (ORFs) in PeptideAtlas. We find that almost half belong to coding genes that are missing from GENCODE and other reference sets. Most of the remaining ORFs were not conserved beyond human, however, and their peptide confirmation was restricted to cancer cell lines. We show that this is strong evidence for aberrant translation, raising important questions about the extent of aberrant translation and how these ORFs should be annotated in reference genomes.

Safety assessment and exploration of the mechanism of toxic effects of diallyl trisulfide: Based on acute and subacute toxicity and proteomics experiments

Ethnopharmacological relevanceGarlic (Allium sativum L.) is a widely consumed spice and condiment around the world, applied both as a food and as a traditional medicine, and is a natural strengthening agent for the body's circulatory and nervous systems. Diallyl trisulfide (DATS) is the major volatile organosulfur phytochemical found in garlic, with antithrombotic, anticoagulant, and antiplatelet activities as well as antioxidant, anti-infective, and other pharmacological effects. However, the safe dose and the underlying mechanisms of its toxic effects remain elusive. Aim of the studyDATS, an important pharmacologically active compound found in garlic, has garnered attention for its ability to fight cancer, antioxidant, anti-infective, and cardioprotective. The aim of this study was to evaluate the safety of DATS and to elucidate the potential mechanisms of its toxicity. Materials and methodsIn this study, ICR mice were selected for acute and subacute toxicity experiments according to OECD guidelines. The toxicity profile of DATS was analyzed by computer prediction software. Also, key differential proteins in spleen and serum were analyzed by proteomics. The binding stability of DAST to differential proteins was analyzed by molecular docking. Additionally, the regulatory relationship between DATS and differential proteins was verified by Western blot and ELISA experiments. ResultsThe results showed that the LD50 value of DATS in acute toxicity was 188.67 mg/kg. In subacute toxicity, water consumption and food intake were reduced in both male and female mice. In addition, the spleen and small intestinal organ coefficients were significantly elevated in male mice at the high dose of DATS; the blood biochemical indices ALB and TP were also significantly elevated. HE staining results showed significant damage to the spleen, liver, small intestine, and kidney of mice at high doses of DATS. Spleen and serum proteomics analyses showed that DATS significantly inhibited ZBP1 expression and upregulated TEC. ADMETlab 2.0 software predictions identified DATS as having potential genotoxicity, dermal sensitization, carcinogenicity, and respiratory and ocular toxicity. Docking results showed that the binding energies between DATS and TEC protein (PDB: 6F3F) and ZBP1 protein (PDB: 4KA4) were −3.7 kcal/mol, −2.4 kcal/mol, respectively. Western blot results showed that DATS-H significantly inhibited the expression of ZBP1 (only in male mice) and Bcl-2 proteins. ELISA results showed that DATS-H significantly increased the level of TEC protein both in male and female mice. ConclusionsLong-term administration of high-dose DATS may carry some risk of toxicity. Based on the amount of DATS in garlic, it is recommended that adults should not take more than 359 mg of DATS and 84.5 g of garlic per day. The mechanism of toxicity may be related to the fact that DATS significantly inhibits ZBP1 expression, upregulates TEC, and promotes apoptosis. This study provides valuable toxicological data for the effective evaluation of the long-term toxicity of DATS and offers an additional experimental basis for developing DATS as a healthy food or drug.

Chromatographic properties of deamidated peptides with Asn-Gly sequences in proteomic bottom-up experiments

Studies surrounding deamidation have relied on the chromatographic and mass spectrometric differentiation of Asn containing peptides and their isomeric Asp and isoAsp products. The development of mass spectrometry analytical techniques and characterization of isomer specific fragmentation patterns has permitted the investigation of some deamidation species but has struggled to remain effective when applied and on complex samples or in high throughput scenarios. On the other hand, chromatographic separations can provide additional information to facilitate detection of deamidation. In this work the retention characteristics of deamidation products have been reported in reversed-phase separations using formic acid as an ion-pairing modifier. We found three major elution patterns depending on primary and secondary structure of Asn-Gly containing tryptic peptides. Random coil, helical conformations, and N-terminal positioning of Asn usually result in Asn < isoAsp < Asp, isoAsp < Asn < Asp, and Asn < Asp < isoAsp elution order, respectively. These trends, found from the analyses of proteomic samples, were subsequently confirmed via analytical scale UV-HPLC. Additionally, we determined the retention shifts following deamidation for twenty various separation settings used as a first-dimension fractionation for high-throughput proteomic 2D LC-MS/MS analyses.

Serum proteomics for the identification of biomarkers to flag predilection of COVID19 patients to various organ morbidities

BackgroundCOVID19 is a pandemic that has affected millions around the world since March 2020. While many patients recovered completely with mild illness, many patients succumbed to various organ morbidities. This heterogeneity in the clinical presentation of COVID19 infection has posed a challenge to clinicians around the world. It is therefore crucial to identify specific organ-related morbidity for effective treatment and better patient outcomes. We have carried out serum-based proteomic experiments to identify protein biomarkers that can flag organ dysfunctions in COVID19 patients.MethodsCOVID19 patients were screened and tested at various hospitals across New Delhi, India. 114 serum samples from these patients, with and without organ morbidities were collected and annotated based on clinical presentation and treatment history. Of these, 29 samples comprising of heart, lung, kidney, gastrointestinal, liver, and neurological morbidities were considered for the discovery phase of the experiment. Proteins were isolated, quantified, trypsin digested, and the peptides were subjected to liquid chromatography assisted tandem mass spectrometry analysis. Data analysis was carried out using Proteome Discoverer software. Fold change analysis was carried out on MetaboAnalyst. KEGG, Reactome, and Wiki Pathway analysis of differentially expressed proteins were carried out using the STRING database. Potential biomarker candidates for various organ morbidities were validated using ELISA.Results254 unique proteins were identified from all the samples with a subset of 12–31 differentially expressed proteins in each of the clinical phenotypes. These proteins establish complement and coagulation cascade pathways in the pathogenesis of the organ morbidities. Validation experiments along with their diagnostic parameters confirm Secreted Protein Acidic and Rich in Cysteine, Cystatin C, and Catalase as potential biomarker candidates that can flag cardiovascular disease, renal disease, and respiratory disease, respectively.ConclusionsLabel free serum proteomics shows differential protein expression in COVID19 patients with morbidity as compared to those without morbidity. Identified biomarker candidates hold promise to flag organ morbidities in COVID19 for efficient patient care.

Using in vivo intact structure for system-wide quantitative analysis of changes in proteins

Mass spectrometry-based methods can provide a global expression profile and structural readout of proteins in complex systems. Preserving the in vivo conformation of proteins in their innate state is challenging during proteomic experiments. Here, we introduce a whole animal in vivo protein footprinting method using perfusion of reagents to add dimethyl labels to exposed lysine residues on intact proteins which provides information about protein conformation. When this approach is used to measure dynamic structural changes during Alzheimer’s disease (AD) progression in a mouse model, we detect 433 proteins that undergo structural changes attributed to AD, independent of aging, across 7 tissues. We identify structural changes of co-expressed proteins and link the communities of these proteins to their biological functions. Our findings show that structural alterations of proteins precede changes in expression, thereby demonstrating the value of in vivo protein conformation measurement. Our method represents a strategy for untangling mechanisms of proteostasis dysfunction caused by protein misfolding. In vivo whole-animal footprinting should have broad applicability for discovering conformational changes in systemic diseases and for the design of therapeutic interventions.

The HSP90/R2TP Quaternary Chaperone Scaffolds Assembly of the TSC Complex

The R2TP chaperone is composed of the RUVBL1/RUVBL2 AAA+ ATPases and two adapter proteins, RPAP3 and PIH1D1. Together with HSP90, it functions in the assembly of macromolecular complexes that are often involved in cell proliferation. Here, proteomic experiments using the isolated PIH domain reveals additional R2TP partners, including the Tuberous Sclerosis Complex (TSC) and many transcriptional complexes. The TSC is a key regulator of mTORC1 and is composed of TSC1, TSC2 and TBC1D7. We show a direct interaction of TSC1 with the PIH phospho-binding domain of PIH1D1, which is, surprisingly, phosphorylation independent. Via the use of mutants and KO cell lines, we observe that TSC2 makes independent interactions with HSP90 and the TPR domains of RPAP3. Moreover, inactivation of PIH1D1 or the RUVBL1/2 ATPase activity inhibits the association of TSC1 with TSC2. Taken together, these data suggest a model in which the R2TP recruits TSC1 via PIH1D1 and TSC2 via RPAP3 and HSP90, and use the chaperone-like activities of RUVBL1/2 to stimulate their assembly.

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.

Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of in silico generated spectral libraries. However, the generation of high-quality spectral libraries for DIA data analysis remains a challenge, particularly because most such libraries are generated directly from data-dependent acquisition (DDA) data or are from in silico prediction using models trained on DDA data. In this study, we developed Carafe, a tool that generates high-quality experiment-specific in silico spectral libraries by training deep learning models directly on DIA data. We demonstrate the performance of Carafe on a wide range of DIA datasets, where we observe improved fragment ion intensity prediction and peptide detection relative to existing pretrained DDA models.

Hu.MAP3.0: Atlas of human protein complexes by integration of > 25,000 proteomic experiments.

Macromolecular protein complexes carry out most functions in the cell including essential functions required for cell survival. Unfortunately, we lack the subunit composition for all human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify > 15,000 human protein complexes. We show our map of protein complexes is highly accurate and more comprehensive than previous maps, placing ~75% of human proteins into their physical contexts. We globally characterize our complexes using protein co-variation data (ProteomeHD.2) and identify co-varying complexes suggesting common functional associations. Our map also generates testable functional hypotheses for 472 uncharacterized proteins which we support using AlphaFold modeling. Additionally, we use AlphaFold modeling to identify 511 mutually exclusive protein pairs in hu.MAP3.0 complexes suggesting complexes serve different functional roles depending on their subunit composition. We identify expression as the primary way cells and organisms relieve the conflict of mutually exclusive subunits. Finally, we import our complexes to EMBL-EBI's Complex Portal (https://www.ebi.ac.uk/complexportal/home) as well as provide complexes through our hu.MAP3.0 web interface (https://humap3.proteincomplexes.org/). We expect our resource to be highly impactful to the broader research community.

GingisREX: A Complementary Enzyme for the Detection of Bacterial Proteins.

Reliable enzymatic digestion underscores successful mass-spectrometry-based proteomics experiments. In this study, we compare the use of the arginine-specific protease, GingisREX, against a more traditional approach in the identification of Escherichia coli proteins. An increased number of protein identifications were noted when GingisREX was used compared to a trypsin/lys-C mixture. This improvement was attributed to the generation of fewer peptides per protein, resulting in a simpler peptide mixture. Furthermore, GingisREX exhibited increased digestion efficiency, fewer missed cleavages, and improved MS/MS data quality for higher molecular weight peptides. The data here establish GingisREX to be a protease complementary to trypsin for enhanced detection of bacterial proteins. With further optimization, GingisREX could prove to be an effective alternative to trypsin for identifying host cell proteins in biotherapeutics.

Use of a Novel Whole Blood Separation and Transport Device for Targeted and Untargeted Proteomics.

There is significant interest in developing alternatives to traditional blood transportation and separation methods, which often require centrifugation and cold storage to preserve specimen integrity. Here we provide new performance findings that characterize a novel device that separates whole blood via lateral flow then dries the isolated components for room temperature storage and transport. Untargeted proteomics was performed on non-small cell lung cancer (NSCLC) and normal healthy plasma applied to the device or prepared neat. Significantly, proteomic profiles from the storage device were more reproducible than from neat plasma. Proteins depleted or absent in the device preparation were shown to be absorbed onto the device membrane through largely hydrophilic interactions. Use of the device did not impact proteins relevant to an NSCLC clinical immune classifier. The device was also evaluated for use in targeted proteomics experiments using multiple-reaction monitoring (MRM) mass spectrometry. Intra-specimen detection intensity for protein targets between neat and device preparations showed a strong correlation, and device variation was comparable to the neat after normalization. Inter-specimen measurements between the device and neat preparations were also highly concordant. These studies demonstrate that the lateral flow device is a viable blood separation and transportation tool for untargeted and targeted proteomics applications.

Identification of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV nonstructural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose-response follow-up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC50 of 58 ± 17 nM, and further analysis with time-dependent inhibition studies yielded a kinact /KI of 6.4 × 103 M-1s-1. LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity in proteomic experiments or against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the identification and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic.