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Garcia-Viloca M, Bayascas JR, Lluch JM, González-Lafont À. Molecular Insights into the Regulation of 3-Phosphoinositide-Dependent Protein Kinase 1: Modeling the Interaction between the Kinase and the Pleckstrin Homology Domains. ACS OMEGA 2022; 7:25186-25199. [PMID: 35910176 PMCID: PMC9330272 DOI: 10.1021/acsomega.2c02020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The 3-phosphoinositide-dependent protein kinase 1 (PDK1) K465E mutant kinase can still activate protein kinase B (PKB) at the membrane in a phosphatidylinositol-3,4,5-trisphosphate (PIP3, PtdIns(3,4,5)P3) independent manner. To understand this new PDK1 regulatory mechanism, docking and molecular dynamics calculations were performed for the first time to simulate the wild-type kinase domain-pleckstrin homology (PH) domain complex with PH-in and PH-out conformations. These simulations were then compared to the PH-in model of the KD-PH(mutant K465E) PDK1 complex. Additionally, three KD-PH complexes were simulated, including a substrate analogue bound to a hydrophobic pocket (denominated the PIF-pocket) substrate-docking site. We find that only the PH-out conformation, with the PH domain well-oriented to interact with the cellular membrane, is active for wild-type PDK1. In contrast, the active conformation of the PDK1 K465E mutant is PH-in, being ATP-stable at the active site while the PIF-pocket is more accessible to the peptide substrate. We corroborate that both the docking-site binding and the catalytic activity are in fact enhanced in knock-in mouse samples expressing the PDK1 K465E protein, enabling the phosphorylation of PKB in the absence of PIP3 binding.
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Affiliation(s)
- Mireia Garcia-Viloca
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Jose Ramón Bayascas
- Institut
de Neurociències, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
- Department
of Biochemistry and Molecular Biology, Biochemistry Unit of the School
of Medicine, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - José M. Lluch
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institut
de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Àngels González-Lafont
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institut
de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
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Engineered Allosteric Regulation of Protein Function. J Mol Biol 2022; 434:167620. [PMID: 35513109 DOI: 10.1016/j.jmb.2022.167620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/27/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022]
Abstract
Allosteric regulation of proteins has been utilized to study various aspects of cell signaling, from unicellular events to organism-wide phenotypes. However, traditional methods of allosteric regulation, such as constitutively active mutants and inhibitors, lack tight spatiotemporal control. This often leads to unintended signaling consequences that interfere with data interpretation. To overcome these obstacles, researchers employed protein engineering approaches that enable tight control of protein function through allosteric mechanisms. These methods provide high specificity as well as spatial and temporal precision in regulation of protein activity in vitro and in vivo. In this review, we focus on the recent advancements in engineered allosteric regulation and discuss the various bioengineered allosteric techniques available now, from chimeric GPCRs to chemogenetic and optogenetic switches. We highlight the benefits and pitfalls of each of these techniques as well as areas in which future improvements can be made. Additionally, we provide a brief discussion on implementation of engineered allosteric regulation approaches, demonstrating that these tools can shed light on elusive biological events and have the potential to be utilized in precision medicine.
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Bailly C. Atractylenolides, essential components of Atractylodes-based traditional herbal medicines: Antioxidant, anti-inflammatory and anticancer properties. Eur J Pharmacol 2020; 891:173735. [PMID: 33220271 DOI: 10.1016/j.ejphar.2020.173735] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 12/20/2022]
Abstract
The rhizome of the plant Atractylodes macrocephala Koidz is the major constituent of the Traditional Chinese Medicine Baizhu, frequently used to treat gastro-intestinal diseases. Many traditional medicine prescriptions based on Baizhu and the similar preparation Cangzhu are used in China, Korea and Japan as Qi-booster. These preparations contain atractylenolides, a small group of sesquiterpenoids endowed with antioxidant and anti-inflammatory properties. Atractylenolides I, II and III also display significant anticancer properties, reviewed here. The capacity of AT-I/II/IIII to inhibit cell proliferation and to induce cancer cell death have been analyzed, together with their effects of angiogenesis, metastasis, cell differentiation and stemness. The immune-modulatory properties of ATs are discussed. AT-I has been tested clinically for the treatment of cancer-induced cachexia with encouraging results. ATs, alone or combined with cytotoxic drugs, could be useful to treat cancers or to reduce side effects of radio and chemotherapy. Several signaling pathways have been implicated in their multi-targeted mechanisms of action, in particular those involving the central regulators TLR4, NFκB and Nrf2. A drug-induced reduction of inflammatory cytokines production (TNFα, IL-6) also characterizes these molecules which are generally weakly cytotoxic and well tolerated in vivo. Inhibition of Janus kinases (notably JAK2 and JAK3 targeted by AT-I and AT-III, respectively) has been postulated. Information about their metabolism and toxicity are limited but the long-established traditional use of the Atractylodes and the diversity of anticancer effects reported with AT-I and AT-III should encourage further studies with these molecules and structurally related natural products.
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Ghode A, Gross LZF, Tee WV, Guarnera E, Berezovsky IN, Biondi RM, Anand GS. Synergistic Allostery in Multiligand-Protein Interactions. Biophys J 2020; 119:1833-1848. [PMID: 33086047 PMCID: PMC7677135 DOI: 10.1016/j.bpj.2020.09.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/31/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023] Open
Abstract
Amide hydrogen-deuterium exchange mass spectrometry is powerful for describing combinatorial coupling effects of a cooperative ligand pair binding at noncontiguous sites: adenosine at the ATP-pocket and a docking peptide (PIFtide) at the PIF-pocket, on a model protein kinase PDK1. Binding of two ligands to PDK1 reveal multiple hotspots of synergistic allostery with cumulative effects greater than the sum of individual effects mediated by each ligand. We quantified this synergism and ranked these hotspots using a difference in deuteration-based approach, which showed that the strongest synergistic effects were observed at three of the critical catalytic loci of kinases: the αB-αC helices, and HRD-motif loop, and DFG-motif. Additionally, we observed weaker synergistic effects at a distal GHI-subdomain locus. Synergistic changes in deuterium exchange observed at a distal site but not at the intermediate sites of the large lobe of the kinase reveals allosteric propagation in proteins to operate through two modes. Direct electrostatic interactions between polar and charged amino acids that mediate targeted relay of allosteric signals, and diffused relay of allosteric signals through soft matter-like hydrophobic core amino acids. Furthermore, we provide evidence that the conserved β-3 strand lysine of protein kinases (Lys111 of PDK1) functions as an integrator node to coordinate allosteric coupling of the two ligand-binding sites. It maintains indirect interactions with the ATP-pocket and mediates a critical salt bridge with a glutamate (Glu130) of αC helix, which is conserved across all kinases. In summary, allosteric propagation in cooperative, dual-liganded enzyme targets is bidirectional and synergistic and offers a strategy for combinatorial drug development.
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Affiliation(s)
- Abhijeet Ghode
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Lissy Z F Gross
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Wei-Ven Tee
- Department of Biological Sciences, National University of Singapore, Singapore; Bioinformatics Institute, Agency for Science, Technology and Research, Matrix, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute, Agency for Science, Technology and Research, Matrix, Singapore
| | - Igor N Berezovsky
- Department of Biological Sciences, National University of Singapore, Singapore; Bioinformatics Institute, Agency for Science, Technology and Research, Matrix, Singapore
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore.
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Zhang M, Jang H, Nussinov R. PI3K inhibitors: review and new strategies. Chem Sci 2020; 11:5855-5865. [PMID: 32953006 PMCID: PMC7472334 DOI: 10.1039/d0sc01676d] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
The search is on for effective specific inhibitors for PI3Kα mutants. PI3Kα, a critical lipid kinase, has two subunits, catalytic and inhibitory. PIK3CA, the gene that encodes the p110α catalytic subunit is a highly mutated protein in cancer. Dysregulation of PI3Kα signalling is commonly associated with tumorigenesis and drug resistance. Despite its vast importance, only recently the FDA approved the first drug (alpelisib by Novartis) for breast cancer. A second (GDC0077), classified as PI3Kα isoform-specific, is undergoing clinical trials. Not surprisingly, these ATP-competitive drugs commonly elicit severe concentration-dependent side effects. Here we briefly review PI3Kα mutations, focus on PI3K drug repertoire and propose new, to-date unexplored PI3Kα therapeutic strategies. These include (1) an allosteric and orthosteric inhibitor combination and (2) taking advantage of allosteric rescue mutations to guide drug discovery.
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Affiliation(s)
- Mingzhen Zhang
- Computational Structural Biology Section , Frederick National Laboratory for Cancer Research , National Cancer Institute at Frederick , Frederick , MD 21702 , USA . ; Tel: +1-301-846-5579
| | - Hyunbum Jang
- Computational Structural Biology Section , Frederick National Laboratory for Cancer Research , National Cancer Institute at Frederick , Frederick , MD 21702 , USA . ; Tel: +1-301-846-5579
| | - Ruth Nussinov
- Computational Structural Biology Section , Frederick National Laboratory for Cancer Research , National Cancer Institute at Frederick , Frederick , MD 21702 , USA . ; Tel: +1-301-846-5579
- Department of Human Molecular Genetics and Biochemistry , Sackler School of Medicine , Tel Aviv University , Tel Aviv 69978 , Israel
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