1
|
Kuthe PV, Muzaffar-Ur-Rehman M, Chandu A, Prashant KS, Sankarnarayanan M. Unlocking nitrogen compounds' promise against malaria: A comprehensive review. Arch Pharm (Weinheim) 2024:e2400222. [PMID: 38837417 DOI: 10.1002/ardp.202400222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024]
Abstract
Plasmodium parasites are the primary cause of malaria, leading to high mortality rates, which require clinical attention. Many of the medications used in the treatment have resulted in resistance over time. Artemisinin combination therapy (ACT) has shown significant results for the treatment. However, mutations in the parasite have resulted in resistance, leading to decreased efficiency of the medications that are currently being used. Therefore, there is a critical need to find novel scaffolds that are safe, effective, and of economic advantage. Literature has reported several potent molecules with diverse scaffolds designed, synthesized, and evaluated against different strains of Plasmodium. With this growing list of compounds, it is essential to collect the data in one place to gain a concise overview of the emerging scaffolds in recent years. For this purpose, nitrogen-containing heterocycles such as β-carboline, imidazole, quinazoline, quinoline, thiazole, and thiophene have been highly explored due to their wide biological applications. Besides these, another scaffold, benzodiazepine, which is majorly used as a central nervous system depressant, is emerging as an anti-malarial agent. Hence, this review centers on the latest medication advancements designed to combat malaria, emphasizing special attention to 1,4-benzodiazepines as a novel scaffold for antimalarial drug discovery.
Collapse
Affiliation(s)
- Pranali Vijaykumar Kuthe
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Mohammad Muzaffar-Ur-Rehman
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Ala Chandu
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Kirad Shivani Prashant
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Murugesan Sankarnarayanan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
| |
Collapse
|
2
|
Bailey BL, Nguyen W, Cowman AF, Sleebs BE. Chemo-proteomics in antimalarial target identification and engagement. Med Res Rev 2023; 43:2303-2351. [PMID: 37232495 PMCID: PMC10947479 DOI: 10.1002/med.21975] [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] [Received: 06/22/2022] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Humans have lived in tenuous battle with malaria over millennia. Today, while much of the world is free of the disease, areas of South America, Asia, and Africa still wage this war with substantial impacts on their social and economic development. The threat of widespread resistance to all currently available antimalarial therapies continues to raise concern. Therefore, it is imperative that novel antimalarial chemotypes be developed to populate the pipeline going forward. Phenotypic screening has been responsible for the majority of the new chemotypes emerging in the past few decades. However, this can result in limited information on the molecular target of these compounds which may serve as an unknown variable complicating their progression into clinical development. Target identification and validation is a process that incorporates techniques from a range of different disciplines. Chemical biology and more specifically chemo-proteomics have been heavily utilized for this purpose. This review provides an in-depth summary of the application of chemo-proteomics in antimalarial development. Here we focus particularly on the methodology, practicalities, merits, and limitations of designing these experiments. Together this provides learnings on the future use of chemo-proteomics in antimalarial development.
Collapse
Affiliation(s)
- Brodie L. Bailey
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Gao P, Chen J, Sun P, Wang J, Tang H, Xia F, Gu L, Zhang H, Wang C, Wong YK, Zhu Y, Xu C, Wang J. Chemical proteomic profiling with photoaffinity labeling strategy identifies antimalarial targets of artemisinin. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
|
5
|
Nardella F, Dobrescu I, Hassan H, Rodrigues F, Thiberge S, Mancio-Silva L, Tafit A, Jallet C, Cadet-Daniel V, Goussin S, Lorthiois A, Menon Y, Molinier N, Pechalrieu D, Long C, Sautel F, Matondo M, Duchateau M, Médard G, Witkowski B, Scherf A, Halby L, Arimondo PB. Hemisynthetic alkaloids derived from trilobine are antimalarials with sustained activity in multidrug-resistant Plasmodium falciparum. iScience 2023; 26:105940. [PMID: 36718363 PMCID: PMC9883252 DOI: 10.1016/j.isci.2023.105940] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/23/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Malaria eradication requires the development of new drugs to combat drug-resistant parasites. We identified bisbenzylisoquinoline alkaloids isolated from Cocculus hirsutus that are active against Plasmodium falciparum blood stages. Synthesis of a library of 94 hemi-synthetic derivatives allowed to identify compound 84 that kills multi-drug resistant clinical isolates in the nanomolar range (median IC50 ranging from 35 to 88 nM). Chemical optimization led to compound 125 with significantly improved preclinical properties. 125 delays the onset of parasitemia in Plasmodium berghei infected mice and inhibits P. falciparum transmission stages in vitro (culture assays), and in vivo using membrane feeding assay in the Anopheles stephensi vector. Compound 125 also impairs P. falciparum development in sporozoite-infected hepatocytes, in the low micromolar range. Finally, by chemical pull-down strategy, we characterized the parasite interactome with trilobine derivatives, identifying protein partners belonging to metabolic pathways that are not targeted by the actual antimalarial drugs or implicated in drug-resistance mechanisms.
Collapse
Affiliation(s)
- Flore Nardella
- Biology of Host-Parasite Interaction, Department of Parasites and Insect Vectors, Institut Pasteur, Université de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Irina Dobrescu
- Biology of Host-Parasite Interaction, Department of Parasites and Insect Vectors, Institut Pasteur, Université de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Haitham Hassan
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris-Cité, UMR n°3523, CNRS, 28 Rue du Dr Roux, 75015 Paris, France
| | - Fabien Rodrigues
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris-Cité, UMR n°3523, CNRS, 28 Rue du Dr Roux, 75015 Paris, France
| | - Sabine Thiberge
- Biology of Host-Parasite Interaction, Department of Parasites and Insect Vectors, Institut Pasteur, Université de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, 75015 Paris, France,Center for Production and Infection of Anopheles (CEPIA), Center for Animal Resources and Research, Institut Pasteur, 75015 Paris, France
| | - Liliana Mancio-Silva
- Biology of Host-Parasite Interaction, Department of Parasites and Insect Vectors, Institut Pasteur, Université de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Ambre Tafit
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris-Cité, UMR n°3523, CNRS, 28 Rue du Dr Roux, 75015 Paris, France
| | - Corinne Jallet
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris-Cité, UMR n°3523, CNRS, 28 Rue du Dr Roux, 75015 Paris, France
| | - Véronique Cadet-Daniel
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris-Cité, UMR n°3523, CNRS, 28 Rue du Dr Roux, 75015 Paris, France
| | - Stéphane Goussin
- Center for Production and Infection of Anopheles (CEPIA), Center for Animal Resources and Research, Institut Pasteur, 75015 Paris, France
| | - Audrey Lorthiois
- Center for Production and Infection of Anopheles (CEPIA), Center for Animal Resources and Research, Institut Pasteur, 75015 Paris, France
| | - Yoann Menon
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et Développement Pierre Fabre, 3 Avenue Hubert Curien, 31035 Toulouse Cedex 01, France
| | - Nicolas Molinier
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et Développement Pierre Fabre, 3 Avenue Hubert Curien, 31035 Toulouse Cedex 01, France
| | - Dany Pechalrieu
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et Développement Pierre Fabre, 3 Avenue Hubert Curien, 31035 Toulouse Cedex 01, France
| | - Christophe Long
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et Développement Pierre Fabre, 3 Avenue Hubert Curien, 31035 Toulouse Cedex 01, France
| | - François Sautel
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et Développement Pierre Fabre, 3 Avenue Hubert Curien, 31035 Toulouse Cedex 01, France
| | - Mariette Matondo
- Proteomics Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, Université de Paris-Cité, CNRS USR 2000, 28 rue du Dr Roux, 75015 Paris, France
| | - Magalie Duchateau
- Proteomics Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, Université de Paris-Cité, CNRS USR 2000, 28 rue du Dr Roux, 75015 Paris, France
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, 85354 Freising, Germany
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Pasteur Institute in Cambodia, Phnom Penh 12201, Cambodia
| | - Artur Scherf
- Biology of Host-Parasite Interaction, Department of Parasites and Insect Vectors, Institut Pasteur, Université de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, 75015 Paris, France,Corresponding author
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris-Cité, UMR n°3523, CNRS, 28 Rue du Dr Roux, 75015 Paris, France
| | - Paola B. Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris-Cité, UMR n°3523, CNRS, 28 Rue du Dr Roux, 75015 Paris, France,USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et Développement Pierre Fabre, 3 Avenue Hubert Curien, 31035 Toulouse Cedex 01, France,Corresponding author
| |
Collapse
|
6
|
Deng H, Lei Q, Yang N, Dai S, Peng H, Yang K, Xiao Z, Wang D, Yu Z, Li N, Li W. Expanded Application of a Photoaffinity Probe to Study Epidermal Growth Factor Receptor Tyrosine Kinase with Functional Activity. Anal Chem 2022; 94:10118-10126. [PMID: 35729862 DOI: 10.1021/acs.analchem.2c01340] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The abnormal activation of the epidermal growth factor receptor (EGFR) is strongly associated with cancer invasion and metastasis. Tools and methods are required to study and visualize EGFR activation under (patho)physiological conditions. Here, we report the development of a two-step photoaffinity probe (HX101) by incorporation of a diazirine as a photoreactive group and an alkyne as a ligation handle to quantitively study EGFR kinase activity in native cellular contexts and human tissue slices. HX101 is a multifunctional probe based on the pharmacophore of the EGFR tyrosine kinase inhibitor (EGFR-TKI) and can covalently target the EGFR upon photoactivation. The incorporated alkyne serves as a versatile ligation handle and enables HX101 to introduce distinct reporter groups (e.g., fluorophore and biotin) via click chemistry. With variable reporter tags, HX101 enables visualization and target engagement studies of the active EGFR in a panel of cancer cells using flow cytometry, confocal microscopy, and mass spectrometry. Furthermore, as a proof of concept study, we applied HX101 in stochastic optical reconstruction microscopy super-resolution imaging to study EGFR activation in live cells. Importantly, HX101 was also applied to visualize EGFR mutant activity in tumor tissues from lung cancer patients for prediction of EGFR-TKI sensitivity. Altogether, our results demonstrate the wide application of a selective photoaffinity probe in multi-modal assessment/visualization of EGFR activity in both live cells and tissue slices. We anticipate that these diverse applications can facilitate the translation of a strategically functionalized probe into medical use.
Collapse
Affiliation(s)
- Hui Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Na Yang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shengkun Dai
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Huipai Peng
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Kai Yang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Zhaolin Xiao
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Dongpeng Wang
- Biological Science Instruments Division, Nikon Instruments (Shanghai), Chengdu, Sichuan, 610041, China
| | - Zhiyi Yu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Nan Li
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.,Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| |
Collapse
|
7
|
Carvalho L, Bernardes GJL. The Impact of Activity-based Protein Profiling in Malaria Drug Discovery. ChemMedChem 2022; 17:e202200174. [PMID: 35506504 PMCID: PMC9401580 DOI: 10.1002/cmdc.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/02/2022] [Indexed: 11/09/2022]
Abstract
Activity-based protein profiling (ABPP) is an approach used at the interface of chemical biology and proteomics that uses small molecular probes to provide dynamic fingerprints of enzymatic activity in complex proteomes. Malaria is a disease caused by Plasmodium parasites with a significant death burden and for which new therapies are actively being sought. Here, we compile the main achievements from ABPP studies in malaria and highlight the probes used and the different downstream platforms for data analysis. ABPP has excelled at studying Plasmodium cysteine proteases and serine hydrolase families, the targeting of the proteasome and metabolic pathways, and in the deconvolution of targets and mechanisms of known antimalarials. Despite the major impact in the field, many antimalarials and enzymatic families in Plasmodium remain to be studied, which suggests ABPP will be an evergreen technique in the field.
Collapse
Affiliation(s)
- Luis Carvalho
- University of Cambridge, Yusuf Hamied Department of Chemistry, Lensfield Rd, Yusuf Hamied Department of Chemistry, CB2 1EW, Cambridge, UNITED KINGDOM
| | - Gonçalo J L Bernardes
- University of Cambridge Department of Chemistry, Yusuf Hamied Department of Chemistry, Lensfield Rd, Yusuf Hamied Department of Chemistry, CB2 1EW, Cambridge, UNITED KINGDOM
| |
Collapse
|
8
|
Lu KY, Mansfield CR, Fitzgerald MC, Derbyshire ER. Chemoproteomics for Plasmodium Parasite Drug Target Discovery. Chembiochem 2021; 22:2591-2599. [PMID: 33999499 PMCID: PMC8373781 DOI: 10.1002/cbic.202100155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/16/2021] [Indexed: 12/16/2022]
Abstract
Emerging Plasmodium parasite drug resistance is threatening progress towards malaria control and elimination. While recent efforts in cell-based, high-throughput drug screening have produced first-in-class drugs with promising activities against different Plasmodium life cycle stages, most of these antimalarial agents have elusive mechanisms of action. Though challenging to address, target identification can provide valuable information to facilitate lead optimization and preclinical drug prioritization. Recently, proteome-wide methods for direct assessment of drug-protein interactions have emerged as powerful tools in a number of systems, including Plasmodium. In this review, we will discuss current chemoproteomic strategies that have been adapted to antimalarial drug target discovery, including affinity- and activity-based protein profiling and the energetics-based techniques thermal proteome profiling and stability of proteins from rates of oxidation. The successful application of chemoproteomics to the Plasmodium blood stage highlights the potential of these methods to link inhibitors to their molecular targets in more elusive Plasmodium life stages and intracellular pathogens in the future.
Collapse
Affiliation(s)
- Kuan-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
| | - Christopher R Mansfield
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Emily R Derbyshire
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| |
Collapse
|
9
|
Cichocki B, Khobragade V, Donzel M, Cotos L, Blandin S, Schaeffer-Reiss C, Cianférani S, Strub JM, Elhabiri M, Davioud-Charvet E. A Class of Valuable (Pro-)Activity-Based Protein Profiling Probes: Application to the Redox-Active Antiplasmodial Agent, Plasmodione. JACS AU 2021; 1:669-689. [PMID: 34056636 PMCID: PMC8154199 DOI: 10.1021/jacsau.1c00025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plasmodione (PD) is a potent antimalarial redox-active drug acting at low nM range concentrations on different malaria parasite stages. In this study, in order to determine the precise PD protein interactome in parasites, we developed a class of (pro-)activity-based protein profiling probes (ABPP) as precursors of photoreactive benzophenone-like probes based on the skeleton of PD metabolites (PDO) generated in a cascade of redox reactions. Under UV-photoirradiation, we clearly demonstrate that benzylic oxidation of 3-benzylmenadione 11 produces the 3-benzoylmenadione probe 7, allowing investigation of the proof-of-concept of the ABPP strategy with 3-benzoylmenadiones 7-10. The synthesized 3-benzoylmenadiones, probe 7 with an alkyne group or probe 9 with -NO2 in para position of the benzoyl chain, were found to be the most efficient photoreactive and clickable probes. In the presence of various H-donor partners, the UV-irradiation of the photoreactive ABPP probes generates different adducts, the expected "benzophenone-like" adducts (pathway 1) in addition to "benzoxanthone" adducts (via two other pathways, 2 and 3). Using both human and Plasmodium falciparum glutathione reductases, three protein ligand binding sites were identified following photolabeling with probes 7 or 9. The photoreduction of 3-benzoylmenadiones (PDO and probe 9) promoting the formation of both the corresponding benzoxanthone and the derived enone could be replaced by the glutathione reductase-catalyzed reduction step. In particular, the electrophilic character of the benzoxanthone was evidenced by its ability to alkylate heme, as a relevant event supporting the antimalarial mode of action of PD. This work provides a proof-of-principle that (pro-)ABPP probes can generate benzophenone-like metabolites enabling optimized activity-based protein profiling conditions that will be instrumental to analyze the interactome of early lead antiplasmodial 3-benzylmenadiones displaying an original and innovative mode of action.
Collapse
Affiliation(s)
- Bogdan
Adam Cichocki
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Vrushali Khobragade
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Maxime Donzel
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Leandro Cotos
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Stephanie Blandin
- Université
de Strasbourg−CNRS−INSERM UPR9022/U1257, Mosquito Immune Responses (MIR), F-67000 Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Jean-Marc Strub
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Mourad Elhabiri
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Elisabeth Davioud-Charvet
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| |
Collapse
|
10
|
Ha J, Park H, Park J, Park SB. Recent advances in identifying protein targets in drug discovery. Cell Chem Biol 2020; 28:394-423. [PMID: 33357463 DOI: 10.1016/j.chembiol.2020.12.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Phenotype-based screening has emerged as an alternative route for discovering new chemical entities toward first-in-class therapeutics. However, clarifying their mode of action has been a significant bottleneck for drug discovery. For target protein identification, conventionally bioactive small molecules are conjugated onto solid supports and then applied to isolate target proteins from whole proteome. This approach requires a high binding affinity between bioactive small molecules and their target proteins. Besides, the binding affinity can be significantly hampered after structural modifications of bioactive molecules with linkers. To overcome these limitations, two major strategies have recently been pursued: (1) the covalent conjugation between small molecules and target proteins using photoactivatable moieties or electrophiles, and (2) label-free target identification through monitoring target engagement by tracking the thermal, proteolytic, or chemical stability of target proteins. This review focuses on recent advancements in target identification from covalent capturing to label-free strategies.
Collapse
Affiliation(s)
- Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Hankum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea.
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea; CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea.
| |
Collapse
|
11
|
Benns HJ, Wincott CJ, Tate EW, Child MA. Activity- and reactivity-based proteomics: Recent technological advances and applications in drug discovery. Curr Opin Chem Biol 2020; 60:20-29. [PMID: 32768892 DOI: 10.1016/j.cbpa.2020.06.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Activity-based protein profiling (ABPP) is recognized as a powerful and versatile chemoproteomic technology in drug discovery. Central to ABPP is the use of activity-based probes to report the activity of specific enzymes or reactivity of amino acid types in complex biological systems. Over the last two decades, ABPP has facilitated the identification of new drug targets and discovery of lead compounds in human and infectious disease. Furthermore, as part of a sustained global effort to illuminate the druggable proteome, the repertoire of target classes addressable with activity-based probes has vastly expanded in recent years. Here, we provide an overview of ABPP and summarise the major technological advances with an emphasis on probe development.
Collapse
Affiliation(s)
- Henry James Benns
- Department of Life Sciences, London, UK; Department of Chemistry, Imperial College London, London, UK
| | | | | | | |
Collapse
|
12
|
Carolino K, Winzeler EA. The antimalarial resistome - finding new drug targets and their modes of action. Curr Opin Microbiol 2020; 57:49-55. [PMID: 32682267 PMCID: PMC7763834 DOI: 10.1016/j.mib.2020.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022]
Abstract
To this day, malaria remains a global burden, affecting millions of people, especially those in sub-Saharan Africa and Asia. The rise of drug resistance to current antimalarial treatments, including artemisinin-based combination therapies, has made discovering new small molecule compounds with novel modes of action an urgent matter. The concerted effort to construct enormous compound libraries and develop high-throughput phenotypic screening assays to find compounds effective at specifically clearing malaria-causing Plasmodium parasites at any stage of the life cycle has provided many antimalarial prospects, but does not indicate their target or mode of action. Here, we review recent advances in antimalarial drug discovery efforts, focusing on the following 'omics' approaches in mode of action studies: IVIEWGA, CETSA, metabolomic profiling.
Collapse
Affiliation(s)
- Krypton Carolino
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States.
| |
Collapse
|
13
|
Guillon J, Cohen A, Boudot C, Valle A, Milano V, Das RN, Guédin A, Moreau S, Ronga L, Savrimoutou S, Demourgues M, Reviriego E, Rubio S, Ferriez S, Agnamey P, Pauc C, Moukha S, Dozolme P, Nascimento SD, Laumaillé P, Bouchut A, Azas N, Mergny JL, Mullié C, Sonnet P, Courtioux B. Design, synthesis, and antiprotozoal evaluation of new 2,4-bis[(substituted-aminomethyl)phenyl]quinoline, 1,3-bis[(substituted-aminomethyl)phenyl]isoquinoline and 2,4-bis[(substituted-aminomethyl)phenyl]quinazoline derivatives. J Enzyme Inhib Med Chem 2020; 35:432-459. [PMID: 31899980 PMCID: PMC6968685 DOI: 10.1080/14756366.2019.1706502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
A series of new 2,4-bis[(substituted-aminomethyl)phenyl]quinoline, 1,3-bis[(substituted-aminomethyl)phenyl]isoquinoline, and 2,4-bis[(substituted-aminomethyl)phenyl]quinazoline derivatives was designed, synthesised, and evaluated in vitro against three protozoan parasites (Plasmodium falciparum, Leishmania donovani, and Trypanosoma brucei brucei). Biological results showed antiprotozoal activity with IC50 values in the µM range. In addition, the in vitro cytotoxicity of these original molecules was assessed with human HepG2 cells. The quinoline 1c was identified as the most potent antimalarial candidate with a ratio of cytotoxic to antiparasitic activities of 97 against the P. falciparum CQ-sensitive strain 3D7. The quinazoline 3h was also identified as the most potent trypanosomal candidate with a selectivity index (SI) of 43 on T. brucei brucei strain. Moreover, as the telomeres of the parasites P. falciparum and Trypanosoma are possible targets of this kind of nitrogen heterocyclic compounds, we have also investigated stabilisation of the Plasmodium and Trypanosoma telomeric G-quadruplexes by our best compounds through FRET melting assays.
Collapse
Affiliation(s)
- Jean Guillon
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Anita Cohen
- IRD, AP-HM, SSA, VITROME, Aix-Marseille University, Marseille, France
| | - Clotilde Boudot
- INSERM U1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, Limoges, France
| | - Alessandra Valle
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Vittoria Milano
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Rabindra Nath Das
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Aurore Guédin
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Stéphane Moreau
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Luisa Ronga
- PREM UMR5254 - UPPA/CNRS, Technopole Hélioparc, Université de Pau, Pau, France
| | - Solène Savrimoutou
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Maxime Demourgues
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Elodie Reviriego
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Sandra Rubio
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Sandie Ferriez
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Patrice Agnamey
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Cécile Pauc
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Serge Moukha
- Université de Bordeaux, Laboratoire de Toxicologie et d'Hygiène Appliquée - INRA, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Pascale Dozolme
- Université de Bordeaux, Laboratoire de Toxicologie et d'Hygiène Appliquée - INRA, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Sophie Da Nascimento
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Pierre Laumaillé
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Anne Bouchut
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Nadine Azas
- IRD, AP-HM, SSA, VITROME, Aix-Marseille University, Marseille, France
| | - Jean-Louis Mergny
- INSERM U1212, UMR CNRS 5320, ARNA Laboratory, UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France.,Institut Curie, Université Paris-Saclay, CNRS-UMR 9187, INSERM U1196, Université Paris-Saclay, Orsay, France.,Institute of Biophysics of the CAS, Brno, Czech Republic
| | - Catherine Mullié
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Pascal Sonnet
- UFR de Pharmacie, AGIR (Agents Infectieux, Résistance et chimiothérapie), Université de Picardie Jules Verne, Amiens,France
| | - Bertrand Courtioux
- INSERM U1094, Tropical Neuroepidemiology, Institute of Neuroepidemiology and Tropical Neurology, Université de Limoges, Limoges, France
| |
Collapse
|
14
|
Deng H, Lei Q, Wu Y, He Y, Li W. Activity-based protein profiling: Recent advances in medicinal chemistry. Eur J Med Chem 2020; 191:112151. [PMID: 32109778 DOI: 10.1016/j.ejmech.2020.112151] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 02/05/2023]
Abstract
Activity-based protein profiling (ABPP) has become an emerging chemical proteomic approach to illustrate the interaction mechanisms between compounds and proteins. This approach has combined organic synthesis, biochemistry, cell biology, biophysics and bioinformatics to accelerate the process of drug discovery in target identification and validation, as well as in the stage of lead discovery and optimization. This review will summarize new developments and applications of ABPP in medicinal chemistry. Here, we mainly described the design principles of activity-base probes (ABPs) and general workflows of ABPP approach. Moreover, we discussed various basic and advanced ABPP strategies and their applications in medicinal chemistry, including competitive and comparative ABPP, two-step ABPP, fluorescence polarization ABPP (FluoPol-ABPP) and ABPs for visualization. In conclusion, this review will give a general overview of the applications of ABPP as a powerful and efficient technique in medicinal chemistry.
Collapse
Affiliation(s)
- Hui Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yangping Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yang He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| |
Collapse
|
15
|
Evaluation of 4-Amino 2-Anilinoquinazolines against Plasmodium and Other Apicomplexan Parasites In Vitro and in a P. falciparum Humanized NOD- scid IL2Rγ null Mouse Model of Malaria. Antimicrob Agents Chemother 2019; 63:AAC.01804-18. [PMID: 30559138 DOI: 10.1128/aac.01804-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/10/2018] [Indexed: 11/20/2022] Open
Abstract
A series of 4-amino 2-anilinoquinazolines optimized for activity against the most lethal malaria parasite of humans, Plasmodium falciparum, was evaluated for activity against other human Plasmodium parasites and related apicomplexans that infect humans and animals. Four of the most promising compounds from the 4-amino 2-anilinoquinazoline series were equally as effective against the asexual blood stages of the zoonotic P. knowlesi, suggesting that they could also be effective against the closely related P. vivax, another important human pathogen. The 2-anilinoquinazoline compounds were also potent against an array of P. falciparum parasites resistant to clinically available antimalarial compounds, although slightly less so than against the drug-sensitive 3D7 parasite line. The apicomplexan parasites Toxoplasma gondii, Babesia bovis, and Cryptosporidium parvum were less sensitive to the 2-anilinoquinazoline series with a 50% effective concentration generally in the low micromolar range, suggesting that the yet to be discovered target of these compounds is absent or highly divergent in non-Plasmodium parasites. The 2-anilinoquinazoline compounds act as rapidly as chloroquine in vitro and when tested in rodents displayed a half-life that contributed to the compound's capacity to clear P. falciparum blood stages in a humanized mouse model. At a dose of 50 mg/kg of body weight, adverse effects to the humanized mice were noted, and evaluation against a panel of experimental high-risk off targets indicated some potential off-target activity. Further optimization of the 2-anilinoquinazoline antimalarial class will concentrate on improving in vivo efficacy and addressing adverse risk.
Collapse
|
16
|
Veale CGL. Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease. ChemMedChem 2019; 14:386-453. [PMID: 30614200 DOI: 10.1002/cmdc.201800755] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 12/13/2022]
Abstract
The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.
Collapse
Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| |
Collapse
|
17
|
D'Ascenzio M, Pugh KM, Konietzny R, Berridge G, Tallant C, Hashem S, Monteiro O, Thomas JR, Schirle M, Knapp S, Marsden B, Fedorov O, Bountra C, Kessler BM, Brennan PE. An Activity-Based Probe Targeting Non-Catalytic, Highly Conserved Amino Acid Residues within Bromodomains. Angew Chem Int Ed Engl 2019; 58:1007-1012. [PMID: 30589164 PMCID: PMC6492141 DOI: 10.1002/anie.201807825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/20/2018] [Indexed: 12/27/2022]
Abstract
Bromodomain-containing proteins are epigenetic modulators involved in a wide range of cellular processes, from recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl-lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule-based approach to covalently modify recombinant and endogenous bromodomain-containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag allowed in-gel visualization and pull-down of the desired bromodomains.
Collapse
Affiliation(s)
- Melissa D'Ascenzio
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Kathryn M. Pugh
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | | | - Georgina Berridge
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Cynthia Tallant
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Shaima Hashem
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | - Octovia Monteiro
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Jason R. Thomas
- Novartis Institute for BioMedical Research (NIBR)180 Massachusetts AveCambridgeMA02139USA
| | - Markus Schirle
- Novartis Institute for BioMedical Research (NIBR)180 Massachusetts AveCambridgeMA02139USA
| | - Stefan Knapp
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Brian Marsden
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | - Oleg Fedorov
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Chas Bountra
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | | | - Paul E. Brennan
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| |
Collapse
|
18
|
D'Ascenzio M, Pugh KM, Konietzny R, Berridge G, Tallant C, Hashem S, Monteiro O, Thomas JR, Schirle M, Knapp S, Marsden B, Fedorov O, Bountra C, Kessler BM, Brennan PE. An Activity‐Based Probe Targeting Non‐Catalytic, Highly Conserved Amino Acid Residues within Bromodomains. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Melissa D'Ascenzio
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Kathryn M. Pugh
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Rebecca Konietzny
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Georgina Berridge
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Cynthia Tallant
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Shaima Hashem
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | - Octovia Monteiro
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Jason R. Thomas
- Novartis Institute for BioMedical Research (NIBR) 180 Massachusetts Ave Cambridge MA 02139 USA
| | - Markus Schirle
- Novartis Institute for BioMedical Research (NIBR) 180 Massachusetts Ave Cambridge MA 02139 USA
| | - Stefan Knapp
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University 60438 Frankfurt am Main Germany
| | - Brian Marsden
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | - Oleg Fedorov
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Chas Bountra
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | | | - Paul E. Brennan
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| |
Collapse
|