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Messing S, Widmeyer SRT, Denson JP, Mehalko J, Wall VE, Drew M, Snead K, Hong M, Grose C, Esposito D, Gillette W. Improved production of class I phosphatidylinositol 4,5-bisphosphate 3-kinase. Protein Expr Purif 2025; 225:106582. [PMID: 39173964 DOI: 10.1016/j.pep.2024.106582] [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: 07/02/2024] [Revised: 08/05/2024] [Accepted: 08/18/2024] [Indexed: 08/24/2024]
Abstract
Phosphatidylinositol 4,5-bisphosphate 3-kinases (PI3K) are a family of kinases whose activity affects pathways needed for basic cell functions. As a result, PI3K is one of the most mutated genes in all human cancers and serves as an ideal therapeutic target for cancer treatment. Expanding on work done by other groups we improved protein yield to produce stable and pure protein using a variety of modifications including improved solubility tag, novel expression modalities, and optimized purification protocol and buffer. By these means, we achieved a 40-fold increase in yield for p110α/p85α and a 3-fold increase in p110α. We also used these protocols to produce comparable constructs of the β and δ isoforms of PI3K. Increased yield enhanced the efficiency of our downstream high throughput drug discovery efforts on the PIK3 family of kinases.
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Affiliation(s)
- Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
| | - Stephanie R T Widmeyer
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Vanessa E Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Min Hong
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Carissa Grose
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
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2
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Yuan F, Li T, Xu X, Chen T, Cao Z. Identification of Novel PI3Kα Inhibitor Against Gastric Cancer: QSAR-, Molecular Docking-, and Molecular Dynamics Simulation-Based Analysis. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04898-3. [PMID: 38507171 DOI: 10.1007/s12010-024-04898-3] [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] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Gastric cancer (GC) is a malignant tumor with global incidence and death ranking fifth and fourth, respectively. GC patients nevertheless have a poor prognosis despite the effectiveness of more advanced chemotherapy and surgical treatment options. The second most frequently mutated gene in GC is PI3Kalpha, a confirmed oncogene that results in abnormal PI3K/AKT/mTOR signaling, causing enhanced translation, proliferation, and survival, and is mutated in 7-25% of GC patients. The protein PI3Kalpha was targeted in the present study by utilizing machine learning (ML), molecular docking, and simulation. A total of 9214 molecules from the DrugBank database were chosen for the first screening. A training set for 6770 compounds tested against PI3Kalpha was assessed to create a quantitative structure-activity relationship-based machine learning model using five different classification algorithms: random forest, random tree, J48 pruned tree, decision stump, and REPTree. Furthermore, consideration was given to the random forest classifier for screening based on its performance index (Kappa statistics, ROC, and MCC). Overall, 1539 of the 9214 drug bank compounds were predicted to be active. Thereafter, three pharmacological filters, Lipinski's rule, Ghose filter, and Veber rule, were applied to test the drug-like properties of the screened compounds. Twenty-six of 1593 compounds showed excellent drug-like properties and were further considered for molecular docking. Thereafter, two compounds were screened as hits because they possessed the molecular docked position with the lowest binding energy and an excellent bonding profile. The binding stability of the selected compounds was further assessed through molecular dynamics simulations for up to 100 ns. Furthermore, compound 1-(3-(2,4-dimethylthiazol-5-YL)-4-oxo-2,4-dihydroindeno[1,2-C]pyrazol-5-YL)-3-(4-methylpiperazin-1-YL) urea was selected as a potential hit in the final screening by analyzing a number of parameters, including the Rg, RMSD, RMSF, H bonding, and SASA profile. Therefore, we conclude that compound 1-(3-(2, 4-dimethylthiazol-5-YL)-4-oxo-2,4-dihydroindeno[1,2-C]pyrazol-5-YL)-3-(4-methylpiperazin-1-YL) urea has efficient inhibitory potential against PI3Kalpha protein and could be utilized for the development of effective drugs against GC.
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Affiliation(s)
- Fang Yuan
- First Clinical College of Shandong, University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Lixia District, Jinan City, 250014, Shandong Province, China
- The First Department of Digestion, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42 Wenhuaxi Road, Jinan City, 250011, Shandong Province, China
| | - Ting Li
- Department of the Cancer Center, Shandong Provincial Third Hospital, Shandong University, No. 11, Wuyingshan Road, Jinan City, 250000, Shandong Province, China
| | - Xinjie Xu
- TCM Department, Second Affiliated Hospital of Shandong First Medical University, No. 366 Taishan Street, Taian, 271000, China
| | - Ting Chen
- First Clinical College of Shandong, University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Lixia District, Jinan City, 250014, Shandong Province, China
- The First Department of Digestion, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42 Wenhuaxi Road, Jinan City, 250011, Shandong Province, China
| | - Zhiqun Cao
- First Clinical College of Shandong, University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Lixia District, Jinan City, 250014, Shandong Province, China.
- The First Department of Digestion, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42 Wenhuaxi Road, Jinan City, 250011, Shandong Province, China.
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Jani V, Sonavane U, Sawant S. Structural insights into the activation mechanism of phosphoinositide 3-kinase alpha. Comput Biol Chem 2024; 108:107994. [PMID: 38043374 DOI: 10.1016/j.compbiolchem.2023.107994] [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: 06/28/2023] [Revised: 11/22/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
Phosphoinositide 3-kinases (PI3Ks) are lipid kinases known to regulate important cellular functions by phosphorylating the inositol ring of inositol-phospholipids (PtdIns) at 3' position. The PI3Kα is a heterodimer and the activation of the catalytic subunit (p110α) is regulated by its regulatory subunit (p85α). The current work deals with studying the activation mechanism of the PI3Kα using multi micro-second molecular dynamic simulations. Structural changes involved in activation mechanism is studied by gradually releasing the inhibitory effects of different domains of regulatory subunit namely, n-terminal SH2 (nSH2) and inter SH2 (iSH2). The observation shows that even in the presence of n-terminal and inter SH2 domain (niSH2) of regulatory subunit, the catalytic domain has some intrinsic activation activity and the presence of c-terminal SH2 (cSH2) domain may be required for complete inhibition. The release of nSH2 domain leads to loss of interactions between iSH2 domain (regulatory subunit) and C2 and kinase domain (catalytic subunit). The study shows that early events in the activation mechanism involve the movement of the ABD domain of the catalytic subunit along with the linker region between ABD and RBD region which may lead to movement of ABD closer to the CLobe of the kinase domain. This movement is essentially as it triggers the rearrangement of CLobe especially the catalytic loop and activation loop which bring catalytic important residues closer to ATP and PIP2(phosphatidylinositol-4,5-bisphosphate). Water mediated interaction analysis reveal that water may be playing an important role in the transfer of phosphate from ATP to PIP2. The study shows that initial signal for release of inhibitory effect of the regulatory subunit might be propagated through the linker region between ABD and RBD through allosteric effect to different regions of the protein. These understanding of early events during the activation mechanism may help in the design of better therapeutic targeting PI3K.
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Affiliation(s)
- Vinod Jani
- HPC-M&BA group, Centre for Development of Advanced computing, Pune 411008, India; Bioinformatics centre, SSP University, Pune 411007, India
| | - Uddhavesh Sonavane
- HPC-M&BA group, Centre for Development of Advanced computing, Pune 411008, India.
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Zhao S, Liu H, Wang H, He X, Tang J, Qi S, Yang R, Xie J. Inhibition of phosphatidylinositol 3-kinase catalytic subunit alpha by miR-203a-3p reduces hypertrophic scar formation via phosphatidylinositol 3-kinase/AKT/mTOR signaling pathway. BURNS & TRAUMA 2024; 12:tkad048. [PMID: 38179473 PMCID: PMC10762504 DOI: 10.1093/burnst/tkad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/24/2023] [Accepted: 09/12/2023] [Indexed: 01/06/2024]
Abstract
Background Hypertrophic scar (HS) is a common fibroproliferative skin disease that currently has no truly effective therapy. Given the importance of phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) in hypertrophic scar formation, the development of therapeutic strategies for endogenous inhibitors against PIK3CA is of great interest. Here, we explored the molecular mechanisms underlying the protective effects of miR-203a-3p (PIK3CA inhibitor) against excessive scar. Methods Bioinformatic analysis, immunohistochemistry, immunofluorescence, miRNA screening and fluorescence in situ hybridization assays were used to identify the possible pathways and target molecules mediating HS formation. A series of in vitro and in vivo experiments were used to clarify the role of PIK3CA and miR-203a-3p in HS. Mechanistically, transcriptomic sequencing, immunoblotting, dual-luciferase assay and rescue experiments were executed. Results Herein, we found that PIK3CA and the phosphatidylinositol 3-kinase (PI3K)/AKT/mTOR pathway were upregulated in scar tissues and positively correlated with fibrosis. We then identified miR-203a-3p as the most suitable endogenous inhibitor of PIK3CA. miR-203a-3p suppressed the proliferation, migration, collagen synthesis and contractility as well as the transdifferentiation of fibroblasts into myofibroblasts in vitro, and improved the morphology and histology of scars in vivo. Mechanistically, miR-203a-3p attenuated fibrosis by inactivating the PI3K/AKT/mTOR pathway by directly targeting PIK3CA. Conclusions PIK3CA and the PI3K/AKT/mTOR pathway are actively involved in scar fibrosis and miR-203a-3p might serve as a potential strategy for hypertrophic scar therapy through targeting PIK3CA and inactivating the PI3K/AKT/mTOR pathway.
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Affiliation(s)
- Shixin Zhao
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
- Guangdong Provincial Engineering Technology Research Center of Burn and Wound Accurate Diagnosis and Treatment Key Technology and Series of Products, Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
| | - Hengdeng Liu
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
- Guangdong Provincial Engineering Technology Research Center of Burn and Wound Accurate Diagnosis and Treatment Key Technology and Series of Products, Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
| | - Hanwen Wang
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
- Guangdong Provincial Engineering Technology Research Center of Burn and Wound Accurate Diagnosis and Treatment Key Technology and Series of Products, Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
| | - Xuefeng He
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
- Guangdong Provincial Engineering Technology Research Center of Burn and Wound Accurate Diagnosis and Treatment Key Technology and Series of Products, Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
| | - Jinming Tang
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
- Guangdong Provincial Engineering Technology Research Center of Burn and Wound Accurate Diagnosis and Treatment Key Technology and Series of Products, Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
| | - Shaohai Qi
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
- Guangdong Provincial Engineering Technology Research Center of Burn and Wound Accurate Diagnosis and Treatment Key Technology and Series of Products, Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
| | - Ronghua Yang
- Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, South China University of technology, No. 1 Panfu Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
| | - Julin Xie
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
- Guangdong Provincial Engineering Technology Research Center of Burn and Wound Accurate Diagnosis and Treatment Key Technology and Series of Products, Sun Yat-Sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, Guangdong, 510062, China
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5
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Vogt PK, Hart JR, Yang S, Zhou Q, Yang D, Wang MW. Structural and mechanistic insights provided by single particle cryo-EM analysis of phosphoinositide 3-kinase (PI3Kα). Biochim Biophys Acta Rev Cancer 2023; 1878:188947. [PMID: 37394020 PMCID: PMC10530483 DOI: 10.1016/j.bbcan.2023.188947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
Recent cryo-electron microscopic (cryo-EM) investigations have succeeded in the analysis of various structural conformations and functional states of PI3Kα, a dimer consisting of the catalytic subunit p110α and the regulatory subunit p85α of class IA of phosphoinositide 3-kinase. High resolution structures have been obtained of the unliganded and of BYL-719-bound PI3Kα. The latter provides information on excessively flexible domains of p85α that are then further analyzed with nanobodies and CXMS (chemical cross-linking, digestion and mass spectrometry). Analysis of p110α helical and kinase domain mutations reveals mutant-specific features that can be linked to the gain of function in enzymatic and signaling activities.
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Affiliation(s)
- Peter K Vogt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States of America.
| | - Jonathan R Hart
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States of America
| | - Su Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States of America
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ming-Wei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Research Center for Deepsea Bioresources, Sanya 572025, China; Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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6
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Gong GQ, Bilanges B, Allsop B, Masson GR, Roberton V, Askwith T, Oxenford S, Madsen RR, Conduit SE, Bellini D, Fitzek M, Collier M, Najam O, He Z, Wahab B, McLaughlin SH, Chan AWE, Feierberg I, Madin A, Morelli D, Bhamra A, Vinciauskaite V, Anderson KE, Surinova S, Pinotsis N, Lopez-Guadamillas E, Wilcox M, Hooper A, Patel C, Whitehead MA, Bunney TD, Stephens LR, Hawkins PT, Katan M, Yellon DM, Davidson SM, Smith DM, Phillips JB, Angell R, Williams RL, Vanhaesebroeck B. A small-molecule PI3Kα activator for cardioprotection and neuroregeneration. Nature 2023; 618:159-168. [PMID: 37225977 PMCID: PMC7614683 DOI: 10.1038/s41586-023-05972-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/17/2023] [Indexed: 05/26/2023]
Abstract
Harnessing the potential beneficial effects of kinase signalling through the generation of direct kinase activators remains an underexplored area of drug development1-5. This also applies to the PI3K signalling pathway, which has been extensively targeted by inhibitors for conditions with PI3K overactivation, such as cancer and immune dysregulation. Here we report the discovery of UCL-TRO-1938 (referred to as 1938 hereon), a small-molecule activator of the PI3Kα isoform, a crucial effector of growth factor signalling. 1938 allosterically activates PI3Kα through a distinct mechanism by enhancing multiple steps of the PI3Kα catalytic cycle and causes both local and global conformational changes in the PI3Kα structure. This compound is selective for PI3Kα over other PI3K isoforms and multiple protein and lipid kinases. It transiently activates PI3K signalling in all rodent and human cells tested, resulting in cellular responses such as proliferation and neurite outgrowth. In rodent models, acute treatment with 1938 provides cardioprotection from ischaemia-reperfusion injury and, after local administration, enhances nerve regeneration following nerve crush. This study identifies a chemical tool to directly probe the PI3Kα signalling pathway and a new approach to modulate PI3K activity, widening the therapeutic potential of targeting these enzymes through short-term activation for tissue protection and regeneration. Our findings illustrate the potential of activating kinases for therapeutic benefit, a currently largely untapped area of drug development.
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Affiliation(s)
- Grace Q Gong
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Benoit Bilanges
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Ben Allsop
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Glenn R Masson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Victoria Roberton
- UCL Centre for Nerve Engineering, UCL School of Pharmacy, University College London, London, UK
| | - Trevor Askwith
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Sally Oxenford
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Ralitsa R Madsen
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Sarah E Conduit
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Dom Bellini
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martina Fitzek
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | - Matt Collier
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | - Osman Najam
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - Zhenhe He
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - Ben Wahab
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff, UK
| | | | - A W Edith Chan
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | | | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Daniele Morelli
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Amandeep Bhamra
- Proteomics Research Translational Technology Platform, Cancer Institute, University College London, London, UK
| | - Vanesa Vinciauskaite
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
| | | | - Silvia Surinova
- Proteomics Research Translational Technology Platform, Cancer Institute, University College London, London, UK
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | | | - Matthew Wilcox
- UCL Centre for Nerve Engineering, UCL School of Pharmacy, University College London, London, UK
| | - Alice Hooper
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Chandni Patel
- Drug Discovery Group, Translational Research Office, University College London, London, UK
| | - Maria A Whitehead
- Cell Signalling, Cancer Institute, University College London, London, UK
| | - Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | | | | | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Derek M Yellon
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - Sean M Davidson
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - David M Smith
- Emerging Innovations, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - James B Phillips
- UCL Centre for Nerve Engineering, UCL School of Pharmacy, University College London, London, UK
| | - Richard Angell
- Drug Discovery Group, Translational Research Office, University College London, London, UK
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff, UK
| | - Roger L Williams
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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7
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Hou X, Chen D, Wang Y, Cui B, Xu H, Wang Y, Chen H, Wang D, Chen Y, Cheng T, Dai X. Network analysis to explore the pharmacological mechanism of Shenmai injection in treating granulocytopenia and evidence-based medicine approach validation. Medicine (Baltimore) 2023; 102:e33825. [PMID: 37335746 DOI: 10.1097/md.0000000000033825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Shenmai injection is frequently utilized in China to clinically treat granulocytopenia in oncology patients following chemotherapy. Despite this, the drug's therapeutic benefits remain a topic of contention, and its active components and potential treatment targets have yet to be established. The present study utilizes a network pharmacology approach to investigate the drug's active ingredients and possible therapeutic targets, and to evaluate the effectiveness of Shenmai injection in treating granulocytopenia through meta-analysis. METHODS In our subject paper, we utilized the TCMID database to investigate the active ingredients present in red ginseng and ophiopogon japonicus. To further identify molecular targets, we employed SuperPred, as well as OMIM, Genecards, and DisGeNET databases. Our focus was on targets associated with granulocytopenia. The DAVID 6.8 database was utilized to perform gene ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Additionally, a protein-protein interaction network was established. The resulting "drug-key component-potential target-core pathway" network was used to predict the mechanism of action of Shenmai injection in the treatment of granulocytopenia. In order to evaluate the quality of the studies included in our analysis, we utilized the Cochrane Reviewers' Handbook. We then conducted a meta-analysis of the clinical curative effect of Shenmai injection for granulocytopenia, utilizing the Cochrane Collaboration's RevMan 5.3 software. RESULTS After conducting a thorough screening, the study identified 5 primary ingredients of Shenmai injection - ophiopogonoside a, β-patchoulene, ginsenoside rf, ginsenoside re, and ginsenoside rg1-that can potentially target 5 essential proteins: STAT3, TLR4, PIK3CA, PIK3R1, and GRB2. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that Shenmai injection can be beneficial in treating granulocytopenia by interacting with pathways such as HIF-1 signaling, T-cell receptor signaling, PI3K-Akt signaling, chemokine signaling, and FoxO signaling. The results of meta-analysis indicate that the treatment group exhibited superior performance in terms of both efficiency and post-treatment leukocyte count when compared to the control group. CONCLUSION In summary, studies in network pharmacology demonstrate that Shenmai injection exerts an impact on granulocytopenia via various components, targets, and mechanisms. Additionally, evidence-based studies provide strong support for the effectiveness of Shenmai injection in preventing and treating granulocytopenia.
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Affiliation(s)
- Xianbing Hou
- Department of Oncology, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Dandan Chen
- Department of Rehabilitation, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Yao Wang
- Department of Oncology, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Bixian Cui
- Department of Oncology, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Hui Xu
- Department of Oncology, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Yuanyuan Wang
- Department of Oncology, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Hongzhou Chen
- Department of Oncology, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Dan Wang
- Department of Nursing, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Ying Chen
- Department of Nursing, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Tongfei Cheng
- Department of Nursing, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
| | - Xiaojun Dai
- Department of Nursing, Fenghua Hospital of Traditional Chinese Medicine, Ningbo, China
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8
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Kotzampasi DM, Premeti K, Papafotika A, Syropoulou V, Christoforidis S, Cournia Z, Leondaritis G. The orchestrated signaling by PI3Kα and PTEN at the membrane interface. Comput Struct Biotechnol J 2022; 20:5607-5621. [PMID: 36284707 PMCID: PMC9578963 DOI: 10.1016/j.csbj.2022.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
The oncogene PI3Kα and the tumor suppressor PTEN represent two antagonistic enzymatic activities that regulate the interconversion of the phosphoinositide lipids PI(4,5)P2 and PI(3,4,5)P3 in membranes. As such, they are defining components of phosphoinositide-based cellular signaling and membrane trafficking pathways that regulate cell survival, growth, and proliferation, and are often deregulated in cancer. In this review, we highlight aspects of PI3Kα and PTEN interplay at the intersection of signaling and membrane trafficking. We also discuss the mechanisms of PI3Kα- and PTEN- membrane interaction and catalytic activation, which are fundamental for our understanding of the structural and allosteric implications on signaling at the membrane interface and may aid current efforts in pharmacological targeting of these proteins.
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Affiliation(s)
- Danai Maria Kotzampasi
- Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
- Department of Biology, University of Crete, Heraklion 71500, Greece
| | - Kyriaki Premeti
- Laboratory of Pharmacology, Faculty of Medicine, University of Ioannina, Ioannina 45110, Greece
| | - Alexandra Papafotika
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece
- Biomedical Research Institute, Foundation for Research and Technology, Ioannina 45110, Greece
| | - Vasiliki Syropoulou
- Laboratory of Pharmacology, Faculty of Medicine, University of Ioannina, Ioannina 45110, Greece
| | - Savvas Christoforidis
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece
- Biomedical Research Institute, Foundation for Research and Technology, Ioannina 45110, Greece
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
| | - George Leondaritis
- Laboratory of Pharmacology, Faculty of Medicine, University of Ioannina, Ioannina 45110, Greece
- Institute of Biosciences, University Research Center of Ioannina, Ioannina 45110, Greece
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9
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Vique‐Sánchez JL, Benítez‐Cardoza CG. A Potential PIK3CA Inhibitor to Develop an Anticancer Drug. ChemistrySelect 2022. [DOI: 10.1002/slct.202202301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Vasan N, Cantley LC. At a crossroads: how to translate the roles of PI3K in oncogenic and metabolic signalling into improvements in cancer therapy. Nat Rev Clin Oncol 2022; 19:471-485. [PMID: 35484287 PMCID: PMC11215755 DOI: 10.1038/s41571-022-00633-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2022] [Indexed: 12/14/2022]
Abstract
Numerous agents targeting various phosphatidylinositol 3-kinase (PI3K) pathway components, including PI3K, AKT and mTOR, have been tested in oncology clinical trials, resulting in regulatory approvals for the treatment of selected patients with breast cancer, certain other solid tumours or particular haematological malignancies. However, given the prominence of PI3K signalling in cancer and the crucial role of this pathway in linking cancer growth with metabolism, these clinical results could arguably be improved upon. In this Review, we discuss past and present efforts to overcome the somewhat limited clinical efficacy of PI3Kα pathway inhibitors, including optimization of inhibitor specificity, patient selection and biomarkers across cancer types, with a focus on breast cancer, as well as identification and abrogation of signalling-related and metabolic mechanisms of resistance, and interventions to improve management of prohibitive adverse events. We highlight the advantages and limitations of laboratory-based model systems used to study the PI3K pathway, and propose technologies and experimental inquiries to guide the future clinical deployment of PI3K pathway inhibitors in the treatment of cancer.
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Affiliation(s)
- Neil Vasan
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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11
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Jiang Y, Xie YZ, Peng CW, Yao KN, Lin XY, Zhan SF, Zhuang HF, Huang HT, Liu XH, Huang XF, Li H. Modeling Kaempferol as a Potential Pharmacological Agent for COVID-19/PF Co-Occurrence Based on Bioinformatics and System Pharmacological Tools. Front Pharmacol 2022; 13:865097. [PMID: 35754492 PMCID: PMC9214245 DOI: 10.3389/fphar.2022.865097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: People suffering from coronavirus disease 2019 (COVID-19) are prone to develop pulmonary fibrosis (PF), but there is currently no definitive treatment for COVID-19/PF co-occurrence. Kaempferol with promising antiviral and anti-fibrotic effects is expected to become a potential treatment for COVID-19 and PF comorbidities. Therefore, this study explored the targets and molecular mechanisms of kaempferol against COVID-19/PF co-occurrence by bioinformatics and network pharmacology. Methods: Various open-source databases and Venn Diagram tool were applied to confirm the targets of kaempferol against COVID-19/PF co-occurrence. Protein-protein interaction (PPI), MCODE, key transcription factors, tissue-specific enrichment, molecular docking, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to clarify the influential molecular mechanisms of kaempferol against COVID-19 and PF comorbidities. Results: 290 targets and 203 transcription factors of kaempferol against COVID-19/PF co-occurrence were captured. Epidermal growth factor receptor (EGFR), proto-oncogene tyrosine-protein kinase SRC (SRC), mitogen-activated protein kinase 3 (MAPK3), mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 8 (MAPK8), RAC-alpha serine/threonine-protein kinase (AKT1), transcription factor p65 (RELA) and phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (PIK3CA) were identified as the most critical targets, and kaempferol showed effective binding activities with the above critical eight targets. Further, anti-COVID-19/PF co-occurrence effects of kaempferol were associated with the regulation of inflammation, oxidative stress, immunity, virus infection, cell growth process and metabolism. EGFR, interleukin 17 (IL-17), tumor necrosis factor (TNF), hypoxia inducible factor 1 (HIF-1), phosphoinositide 3-kinase/AKT serine/threonine kinase (PI3K/AKT) and Toll-like receptor signaling pathways were identified as the key anti-COVID-19/PF co-occurrence pathways. Conclusion: Kaempferol is a candidate treatment for COVID-19/PF co-occurrence. The underlying mechanisms may be related to the regulation of critical targets (EGFR, SRC, MAPK3, MAPK1, MAPK8, AKT1, RELA, PIK3CA and so on) and EGFR, IL-17, TNF, HIF-1, PI3K/AKT and Toll-like receptor signaling pathways. This study contributes to guiding development of new drugs for COVID-19 and PF comorbidities.
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Affiliation(s)
- Yong Jiang
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Yi-Zi Xie
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chen-Wen Peng
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kai-Nan Yao
- Shenzhen Bao'an District Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xue-Ying Lin
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shao-Feng Zhan
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hong-Fa Zhuang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hui-Ting Huang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiao-Hong Liu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiu-Fang Huang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hang Li
- Shenzhen Bao'an District Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
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12
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Xu J, Jiang AM, Zhang C, Zheng Y, Zhang T, Zhou L. Potential of eight mutations for marker-assisted breeding in Chinese Lulai black pigs. CANADIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1139/cjas-2021-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular marker-assisted selection (MAS) provides an efficient tool for pig breeding. In this study, according to the literature, we selected eight effective or causal mutations from eight functional genes, including five causal mutations in PHKG1 (rs330928088), MUC13 (rs319699771), IGF2 (g.3072G>A), VRTN (g.20311_20312ins291) and MYH3 (XM_013981330.2:g.-1805_-1810del) genes, and three effective mutations in LIPE (rs328830166), LEPR (rs45435518) and MC4R (rs81219178) genes, to investigate the potential breeding effect of them in 418 Lulai pigs. The linear model was used to analyze the association between mutations and intramuscular fat (IMF) content, average backfat thickness (ABT) and muscle moisture percent (MMP). The results revealed that among the four effective mutations, only the mutation in the LEPR gene, which affect IMF deposition, was significantly associated with IMF content. However, the other molecular markers were not significantly associated with the affected traits reported in previous studies, and these mutations are ineffective for MAS in the Lulai black pig population. Therefore, causal mutations in PHKG1, IGF2 and VRTN genes, and an effective mutation in LEPR gene could be used as effective breeding makers for MAS in Lulai pigs. These results can provide helpful information for further breeding in Lulai black pigs.
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Affiliation(s)
- Jing Xu
- Qingdao Agricultural University, 98431, Qingdao, China, 266109
| | - Ai mei Jiang
- Jiaozhou City Bureau of Agriculture and Rural Affairs, Qingdao, China
| | | | | | - Tingrong Zhang
- Qingdao Agricultural University, 98431, Qingdao, China, 266109
| | - Lisheng Zhou
- Qingdao Agricultural University, 98431, Qingdao, China, 266109
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13
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Maliszewski D, Drozdowska D. Recent Advances in the Biological Activity of s-Triazine Core Compounds. Pharmaceuticals (Basel) 2022; 15:221. [PMID: 35215333 PMCID: PMC8875733 DOI: 10.3390/ph15020221] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022] Open
Abstract
An effective strategy for successful chemotherapy relies on creating compounds with high selectivity against cancer cells compared to normal cells and relatively low cytotoxicity. One such approach is the discovery of critical points in cancer cells, i.e., where specific enzymes that are potential therapeutic targets are generated. Triazine is a six-membered heterocyclic ring compound with three nitrogen replacing carbon-hydrogen units in the benzene ring structure. The subject of this review is the symmetrical 1,3,5-triazine, known as s-triazine. 1,3,5-triazine is one of the oldest heterocyclic compounds available. Because of its low cost and high availability, it has attracted researcher attention for novel synthesis. s-Triazine has a weak base, it has much weaker resonance energy than benzene, therefore, nucleophilic substitution is preferred to electrophilic substitution. Heterocyclic bearing a symmetrical s-triazine core represents an interesting class of compounds possessing a wide spectrum of biological properties such as anti-cancer, antiviral, fungicidal, insecticidal, bactericidal, herbicidal and antimicrobial, antimalarial agents. They also have applications as dyes, lubricants, and analytical reagents. Hence, the group of 1,3,5-triazine derivatives has developed over the years. Triazine is not only the core amongst them, but is also a factor increasing the kinetic potential of the entire derivatives. Modifying the structure and introducing new substituents makes it possible to obtain compounds with broad inhibitory activity on processes such as proliferation. In some cases, s-triazine derivatives induce cell apoptosis. In this review we will present currently investigated 1,3,5-triazine derivatives with anti-cancer activities, with particular emphasis on their inhibition of enzymes involved in the process of tumorigenesis.
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Affiliation(s)
- Dawid Maliszewski
- Department of Organic Chemistry, Medical University of Bialystok, 15-222 Białystok, Poland
| | - Danuta Drozdowska
- Department of Organic Chemistry, Medical University of Bialystok, 15-222 Białystok, Poland
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14
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Class I PI3K Biology. Curr Top Microbiol Immunol 2022; 436:3-49. [DOI: 10.1007/978-3-031-06566-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Jin N, Keam B, Cho J, Lee MJ, Kim HR, Torosyan H, Jura N, Ng PK, Mills GB, Li H, Zeng Y, Barbash Z, Tarcic G, Kang H, Bauman JE, Kim MO, VanLandingham NK, Swaney DL, Krogan NJ, Johnson DE, Grandis JR. Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma. J Clin Invest 2021; 131:e150335. [PMID: 34779417 PMCID: PMC8592538 DOI: 10.1172/jci150335] [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: 04/07/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022] Open
Abstract
Alpelisib selectively inhibits the p110α catalytic subunit of PI3Kα and is approved for treatment of breast cancers harboring canonical PIK3CA mutations. In head and neck squamous cell carcinoma (HNSCC), 63% of PIK3CA mutations occur at canonical hotspots. The oncogenic role of the remaining 37% of PIK3CA noncanonical mutations is incompletely understood. We report a patient with HNSCC with a noncanonical PIK3CA mutation (Q75E) who exhibited a durable (12 months) response to alpelisib in a phase II clinical trial. Characterization of all 32 noncanonical PIK3CA mutations found in HNSCC using several functional and phenotypic assays revealed that the majority (69%) were activating, including Q75E. The oncogenic impact of these mutations was validated in 4 cellular models, demonstrating that their activity was lineage independent. Further, alpelisib exhibited antitumor effects in a xenograft derived from a patient with HNSCC containing an activating noncanonical PIK3CA mutation. Structural analyses revealed plausible mechanisms for the functional phenotypes of the majority of the noncanonical PIK3CA mutations. Collectively, these findings highlight the importance of characterizing the function of noncanonical PIK3CA mutations and suggest that patients with HNSCC whose tumors harbor activating noncanonical PIK3CA mutations may benefit from treatment with PI3Kα inhibitors.
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Affiliation(s)
- Nan Jin
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Bhumsuk Keam
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Janice Cho
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Michelle J. Lee
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Yonsei Cancer Center, Seoul, South Korea
| | | | - Natalia Jura
- Cardiovascular Research Institute and
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - Patrick K.S. Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Gordon B. Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Hua Li
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Yan Zeng
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | | | | | - Hyunseok Kang
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Julie E. Bauman
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Mi-Ok Kim
- Department of Epidemiology and Biostatistics and
| | - Nathan K. VanLandingham
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Danielle L. Swaney
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Daniel E. Johnson
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Jennifer R. Grandis
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
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16
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Roskoski R. Properties of FDA-approved small molecule phosphatidylinositol 3-kinase inhibitors prescribed for the treatment of malignancies. Pharmacol Res 2021; 168:105579. [PMID: 33774181 DOI: 10.1016/j.phrs.2021.105579] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
The discovery of the phosphatidylinositol 3-kinase (PI 3-kinase) pathway was a major advance in understanding eukaryotic signal transduction. The high frequency of PI 3-kinase pathway mutations in many cancers stimulated the development of drugs targeting these oncogenic mutants. The PI 3-kinases are divided into three classes and Class I PI 3-kinases, which catalyze the phosphorylation of phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2) to generate phosphatidylinositol-3,4,5-trisphosphate (PIP3), are the main subject of this review. The class I PI 3-kinases are made up of p110α, p110β, p110δ, and p110γ catalytic subunits. These catalytic subunits are constitutively bound to regulatory subunits (p85α, p85β, p55γ, p101, and p87 proteins). The p85/p55 regulatory subunits heterodimerize with p110α or p110δ thereby forming complexes that are regulated chiefly by receptor protein-tyrosine kinases. The p101 and p87 subunits heterodimerize with p110γ to form complexes that are regulated mainly by G protein-coupled receptors (GPCRs). Complexes containing the p110β subunit are activated by receptor protein-tyrosine kinases as well as GPCRs. Following the generation of PIP3, the AKT and mTOR protein-serine/threonine kinases are activated leading to cell growth, proliferation, and survival. Like protein kinases, the PI 3-kinase domains consist of a bilobed structure connected by a hinge-linker segment. ATP and most PI 3-kinase and protein kinase inhibitors form hydrogen bonds with hinge residues. The small and large lobes of PI 3-kinases and protein kinases have a very similar three-dimensional structure called the protein kinase fold. Both PI 3-kinases and eukaryotic protein kinases possess an activation segment that begins with a DFG triad (Asp-Phe-Gly); the activation segment of protein kinases usually ends with an APE (Ala-Pro-Glu) signature while that of PI 3-kinases ends with a PFxLT (Pro-Phe-Xxx-Leu-Thr) signature. Dormant PI 3-kinases have a collapsed activation loop and active PI 3-kinases have an extended activation loop. The distance between the α-carbon atom of the DFG-D residue at the beginning of the activation loop and that of the PFxLT-F residue at the end of the activation loop in dormant PI 3-kinases is about 13 Å; this distance in active PI 3-kinases is about 18 Å. The protein kinase catalytic loop has an HRD (His-Arg-Asp) signature while that of the PI 3-kinases reverses the order with a DRH triad. Alpelisib is an orally effective FDA-approved PI 3-kinase-α inhibitor used for the treatment of breast cancer. Copanlisib, duvelisib, idelalisib, and umbralisib are PI 3-kinase-δ inhibitors that are approved for the third-line treatment of follicular lymphomas and other hematological disorders. Copanlisib is also a potent inhibitor of PI 3-kinase-α. Of the five approved drugs, all are orally bioavailable except copanlisib. Idelalisib interacts with the active conformation of PI 3-kinase-δ and is classified as a type I inhibitor. Alpelisib and copanlisib interact with inactive PI 3-kinase-α and PI 3-kinase-γ, respectively, and are classified as a type I½ antagonists. Except for umbralisib with a molecular weight of 571.5, all five drugs conform to the Lipinski rule of five for oral effectiveness. Copanlisib, however, must be given intravenously. Alpelisib and copanlisib inhibit PI 3-kinase-α, which is involved in insulin signaling, and both drugs promote insulin-resistance and produce hyperglycemia. The five FDA-approved PI 3-kinase inhibitors produce significant on-target toxicities, more so than many approved protein kinase antagonists. The development of PI 3-kinase inhibitors with fewer toxicities is an important long-term therapeutic goal.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742-8814, United States.
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17
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Erguven M, Karakulak T, Diril MK, Karaca E. How Far Are We from the Rapid Prediction of Drug Resistance Arising Due to Kinase Mutations? ACS OMEGA 2021; 6:1254-1265. [PMID: 33490784 PMCID: PMC7818309 DOI: 10.1021/acsomega.0c04672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
In all living organisms, protein kinases regulate various cell signaling events through phosphorylation. The phosphorylation occurs upon transferring an ATP's terminal phosphate to a target residue. Because of the central role of protein kinases in several proliferative pathways, point mutations occurring within the kinase's ATP-binding site can lead to a constitutively active enzyme, and ultimately, to cancer. A select set of these point mutations can also make the enzyme drug resistant toward the available kinase inhibitors. Because of technical and economical limitations, rapid experimental exploration of the impact of these mutations remains to be a challenge. This underscores the importance of kinase-ligand binding affinity prediction tools that are poised to measure the efficacy of inhibitors in the presence of kinase mutations. To this end, here, we compare the performances of six web-based scoring tools (DSX-ONLINE, KDEEP, HADDOCK2.2, PDBePISA, Pose&Rank, and PRODIGY-LIG) in assessing the impact of kinase mutations on their interactions with their inhibitors. This assessment is carried out on a new structure-based BINDKIN benchmark we compiled. BINDKIN contains wild-type and mutant structure pairs of kinase-inhibitor complexes, together with their corresponding experimental binding affinities (in the form of IC50, K d, and K i). The performance of various web servers over BINDKIN shows that they cannot predict the binding affinities (ΔGs) of wild-type and mutant cases directly. Still, they could catch whether a mutation improves or worsens the ligand binding (ΔΔGs) where the highest Pearson's R correlation coefficient is reached by DSX-ONLINE over the K i dataset. When homology models are used instead of K i-associated crystal structures, DSX-ONLINE loses its predictive capacity. These results highlight that there is room to improve the available scoring functions to estimate the impact of protein kinase point mutations on inhibitor binding. The BINDKIN benchmark with all related results is freely accessible online (https://github.com/CSB-KaracaLab/BINDKIN).
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Affiliation(s)
- Mehmet Erguven
- Izmir
Biomedicine and Genome Center, 35330 Izmir, Turkey
- Izmir
International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Tülay Karakulak
- Izmir
Biomedicine and Genome Center, 35330 Izmir, Turkey
- Izmir
International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - M. Kasim Diril
- Izmir
Biomedicine and Genome Center, 35330 Izmir, Turkey
- Izmir
International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Ezgi Karaca
- Izmir
Biomedicine and Genome Center, 35330 Izmir, Turkey
- Izmir
International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
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18
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Sahu MK, Kaushik K, Das A, Jha H. In vitro and in silico antioxidant and antiproliferative activity of rhizospheric fungus Talaromyces purpureogenus isolate-ABRF2. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00303-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractThe present study evaluated the potential biological activities of rhizospheric fungi isolated from the Achanakmar Biosphere Reserve, India. Fungus, Talaromyces purpureogenus isolate-ABRF2 from the soil of the Achanakmar biosphere was characterized by using morphological, biochemical and molecular techniques. Fungus was screened for the production of secondary metabolites using a specific medium. The metabolites were extracted using a suitable solvent and each fraction was subsequently evaluated for their antioxidant, antimicrobial, antiproliferative and anti-aging properties. The ethanolic extract depicted the highest antioxidant activity with 83%, 79%, 80% and 74% as assessed by ferric reducing power, 2,2-diphenyl 1-picrylhydrazyl, 2,2′-azino-bis3-ethylbenzthiazoline-6-sulfonic and phosphomolybdenum assays, respectively. Similarly, ethanolic extracts depicted marked antimicrobial activity as compared with standard antibiotics and antifungal agents as well as demonstrated significant antiproliferative property against a panel of mammalian cancer cell lines. Furthermore, different fractions of the purified ethanolic extract obtained using adsorption column chromatography were evaluated for antiproliferative property and identification of an active metabolite in the purified fraction using gas chromatography–mass spectroscopy and nuclear magnetic resonance techniques yielded 3-methyl-4-oxo-pentanoic acid. Thus, the present study suggests that the active metabolite 3-methyl-4-oxo-pentanoic acid extracted from Talaromyces purpureogenus isolate-ABRF2 has a potential antiproliferative, anti-aging, and antimicrobial therapeutic properties that will be further evaluated using in vivo studies in future.
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19
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Zhang M, Jang H, Nussinov R. Structural Features that Distinguish Inactive and Active PI3K Lipid Kinases. J Mol Biol 2020; 432:5849-5859. [PMID: 32918948 PMCID: PMC8916166 DOI: 10.1016/j.jmb.2020.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/10/2020] [Accepted: 09/02/2020] [Indexed: 12/25/2022]
Abstract
PI3K lipid kinases signal through the PI3K/Akt pathway, regulating cell growth and proliferation. While the structural features that distinguish between the active and inactive states of protein kinases are well established, that has not been the case for lipid kinases, and neither was the structural mechanism controlling the switch between the two states. Class I PI3Ks are obligate heterodimers with catalytic and regulatory subunits. Here, we analyze PI3K crystal structures. Structures with the nSH2 (inactive state) are featured by collapsed activation loop (a-loop) and an IN kinase domain helix 11 (kα11). In the active state, the a-loop is extended and kα11 in the OUT conformation. Our analysis suggests that the nSH2 domain in the regulatory subunit regulates activation, catalysis and autoinhibition through the a-loop. Inhibition, activation and catalytic scenarios are shared by class IA PI3Ks; the activation is mimicked by oncogenic mutations and the inhibition offers an allosteric inhibitor strategy.
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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
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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20
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Mansour MA, Lasheen DS, Gaber HM, Abouzid KAM. Elaborating piperazinyl-furopyrimidine based scaffolds as phosphoinositol-3-kinase enzyme alpha (PI3Kα) inhibitors to combat pancreatic cancer. RSC Adv 2020; 10:32103-32112. [PMID: 35518146 PMCID: PMC9056536 DOI: 10.1039/d0ra06428a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022] Open
Abstract
Phosphoinositol-3-kinase enzyme (PI3K) plays a crucial role in driving oncogenic growth in various mammalian cells, particularly pancreatic cells. In the current study a series of novel furo[2,3-d]pyrimidine based-compounds were designed and synthesized as potential PI3K-α inhibitors. In accordance to the structure–activity relationship (SAR) studies of known PI3K-α inhibitors, different linkers including amide, urea and ether were attached to a piperazinyl furo[2,3-d]pyrimidine core. The synthesized compounds that revealed moderate PI3K-α inhibitory activity were tested for their anti-proliferative activities against pancreatic carcinoma on the PANC-1 cell line. Compounds 7b and 8a showed the highest anti-proliferative activity with IC50 values of 4.5 μM and 6 μM, respectively and relatively, the best in vitro PI3K inhibition ability within the newly synthesized compounds. Additionally, all the newly synthesized final compounds were tested on 60 human cancer cell lines. A docking study was carried out on the PI3K-α active site showing a comparable binding mode to that of FDA approved PI3K-α inhibitors. These newly discovered lipid kinase inhibitors could be considered as potential candidates for the development of new targeted anticancer agents. Phosphoinositol-3-kinase alpha (PI3K-α) enzyme inhibition to combat pancreatic cancer.![]()
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Affiliation(s)
- Mai A Mansour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Badr University in Cairo Egypt
| | - Deena S Lasheen
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University Abbassia Cairo 11566 Egypt
| | - Hatem M Gaber
- National Organization for Drug Control and Research Egypt
| | - Khaled A M Abouzid
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University Abbassia Cairo 11566 Egypt .,Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City Sadat City Menoufia Egypt
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21
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Galdadas I, Gervasio FL, Cournia Z. Unravelling the effect of the E545K mutation on PI3Kα kinase. Chem Sci 2020; 11:3511-3515. [PMID: 34703536 PMCID: PMC8493679 DOI: 10.1039/c9sc05903b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
PI3Kα controls several cellular processes and its aberrant signalling is implicated in tumorigenesis. One of its hotspot mutations, E545K, increases PI3Kα lipid kinase activity, but its mode of action is only partially understood. Here, we perform biased and unbiased molecular dynamics simulations of PI3Kα and uncover, for the first time, the free energy landscape of the E545K PI3Kα mutant. We reveal the mechanism by which E545K leads to PI3Kα activation in atomic-level detail, which is considerably more complex than previously thought.
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Affiliation(s)
- Ioannis Galdadas
- Department of Chemistry, University College London London WC1E 6BT UK
| | - Francesco Luigi Gervasio
- Department of Chemistry, University College London London WC1E 6BT UK
- Institute of Structural and Molecular Biology, University College London London WC1E 6BT UK
- Pharmaceutical Sciences, University of Geneva Geneva CH-1211 Switzerland
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens Athens 11527 Greece
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22
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Allosteric Activation of PI3Kα Results in Dynamic Access to Catalytically Competent Conformations. Structure 2020; 28:465-474.e5. [PMID: 32049032 DOI: 10.1016/j.str.2020.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/21/2019] [Accepted: 01/16/2020] [Indexed: 11/30/2022]
Abstract
Class I phosphoinositide-3-kinases (PI3Ks) phosphorylate PIP2 at its 3' inositol position to generate PIP3, a second messenger that influences signaling cascades regulating cellular growth, survival, and proliferation. Previous studies have suggested that PI3Kα activation involves dislodging the p85α nSH2 domain from the p110α catalytic subunit by binding activated receptor tyrosine kinases. We carried out molecular dynamics simulations to determine, mechanistically and structurally, how PI3Kα conformations are influenced by physiological effectors and the nSH2 domain. We demonstrate that changes in protein dynamics mediated by allosteric regulation significantly increase the population of catalytically competent states without changing the enzyme ground-state structure. Furthermore, we demonstrate that modulation of active-site residue interactions with enzyme substrates can reciprocally influence nSH2 domain dynamics. Together, these results suggest that dynamic allostery plays a role in populating the catalytically competent conformation of PI3Kα, and provide a key platform for the design of novel chemotherapeutic PI3Kα inhibitors.
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23
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Vasan N, Razavi P, Johnson JL, Shao H, Shah H, Antoine A, Ladewig E, Gorelick A, Lin TY, Toska E, Xu G, Kazmi A, Chang MT, Taylor BS, Dickler MN, Jhaveri K, Chandarlapaty S, Rabadan R, Reznik E, Smith ML, Sebra R, Schimmoller F, Wilson TR, Friedman LS, Cantley LC, Scaltriti M, Baselga J. Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors. Science 2019; 366:714-723. [PMID: 31699932 PMCID: PMC7173400 DOI: 10.1126/science.aaw9032] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022]
Abstract
Activating mutations in PIK3CA are frequent in human breast cancer, and phosphoinositide 3-kinase alpha (PI3Kα) inhibitors have been approved for therapy. To characterize determinants of sensitivity to these agents, we analyzed PIK3CA-mutant cancer genomes and observed the presence of multiple PIK3CA mutations in 12 to 15% of breast cancers and other tumor types, most of which (95%) are double mutations. Double PIK3CA mutations are in cis on the same allele and result in increased PI3K activity, enhanced downstream signaling, increased cell proliferation, and tumor growth. The biochemical mechanisms of dual mutations include increased disruption of p110α binding to the inhibitory subunit p85α, which relieves its catalytic inhibition, and increased p110α membrane lipid binding. Double PIK3CA mutations predict increased sensitivity to PI3Kα inhibitors compared with single-hotspot mutations.
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Affiliation(s)
- Neil Vasan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Pedram Razavi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jared L Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hong Shao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alesia Antoine
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erik Ladewig
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Gorelick
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ting-Yu Lin
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Eneda Toska
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guotai Xu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abiha Kazmi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maura N Dickler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Eli Lilly and Company, Indianapolis, IN, USA
| | - Komal Jhaveri
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raul Rabadan
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | | | | | | | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - José Baselga
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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24
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Halder AK, Cordeiro MNDS. Development of Multi-Target Chemometric Models for the Inhibition of Class I PI3K Enzyme Isoforms: A Case Study Using QSAR-Co Tool. Int J Mol Sci 2019; 20:ijms20174191. [PMID: 31461863 PMCID: PMC6747073 DOI: 10.3390/ijms20174191] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 12/12/2022] Open
Abstract
The present work aims at establishing multi-target chemometric models using the recently launched quantitative structure–activity relationship (QSAR)-Co tool for predicting the activity of inhibitor compounds against different isoforms of phosphoinositide 3-kinase (PI3K) under various experimental conditions. The inhibitors of class I phosphoinositide 3-kinase (PI3K) isoforms have emerged as potential therapeutic agents for the treatment of various disorders, especially cancer. The cell-based enzyme inhibition assay results of PI3K inhibitors were curated from the CHEMBL database. Factors such as the nature and mutation of cell lines that may significantly alter the assay outcomes were considered as important experimental elements for mt-QSAR model development. The models, in turn, were developed using two machine learning techniques as implemented in QSAR-Co: linear discriminant analysis (LDA) and random forest (RF). Both techniques led to models with high accuracy (ca. 90%). Several molecular fragments were extracted from the current dataset, and their quantitative contributions to the inhibitory activity against all the proteins and experimental conditions under study were calculated. This case study also demonstrates the utility of QSAR-Co tool in solving multi-factorial and complex chemometric problems. Additionally, the combination of different in silico methods employed in this work can serve as a valuable guideline to speed up early discovery of PI3K inhibitors.
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Affiliation(s)
- Amit Kumar Halder
- Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal
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25
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Miller MS, Thompson PE, Gabelli SB. Structural Determinants of Isoform Selectivity in PI3K Inhibitors. Biomolecules 2019; 9:biom9030082. [PMID: 30813656 PMCID: PMC6468644 DOI: 10.3390/biom9030082] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 01/17/2023] Open
Abstract
Phosphatidylinositol 3-kinases (PI3Ks) are important therapeutic targets for the treatment of cancer, thrombosis, and inflammatory and immune diseases. The four highly homologous Class I isoforms, PI3K, PI3K, PI3K and PI3K have unique, non-redundant physiological roles and as such, isoform selectivity has been a key consideration driving inhibitor design and development. In this review, we discuss the structural biology of PI3Ks and how our growing knowledge of structure has influenced the medicinal chemistry of PI3K inhibitors. We present an analysis of the available structure-selectivity-activity relationship data to highlight key insights into how the various regions of the PI3K binding site influence isoform selectivity. The picture that emerges is one that is far from simple and emphasizes the complex nature of protein-inhibitor binding, involving protein flexibility, energetics, water networks and interactions with non-conserved residues.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia.
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Departments of Medicine, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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26
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Zhang M, Jang H, Nussinov R. The mechanism of PI3Kα activation at the atomic level. Chem Sci 2019; 10:3671-3680. [PMID: 30996962 PMCID: PMC6430085 DOI: 10.1039/c8sc04498h] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/19/2019] [Indexed: 12/19/2022] Open
Abstract
PI3K lipid kinases phosphorylate PIP2 to PIP3 in the PI3K/Akt/mTOR pathway to regulate cellular processes. They are frequently mutated in cancer. Here we determine the PI3Kα activation mechanism at the atomic level. Unlike protein kinases where the substrate abuts the ATP, crystal structures indicate that in PI3Kα, the distance between the γ phosphate of the ATP and the PIP2 lipid substrate is over 6 Å, much too far for the phosphoryl transfer, raising the question of how catalysis is executed. PI3Kα has two subunits, the catalytic p110α and the regulatory p85α. Our simulations show that release of the autoinhibition exerted by the nSH2 domain of the p85α triggers significant conformational change in p110α, leading to the exposure of the kinase domain for membrane interaction. Structural rearrangement in the C-lobe of the kinase domain reduces the distance between the ATP γ-phosphate and the substrate, offering an explanation as to how phosphoryl transfer is executed. An alternative mechanism may involve ATP relocation. This mechanism not only explains how oncogenic mutations promote PI3Kα activation by facilitating nSH2 release, or nSH2-release-induced, allosteric motions; it also offers an innovative, PI3K isoform-specific drug discovery principle. Rather than competing with nanomolar range ATP in the ATP-binding pocket and contending with ATP pocket conservation and massive binding targets, this mechanism suggests blocking the PI3Kα sequence-specific cavity between the ATP-binding pocket and the substrate binding site. Targeting isoform-specific residues in the cavity may prevent PIP2 phosphorylation.
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Affiliation(s)
- Mingzhen Zhang
- Computational Structural Biology Section , Basic Science Program , Frederick National Laboratory for Cancer Research , Frederick , MD 21702 , USA .
| | - Hyunbum Jang
- Computational Structural Biology Section , Basic Science Program , Frederick National Laboratory for Cancer Research , Frederick , MD 21702 , USA .
| | - Ruth Nussinov
- Computational Structural Biology Section , Basic Science Program , Frederick National Laboratory for Cancer Research , Frederick , MD 21702 , USA . .,Department of Human Molecular Genetics and Biochemistry , Sackler School of Medicine , Tel Aviv University , Tel Aviv 69978 , Israel
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27
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Irvine WA, Flanagan JU, Allison JR. Computational Prediction of Amino Acids Governing Protein-Membrane Interaction for the PIP3 Cell Signaling System. Structure 2019; 27:371-380.e3. [DOI: 10.1016/j.str.2018.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/13/2018] [Accepted: 10/18/2018] [Indexed: 10/27/2022]
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28
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Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II. Molecules 2019; 24:molecules24030496. [PMID: 30704096 PMCID: PMC6384729 DOI: 10.3390/molecules24030496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 11/17/2022] Open
Abstract
Advances in synchrotron technology are changing the landscape of macromolecular crystallography. The two recently opened beamlines at NSLS-II-AMX and FMX-deliver high-flux microfocus beams that open new possibilities for crystallographic data collection. They are equipped with state-of-the-art experimental stations and automation to allow data collection on previously intractable crystals. Optimized data collection strategies allow users to tailor crystal positioning to optimally distribute the X-ray dose over its volume. Vector data collection allows the user to define a linear trajectory along a well diffracting volume of the crystal and perform rotational data collection while moving along the vector. This is particularly well suited to long, thin crystals. We describe vector data collection of three proteins-Akt1, PI3Kα, and CDP-Chase-to demonstrate its application and utility. For smaller crystals, we describe two methods for multicrystal data collection in a single loop, either manually selecting multiple centers (using H108A-PHM as an example), or "raster-collect", a more automated approach for a larger number of crystals (using CDP-Chase as an example).
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29
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Abstract
Carbohydrate kinases activate a wide variety of monosaccharides by adding a phosphate group, usually from ATP. This modification is fundamental to saccharide utilization, and it is likely a very ancient reaction. Modern organisms contain carbohydrate kinases from at least five main protein families. These range from the highly specialized inositol kinases, to the ribokinases and galactokinases, which belong to families that phosphorylate a wide range of substrates. The carbohydrate kinases utilize a common strategy to drive the reaction between the sugar hydroxyl and the donor phosphate. Each sugar is held in position by a network of hydrogen bonds to the non-reactive hydroxyls (and other functional groups). The reactive hydroxyl is deprotonated, usually by an aspartic acid side chain acting as a catalytic base. The deprotonated hydroxyl then attacks the donor phosphate. The resulting pentacoordinate transition state is stabilized by an adjacent divalent cation, and sometimes by a positively charged protein side chain or the presence of an anion hole. Many carbohydrate kinases are allosterically regulated using a wide variety of strategies, due to their roles at critical control points in carbohydrate metabolism. The evolution of a similar mechanism in several folds highlights the elegance and simplicity of the catalytic scheme.
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30
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Shears SB, Wang H. Inositol phosphate kinases: Expanding the biological significance of the universal core of the protein kinase fold. Adv Biol Regul 2019; 71:118-127. [PMID: 30392847 PMCID: PMC9364425 DOI: 10.1016/j.jbior.2018.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 05/06/2023]
Abstract
The protein kinase family is characterized by substantial conservation of architectural elements that are required for both ATP binding and phosphotransferase activity. Many of these structural features have also been identified in homologous enzymes that phosphorylate a variety of alternative, non-protein substrates. A comparative structural analysis of these different kinase sub-classes is a portal to a greater understanding of reaction mechanisms, enzyme regulation, inhibitor-development strategies, and superfamily-level evolutionary relationships. To serve such advances, we review structural elements of the protein kinase fold that are conserved in the subfamily of inositol phosphate kinases (InsPKs) that share a PxxxDxKxG catalytic signature: inositol 1,4,5-trisphosphate kinase (IP3K), inositol hexakisphosphate kinase (IP6K), and inositol polyphosphate multikinase (IPMK). We describe conservation of the fundamental two-lobe kinase architecture: an N-lobe constructed upon an anti-parallel β-strand scaffold, which is coupled to a largely helical C-lobe by a single, adenine-binding hinge. This equivalency also includes a G-loop that embraces the β/γ-phosphates of ATP, a transition-state stabilizing residue (Lys/His), and a Mg-positioning aspartate residue within a catalytic triad. Furthermore, we expand this list of conserved structural features to include some not previously identified in InsPKs: a 'gatekeeper' residue in the N-lobe, and an 'αF'-like helix in the C-lobe that anchors two structurally-stabilizing, hydrophobic spines, formed from non-consecutive residues that span the two lobes. We describe how this wide-ranging structural homology can be exploited to develop lead inhibitors of IP6K and IPMK, by using strategies similar to those that have generated ATP-competing inhibitors of protein-kinases. We provide several examples to illustrate how such an approach could benefit human health.
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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31
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Ma Q, Gabelli SB, Raben DM. Diacylglycerol kinases: Relationship to other lipid kinases. Adv Biol Regul 2019; 71:104-110. [PMID: 30348515 PMCID: PMC6347529 DOI: 10.1016/j.jbior.2018.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 04/17/2023]
Abstract
Lipid kinases regulate a wide variety of cellular functions and have emerged as one the most promising targets for drug design. Diacylglycerol kinases (DGKs) are a family of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PtdOH). Despite the critical role in lipid biosynthesis, both DAG and PtdOH have been shown as bioactive lipids mediating a number of signaling pathways. Although there is increasing recognition of their role in signaling systems, our understanding of the key enzyme which regulate the balance of these two lipid messages remain limited. Solved structures provide a wealth of information for understanding the function and regulation of these enzymes. Solving the structures of mammalian DGKs by traditional NMR and X-ray crystallography approaches have been challenging and so far, there are still no three-dimensional structures of these DGKs. Despite this, some insights may be gained by examining the similarities and differences between prokaryotic DGKs and other mammalian lipid kinases. This review focuses on summarizing and comparing the structure of prokaryotic and mammalian DGKs as well as two other lipid kinases: sphingosine kinase and phosphatidylinositol-3-kinase. How these known lipid kinases structures relate to mammalian DGKs will also be discussed.
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Affiliation(s)
- Qianqian Ma
- The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Sandra B Gabelli
- The Department of Biophysics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel M Raben
- The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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32
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Hervieu A, Kermorgant S. The Role of PI3K in Met Driven Cancer: A Recap. Front Mol Biosci 2018; 5:86. [PMID: 30406111 PMCID: PMC6207648 DOI: 10.3389/fmolb.2018.00086] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/10/2018] [Indexed: 12/27/2022] Open
Abstract
The Receptor Tyrosine Kinase (RTK) Met, overexpressed or mutated in cancer, plays a major role in cancer progression and represents an attractive target for cancer therapy. However RTK inhibitors can lead to drug resistance, explaining the necessity to develop therapies that target downstream signaling. Phosphatidylinositide 3-kinase (PI3K) is one of the most deregulated pathways in cancer and implicated in various types of cancer. PI3K signaling is also a major signaling pathway downstream of RTK, including Met. PI3K major effectors include Akt and "mechanistic Target of Rapamycin" (mTOR), which each play key roles in numerous and various cell functions. Advancements made due to the development of molecular and pharmaceutical tools now allow us to delve into the roles of each independently. In this review, we summarize the current understanding we possess of the activation and role of PI3K/Akt/mTOR, downstream of Met, in cancer.
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Affiliation(s)
- Alexia Hervieu
- Signal Transduction and Molecular Pharmacology Team, Cancer Therapeutics Division, Institute of Cancer Research, Sutton, United Kingdom
- Spatial Signalling Team, Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Stéphanie Kermorgant
- Spatial Signalling Team, Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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