role of proteomics in drug discovery slideshare

Drug Discov. Proteomics has evolved to address increasingly complex biological questions, unravel new intracellular signaling pathways leading to new therapeutic targets and has helped decipher key pathway modulators and biomarkers [Citation1]. Gillet, L. C. et al. In addition to being a powerful tool for biomarker discovery, clinical proteomics can add significant value to drug discovery and development in many other ways independent of biomarkers. Disrupt the hydrogen-bonding network between water molecules, thereby perturbing the stability of the native state of other molecules in the solution, in particlular, biological macromolecules. A biomarker used to identify individuals who are more likely than similar individuals without the biomarker to experience a favorable or unfavorable effect from exposure to a medical product or an environmental agent. These common steps typically include: 1) selection of an appropriate, disease-relevant input material for the chemoproteomics experiment; 2) treatment of proteome with either free compound (for competitive workflows or workflows based on a broad specificity enrichment steps) or functionalized probe; 3) separation of proteins interacting with compound or probe in step 2) from background by e.g. Science 356, 10841087 (2017). AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics, https://doi.org/10.1101/2021.01.25.427969, https://www.proteinatlas.org/search/protein_class%3AFDA+approved+drug+targets, Validity of serum neurofilament light chain as a prognostic biomarker of disease activity in multiple sclerosis, Sign up for Nature Briefing: Translational Research. Nat. Chem. Cell Proteom. Mol. Science 341, 8487 (2013). Bach, S. et al. For some analyses that are routinely performed there is still some guess work involved, or at least incorporation of algorithms that make assumptions about the data that is being used as a database or to interpret downstream analyses. TOMAHAQ comprises a complex MS scan sequence including a peptide sequencing scan where a synthetic peptide identification triggers an offset analysis on the endogenous target peptide. Registered in England & Wales No. Tsiamis, V. et al. By optimization of several mass spectrometric instrument parameters including MS automatic gain control (AGC) and ion injection time settings in MS/MS analysis (e.g., 5E5 and 300ms, respectively, which is significantly higher than that used in typical bulk analysis), further improvements in sensitivity were observed. Early versions of mass spectrometers ran on rudimentary embedded computers utilizing custom code bases developed specifically for the mass spectrometer control. Finally, global proteomic profiling has seen renewed interest in the context of compound target identification and mechanism of action studies. van Esbroeck, A. C. M. et al. It also discusses current limitations, and areas of rapid growth in the field in addition to new technologies and approaches on the horizon that have the potential to be highly impactful on how proteomics shapes the next set of drug targets, therapeutic modalities, biomarkers, diagnostics and clinical endpoints, assays and diagnostics associated with the biotherapeutic and small molecule drug research. 18, 83 (2017). Depending on the intended use, the requirements for biomarker validation can vary significantly. 18, 14011412 (2011). A. et al. The size of the human proteome: the width and depth. Global quantification of mammalian gene expression control. Nat. Sample manipulation in volumes < 200 nL, minimizes sample loss by reducing exposure to potentially adherent surfaces. A dynamic protein interaction landscape of the human centrosome-cilium interface. 38, 365373 (2020). This step is critical; virtually any differential expression experiment will discover proteins that are up or down regulated between but few if any are actually potential clinical biomarkers. Borrebaeck, C. A. Building on this finding, studies from Ruiz Cuevas et al. PubMed Central An endpoint supported by a clear mechanistic rationale and clinical data providing strong evidence that an effect on the surrogate endpoint predicts a specific clinical benefit. Suppression of inflammation by a synthetic histone mimic. & Meissner, F. Dissecting intercellular signaling with mass spectrometry-based proteomics. 26, 13671372 (2008). In addition, such electrophilic probes can be used for protein level enrichment analyses and have been shown to provide overlapping but not identical information to isoTOP-ABPP-like approaches, e.g., shown for selectivity profiling for KRAS G12C inhibitors [Citation102]. The panel was designed based on cross sectional studies, it is perhaps not surprising that while many replicated as diagnostic candidates only a few emerged as monitoring biomarkers and highlights the importance of aligning the discovery experiments with the ultimate intended use. Pankow, S. et al. 18, 699710 (2011). The mechanism of photoaffinity labeling. This is a pivotal process, and a lot rides on its success, thus, efficiency is absolutely critical, but mainly for two key points: Biol. Chemical proteomics uncovers EPHA2 as a mechanism of acquired resistance to small molecule EGFR kinase inhibition. People also read lists articles that other readers of this article have read. Collagen neoepitope peptides were identified by data dependent proteomics in an ex vivo cartilage explant model [Citation141]. Chem. Paolini, G. V., Shapland, R. H. B., van Hoorn, W. P., Mason, J. S. & Hopkins, A. L. Global mapping of pharmacological space. Chem. Piazza, I. et al. & Charpentier, E. Genome editing. 29, 255265 (2011). Drug Development. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Chem. This article contains the first description of the efficacy of glivec/imatinib in chronic myeloid leukaemia. Nat. 196, 801810 (2012). 12, 20402050 (2017). Our aim is to deliver innovative tools that make drug development more efficient, more cost-effective, and more successful. The area most impacted by these improvements to computational power has been multiplexed global proteome quantification. Cell Rep. 8, 10371048 (2014). 18, 40274037 (2019). HATRIC-based identification of receptors for orphan ligands. Discovery of a functional covalent ligand targeting an intrinsically disordered cysteine within MYC. Chem. Cell 69, 517532 e511 (2018). PubMed Central Protein kinases are among the most exploited targets in modern drug discovery due to key roles these enzymes play in human diseases including cancer. Budayeva, H. G. & Kirkpatrick, D. S. Monitoring protein communities and their responses to therapeutics. As the above examples illustrate, a variety of different types of biomarkers are important for successful drug development. Chem. Design, synthesis and selection of DNA-encoded small-molecule libraries. 23, 608618 (2016). Soc. Nat. A genetic perturbation technique that allows sequence-specific activation of transcription. Secondary pharmacology data to assess potential off-target activity of new drugs: a regulatory perspective. High throughput discovery of functional protein modifications by Hotspot Thermal Profiling. Nat. Defines the theoretical relationship between the measured IC50 of a competitive inhibitor of a given Ki, the concentration of labelled ligand and the Kd of the ligandreceptor interaction. Although there have been over 100 published studies to identify potential diagnostic and prognostic biomarkers for Alzheimers Disease (AD) in cerebrospinal fluid (CSF) [Citation148], a key drug development need is for monitoring biomarkers. 24 November 2022, Access Nature and 54 other Nature Portfolio journals, Get Nature+, our best-value online-access subscription, Receive 12 print issues and online access, Get just this article for as long as you need it, Prices may be subject to local taxes which are calculated during checkout. Geyer, P. E. et al. Thank you for visiting nature.com. Medium submitted to regulatory agencies, included in the label. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. While the focus of biomarker discovery reported in the literature has been the identification of diagnostic tools, biomarkers play other critical roles in the clinical development of novel therapeutics. Chemoproteomics provides an unbiased map of physical interactions of a compound with cellular proteins that includes the efficacy or on-target for which the physical binding event functionally results in the observed cellular phenotypic response. By combining nanoPOTS with high sensitivity tandem mass spectrometry (MS/MS), Zhu et al. Cell 180, 605632 (2020). Mund, A. et al. J. Proteome Res. BReast CAncer genes 1 and 2 (BRCA1/2) mutations may be used as predictive biomarkers when evaluating women with platinum-sensitive ovarian cancer, to identify patients likely to respond to Poly (ADP-ribose) polymerase (PARP) inhibitors [. developed a technique boosting to amplify signal with isobaric labeling (iBASIL) to quantify phosphorylation in a small number of cells, for highly effective analysis of proteins in single cells. Nature 369, 756758 (1994). Permission will be required if your reuse is not covered by the terms of the License. Specificity of protein covalent modification by the electrophilic proteasome inhibitor carfilzomib in human cells. USA 70, 25672571 (1973). Nat. Accordingly, the general workflow has been applied successfully not only to target deconvolution for bioactive compounds such as for nimbolide (E3 ligase RNF114) [Citation93] or dimethyl fumarate (kinase complexes PKC-CD28 [Citation94] and IRAK44-Myd88 [Citation95]) but also to large scale mapping of protein interactors and ligandable pockets in living cells using electrophile libraries [Citation96]. Several approaches use differences in susceptibility to limited proteolysis upon compound treatment to identify proteome-wide compound interaction, including DARTS [Citation110] and LiP-MS [Citation111]. Opin. Future Med. The authors declare no competing interests. J. J. Pharmacol. Reducing sample preparation time and the number of adherent surfaces that come into contact with it, can all contribute to more sensitive analyses. As proteins constitute the majority of targets in drug development, these workflows have become indispensable at various stages of the drug discovery process: in phenotypic or cell-based drug discovery, where screening of large compound libraries in a cellular or organismal model of disease is used to identify chemical starting points, chemoproteomics can generate target hypotheses and in extension provide information about the mechanism of action (MoA) by which the compound exerts its phenotypic effect. Cell 168, 527541.e529 (2017). Therefore, approaches that enable live cell applications are increasingly gaining popularity. 54, 63426363 (2011). Boike, L. et al. Peer reviewers on this manuscript have no relevant financial or other relationships to disclose. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Science 360, eaao4927 (2018). In addition, reduced sample complexity is often correlated with easier data analysis (no chemical tag modification to add to the search parameters, no deconvolution of data needed as is required with a multiplexing approach). While large, standardized studies offer the best opportunity to collect data that can be directly compared, there is currently an effort to make the numerous, bespoke quantitative proteomic analyses more amenable to re-analysis from non-experts. A biomarker used for internal decision making may need less validation than a biomarker used to support the approval or use of a novel therapeutic. Hughes, J. P., Rees, S., Kalindjian, S. B. Building upon the MassIVE Knowledge Base [Citation65], MassIVE.quant includes experimental design information commonly lacking in public data repositories. the iodoacetamide-based probe for cysteine as used in the competitive isoTOP-ABPP workflow [Citation90]. Anal. Historically, the focus has been on identification of functionally relevant interactions such as efficacy target identification where complementary, in particular genetic approaches were required to prioritize physical interactors identified by chemoproteomics hits by functional relevance (and vice versa since genetic screening hits often include additional components of the target biology network). While these are becoming increasingly available, including for lysine [Citation97], methionine [Citation98] and tyrosine [Citation99], the identification of novel probes that are more robust and allow access to additional amino acids remains of high importance. Ballell, L. et al. Structural studies yield important insights into protein function, the "druggability" of protein targets for drug discovery, and drug design. Chemical proteomics approaches for identifying the cellular targets of natural products. Rapid Commun. Article Colca, J. R. et al. Drug Discov. Overlaying these genome-wide multi-omics datasets can reveal novel networks [Citation48]. 16, 269280 (2015). For example, Overmyer et al. Drug Discov. Recent advances in sample collection and processing, separation chemistries, ionization and mass spectrometric instrumentation as well as data collection and curation techniques now make it possible to quantify > 1000 proteins from a single cell. Thiazolidinediones are acute, specific inhibitors of the mitochondrial pyruvate carrier. Rutkowska, A. et al. J. Chem. J. Anal. Ponomarenko, E. A. et al. This is a very important parameter to optimize if one wishes to obtain the levels of sensitivity routinely appreciated by our genomic counterparts. These include analyzing novel targets, understanding disease mechanisms, structure-based drug design, and discovering the mode of action of lead compounds. Huang, J. X. et al. Combining multiple omics results resulted in clusters enriched in severe COVID-19 cases, such as a cluster that included the protein gelsolin (GSN) and the metabolite citrate. Nat. Thermal proteome profiling monitors ligand interactions with cellular membrane proteins. 33, 990995 (2015). 16, 11111119 (2020). MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins. Analysis of the root cause of drug development failures have consistently found that efficacy and safety are the major contributors to the low success rate in clinical trials [Citation71]. The rise of proteomics in advancing drug discovery and human health; Editorial Article: . Drug discovery is a lengthy and highly expensive process that uses a variety of tools from diverse fields. A commonly used strategy to increase proteome coverage is to use pre-fractionation. Sinitcyn, P., Rudolph, J. D. & Cox, J. Computational methods for understanding mass spectrometrybased shotgun proteomics data. Vinken, M. The adverse outcome pathway concept: a pragmatic tool in toxicology. Recently, Ouldali et al. The SysteMHC Atlas project. J. Mol. Nat. Front. capturing the experimental meta data associated with a mass spectrometry experiment is vital to re-analysis. For the Cellular Thermal Shift Assay (CETSA) [Citation103] and its coupling with a quantitative MS-based read-out for proteome-wide analysis (also called Thermal Proteome Profiling, TPP) [Citation104], the compound-induced stabilization in cells or lysate is detected as protection from heat-induced denaturation by quantifying non-denatured protein in the supernatant after a centrifugation step. Performing comparisons of multi-omics data is not trivial and requires a deep understanding of the complexity and caveats of each -omic approach. Engl. For more information please visit our Permissions help page. Koch, H., Busto, M. E., Kramer, K., Medard, G. & Kuster, B. Paananen, J. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Broad-spectrum kinase profiling in live cells with lysine-targeted sulfonyl fluoride probes. Cell 149, 307321 (2012). Gehringer, M. & Laufer, S. A. The method was used to analyze 1294 plasma samples in a human weight loss study [Citation151]. J. Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities. 120, 1432 (2011). Chem. J. Weissman and colleagues used this approach to identify 3,455 ORFs distinct from annotated coding sequences [Citation44]. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. Ligand and target discovery by fragment-based screening in human cells. Nat. Franco-Serrano, L. et al. Single molecule protein detection is currently possible through DNA-linked antibodies [Citation30] or fluorescently-labeled protein specific aptamers [Citation31]. Rev. Global profiling of lysine reactivity and ligandability in the human proteome. Nature 545, 505509 (2017). Today 21, 8289 (2016). The challenges associated with proteomics-based biomarker discovery, referred to as the discovery to validation gap, have been reviewed previously [Citation133136] and a number of factors have been identified that contribute to the failure to validate discovery findings. 9, 15401553 (2010). Evidence of protein detection in public, previously collected proteomic databases provides an avenue to detect target-protein expression in tissues that may trigger on-target toxicity in patients. Rev. Bos, J. 15, 679698 (2016). B V V S Hanagal Shri Kumareshwar College of Pharmacy, Bagalkote 1.4k views 44 slides protein microarray Soc. Schauer, N. J. et al. Nanopores have demonstrated the ability to discriminate phosphorylated from non-phosphorylated proteins [Citation39], but the challenge of discriminating all possible amino acid side chain modifications (e.g., acetylation, methylation, glycosylation) still remains unmet. Cell Biol. Again, key points for method development in the coming years will aim to further increase throughput, sensitivity and ease of application for the various covalent chemoproteomics workflows. Soc. These probes can be target family-specific such as the fluorophosphonate-based probes for serines hydrolases [Citation88] which have e.g. Schirle, M. & Jenkins, J. L. Identifying compound efficacy targets in phenotypic drug discovery. 14, 206214 (2018). Chem. Org. Biotechnol. Nat. This article reports the discovery of JQ1 as a selective inhibitor of BET proteins. By focusing on low-level phospho-tyrosine and immunopeptidomic samples they demonstrate that quantitative dynamic range decreases 2 to 6-fold when a carrier proteome is employed. 42, D1091D1097 (2014). Finally, 4) the interacting proteins are detected and quantified vs. an untreated control using typically quantitative mass spectrometry. Furthermore, it also has a vital role in drug development as target molecules. Nat. Oncogene 30, 41634174 (2011). 17, 6574 (2010). A subcellular map of the human proteome. The development of novel drugs is time consuming, expensive, challenging and risky. 9, 1519 (2018). Felix Meissner or Marcus Bantscheff. Table 1 describes several types of biomarkers used in drug development, as defined in the BEST document as well as examples from the BEST document and literature, with an emphasis on protein and proteomics related biomarkers. Kambe, T., Correia, B. E., Niphakis, M. J. Chem. Neurosci. Transl. 17, 24482461 (2018). Angew. Lappano, R. & Maggiolini, M. G protein-coupled receptors: novel targets for drug discovery in cancer. 75, 18951904 (2003). One of the major factors driving the cost of drug development is the high cost of failure, in particular failures in clinical development. Bantscheff, M., Scholten, A. Soc. Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes. Cell Chem. Drug Discov. PubMed Central Struct. Weerapana, E. et al. [Citation91,Citation92],) which differ in aspects including the exact probe design with either pre-installed or latent affinity handle as well as quantitative MS strategy with the final sample consisting of enriched probe-labeled peptides. This association makes functional sense because GNS is a Ca2+-activated actin-severing protein and citrate is a calcium chelator. 30, 17971803 (2017). Scott, D. E., Bayly, A. R., Abell, C. & Skidmore, J. Tsvetanova, N. G. et al. The same team went on to demonstrate that combined microfluidic nanodroplet technology with tandem mass tag (TMT) isobaric labeling could significantly improve analysis throughput and proteome coverage for low levels of mammalian cells. Virreira Winter, S. et al. The proteomics database information that is available shows that it can be used for basic research, drug discovery, or decision making in the clinic. The same advances in throughput, proteome coverage, and quantitation that are improving biomarker candidate discovery will accelerate these applications as well. ACS Chem. Am. This is supported by the fact that the authors found 240 HLA-I associated peptides from these distinct ORFs. Nat. One thousand and one software for proteomics: tales of the toolmakers of science. Nature 528, 510516 (2015). Sci. Biomarker candidate discovery relies on accurate differential analysis across large sample sets. 13, 162164 (2014). 12, 569 (2013). Kim, W. et al. Jones, L. H. Cell permeable affinity- and activity-based probes. The above two references describe some of the deepest and information-rich high-quality interactome studies to date. 63, 2030 (2020). 7, 13042 (2016). Rev. Br. The emerging role of mass spectrometry-based proteomics in drug discovery. Although a general consensus regarding the optimal approach to quantitative proteomics for biomarker candidate discovery has not yet emerged, the field is rapidly advancing and the future looks very promising. And while multi-omic integration is still evolving, examples of disease-relevant studies are starting to emerge. Chem. Nat. Selectively targeting the kinome-conserved lysine of PI3K as a general approach to covalent kinase inhibition. This paper introduces the most frequently used and free software suite in proteomics. A selective inhibitor reveals PI3Kgamma dependence of T(H)17 cell differentiation. Int. Nat. Proteom. Cell 131, 11901203 (2007). 32, 10361044 (2014). This approach has proven to be most successful for soluble proteins that retain binding competence under generic cell lysis conditions such as the E3 ligase substrate receptor CRBN as the target of thalidomide [Citation75] or Annexin A2 as a target of bleomycin in bleomycin-induced pulmonary fibrosis (PMID: 29,172,997). Mol. At present, proteomics is used pre-clinically for target identification and characterization, drug candidate selection and characterization, and clinically for biomarker discovery and development. A proximity biotinylation map of a human cell. Riley, N. M., Hebert, A. S. & Coon, J. J. Proteomics moves into the fast lane. This approach is attractive because it has the potential to sequence peptides in an unbiased manner and could potentially be used to specifically sequence post-translationally modified peptides. 20, 554570 (2012). Acetylation site specificities of lysine deacetylase inhibitors in human cells. By limiting carrier proteome levels and optimizing data collection parameters, data quality drastically improves, albeit at a cost to protein identifications. In addition to the sensitivity improvements discussed in section 2. Google Scholar. Science 327, 13451350 (2010). Muller, T. et al. The chip consists of a glass spacer, sealed to a membrane-coated glass slide to minimize evaporation of the nanowell contents during the various incubation steps. N-terminomic proteomic profiling (TAILS) was used to identify novel substrates of HtrA1, a serine hydrolase associated with increased risk of age-related macular degeneration (AMD) in preclinical models. Fueling open-source drug discovery: 177 small-molecule leads against tuberculosis.

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