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Eshaq AM, Flanagan TW, Hassan SY, Al Asheikh SA, Al-Amoudi WA, Santourlidis S, Hassan SL, Alamodi MO, Bendhack ML, Alamodi MO, Haikel Y, Megahed M, Hassan M. Non-Receptor Tyrosine Kinases: Their Structure and Mechanistic Role in Tumor Progression and Resistance. Cancers (Basel) 2024; 16:2754. [PMID: 39123481 PMCID: PMC11311543 DOI: 10.3390/cancers16152754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/30/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Protein tyrosine kinases (PTKs) function as key molecules in the signaling pathways in addition to their impact as a therapeutic target for the treatment of many human diseases, including cancer. PTKs are characterized by their ability to phosphorylate serine, threonine, or tyrosine residues and can thereby rapidly and reversibly alter the function of their protein substrates in the form of significant changes in protein confirmation and affinity for their interaction with protein partners to drive cellular functions under normal and pathological conditions. PTKs are classified into two groups: one of which represents tyrosine kinases, while the other one includes the members of the serine/threonine kinases. The group of tyrosine kinases is subdivided into subgroups: one of them includes the member of receptor tyrosine kinases (RTKs), while the other subgroup includes the member of non-receptor tyrosine kinases (NRTKs). Both these kinase groups function as an "on" or "off" switch in many cellular functions. NRTKs are enzymes which are overexpressed and activated in many cancer types and regulate variable cellular functions in response to extracellular signaling-dependent mechanisms. NRTK-mediated different cellular functions are regulated by kinase-dependent and kinase-independent mechanisms either in the cytoplasm or in the nucleus. Thus, targeting NRTKs is of great interest to improve the treatment strategy of different tumor types. This review deals with the structure and mechanistic role of NRTKs in tumor progression and resistance and their importance as therapeutic targets in tumor therapy.
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Affiliation(s)
- Abdulaziz M. Eshaq
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Thomas W. Flanagan
- Department of Pharmacology and Experimental Therapeutics, LSU Health Sciences Center, New Orleans, LA 70112, USA;
| | - Sofie-Yasmin Hassan
- Department of Pharmacy, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany;
| | - Sara A. Al Asheikh
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Waleed A. Al-Amoudi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Simeon Santourlidis
- Institute of Cell Therapeutics and Diagnostics, University Medical Center of Duesseldorf, 40225 Duesseldorf, Germany;
| | - Sarah-Lilly Hassan
- Department of Chemistry, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany;
| | - Maryam O. Alamodi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Marcelo L. Bendhack
- Department of Urology, Red Cross University Hospital, Positivo University, Rua Mauá 1111, Curitiba 80030-200, Brazil;
| | - Mohammed O. Alamodi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Youssef Haikel
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France;
- Department of Operative Dentistry and Endodontics, Dental Faculty, 67000 Strasbourg, France
- Pôle de Médecine et Chirurgie Bucco-Dentaire, Hôpital Civil, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France
| | - Mossad Megahed
- Clinic of Dermatology, University Hospital of Aachen, 52074 Aachen, Germany;
| | - Mohamed Hassan
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France;
- Department of Operative Dentistry and Endodontics, Dental Faculty, 67000 Strasbourg, France
- Research Laboratory of Surgery-Oncology, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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Momin AA, Mendes T, Barthe P, Faure C, Hong S, Yu P, Kadaré G, Jaremko M, Girault JA, Jaremko Ł, Arold ST. PYK2 senses calcium through a disordered dimerization and calmodulin-binding element. Commun Biol 2022; 5:800. [PMID: 35945264 PMCID: PMC9363500 DOI: 10.1038/s42003-022-03760-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
Multidomain kinases use many ways to integrate and process diverse stimuli. Here, we investigated the mechanism by which the protein tyrosine kinase 2-beta (PYK2) functions as a sensor and effector of cellular calcium influx. We show that the linker between the PYK2 kinase and FAT domains (KFL) encompasses an unusual calmodulin (CaM) binding element. PYK2 KFL is disordered and engages CaM through an ensemble of transient binding events. Calcium increases the association by promoting structural changes in CaM that expose auxiliary interaction opportunities. KFL also forms fuzzy dimers, and dimerization is enhanced by CaM binding. As a monomer, however, KFL associates with the PYK2 FERM-kinase fragment. Thus, we identify a mechanism whereby calcium influx can promote PYK2 self-association, and hence kinase-activating trans-autophosphorylation. Collectively, our findings describe a flexible protein module that expands the paradigms for CaM binding and self-association, and their use for controlling kinase activity. Protein tyrosine kinase 2-beta is shown to function as a sensor and effector of cellular calcium influx through self-association.
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Affiliation(s)
- Afaque A Momin
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tiago Mendes
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Philippe Barthe
- Centre de Biologie Structurale (CBS), University Montpellier, INSERM U1054, CNRS UMR 5048, 34090, Montpellier, France
| | - Camille Faure
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - SeungBeom Hong
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Piao Yu
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gress Kadaré
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Mariusz Jaremko
- Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Antoine Girault
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Łukasz Jaremko
- Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Centre de Biologie Structurale (CBS), University Montpellier, INSERM U1054, CNRS UMR 5048, 34090, Montpellier, France.
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Sunderhaus A, Imran R, Enoh E, Adedeji A, Obafemi T, Abdel Aziz MH. Comparative expression of soluble, active human kinases in specialized bacterial strains. PLoS One 2022; 17:e0267226. [PMID: 35439268 PMCID: PMC9017934 DOI: 10.1371/journal.pone.0267226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/05/2022] [Indexed: 11/19/2022] Open
Abstract
Kinases act as molecular switches for cellular functions and are involved in multiple human pathogeneses, most notably cancer. There is a continuous need for soluble and active kinases for in-vitro drug discovery and structural biology purposes. Kinases remain challenging to express using Escherichia coli, the most widely utilized host for heterologous expression. In this work, four bacterial strains, BL21 (DE3), BL21 (DE3) pLysS, Rosetta, and Arctic Express, were chosen for parallel expression trials along with BL21 (DE3) complemented with folding chaperones DnaJ/K and GroEL/ES to compare their performance in producing soluble and active human kinases. Three representative diverse kinases were studied, Epidermal Growth Factor Receptor kinase domain, Aurora Kinase A kinase domain, and Mitogen-activated protein Kinase Kinase. The genes encoding the kinases were subcloned into pET15b bacterial plasmid and transformed into the bacterial strains. Soluble kinase expression was tested using different IPTG concentrations (1–0.05 mM) at varying temperatures (37°C– 10°C) and induction times (3–24 hours). The optimum conditions for each kinase in all strains were then used for 1L large scale cultures from which each kinase was purified to compare yield, purity, oligomerization status, and activity. Although using specialized strains achieved improvements in yield and/or activity for the three kinases, none of the tested strains was universally superior, highlighting the individuality in kinase expression.
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Affiliation(s)
- Allison Sunderhaus
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, United States of America
| | - Ramsha Imran
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, United States of America
| | - Elanzou Enoh
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, United States of America
| | - Adesola Adedeji
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, United States of America
| | - Taiye Obafemi
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, United States of America
| | - May H. Abdel Aziz
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, United States of America
- * E-mail:
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Characterization of Phosphorylation Status and Kinase Activity of Src Family Kinases Expressed in Cell-Based and Cell-Free Protein Expression Systems. Biomolecules 2021; 11:biom11101448. [PMID: 34680080 PMCID: PMC8533471 DOI: 10.3390/biom11101448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/25/2022] Open
Abstract
The production of heterologous proteins is an important procedure for biologists in basic and applied sciences. A variety of cell-based and cell-free protein expression systems are available to achieve this. The expression system must be selected carefully, especially for target proteins that require post-translational modifications. In this study, human Src family kinases were prepared using six different protein expression systems: 293 human embryonic kidney cells, Escherichia coli, and cell-free expression systems derived from rabbit reticulocytes, wheat germ, insect cells, or Escherichia coli. The phosphorylation status of each kinase was analyzed by Phos-tag SDS-PAGE. The kinase activities were also investigated. In the eukaryotic systems, multiple phosphorylated forms of the expressed kinases were observed. In the rabbit reticulocyte lysate system and 293 cells, differences in phosphorylation status between the wild-type and kinase-dead mutants were observed. Whether the expressed kinase was active depended on the properties of both the kinase and each expression system. In the prokaryotic systems, Src and Hck were expressed in autophosphorylated active forms. Clear differences in post-translational phosphorylation among the protein expression systems were revealed. These results provide useful information for preparing functional proteins regulated by phosphorylation.
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Sunderhaus A, Imran R, Goudelock A, Nassar M, Cooper K, Patterson D, Abdel Aziz MH. Engineering soluble artificial epidermal growth factor receptor mimics capable of spontaneous in vitro dimerization. Biotechnol Bioeng 2021; 118:1466-1475. [PMID: 33331661 DOI: 10.1002/bit.27659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/08/2020] [Accepted: 12/12/2020] [Indexed: 12/11/2022]
Abstract
Epidermal growth factor receptor (EGFR) is a clinically validated target for a multitude of human cancers. The receptor is activated upon ligand binding through a critical dimerization step. Dimerization can be replicated in vitro by locally concentrating the receptor kinase domains on the surface of lipid-based vesicles. In this study we investigated the use of coiled coils to induce spontaneous receptor kinase domain dimerization in vitro to form non-membrane-bound artificial receptor mimics in solution. Two engineered forms of EGFR kinase domain fused to coiled coil complementary peptides were designed to self-associate upon mixing. Two fusion protein species (P3-EGFR and P4-EGFR) independently showed the same activity and polymerization profile known to exist with EGFR kinase domains. Upon mixing the two species, coiled coil heterodimers were formed that induced EGFR association to form dimers of the kinase domains. This was accompanied by 11.5-fold increase in the phosphorylation rate indicative of kinase domain activation equivalent to the levels achieved using vesicle localization and mimicking in vivo ligand-induced activation. This study presents a soluble tyrosine kinase receptor mimic capable of spontaneous in vitro activation that can facilitate functional and drug discovery studies for this clinically important receptor class.
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Affiliation(s)
- Allison Sunderhaus
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Ramsha Imran
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Amanda Goudelock
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Manon Nassar
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, Tyler, Texas, USA
| | - Kendall Cooper
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, Tyler, Texas, USA
| | - Dustin Patterson
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, Tyler, Texas, USA
| | - May H Abdel Aziz
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
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A scalable insect cell-based production process of the human recombinant BMX for in-vitro covalent ligand high-throughput screening. Bioprocess Biosyst Eng 2020; 44:209-215. [PMID: 32816073 DOI: 10.1007/s00449-020-02421-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
Abstract
Bone Marrow Tyrosine kinase in the chromosome X (BMX) is a TEC family kinase associated with numerous pathological pathways in cancer cells. Covalent inhibition of BMX activity holds promise as a therapeutic approach against cancer. To screen for potent and selective covalent BMX inhibitors, large quantities of highly pure BMX are normally required which is challenging with the currently available production and purification processes. Here, we developed a scalable production process for the human recombinant BMX (hrBMX) using the insect cell-baculovirus expression vector system. Comparable expression levels were obtained in small-scale shake flasks (13 mL) and in stirred-tank bioreactors (STB, 5 L). A two-step chromatographic-based process was implemented, reducing purification times by 75% when compared to traditional processes, while maintaining hrBMX stability. The final production yield was 24 mg of purified hrBMX per litter of cell culture, with a purity of > 99%. Product quality was assessed and confirmed through a series of biochemical and biophysical assays, including circular dichroism and dynamic light scattering. Overall, the platform herein developed was capable of generating 100 mg purified hrBMX from 5 L STB in just 34 days, thus having the potential to assist in-vitro covalent ligand high-throughput screening for BMX activity inhibition.
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