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van der Zouwen AJ, Jeucken A, van der Pol E, Boerema G, Slotboom DJ, Witte MD. The linkage-type and the exchange molecule affect the protein-labeling efficiency of iminoboronate probes. Org Biomol Chem 2023; 21:9173-9181. [PMID: 37947354 PMCID: PMC10686633 DOI: 10.1039/d3ob01269g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Reversible bioorthogonal conjugation reactions have been exploited in the chemoproteomic field to prepare protein labeling reagents and to visualize labeled proteins. We recently demonstrated that reversible iminoboronates can be used to prepare probes from fragment libraries and that the linkage subsequently can be used to detect the labeled proteins. In this study, we determined the effect of the stability of the iminoboronate linkage on the efficiency of the labeling protocol. Our study reveals that the linkage should be stable enough to allow for efficient targeting, but should be labile enough to detect the labeled protein. Acyl hydrazides were identified as the most suitable handles for the probe synthesis step. Anthranilic hydrazides and N-hydroxy semicarbazides were found to be the most efficient read-out molecules. With these novel exchange molecules, native probe-labeled proteins could be visualized under physiological conditions.
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Affiliation(s)
- Antonie J van der Zouwen
- Chemical Biology II, Stratingh Institute for Chemistry, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Aike Jeucken
- Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG Groningen, The Netherlands
| | - Elske van der Pol
- Chemical Biology II, Stratingh Institute for Chemistry, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Gerben Boerema
- Chemical Biology II, Stratingh Institute for Chemistry, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Dirk J Slotboom
- Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG Groningen, The Netherlands
| | - Martin D Witte
- Chemical Biology II, Stratingh Institute for Chemistry, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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2
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Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
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Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
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3
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Pun FW, Ozerov IV, Zhavoronkov A. AI-powered therapeutic target discovery. Trends Pharmacol Sci 2023; 44:561-572. [PMID: 37479540 DOI: 10.1016/j.tips.2023.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/23/2023]
Abstract
Disease modeling and target identification are the most crucial initial steps in drug discovery, and influence the probability of success at every step of drug development. Traditional target identification is a time-consuming process that takes years to decades and usually starts in an academic setting. Given its advantages of analyzing large datasets and intricate biological networks, artificial intelligence (AI) is playing a growing role in modern drug target identification. We review recent advances in target discovery, focusing on breakthroughs in AI-driven therapeutic target exploration. We also discuss the importance of striking a balance between novelty and confidence in target selection. An increasing number of AI-identified targets are being validated through experiments and several AI-derived drugs are entering clinical trials; we highlight current limitations and potential pathways for moving forward.
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Affiliation(s)
- Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong; Insilico Medicine MENA, 6F IRENA Building, Abu Dhabi, United Arab Emirates; Buck Institute for Research on Aging, Novato, CA, USA.
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bioTCIs: Middle-to-Macro Biomolecular Targeted Covalent Inhibitors Possessing Both Semi-Permanent Drug Action and Stringent Target Specificity as Potential Antibody Replacements. Int J Mol Sci 2023; 24:ijms24043525. [PMID: 36834935 PMCID: PMC9968108 DOI: 10.3390/ijms24043525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Monoclonal antibody therapies targeting immuno-modulatory targets such as checkpoint proteins, chemokines, and cytokines have made significant impact in several areas, including cancer, inflammatory disease, and infection. However, antibodies are complex biologics with well-known limitations, including high cost for development and production, immunogenicity, a limited shelf-life because of aggregation, denaturation, and fragmentation of the large protein. Drug modalities such as peptides and nucleic acid aptamers showing high-affinity and highly selective interaction with the target protein have been proposed alternatives to therapeutic antibodies. The fundamental limitation of short in vivo half-life has prevented the wide acceptance of these alternatives. Covalent drugs, also known as targeted covalent inhibitors (TCIs), form permanent bonds to target proteins and, in theory, eternally exert the drug action, circumventing the pharmacokinetic limitation of other antibody alternatives. The TCI drug platform, too, has been slow in gaining acceptance because of its potential prolonged side-effect from off-target covalent binding. To avoid the potential risks of irreversible adverse drug effects from off-target conjugation, the TCI modality is broadening from the conventional small molecules to larger biomolecules possessing desirable properties (e.g., hydrolysis resistance, drug-action reversal, unique pharmacokinetics, stringent target specificity, and inhibition of protein-protein interactions). Here, we review the historical development of the TCI made of bio-oligomers/polymers (i.e., peptide-, protein-, or nucleic-acid-type) obtained by rational design and combinatorial screening. The structural optimization of the reactive warheads and incorporation into the targeted biomolecules enabling a highly selective covalent interaction between the TCI and the target protein is discussed. Through this review, we hope to highlight the middle to macro-molecular TCI platform as a realistic replacement for the antibody.
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Franco AR, Artusa V, Peri F. Use of Fluorescent Chemical Probes in the Study of Toll-like Receptors (TLRs) Trafficking. Methods Mol Biol 2023; 2700:57-74. [PMID: 37603174 DOI: 10.1007/978-1-0716-3366-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Fluorescent chemical probes are used nowadays as a chemical resource to study the physiology and pharmacology of several important endogenous receptors. Different fluorescent groups have been coupled with known ligands of these receptors, allowing the visualization of their localization and trafficking. One of the most important molecular players of innate immunity and inflammation are the Toll-Like Receptors (TLRs). These Pattern-Recognition Receptors (PRR) have as natural ligands microbial-derived pathogen-associated molecular patterns (PAMPs) and also endogenous molecules called danger-associated molecular patterns (DAMPs). These ligands activate TLRs to start a response that will determine the host's protection and overall cell survival but can also lead to chronic inflammation and autoimmune syndromes. TLRs action is tightly related to their subcellular localization and trafficking. Understanding this trafficking phenomenon can enlighten critical molecular pathways that might allow to decipher the causes of different diseases. In this chapter, the study of function, localization and trafficking of TLRs through the use of chemical probes will be discussed. Furthermore, an example protocol of the use of fluorescent chemical probes to study TLR4 trafficking using high-content analysis will be described.
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Affiliation(s)
- Ana Rita Franco
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Valentina Artusa
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Francesco Peri
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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Gagestein B, Stevens AF, Fazio D, Florea BI, van der Wel T, Bakker AT, Fezza F, Dulk HD, Overkleeft HS, Maccarrone M, van der Stelt M. Chemical Proteomics Reveals Off-Targets of the Anandamide Reuptake Inhibitor WOBE437. ACS Chem Biol 2022; 17:1174-1183. [PMID: 35482948 PMCID: PMC9127799 DOI: 10.1021/acschembio.2c00122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Anandamide or N-arachidonoylethanolamine (AEA) is a signaling lipid that modulates neurotransmitter release via activation of the type 1 cannabinoid receptor (CB1R) in the brain. Termination of anandamide signaling is thought to be mediated via a facilitated cellular reuptake process that utilizes a purported transporter protein. Recently, WOBE437 has been reported as a novel, natural product-based inhibitor of AEA reuptake that is active in cellular and in vivo models. To profile its target interaction landscape, we synthesized pac-WOBE, a photoactivatable probe derivative of WOBE437, and performed chemical proteomics in mouse neuroblastoma Neuro-2a cells. Surprisingly WOBE437, unlike the widely used selective inhibitor of AEA uptake OMDM-1, was found to increase AEA uptake in Neuro-2a cells. In line with this, WOBE437 reduced the cellular levels of AEA and related N-acylethanolamines (NAEs). Using pac-WOBE, we identified saccharopine dehydrogenase-like oxidoreductase (SCCPDH), vesicle amine transport 1 (VAT1), and ferrochelatase (FECH) as WOBE437-interacting proteins in Neuro-2a cells. Further genetic studies indicated that SCCPDH and VAT1 were not responsible for the WOBE437-induced reduction in NAE levels. Regardless of the precise mechanism of action of WOB437 in AEA transport, we have identified SSCPHD, VAT1, and FECH as unprecedented off-targets of this molecule which should be taken into account when interpreting its cellular and in vivo effects.
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Affiliation(s)
- Berend Gagestein
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Anna F. Stevens
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Domenico Fazio
- European Center for Brain Research/IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano 64, Rome 00143, Italy
| | - Bogdan I. Florea
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Tom van der Wel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Alexander T. Bakker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Filomena Fezza
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, Rome 00121, Italy
| | - Hans den Dulk
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Herman S. Overkleeft
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Mauro Maccarrone
- European Center for Brain Research/IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano 64, Rome 00143, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio snc, 67100 L’Aquila, Italy
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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Schmid P, Peñalver L, Böttcher T. A ligand selection strategy to customize small molecule probes for activity-based protein profiling (LS-ABPP). Methods Enzymol 2022; 664:23-58. [PMID: 35331376 DOI: 10.1016/bs.mie.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activity-based probes (ABPs) are the key components of activity-based protein profiling (ABPP). However, designing a probe that shows target-specific as well as site-selective binding can be a challenging and time-consuming task, often requiring complex synthetic procedures to provide a selection of probes from which to choose the ideal one. In this chapter, we present a ligand selection (LS) approach that allows us to rapidly diversify probe molecules in order to meet the steric and electronic demands of the binding site of any target enzyme. The central element of this method is a trifunctional LS probe synthesized from tyrosine in five steps, consisting of a highly reactive pentafluorophenyl (PFP) ester in addition to an electrophilic chloroacetamide warhead, and a bioorthogonal alkyne reporter group. By reacting a variety of primary amine ligands with the PFP ester, a probe library is created and screened for optimal binding characteristics to the target enzyme. With the optimized probe in hand, a compound library is subsequently screened by competitive profiling to identify potential enzyme inhibitors. Conveniently, this protocol is highly adaptable to a large variety of target proteins, representing a valuable tool for enzyme characterization and the discovery of enzyme inhibitors. Here, we apply this method exemplarily to the cysteine protease 3CLpro of the coronavirus SARS-CoV-2.
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Affiliation(s)
- Philipp Schmid
- Faculty of Chemistry, Institute for Biological Chemistry & Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystems Science, University of Vienna, Vienna, Austria
| | - Lilian Peñalver
- Faculty of Chemistry, Institute for Biological Chemistry & Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystems Science, University of Vienna, Vienna, Austria
| | - Thomas Böttcher
- Faculty of Chemistry, Institute for Biological Chemistry & Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystems Science, University of Vienna, Vienna, Austria.
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8
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Pan J, Li M, Yu F, Zhu F, Wang L, Ning D, Hou X, Jiang F. Up-Regulation of p53/miR-628-3p Pathway, a Novel Mechanism of Shikonin on Inhibiting Proliferation and Inducing Apoptosis of A549 and PC-9 Non-Small Cell Lung Cancer Cell Lines. Front Pharmacol 2021; 12:766165. [PMID: 34867391 PMCID: PMC8635033 DOI: 10.3389/fphar.2021.766165] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/07/2021] [Indexed: 12/19/2022] Open
Abstract
Shikonin (SHK) is a pleiotropic agent with remarkable cell growth inhibition activity against various cancer types, especially non–small cell lung cancer (NSCLC), but its molecular mechanism is still unclear. Our previous study found that miR-628-3p could inhibit the growth of A549 cells and induce its apoptosis. Bioinformatics analysis predicted that miR-628-3p promoter sequence contained p53 binding sites. Considering the regulatory effect of SHK on p53, we speculate that SHK may inhibit the growth and induce apoptosis of NSCLC cells by up-regulating miR-628-3p. CCK-8 and EdU assay confirmed the inhibitory effect of SHK on A549 and PC-9 cells. Meanwhile, quantitative reverse transcription–polymerase chain reaction and Western blot showed that SHK could promote the expression of p53 and miR-628-3p in a dose-dependent manner. Overexpression of p53 or miR-628-3p can inhibit the growth and promote apoptosis of A549 and PC-9 cells, while silencing p53 or miR-628-3p has the opposite effect. Dual luciferase reporting assay and ChIP (chromatin immunoprecipitation) assay further verified the direct interaction between p53 and the promoter of miR-628-3p. Gene knockdown for p53 or miR-628-3p confirmed that SHK inhibits the growth and induces apoptosis of A549 and PC-9 cells at least partly by up-regulating p53/miR-628-3p signaling pathway. Therefore, these novel findings provide an alternative approach to target p53/miR-628-3p axis and could be used for the development of new treatment strategies for NSCLC.
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Affiliation(s)
- Jieli Pan
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Meiya Li
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Fenglin Yu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Feiye Zhu
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Linyan Wang
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Dandan Ning
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaoli Hou
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Fusheng Jiang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
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