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Sambur E, Oktay L, Durdağı S. Covalent docking-driven virtual screening of extensive small-molecule libraries against Bruton tyrosine kinase for the identification of highly selective and potent novel therapeutic candidates. J Mol Graph Model 2024; 130:108762. [PMID: 38614067 DOI: 10.1016/j.jmgm.2024.108762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]
Abstract
Bruton tyrosine kinases (BTKs) play critical roles in various diseases, including chronic lymphatic leukemia (CLL), Waldenström Macroglobulinemia, Marginal Zone Lymphoma, Mantle Cell Lymphoma (MCL), and Graft Versus Host diseases. BTKs are a family of tyrosine kinases involved in B lymphocyte signal transduction, development, and maturation. Their overexpression can lead to cancer as they are essential for the activation of the B Cell Receptor (BCR) signaling pathway. Blocking the activation of BTKs presents a promising approach for treating CLL. This study was centered around the identification of small-molecule therapeutics that have an impact on human BTK. The covalently bound Ibrutinib molecule, recognized for its ability to inhibit BTK, was used as the query molecule. IUPAC text files containing molecular fragments of Ibrutinib were employed to virtually screen five different libraries comprising small-molecules, resulting in the screening of over 2.4 million synthesized compounds. Covalent docking simulations were applied to the selected small-molecules obtained through text mining from databases. Potent hit molecules capable of inhibiting BTKs through virtual screening algorithms were identified, paving the way for novel therapeutic strategies in the treatment of CLL.
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Affiliation(s)
- Ezgi Sambur
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey; Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HITMER), Bahçeşehir University, Istanbul, Turkey
| | - Lalehan Oktay
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey; Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HITMER), Bahçeşehir University, Istanbul, Turkey
| | - Serdar Durdağı
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey; Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HITMER), Bahçeşehir University, Istanbul, Turkey; Molecular Therapy Lab, Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul, Turkey.
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2
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McCone JAJ, Teesdale-Spittle PH, Flanagan JU, Harvey JE. A Structure-Activity Investigation of the Fungal Metabolite (-)-TAN-2483B: Inhibition of Bruton's Tyrosine Kinase. Chemistry 2024; 30:e202401051. [PMID: 38629656 DOI: 10.1002/chem.202401051] [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: 03/14/2024] [Indexed: 06/01/2024]
Abstract
The natural product (-)-TAN-2483B is a fungal secondary metabolite which displays promising anti-cancer and immunomodulatory activity. Our previous syntheses of (-)-TAN-2483B and sidechain analogues uncovered inhibitory activity against Bruton's tyrosine kinase (Btk), an established drug target for various leukaemia and immunological diseases. A structure-based computational study using ensemble docking and molecular dynamics was performed to determine plausible binding modes for (-)-TAN-2483B and analogues in the Btk binding site. These hypotheses guided the design of new analogues which were synthesised and their inhibitory activities determined, providing insights into the structural determinants of the furopyranone scaffold that confer both activity and selectivity for Btk. These findings offer new perspectives for generating optimised (-)-TAN-2483B-based kinase inhibitors for the treatment of leukaemia and immunological diseases.
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Affiliation(s)
- Jordan A J McCone
- School of Chemical and Physical Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Paul H Teesdale-Spittle
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- School of Biological Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Jack U Flanagan
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Joanne E Harvey
- School of Chemical and Physical Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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3
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Barragan AM, Ghaby K, Pond MP, Roux B. Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib. J Chem Inf Model 2024; 64:3488-3502. [PMID: 38546820 DOI: 10.1021/acs.jcim.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Covalent inhibitors represent a promising class of therapeutic compounds. Nonetheless, rationally designing covalent inhibitors to achieve a right balance between selectivity and reactivity remains extremely challenging. To better understand the covalent binding mechanism, a computational study is carried out using the irreversible covalent inhibitor of Bruton tyrosine kinase (BTK) ibrutinib as an example. A multi-μs classical molecular dynamics trajectory of the unlinked inhibitor is generated to explore the fluctuations of the compound associated with the kinase binding pocket. Then, the reaction pathway leading to the formation of the covalent bond with the cysteine residue at position 481 via a Michael addition is determined using the string method in collective variables on the basis of hybrid quantum mechanical-molecular mechanical (QM/MM) simulations. The reaction pathway shows a strong correlation between the covalent bond formation and the protonation/deprotonation events taking place sequentially in the covalent inhibition reaction, consistent with a 3-step reaction with transient thiolate and enolates intermediate states. Two possible atomistic mechanisms affecting deprotonation/protonation events from the thiolate to the enolate intermediate were observed: a highly correlated direct pathway involving proton transfer to the Cα of the acrylamide warhead from the cysteine involving one or a few water molecules and a more indirect pathway involving a long-lived enolate intermediate state following the escape of the proton to the bulk solution. The results are compared with experiments by simulating the long-time kinetics of the reaction using kinetic modeling.
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Affiliation(s)
- Angela M Barragan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Kyle Ghaby
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Matthew P Pond
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
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4
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Lin DYW, Kueffer LE, Juneja P, Wales TE, Engen JR, Andreotti AH. Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states. eLife 2024; 12:RP89489. [PMID: 38189455 PMCID: PMC10945472 DOI: 10.7554/elife.89489] [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] [Indexed: 01/09/2024] Open
Abstract
Full-length Bruton's tyrosine kinase (BTK) has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology [PHTH] domain and proline-rich regions [PRR] contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveal only the SH3-SH2-kinase core with no electron density visible for the PHTH-PRR segment. Cryo-electron microscopy (cryoEM) data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. On the way to activation, disassembly of the SH3-SH2-kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with phosphatidylinositol (3,4,5)-trisphosphate. Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.
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Affiliation(s)
- David Yin-wei Lin
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Lauren E Kueffer
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Puneet Juneja
- Cryo-EM Facility, Office of Biotechnology, Iowa State UniversityAmesUnited States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern UniversityBostonUnited States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern UniversityBostonUnited States
| | - Amy H Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmesUnited States
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Panbhare K, Pandey R, Chauhan C, Sinha A, Shukla R, Kaundal RK. Role of NLRP3 Inflammasome in Stroke Pathobiology: Current Therapeutic Avenues and Future Perspective. ACS Chem Neurosci 2024; 15:31-55. [PMID: 38118278 DOI: 10.1021/acschemneuro.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
Neuroinflammation is a key pathophysiological feature of stroke-associated brain injury. A local innate immune response triggers neuroinflammation following a stroke via activating inflammasomes. The nucleotide-binding oligomerization domain leucine-rich repeat and pyrin domain-containing protein 3 (NLRP3) inflammasome has been heavily implicated in stroke pathobiology. Following a stroke, several stimuli have been suggested to trigger the assembly of the NLRP3 inflammasome. Recent studies have advanced the understanding and revealed several new players regulating NLRP3 inflammasome-mediated neuroinflammation. This article discussed recent advancements in NLRP3 assembly and highlighted stroke-induced mitochondrial dysfunction as a major checkpoint to regulating NLRP3 activation. The NLRP3 inflammasome activation leads to caspase-1-dependent maturation and release of IL-1β, IL-18, and gasdermin D. In addition, genetic or pharmacological inhibition of the NLRP3 inflammasome activation and downstream signaling has been shown to attenuate brain infarction and improve the neurological outcome in experimental models of stroke. Several drug-like small molecules targeting the NLRP3 inflammasome are in different phases of development as novel therapeutics for various inflammatory conditions, including stroke. Understanding how these molecules interfere with NLRP3 inflammasome assembly is paramount for their better optimization and/or development of newer NLRP3 inhibitors. In this review, we summarized the assembly of the NLRP3 inflammasome and discussed the recent advances in understanding the upstream regulators of NLRP3 inflammasome-mediated neuroinflammation following stroke. Additionally, we critically examined the role of the NLRP3 inflammasome-mediated signaling in stroke pathophysiology and the development of therapeutic modalities to target the NLRP3 inflammasome-related signaling for stroke treatment.
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Affiliation(s)
- Kartik Panbhare
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, UP 226002, India
| | - Rukmani Pandey
- Department of Psychiatry, Center for Molecular Biology and Genetics of Neurodegeneration, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Chandan Chauhan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, UP 226002, India
| | - Antarip Sinha
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, UP 226002, India
| | - Rahul Shukla
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Lucknow, UP 226002, India
| | - Ravinder K Kaundal
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, UP 226002, India
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6
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Xu B, Liang L, Jiang Y, Zhao Z. Investigating the ibrutinib resistance mechanism of L528W mutation on Bruton's tyrosine kinase via molecular dynamics simulations. J Mol Graph Model 2024; 126:108623. [PMID: 37716293 DOI: 10.1016/j.jmgm.2023.108623] [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: 04/16/2023] [Revised: 08/27/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023]
Abstract
Drug resistance to Bruton's Tyrosine Kinase (BTK) inhibitors presents a challenge in treating B-cell malignancies, and the mechanism behind drug resistance remains unclear. In this study, we focused on the BTK L528W mutation and investigated the underlying mechanisms of resistance to ibrutinib (including prototype and its active metabolite from, PCI-45227) using a combination of bioinformatics analysis, and molecular dynamics (MD) simulations. Protein stability of wild type (WT) BTK and L528W mutant was predicted using DUET, PoPMuSiC, and I-Mutant2.0. We performed MD simulations of six systems, apo-WT, metabolite-WT, prototype-WT and their mutants, to analyze the significant conformational and BTK-inhibitor binding affinity changes induced by the L528W mutation. Results show that the L528W mutation reduces the conformational stability of BTK compared to the WT. Principal component analysis (PCA) based free energy landscape (FEL) analysis shows that the L528W mutant ensemble tends to form more conformation clusters and exhibit higher levels of local minima than the WT counterpart. The interaction analysis reveal that the L528W mutation disrupts the strong hydrogen bond between Cys481 and inhibitors and reduces the number of hydrogen bonds between inhibitors and BTK in the L528W mutant complex structures compared to the WT. Porcupine plot analysis in association with cross-correlation analysis show the high-intensity flexible motion exhibited by the P-loop region. MM/GBSA calculations show that the L528W mutation in metabolite-BTK and prototype-BTK complexes increases binding free energy compared to the WT, with a reduction in binding affinity confirmed by per-residue energy decomposition. Specifically, the binding free energy increases from -57.86 kcal/mol to -48.26 kcal/mol for the metabolite-BTK complex and from -62.04 kcal/mol to -50.55 kcal/mol for the prototype-BTK complex. Overall, our study finds that the L528W mutation reduces BTK stability, decreases binding affinity, and leads to drug resistance and potential disease recurrence.
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Affiliation(s)
- Biyu Xu
- Department of Hematology, Dongguan Institute of Clinical Cancer Research, Affiliated Dongguan Hospital, Southern Medical University, Dongguan City, 523050, Guangdong Province, China; Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, Affiliated Dongguan Hospital, Southern Medical University, Dongguan City, 523050, Guangdong Province, China
| | - Luguang Liang
- Department of Intensive Care Unit, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan City, 523710, Guangdong Province, China
| | - Yirong Jiang
- Department of Hematology, Dongguan Institute of Clinical Cancer Research, Affiliated Dongguan Hospital, Southern Medical University, Dongguan City, 523050, Guangdong Province, China; Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, Affiliated Dongguan Hospital, Southern Medical University, Dongguan City, 523050, Guangdong Province, China.
| | - Zuguo Zhao
- Department of Microbiology and Immunology of Basical Medicine of Guangdong Medical University, Dongguan City, 523808, Guangdong Province, China; Department of Intensive Care Unit, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan City, 523710, Guangdong Province, China.
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7
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Lin DYW, Kueffer LE, Juneja P, Wales TE, Engen JR, Andreotti AH. Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543453. [PMID: 37786675 PMCID: PMC10541622 DOI: 10.1101/2023.06.02.543453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Full-length BTK has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology (PHTH) domain and proline-rich regions (PRR) contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveals only the SH3-SH2-kinase core with no electron density visible for the PHTH-PRR segment. CryoEM data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. On the way to activation, disassembly of the SH3-SH2-kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with PIP3. Membrane-induced dimerizationactivates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to transautophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.
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8
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Alrouji M, Benjamin LS, Alhumaydhi FA, Al Abdulmonem W, Baeesa SS, Rehan M, Shahwan M, Shamsi A, Akhtar A. Unlocking potential inhibitors for Bruton's tyrosine kinase through in-silico drug repurposing strategies. Sci Rep 2023; 13:17684. [PMID: 37848584 PMCID: PMC10582150 DOI: 10.1038/s41598-023-44956-0] [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: 02/20/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023] Open
Abstract
Bruton's tyrosine kinase (BTK) is a non-receptor protein kinase that plays a crucial role in various biological processes, including immune system function and cancer development. Therefore, inhibition of BTK has been proposed as a therapeutic strategy for various complex diseases. In this study, we aimed to identify potential inhibitors of BTK by using a drug repurposing approach. To identify potential inhibitors, we performed a molecular docking-based virtual screening using a library of repurposed drugs from DrugBank. We then used various filtrations followed by molecular dynamics (MD) simulations, principal component analysis (PCA), and Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA) analysis to further evaluate the binding interactions and stability of the top-ranking compounds. Molecular docking-based virtual screening approach identified several repurposed drugs as potential BTK inhibitors, including Eltrombopag and Alectinib, which have already been approved for human use. All-atom MD simulations provided insights into the binding interactions and stability of the identified compounds, which will be helpful for further experimental validation and optimization. Overall, our study demonstrates that drug repurposing is a promising approach to identify potential inhibitors of BTK and highlights the importance of computational methods in drug discovery.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, 11961, Shaqra, Saudi Arabia
| | - Lizy Sonia Benjamin
- College of Nursing, King Khalid University (KKU), Abha, Kingdom of Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 52571, Buraydah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Saleh Salem Baeesa
- Division of Neurosurgery, College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Moyad Shahwan
- College of Pharmacy and Health Sciences, Ajman University, Ajman, UAE
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, UAE
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, UAE.
| | - Atiya Akhtar
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger St., 62529, Abha, Saudi Arabia.
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Yang Y, Chong Z, Vihinen M. PON-Fold: Prediction of Substitutions Affecting Protein Folding Rate. Int J Mol Sci 2023; 24:13023. [PMID: 37629203 PMCID: PMC10455311 DOI: 10.3390/ijms241613023] [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: 06/14/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Most proteins fold into characteristic three-dimensional structures. The rate of folding and unfolding varies widely and can be affected by variations in proteins. We developed a novel machine-learning-based method for the prediction of the folding rate effects of amino acid substitutions in two-state folding proteins. We collected a data set of experimentally defined folding rates for variants and used them to train a gradient boosting algorithm starting with 1161 features. Two predictors were designed. The three-class classifier had, in blind tests, specificity and sensitivity ranging from 0.324 to 0.419 and from 0.256 to 0.451, respectively. The other tool was a regression predictor that showed a Pearson correlation coefficient of 0.525. The error measures, mean absolute error and mean squared error, were 0.581 and 0.603, respectively. One of the previously presented tools could be used for comparison with the blind test data set, our method called PON-Fold showed superior performance on all used measures. The applicability of the tool was tested by predicting all possible substitutions in a protein domain. Predictions for different conformations of proteins, open and closed forms of a protein kinase, and apo and holo forms of an enzyme indicated that the choice of the structure had a large impact on the outcome. PON-Fold is freely available.
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Affiliation(s)
- Yang Yang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China; (Y.Y.); (Z.C.)
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Zhang Chong
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China; (Y.Y.); (Z.C.)
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-221 84 Lund, Sweden
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Kciuk M, Marciniak B, Celik I, Zerroug E, Dubey A, Sundaraj R, Mujwar S, Bukowski K, Mojzych M, Kontek R. Pyrazolo[4,3- e]tetrazolo[1,5- b][1,2,4]triazine Sulfonamides as an Important Scaffold for Anticancer Drug Discovery-In Vitro and In Silico Evaluation. Int J Mol Sci 2023; 24:10959. [PMID: 37446136 DOI: 10.3390/ijms241310959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Pyrazolo[4,3-e]tetrazolo[1,5-b][1,2,4]triazine sulfonamides (MM-compounds) are a relatively new class of heterocyclic compounds that exhibit a wide variety of biological actions, including anticancer properties. Here, we used caspase enzyme activity assays, flow cytometry analysis of propidium iodide (PI)-stained cells, and a DNA laddering assay to investigate the mechanisms of cell death triggered by the MM-compounds (MM134, -6, -7, and -9). Due to inconsistent results in caspase activity assays, we have performed a bromodeoxyuridine (BrdU) incorporation assay, colony formation assay, and gene expression profiling. The compounds' cytotoxic and pro-oxidative properties were also assessed. Additionally, computational studies were performed to demonstrate the potential of the scaffold for future drug discovery endeavors. MM-compounds exhibited strong micromolar (0.06-0.35 µM) anti-proliferative and pro-oxidative activity in two cancer cell lines (BxPC-3 and PC-3). Activation of caspase 3/7 was observed following a 24-h treatment of BxPC-3 cells with IC50 concentrations of MM134, -6, and -9 compounds. However, no DNA fragmentation characteristics for apoptosis were observed in the flow cytometry and DNA laddering analysis. Gene expression data indicated up-regulation of BCL10, GADD45A, RIPK2, TNF, TNFRSF10B, and TNFRSF1A (TNF-R1) following treatment of cells with the MM134 compound. Moreover, in silico studies indicated AKT2 kinase as the primary target of compounds. MM-compounds exhibit strong cytotoxic activity with pro-oxidative, pro-apoptotic, and possibly pro-necroptotic properties that could be employed for further drug discovery approaches.
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Affiliation(s)
- Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
| | - Beata Marciniak
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38280, Turkey
| | - Enfale Zerroug
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 07000, Algeria
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida 274203, Uttar Prades, India
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
| | - Rajamanikandan Sundaraj
- Centre for Drug Discovery, Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - Karol Bukowski
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
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11
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Sun L, Wang Z, Yang Z, Liu X, Dong H. Virtual screening and structure-activity relationship study of novel BTK inhibitors in Traditional Chinese Medicine for the treatment of rheumatoid arthritis. J Biomol Struct Dyn 2023; 41:15219-15233. [PMID: 36914235 DOI: 10.1080/07391102.2023.2188418] [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: 10/31/2022] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
Bruton tyrosine kinase (BTK) is a known drug target for the treatment of autoimmune diseases, including rheumatoid arthritis (RA). In this study, a series of 1-amino-1H-imidazole-5-carboxamide derivatives with good inhibitory activity against BTK were selected to explore the structure-activity relationships of these BTK inhibitors (BTKIs). Furthermore, we concentrated on 182 prescriptions of Traditional Chinese Medicine with therapeutic effects on RA. 54 herbs with a frequency of ≥10 were counted to establish a database containing 4027 ingredients for virtual screening. Five compounds with relatively higher docking scores and better absorption, distribution, metabolism, elimination and toxicity (ADMET) parameters were then selected for higher precision docking. The results demonstrated that the potentially active molecules form hydrogen bond interactions with the hinge region residues Met477, Glu475, glycine-rich P-loop residue Val416, Lys430 and DFG motif Asp539. In particular, they also interact with the key residues Thr474 and Cys481 of BTK. The molecular dynamics (MD) results demonstrated that all five compounds above could bind with BTK stably as its cognate ligand in dynamic conditions. This work identified several potential BTKIs using a computer-aided drug design approach and may provide crucial information for developing novel BTKIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lili Sun
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zixiao Wang
- Department of Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhigang Yang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - XiuJuan Liu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, China
| | - Haiyan Dong
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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12
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Kwak C, Park C, Ko M, Im CY, Moon H, Park YH, Kim SY, Lee S, Kang MG, Kwon HJ, Hong E, Seo JK, Rhee HW. Identification of proteomic landscape of drug-binding proteins in live cells by proximity-dependent target ID. Cell Chem Biol 2022; 29:1739-1753.e6. [PMID: 36272407 DOI: 10.1016/j.chembiol.2022.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/29/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
Direct identification of the proteins targeted by small molecules can provide clues for disease diagnosis, prevention, and drug development. Despite concentrated attempts, there are still technical limitations associated with the elucidation of direct interactors. Herein, we report a target-ID system called proximity-based compound-binding protein identification (PROCID), which combines our direct analysis workflow of proximity-labeled proteins (Spot-ID) with the HaloTag system to efficiently identify the dynamic proteomic landscape of drug-binding proteins. We successfully identified well-known dasatinib-binding proteins (ABL1, ABL2) and confirmed the unapproved dasatinib-binding kinases (e.g., BTK and CSK) in a live chronic myeloid leukemia cell line. PROCID also identified the DNA helicase protein SMARCA2 as a dasatinib-binding protein, and the ATPase domain was confirmed to be the binding site of dasatinib using a proximity ligation assay (PLA) and in cellulo biotinylation assay. PROCID thus provides a robust method to identify unknown drug-interacting proteins in live cells that expedites the mode of action of the drug.
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Affiliation(s)
- Chulhwan Kwak
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Cheolhun Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Minjeong Ko
- Chemical Genomics Leader Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Chun Young Im
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Heegyum Moon
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Young-Hoon Park
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - So Young Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Seungyeon Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ho Jeong Kwon
- Chemical Genomics Leader Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea.
| | - Jeong Kon Seo
- Graduate School of Semiconductor Materials and Devices Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea; UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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13
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Comparison of Intermolecular Interactions of Irreversible and Reversible Inhibitors with Bruton’s Tyrosine Kinase via Molecular Dynamics Simulations. Molecules 2022; 27:molecules27217451. [DOI: 10.3390/molecules27217451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) is a key protein from the TEC family and is involved in B-cell lymphoma occurrence and development. Targeting BTK is therefore an effective strategy for B-cell lymphoma treatment. Since previous studies on BTK have been limited to structure-function analyses of static protein structures, the dynamics of conformational change of BTK upon inhibitor binding remain unclear. Here, molecular dynamics simulations were conducted to investigate the molecular mechanisms of association and dissociation of a reversible (ARQ531) and irreversible (ibrutinib) small-molecule inhibitor to/from BTK. The results indicated that the BTK kinase domain was found to be locked in an inactive state through local conformational changes in the DFG motif, and P-, A-, and gatekeeper loops. The binding of the inhibitors drove the outward rotation of the C-helix, resulting in the upfolded state of Trp395 and the formation of the salt bridge of Glu445-Arg544, which maintained the inactive conformation state. Met477 and Glu475 in the hinge region were found to be the key residues for inhibitor binding. These findings can be used to evaluate the inhibitory activity of the pharmacophore and applied to the design of effective BTK inhibitors. In addition, the drug resistance to the irreversible inhibitor Ibrutinib was mainly from the strong interaction of Cys481, which was evidenced by the mutational experiment, and further confirmed by the measurement of rupture force and rupture times from steered molecular dynamics simulation. Our results provide mechanistic insights into resistance against BTK-targeting drugs and the key interaction sites for the development of high-quality BTK inhibitors. The steered dynamics simulation also offers a means to rapidly assess the binding capacity of newly designed inhibitors.
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14
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Preparation of Novel Pyrazolo[4,3- e]tetrazolo[1,5- b][1,2,4]triazine Sulfonamides and Their Experimental and Computational Biological Studies. Int J Mol Sci 2022; 23:ijms23115892. [PMID: 35682571 PMCID: PMC9180621 DOI: 10.3390/ijms23115892] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Pyrazolo[4,3-e]tetrazolo[1,5-b][1,2,4]triazine sulfonamides constitute a novel class of heterocyclic compounds with broad biological activity, including anticancer properties. Investigated in this study, MM-compounds (MM134, MM136, MM137, and MM139) exhibited cytotoxic and proapoptotic activity against cancer cell lines (BxPC-3, PC-3, and HCT-116) in nanomolar concentrations without causing cytotoxicity in normal cells (L929 and WI38). In silico predictions indicate that tested compounds exhibit favorable pharmacokinetic profiles and may exert anticancer activity through the inhibition of BTK kinase, the AKT-mTOR pathway and PD1-PD-L1 interaction. Our findings point out that these sulfonamide derivatives may constitute a source of new anticancer drugs after optimization.
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15
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Sun SL, Wu SH, Kang JB, Ma YY, Chen L, Cao P, Chang L, Ding N, Xue X, Li NG, Shi ZH. Medicinal Chemistry Strategies for the Development of Bruton's Tyrosine Kinase Inhibitors against Resistance. J Med Chem 2022; 65:7415-7437. [PMID: 35594541 DOI: 10.1021/acs.jmedchem.2c00030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Despite significant efficacy, one of the major limitations of small-molecule Bruton's tyrosine kinase (BTK) agents is the presence of clinically acquired resistance, which remains a major clinical challenge. This Perspective focuses on medicinal chemistry strategies for the development of BTK small-molecule inhibitors against resistance, including the structure-based design of BTK inhibitors targeting point mutations, e.g., (i) developing noncovalent inhibitors from covalent inhibitors, (ii) avoiding steric hindrance from mutated residues, (iii) making interactions with the mutated residue, (iv) modifying the solvent-accessible region, and (v) developing new scaffolds. Additionally, a comparative analysis of multi-inhibitions of BTK is presented based on cross-comparisons between 2916 unique BTK ligands and 283 other kinases that cover 7108 dual/multiple inhibitions. Finally, targeting the BTK allosteric site and uding proteolysis-targeting chimera (PROTAC) as two potential strategies are addressed briefly, while also illustrating the possibilities and challenges to find novel ligands of BTK.
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Affiliation(s)
- Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shi-Han Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ji-Bo Kang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yi-Yuan Ma
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lu Chen
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Peng Cao
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, China
| | - Liang Chang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhi-Hao Shi
- Department of Organic Chemistry, China Pharmaceutical University, Nanjing 211198, China
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16
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Borsari C, Keles E, McPhail JA, Schaefer A, Sriramaratnam R, Goch W, Schaefer T, De Pascale M, Bal W, Gstaiger M, Burke JE, Wymann MP. Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα. J Am Chem Soc 2022; 144:6326-6342. [PMID: 35353516 PMCID: PMC9011356 DOI: 10.1021/jacs.1c13568] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Covalent protein
kinase inhibitors exploit currently noncatalytic
cysteines in the adenosine 5′-triphosphate (ATP)-binding site
via electrophiles directly appended to a reversible-inhibitor scaffold.
Here, we delineate a path to target solvent-exposed cysteines at a
distance >10 Å from an ATP-site-directed core module and produce
potent covalent phosphoinositide 3-kinase α (PI3Kα) inhibitors.
First, reactive warheads are used to reach out to Cys862 on PI3Kα,
and second, enones are replaced with druglike warheads while linkers
are optimized. The systematic investigation of intrinsic warhead reactivity
(kchem), rate of covalent bond formation
and proximity (kinact and reaction space
volume Vr), and integration of structure
data, kinetic and structural modeling, led to the guided identification
of high-quality, covalent chemical probes. A novel stochastic approach
provided direct access to the calculation of overall reaction rates
as a function of kchem, kinact, Ki, and Vr, which was validated with compounds with varied linker
lengths. X-ray crystallography, protein mass spectrometry (MS), and
NanoBRET assays confirmed covalent bond formation of the acrylamide
warhead and Cys862. In rat liver microsomes, compounds 19 and 22 outperformed the rapidly metabolized CNX-1351,
the only known PI3Kα irreversible inhibitor. Washout experiments
in cancer cell lines with mutated, constitutively activated PI3Kα
showed a long-lasting inhibition of PI3Kα. In SKOV3 cells, compounds 19 and 22 revealed PI3Kβ-dependent signaling,
which was sensitive to TGX221. Compounds 19 and 22 thus qualify as specific chemical probes to explore PI3Kα-selective
signaling branches. The proposed approach is generally suited to develop
covalent tools targeting distal, unexplored Cys residues in biologically
active enzymes.
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Affiliation(s)
- Chiara Borsari
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Erhan Keles
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Alexander Schaefer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Rohitha Sriramaratnam
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Wojciech Goch
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Thorsten Schaefer
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Martina De Pascale
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Matthias P Wymann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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17
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Hopkins BT, Bame E, Bajrami B, Black C, Bohnert T, Boiselle C, Burdette D, Burns JC, Delva L, Donaldson D, Grater R, Gu C, Hoemberger M, Johnson J, Kapadnis S, King K, Lulla M, Ma B, Marx I, Magee T, Meissner R, Metrick CM, Mingueneau M, Murugan P, Otipoby KL, Polack E, Poreci U, Prince R, Roach AM, Rowbottom C, Santoro JC, Schroeder P, Tang H, Tien E, Zhang F, Lyssikatos J. Discovery and Preclinical Characterization of BIIB091, a Reversible, Selective BTK Inhibitor for the Treatment of Multiple Sclerosis. J Med Chem 2022; 65:1206-1224. [PMID: 34734694 DOI: 10.1021/acs.jmedchem.1c00926] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multiple Sclerosis is a chronic autoimmune neurodegenerative disorder of the central nervous system (CNS) that is characterized by inflammation, demyelination, and axonal injury leading to permeant disability. In the early stage of MS, inflammation is the primary driver of the disease progression. There remains an unmet need to develop high efficacy therapies with superior safety profiles to prevent the inflammation processes leading to disability. Herein, we describe the discovery of BIIB091, a structurally distinct orthosteric ATP competitive, reversible inhibitor that binds the BTK protein in a DFG-in confirmation designed to sequester Tyr-551, an important phosphorylation site on BTK, into an inactive conformation with excellent affinity. Preclinical studies demonstrated BIB091 to be a high potency molecule with good drug-like properties and a safety/tolerability profile suitable for clinical development as a highly selective, reversible BTKi for treating autoimmune diseases such as MS.
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Affiliation(s)
- Brian T Hopkins
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Eris Bame
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Cheryl Black
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Tonika Bohnert
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Carrie Boiselle
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Doug Burdette
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Jeremy C Burns
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Luisette Delva
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Douglas Donaldson
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Richard Grater
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Chungang Gu
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Marc Hoemberger
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Josh Johnson
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Sudarshan Kapadnis
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kris King
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Mukesh Lulla
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Bin Ma
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Isaac Marx
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Tom Magee
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Robert Meissner
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Claire M Metrick
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Michael Mingueneau
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kevin L Otipoby
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Evelyne Polack
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Urjana Poreci
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Robin Prince
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Allie M Roach
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Chris Rowbottom
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Joseph C Santoro
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Patricia Schroeder
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Hao Tang
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Eric Tien
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Fengmei Zhang
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Joseph Lyssikatos
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
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18
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Bruton's Tyrosine Kinase Inhibitors in Multiple Sclerosis: Pioneering the Path Towards Treatment of Progression? CNS Drugs 2022; 36:1019-1030. [PMID: 36178589 PMCID: PMC9550714 DOI: 10.1007/s40263-022-00951-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/21/2022] [Indexed: 11/03/2022]
Abstract
In multiple sclerosis (MS) persisting disability can derive from acute relapses or, alternatively, from slow and steady deterioration, termed chronic progression. Emerging data suggest that the latter process occurs largely independent from relapse activity or development of new central nervous system (CNS) inflammatory lesions. Pathophysiologically, acute relapses develop as a consequence of de novo CNS infiltration of immune cells, while MS progression appears to be driven by a CNS-trapped inflammatory circuit between CNS-established hematopoietic cells as well as CNS-resident cells, such as microglia, astrocytes, and oligodendrocytes. Within the last decades, powerful therapies have been developed to control relapse activity in MS. All of these agents were primarily designed to systemically target the peripheral immune system and/or to prevent CNS infiltration of immune cells. Based on the above described dichotomy of MS pathophysiology, it is understandable that these agents only exert minor effects on progression and that novel targets within the CNS have to be utilized to control MS progression independent of relapse activity. In this regard, one promising strategy may be the inhibition of the enzyme Bruton's tyrosine kinase (BTK), which is centrally involved in the activation of B cells as well as myeloid cells, such as macrophages and microglia. In this review, we discuss where and to what extent BTK is involved in the immunological and molecular cascades driving MS progression. We furthermore summarize all mechanistic, preclinical, and clinical data on the various BTK inhibitors (evobrutinib, tolebrutinib, fenebrutinib, remibrutinib, orelabrutinib, BIIB091) that are currently in development for treatment of MS, with a particular focus on the potential ability of either drug to control MS progression.
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19
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Ahmadi S, Lotfi S, Afshari S, Kumar P, Ghasemi E. CORAL: Monte Carlo based global QSAR modelling of Bruton tyrosine kinase inhibitors using hybrid descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:1013-1031. [PMID: 34875951 DOI: 10.1080/1062936x.2021.2003429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Global QSAR modelling was performed to predict the pIC50 values of 233 diverse heterocyclic compounds as BTK inhibitors with the Monte Carlo algorithm of CORAL software using the DCW hybrid descriptors extracted from SMILES notations of molecules. The dataset of 233 BTK inhibitors was randomly split into training, invisible training, calibration and validation sets. The index of ideality of correlation was also applied to build and judge the predictability of the QSAR models. Eight global QSAR models based on the hybrid optimal descriptor using two target functions, i.e. TF1 (WIIC = 0) and TF2 (WIIC = 0.2) have been constructed. The statistical parameters of QSAR models computed by TF2 are more reliable and robust and were used to predict the pIC50 values. The model constructed for split 4 via TF2 is regarded as the best model and the numerical values of r2Train, r2Valid, Q2Train and Q2Valid are equal to 0.7981, 0.7429, 0.7898 and 0.6784, respectively. By internal and external validation techniques, the predictability and reliability of the designed models have been assessed. The structural attributes responsible for the increase and decrease of pIC50 of BTK inhibitors were also identified.
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Affiliation(s)
- S Ahmadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - S Lotfi
- Department of Chemistry, Payame Noor University (PNU), Tehran, Iran
| | - S Afshari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - P Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, Haryana, India
| | - E Ghasemi
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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20
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Qiu H, Ali Z, Bowlan J, Caldwell R, Gardberg A, Glaser N, Goutopoulos A, Head J, Johnson T, Maurer C, Georgi K, Grenningloh R, Fang Z, Morandi F, Rohdich F, Schmidt R, Follis AV, Sherer B. Discovery of Covalent Bruton's Tyrosine Kinase Inhibitors with Decreased CYP2C8 Inhibitory Activity. ChemMedChem 2021; 16:3653-3662. [PMID: 34582626 DOI: 10.1002/cmdc.202100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/27/2021] [Indexed: 11/07/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a member of the Tec kinase family that is expressed in cells of hematopoietic lineage. Evidence has shown that inhibition of BTK has clinical benefit for the treatment of a wide array of autoimmune and inflammatory diseases. Previously we reported the discovery of a novel nicotinamide selectivity pocket (SP) series of potent and selective covalent irreversible BTK inhibitors. The top molecule 1 of that series strongly inhibited CYP2C8 (IC50 =100 nM), which was attributed to the bridged linker group. However, our effort on the linker replacement turned out to be fruitless. With the study of the X-ray crystal structure of compound 1, we envisioned the opportunity of removal of this liability via transposition of the linker moiety in 1 from C6 to C5 position of the pyridine core. With this strategy, our optimization led to the discovery of a novel series, in which the top molecule 18 A displayed reduced CYP inhibitory activity and good potency. To further explore this new series, different warheads besides acrylamide, for example cyanamide, were also tested. However, this effort didn't lead to the discovery of molecules with better potency than 18 A. The loss of potency in those molecules could be related to the reduced reactivity of the warhead or reversible binding mode. Further profiling of 18 A disclosed that it had a strong hERG (human Ether-a-go-go Related Gene) inhibition, which could be related to the phenoxyphenyl group.
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Affiliation(s)
- Hui Qiu
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Zahid Ali
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Julian Bowlan
- Repare Therapeutics, 1 Broadway, 15th Floor, Cambridge, MA, 02142, USA
| | - Richard Caldwell
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Anna Gardberg
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA, 02142, USA
| | - Nina Glaser
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Andreas Goutopoulos
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Jared Head
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Theresa Johnson
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | | | - Katrin Georgi
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Roland Grenningloh
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Zhizhou Fang
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Federica Morandi
- Cellular Enzymology, F. Hoffmann-La Roche AG, Konzern-Hauptsitz, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Felix Rohdich
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Ralf Schmidt
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Ariele Viacava Follis
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Brian Sherer
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
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21
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Qiu S, Liu Y, Li Q. A mechanism for localized dynamics-driven activation in Bruton's tyrosine kinase. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210066. [PMID: 34457331 PMCID: PMC8371364 DOI: 10.1098/rsos.210066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/19/2021] [Indexed: 05/28/2023]
Abstract
Bruton's tyrosine kinase (BTK) plays a vital role in mature B-cell proliferation, development and function. Its inhibitors have gradually been applied for the treatment of many B-cell malignancies. However, because of treatment-associated drug resistance or low efficacy, it is urgent to develop new inhibitors and/or improve the efficacy of current inhibitors, where finding the intrinsic activation mechanism becomes the key to solve this problem. Here, we used BTK T474M mutation as a resistance model for inhibitors to study the mechanism of BTK activation and drug resistance by free molecular dynamics simulations. The results showed that the increase of kinase activity of T474M mutation is coming from the conformation change of the activation ring and ATP binding sites located in BTK N-terminus region. Specifically, the Thr474 mutation changed the structure of A-loop and stabilized the binding site of ATP, thus promoting the catalytic ability in the kinase domain. This localized dynamics-driven activation mechanism and resistance mechanism of BTK may provide new ideas for drug development in B-cell malignancies.
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Affiliation(s)
- Simei Qiu
- Institute of Biomechanics/School of Bioscience and Bioengineering, South China University of Technology, Guangzhou People's Republic of China
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou People's Republic of China
| | - Yunfeng Liu
- Institute of Biomechanics/School of Bioscience and Bioengineering, South China University of Technology, Guangzhou People's Republic of China
| | - Quhuan Li
- Institute of Biomechanics/School of Bioscience and Bioengineering, South China University of Technology, Guangzhou People's Republic of China
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou People's Republic of China
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22
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Zain R, Vihinen M. Structure-Function Relationships of Covalent and Non-Covalent BTK Inhibitors. Front Immunol 2021; 12:694853. [PMID: 34349760 PMCID: PMC8328433 DOI: 10.3389/fimmu.2021.694853] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/21/2021] [Indexed: 01/20/2023] Open
Abstract
Low-molecular weight chemical compounds have a longstanding history as drugs. Target specificity and binding efficiency represent major obstacles for small molecules to become clinically relevant. Protein kinases are attractive cellular targets; however, they are challenging because they present one of the largest protein families and share structural similarities. Bruton tyrosine kinase (BTK), a cytoplasmic protein tyrosine kinase, has received much attention as a promising target for the treatment of B-cell malignancies and more recently autoimmune and inflammatory diseases. Here we describe the structural properties and binding modes of small-molecule BTK inhibitors, including irreversible and reversible inhibitors. Covalently binding compounds, such as ibrutinib, acalabrutinib and zanubrutinib, are discussed along with non-covalent inhibitors fenebrutinib and RN486. The focus of this review is on structure-function relationships.
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Affiliation(s)
- Rula Zain
- Department of Laboratory Medicine, Clinical Research Centre, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden.,Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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23
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Guilinger JP, Archna A, Augustin M, Bergmann A, Centrella PA, Clark MA, Cuozzo JW, Däther M, Guié MA, Habeshian S, Kiefersauer R, Krapp S, Lammens A, Lercher L, Liu J, Liu Y, Maskos K, Mrosek M, Pflügler K, Siegert M, Thomson HA, Tian X, Zhang Y, Konz Makino DL, Keefe AD. Novel irreversible covalent BTK inhibitors discovered using DNA-encoded chemistry. Bioorg Med Chem 2021; 42:116223. [PMID: 34091303 DOI: 10.1016/j.bmc.2021.116223] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/24/2022]
Abstract
Libraries of DNA-Encoded small molecules created using combinatorial chemistry and synthetic oligonucleotides are being applied to drug discovery projects across the pharmaceutical industry. The majority of reported projects describe the discovery of reversible, i.e. non-covalent, target modulators. We synthesized multiple DNA-encoded chemical libraries terminated in electrophiles and then used them to discover covalent irreversible inhibitors and report the successful discovery of acrylamide- and epoxide-terminated Bruton's Tyrosine Kinase (BTK) inhibitors. We also demonstrate their selectivity, potency and covalent cysteine engagement using a range of techniques including X-ray crystallography, thermal transition shift assay, reporter displacement assay and intact protein complex mass spectrometry. The epoxide BTK inhibitors described here are the first ever reported to utilize this electrophile for this target.
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Affiliation(s)
| | - Archna Archna
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Martin Augustin
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Andreas Bergmann
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | | | | | - John W Cuozzo
- ZebiAI Inc., 100 Beaver Street, Waltham, MA 02453, USA
| | - Maike Däther
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | | | - Sevan Habeshian
- Laboratory of Therapeutic Proteins and Peptides École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Reiner Kiefersauer
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Stephan Krapp
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Alfred Lammens
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Lukas Lercher
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Julie Liu
- Accent Therapeutics Inc., 65 Hayden Avenue, Lexington, MA 02421, USA
| | - Yanbin Liu
- Cyteir Therapeutics, 128 Spring St, Lexington, MA 02421, USA
| | - Klaus Maskos
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | | | - Klaus Pflügler
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Markus Siegert
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | | | - Xia Tian
- Nurix Therapeutics Inc., 1700 Owens Street, Suite 205 San Francisco, CA 94158, USA
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA
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24
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Shi M, Wang L, Li P, Liu J, Chen L, Xu D. Dasatinib-SIK2 Binding Elucidated by Homology Modeling, Molecular Docking, and Dynamics Simulations. ACS OMEGA 2021; 6:11025-11038. [PMID: 34056256 PMCID: PMC8153941 DOI: 10.1021/acsomega.1c00947] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/06/2021] [Indexed: 02/08/2023]
Abstract
![]()
Salt-inducible kinases
(SIKs) are calcium/calmodulin-dependent
protein kinase (CAMK)-like (CAMKL) family members implicated in insulin
signal transduction, metabolic regulation, inflammatory response,
and other processes. Here, we focused on SIK2, which is a target of
the Food and Drug Administration (FDA)-approved pan inhibitor N-(2-chloro-6-methylphenyl)-2-(6-(4-(2-hydroxyethyl)piperazin-1-yl)-2-methylpyrimidin-4-ylamino)thiazole-5-carboxamide
(dasatinib), and constructed four representative SIK2 structures by
homology modeling. We investigated the interactions between dasatinib
and SIK2 via molecular docking, molecular dynamics simulation, and
binding free energy calculation and found that dasatinib showed strong
binding affinity for SIK2. Binding free energy calculations suggested
that the modification of various dasatinib regions may provide useful
information for drug design and to guide the discovery of novel dasatinib-based
SIK2 inhibitors.
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Affiliation(s)
- Mingsong Shi
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lun Wang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Penghui Li
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jiang Liu
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu, Sichuan 610065, China
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25
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Liu J, Chen C, Wang D, Zhang J, Zhang T. Emerging small-molecule inhibitors of the Bruton's tyrosine kinase (BTK): Current development. Eur J Med Chem 2021; 217:113329. [PMID: 33740548 DOI: 10.1016/j.ejmech.2021.113329] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/12/2021] [Accepted: 02/21/2021] [Indexed: 12/29/2022]
Abstract
Therapy based on Bruton's tyrosine kinase (BTK) inhibitors one of the major treatment options currently recommended for lymphoma patients. The first generation of BTK inhibitor, Ibrutinib, achieved remarkable progress in the treatment of B-cell malignancies, but still has problems with drug-resistance or off-target induced serious side effects. Therefore, numerous new BTK inhibitors were developed to address this unmet medical need. In parallel, the effect of BTK inhibitors against immune-related diseases has been evaluated in clinical trials. This review summarizes recent progress in the research and development of BTK inhibitors, with a focus on structural characteristics and structure-activity relationships. The structure-refinement process of representative pharmacophores as well as their effects on binding affinity, biological activity and pharmacokinetics profiles were analyzed. The advantages and disadvantages of reversible/irreversible BTK inhibitors and their potential implications were discussed to provide a reference for the rational design and development of novel potent BTK inhibitors.
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Affiliation(s)
- Jiakuo Liu
- Pharmaceutical Department, PLA Strategic Support Force Medical Center, No.9 Anxiangbeili Road, Chaoyang District, Beijing, 100101, PR China
| | - Chengjuan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China
| | - Dongmei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China
| | - Jie Zhang
- Pharmaceutical Department, PLA Strategic Support Force Medical Center, No.9 Anxiangbeili Road, Chaoyang District, Beijing, 100101, PR China.
| | - Tiantai Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China.
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26
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Anand GS. Disrupting enzyme fluidity. eLife 2021; 10:65221. [PMID: 33492229 PMCID: PMC7834015 DOI: 10.7554/elife.65221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 11/29/2022] Open
Abstract
A combination of X-ray crystallography, NMR, and mass spectrometry has revealed how diverse small-molecule inhibitors bind Bruton’s tyrosine kinase and alter the conformation of this enzyme.
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Affiliation(s)
- Ganesh Srinivasan Anand
- Department of Chemistry and Huck Institute of Life Sciences, Pennsylvania State University, University Park, United States
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27
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Joseph RE, Amatya N, Fulton DB, Engen JR, Wales TE, Andreotti A. Differential impact of BTK active site inhibitors on the conformational state of full-length BTK. eLife 2020; 9:60470. [PMID: 33226337 PMCID: PMC7834017 DOI: 10.7554/elife.60470] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) is targeted in the treatment of B-cell disorders including leukemias and lymphomas. Currently approved BTK inhibitors, including Ibrutinib, a first-in-class covalent inhibitor of BTK, bind directly to the kinase active site. While effective at blocking the catalytic activity of BTK, consequences of drug binding on the global conformation of full-length BTK are unknown. Here, we uncover a range of conformational effects in full-length BTK induced by a panel of active site inhibitors, including large-scale shifts in the conformational equilibria of the regulatory domains. Additionally, we find that a remote Ibrutinib resistance mutation, T316A in the BTK SH2 domain, drives spurious BTK activity by destabilizing the compact autoinhibitory conformation of full-length BTK, shifting the conformational ensemble away from the autoinhibited form. Future development of BTK inhibitors will need to consider long-range allosteric consequences of inhibitor binding, including the emerging application of these BTK inhibitors in treating COVID-19. Treatments for blood cancers, such as leukemia and lymphoma, rely heavily on chemotherapy, using drugs that target a vulnerable aspect of the cancer cells. B-cells, a type of white blood cell that produces antibodies, require a protein called Bruton’s tyrosine kinase, or BTK for short, to survive. The drug ibrutinib (Imbruvica) is used to treat B-cell cancers by blocking BTK. The BTK protein consists of several regions. One of them, known as the kinase domain, is responsible for its activity as an enzyme (which allows it to modify other proteins by adding a ‘tag’ known as a phosphate group). The other regions of BTK, known as regulatory modules, control this activity. In BTK’s inactive form, the regulatory modules attach to the kinase domain, blocking the regulatory modules from interacting with other proteins. When BTK is activated, it changes its conformation so the regulatory regions detach and become available for interactions with other proteins, at the same time exposing the active kinase domain. Ibrutinib and other BTK drugs in development bind to the kinase domain to block its activity. However, it is not known how this binding affects the regulatory modules. Previous efforts to study how drugs bind to BTK have used a version of the protein that only had the kinase domain, instead of the full-length protein. Now, Joseph et al. have studied full-length BTK and how it binds to five different drugs. The results reveal that ibrutinib and another drug called dasatinib both indirectly disrupt the normal position of the regulatory domains pushing BTK toward a conformation that resembles the activated state. By contrast, the three other compounds studied do not affect the inactive structure. Joseph et al. also examined a mutation in BTK that confers resistance against ibrutinib. This mutation increases the activity of BTK by disrupting the inactive structure, leading to B cells surviving better. Understanding how drug resistance mechanisms can work will lead to better drug treatment strategies for cancer. BTK is also a target in other diseases such as allergies or asthma and even COVID-19. If interactions between partner proteins and the regulatory domain are important in these diseases, then they may be better treated with drugs that maintain the regulatory modules in their inactive state. This research will help to design drugs that are better able to control BTK activity.
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Affiliation(s)
- Raji E Joseph
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - Neha Amatya
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - D Bruce Fulton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Amy Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
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28
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Lee E, Cho H, Lee DK, Ha J, Choi BJ, Jeong JH, Ryu JH, Kang JS, Jeon R. Discovery of 5-Phenoxy-2-aminopyridine Derivatives as Potent and Selective Irreversible Inhibitors of Bruton's Tyrosine Kinase. Int J Mol Sci 2020; 21:ijms21218006. [PMID: 33126415 PMCID: PMC7663149 DOI: 10.3390/ijms21218006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 11/25/2022] Open
Abstract
As a member of the tyrosine protein kinase Tec (TEC) family, Bruton’s tyrosine kinase (BTK) is considered a promising therapeutic target due to its crucial roles in the B cell receptor (BCR) signaling pathway. Although many types of BTK inhibitors have been reported, there is an unmet need to achieve selective BTK inhibitors to reduce side effects. To obtain BTK selectivity and efficacy, we designed a novel series of type II BTK inhibitors which can occupy the allosteric pocket induced by the DFG-out conformation and introduced an electrophilic warhead for targeting Cys481. In this article, we have described the structure–activity relationships (SARs) leading to a novel series of potent and selective piperazine and tetrahydroisoquinoline linked 5-phenoxy-2-aminopyridine irreversible inhibitors of BTK. Compound 18g showed good potency and selectivity, and its biological activity was evaluated in hematological tumor cell lines. The in vivo efficacy of 18g was also tested in a Raji xenograft mouse model, and it significantly reduced tumor size, with 46.8% inhibition compared with vehicle. Therefore, we have presented the novel, potent, and selective irreversible inhibitor 18g as a type II BTK inhibitor.
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Affiliation(s)
- Eun Lee
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea; (E.L.); (H.C.); (D.K.L.); (J.H.); (J.H.J.); (J.-H.R.)
| | - Hyewon Cho
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea; (E.L.); (H.C.); (D.K.L.); (J.H.); (J.H.J.); (J.-H.R.)
| | - Da Kyung Lee
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea; (E.L.); (H.C.); (D.K.L.); (J.H.); (J.H.J.); (J.-H.R.)
| | - JuHyun Ha
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea; (E.L.); (H.C.); (D.K.L.); (J.H.); (J.H.J.); (J.-H.R.)
| | - Byeong Jo Choi
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungcheongbuk-do 28116, Korea; (B.J.C.); (J.S.K.)
| | - Ji Hye Jeong
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea; (E.L.); (H.C.); (D.K.L.); (J.H.); (J.H.J.); (J.-H.R.)
| | - Jae-Ha Ryu
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea; (E.L.); (H.C.); (D.K.L.); (J.H.); (J.H.J.); (J.-H.R.)
| | - Jong Soon Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungcheongbuk-do 28116, Korea; (B.J.C.); (J.S.K.)
| | - Raok Jeon
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea; (E.L.); (H.C.); (D.K.L.); (J.H.); (J.H.J.); (J.-H.R.)
- Correspondence: ; Tel.: +82-2-710-9571
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29
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Targeting protein tyrosine kinase 6 in cancer. Biochim Biophys Acta Rev Cancer 2020; 1874:188432. [PMID: 32956764 DOI: 10.1016/j.bbcan.2020.188432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/27/2020] [Accepted: 09/04/2020] [Indexed: 11/21/2022]
Abstract
Protein tyrosine kinase 6 (PTK6) is the most well studied member of the PTK6 family of intracellular tyrosine kinases. While it is expressed at highest levels in differentiated cells in the regenerating epithelial linings of the gastrointestinal tract and skin, induction and activation of PTK6 is detected in several cancers, including breast and prostate cancer where high PTK6 expression correlates with worse outcome. PTK6 expression is regulated by hypoxia and cell stress, and its kinase activity is induced by several growth factor receptors implicated in cancer including members of the ERBB family, IGFR1 and MET. Activation of PTK6 at the plasma membrane has been associated with the epithelial mesenchymal transition and tumor metastasis. Several lines of evidence indicate that PTK6 has context dependent functions that depend on cell type, intracellular localization and kinase activation. Systemic disruption of PTK6 has been shown to reduce tumorigenesis in mouse models of breast and prostate cancer, and more recently small molecule inhibitors of PTK6 have exhibited efficacy in inhibiting tumor growth in animal models. Here we review data that suggest targeting PTK6 may have beneficial therapeutic outcomes in some cancers.
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30
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Lechner KS, Neurath MF, Weigmann B. Role of the IL-2 inducible tyrosine kinase ITK and its inhibitors in disease pathogenesis. J Mol Med (Berl) 2020; 98:1385-1395. [PMID: 32808093 PMCID: PMC7524833 DOI: 10.1007/s00109-020-01958-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 07/10/2020] [Accepted: 08/04/2020] [Indexed: 01/18/2023]
Abstract
ITK (IL-2-inducible tyrosine kinase) belongs to the Tec family kinases and is mainly expressed in T cells. It is involved in TCR signalling events driving processes like T cell development as well as Th2, Th9 and Th17 responses thereby controlling the expression of pro-inflammatory cytokines. Studies have shown that ITK is involved in the pathogenesis of autoimmune diseases as well as in carcinogenesis. The loss of ITK or its activity either by mutation or by the use of inhibitors led to a beneficial outcome in experimental models of asthma, inflammatory bowel disease and multiple sclerosis among others. In humans, biallelic mutations in the ITK gene locus result in a monogenetic disorder leading to T cell dysfunction; in consequence, mainly EBV infections can lead to severe immune dysregulation evident by lymphoproliferation, lymphoma and hemophagocytic lymphohistiocytosis. Furthermore, patients who suffer from angioimmunoblastic T cell lymphoma have been found to express significantly more ITK. These findings put ITK in the strong focus as a target for drug development.
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Affiliation(s)
- Kristina S Lechner
- Department of Medicine 1, Kussmaul Campus for Medical Research, University of Erlangen-Nürnberg, Hartmannstr.14, 91052, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, Kussmaul Campus for Medical Research, University of Erlangen-Nürnberg, Hartmannstr.14, 91052, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Ulmenweg 18, 91054, Erlangen, Germany
- Ludwig Demling Endoscopy Center of Excellence, Ulmenweg 18, 91054, Erlangen, Germany
| | - Benno Weigmann
- Department of Medicine 1, Kussmaul Campus for Medical Research, University of Erlangen-Nürnberg, Hartmannstr.14, 91052, Erlangen, Germany.
- Medical Immunology Campus Erlangen, Medical Clinic 1, Friedrich-Alexander University Erlangen-Nürnberg, 91052, Erlangen, Germany.
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31
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Pery N, Rizvi NB, Shafiq MI. Development of piperidinyl dipyrrrolopyridine-based dual inhibitors of Janus kinase and Bruton’s tyrosine kinase: a potential therapeutic probability to deal with rheumatoid arthritis. J Mol Model 2020; 26:235. [DOI: 10.1007/s00894-020-04512-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023]
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32
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Impact of amino acid substitution in the kinase domain of Bruton tyrosine kinase and its association with X-linked agammaglobulinemia. Int J Biol Macromol 2020; 164:2399-2408. [PMID: 32784026 DOI: 10.1016/j.ijbiomac.2020.08.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
X-linked agammaglobulinemia (XLA) is a rare disease that affects the immune system, characterized by a serial development of bacterial infection from the onset of infantile age. Bruton tyrosine kinase (BTK) is a non-receptor cytoplasmic kinase that plays a crucial role in the B-lymphocyte maturation. The altered expression, mutation and/or structural variations of BTK are responsible for causing XLA. Here, we have performed extensive sequence and structure analyses of BTK to find deleterious variations and their pathogenic association with XLA. First, we screened the pathogenic variations in the BTK from a pool of publicly available resources, and their pathogenicity/tolerance and stability predictions were carried out. Finally, two pathogenic variations (E589G and M630K) were studied in detail and subjected to all-atom molecular dynamics simulation for 200 ns. Intramolecular hydrogen bonds (H-bonds), secondary structure, and principal component analysis revealed significant conformational changes in variants that support the structural basis of BTK dysfunction in XLA. The free energy landscape analysis revealed the presence of multiple energy minima, suggests that E589G brings a large destabilization and consequently unfolding behavior compared to M630K. Overall, our study suggests that amino acid substitutions, E589G, and M630K, significantly alter the structural conformation and stability of BTK.
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Ma B, Bohnert T, Otipoby KL, Tien E, Arefayene M, Bai J, Bajrami B, Bame E, Chan TR, Humora M, MacPhee JM, Marcotte D, Mehta D, Metrick CM, Moniz G, Polack E, Poreci U, Prefontaine A, Sheikh S, Schroeder P, Smirnakis K, Zhang L, Zheng F, Hopkins BT. Discovery of BIIB068: A Selective, Potent, Reversible Bruton's Tyrosine Kinase Inhibitor as an Orally Efficacious Agent for Autoimmune Diseases. J Med Chem 2020; 63:12526-12541. [PMID: 32696648 DOI: 10.1021/acs.jmedchem.0c00702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Autoreactive B cell-derived antibodies form immune complexes that likely play a pathogenic role in autoimmune diseases. In systemic lupus erythematosus (SLE), these antibodies bind Fc receptors on myeloid cells and induce proinflammatory cytokine production by monocytes and NETosis by neutrophils. Bruton's tyrosine kinase (BTK) is a non-receptor tyrosine kinase that signals downstream of Fc receptors and plays a transduction role in antibody expression following B cell activation. Given the roles of BTK in both the production and sensing of autoreactive antibodies, inhibitors of BTK kinase activity may provide therapeutic value to patients suffering from autoantibody-driven immune disorders. Starting from an in-house proprietary screening hit followed by structure-based rational design, we have identified a potent, reversible BTK inhibitor, BIIB068 (1), which demonstrated good kinome selectivity with good overall drug-like properties for oral dosing, was well tolerated across preclinical species at pharmacologically relevant doses with good ADME properties, and achieved >90% inhibition of BTK phosphorylation (pBTK) in humans.
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Affiliation(s)
- Bin Ma
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Tonika Bohnert
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kevin L Otipoby
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Eric Tien
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Million Arefayene
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Judy Bai
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Eris Bame
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Timothy R Chan
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Humora
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - J Michael MacPhee
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Douglas Marcotte
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Devangi Mehta
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Claire M Metrick
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - George Moniz
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Evelyne Polack
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Urjana Poreci
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Annick Prefontaine
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Sarah Sheikh
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Patricia Schroeder
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Karen Smirnakis
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Lei Zhang
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Fengmei Zheng
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brian T Hopkins
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
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Paul A, Srinivasan N. Genome-wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights. Proteins 2020; 88:1620-1638. [PMID: 32667690 DOI: 10.1002/prot.25981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/26/2020] [Accepted: 07/12/2020] [Indexed: 12/31/2022]
Abstract
Protein Kinase-Like Non-Kinases (PKLNKs), commonly known as "pseudokinases", are homologous to eukaryotic Ser/Thr/Tyr protein kinases (PKs) but lack the crucial aspartate residue in the catalytic loop, indispensable for phosphotransferase activity. Therefore, they are predicted to be "catalytically inactive" enzyme homologs. Analysis of protein-kinase like sequences from Arabidopsis thaliana led to the identification of more than 120 pseudokinases lacking catalytic aspartate, majority of which are closely related to the plant-specific receptor-like kinase family. These pseudokinases engage in different biological processes, enabled by their diverse domain architectures and specific subcellular localizations. Structural comparison of pseudokinases with active and inactive conformations of canonical PKs, belonging to both plant and animal origin, revealed unique structural differences. The currently available crystal structures of pseudokinases show that the loop topologically equivalent to activation segment of PKs adopts a distinct-folded conformation, packing against the pseudoenzyme core, in contrast to the extended and inhibitory geometries observed for active and inactive states, respectively, of catalytic PKs. Salt-bridge between ATP-binding Lys and DFG-Asp as well as hydrophobic interactions between the conserved nonpolar residue C-terminal to the equivalent DFG motif and nonpolar residues in C-helix mediate such a conformation in pseudokinases. This results in enhanced solvent accessibility of the pseudocatalytic loop in pseudokinases that can possibly serve as an interacting surface while associating with other proteins. Specifically, our analysis identified several residues that may be involved in pseudokinase regulation and hints at the repurposing of pseudocatalytic residues to achieve mechanistic control over noncatalytic functions of pseudoenzymes.
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Affiliation(s)
- Anindita Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Jeong S, Sohn YK, Choi Y, Park J, Kim HS. A regulatory SH2 domain-targeting protein binder effectively inhibits the activity of Bruton's tyrosine kinase and its drug-resistant variants. Biochem Biophys Res Commun 2020; 526:8-13. [PMID: 32192770 DOI: 10.1016/j.bbrc.2020.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 01/06/2023]
Abstract
Human Bruton's tyrosine kinase (hBtk) plays a key role in growth and metabolism of B cells, but its dysfunctions cause various B-cell malignancies. Inhibitors targeting the ATP-binding pocket of hBtk have been developed, but they have several drawbacks such as adverse side effects and occurrence of drug-resistant mutations. Here, we present a protein binder which specifically binds to an allosteric regulatory SH2 domain of hBtk. The protein binder effectively inhibited the hBtk activity, indicating a critical role of the SH2 domain in allosteric regulation of the hBtk activity. Cytosolic delivery of the protein binder led to a significant inhibition on the BCR-mediated signaling and viability of B lymphoma cells. The utility of our approach was demonstrated by effective inhibition of drug-resistant hBtk variants by the protein binder. Based on the computationally predicted binding mode, the protein binder is likely to inhibit the hBtk activity by disrupting the interaction between the SH2 domain and kinase domain. The present approach can be used for developing therapeutic agents with improved efficacy for B-cell lymphoma.
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Affiliation(s)
- Sukyo Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Yoo-Kyoung Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Yoonjoo Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Jinho Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
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36
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Recent advance in the development of novel, selective and potent FGFR inhibitors. Eur J Med Chem 2020; 186:111884. [DOI: 10.1016/j.ejmech.2019.111884] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/28/2022]
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Leroux AE, Biondi RM. Renaissance of Allostery to Disrupt Protein Kinase Interactions. Trends Biochem Sci 2019; 45:27-41. [PMID: 31690482 DOI: 10.1016/j.tibs.2019.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions often regulate the activity of protein kinases by allosterically modulating the conformation of the ATP-binding site. Bidirectional allostery implies that reverse modulation (i.e., from the ATP-binding site to the interaction and regulatory sites) must also be possible. Here, we review both the allosteric regulation of protein kinases and recent work describing how compounds binding at the ATP-binding site can promote or inhibit protein kinase interactions at regulatory sites via the reverse mechanism. Notably, the pharmaceutical industry has been developing compounds that bind to the ATP-binding site of protein kinases and potently disrupt protein-protein interactions between target protein kinases and their regulatory interacting partners. Learning to modulate allosteric processes will facilitate the development of protein-protein interaction modulators.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina; Department of Internal Medicine I, University Hospital, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; DKTK German Cancer Consortium (DKTK), Frankfurt, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Guo Y, Liu Y, Hu N, Yu D, Zhou C, Shi G, Zhang B, Wei M, Liu J, Luo L, Tang Z, Song H, Guo Y, Liu X, Su D, Zhang S, Song X, Zhou X, Hong Y, Chen S, Cheng Z, Young S, Wei Q, Wang H, Wang Q, Lv L, Wang F, Xu H, Sun H, Xing H, Li N, Zhang W, Wang Z, Liu G, Sun Z, Zhou D, Li W, Liu L, Wang L, Wang Z. Discovery of Zanubrutinib (BGB-3111), a Novel, Potent, and Selective Covalent Inhibitor of Bruton's Tyrosine Kinase. J Med Chem 2019; 62:7923-7940. [PMID: 31381333 DOI: 10.1021/acs.jmedchem.9b00687] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrant activation of Bruton's tyrosine kinase (BTK) plays an important role in pathogenesis of B-cell lymphomas, suggesting that inhibition of BTK is useful in the treatment of hematological malignancies. The discovery of a more selective on-target covalent BTK inhibitor is of high value. Herein, we disclose the discovery and preclinical characterization of a potent, selective, and irreversible BTK inhibitor as our clinical candidate by using in vitro potency, selectivity, pharmacokinetics (PK), and in vivo pharmacodynamic for prioritizing compounds. Compound BGB-3111 (31a, Zanubrutinib) demonstrates (i) potent activity against BTK and excellent selectivity over other TEC, EGFR and Src family kinases, (ii) desirable ADME, excellent in vivo pharmacodynamic in mice and efficacy in OCI-LY10 xenograft models.
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Diao Y, Fang X, Song P, Lai M, Tong L, Hao Y, Dou D, Liu Y, Ding J, Zhao Z, Xie H, Li H. Discovery and Biological evaluation of pyrimido[4,5-d]pyrimidine-2,4(1H,3H)-dione derivatives as potent Bruton’s tyrosine kinase inhibitors. Bioorg Med Chem 2019; 27:3390-3395. [DOI: 10.1016/j.bmc.2019.06.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 12/14/2022]
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40
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Caldwell RD, Qiu H, Askew BC, Bender AT, Brugger N, Camps M, Dhanabal M, Dutt V, Eichhorn T, Gardberg AS, Goutopoulos A, Grenningloh R, Head J, Healey B, Hodous BL, Huck BR, Johnson TL, Jones C, Jones RC, Mochalkin I, Morandi F, Nguyen N, Meyring M, Potnick JR, Santos DC, Schmidt R, Sherer B, Shutes A, Urbahns K, Follis AV, Wegener AA, Zimmerli SC, Liu-Bujalski L. Discovery of Evobrutinib: An Oral, Potent, and Highly Selective, Covalent Bruton’s Tyrosine Kinase (BTK) Inhibitor for the Treatment of Immunological Diseases. J Med Chem 2019; 62:7643-7655. [DOI: 10.1021/acs.jmedchem.9b00794] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Richard D. Caldwell
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Hui Qiu
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Ben C. Askew
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Andrew T. Bender
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Nadia Brugger
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Montserrat Camps
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Mohanraj Dhanabal
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Vikram Dutt
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Thomas Eichhorn
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Anna S. Gardberg
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Andreas Goutopoulos
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Roland Grenningloh
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Jared Head
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Brian Healey
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Brian L. Hodous
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Bayard R. Huck
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Theresa L. Johnson
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Christopher Jones
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Reinaldo C. Jones
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Igor Mochalkin
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Federica Morandi
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Ngan Nguyen
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Michael Meyring
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Justin R. Potnick
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Dusica Cvetinovic Santos
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Ralf Schmidt
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Brian Sherer
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Adam Shutes
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Klaus Urbahns
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Ariele Viacava Follis
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Ansgar A. Wegener
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Simone C. Zimmerli
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Lesley Liu-Bujalski
- EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), 45 A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
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Abstract
Bruton's tyrosine kinase (BTK) is crucial in B-cell development and survival. The role of BTK as a downstream kinase in the B-cell receptor (BCR) signaling pathway is well described. As a key player in the pathogenesis of B-cell malignancies, targeting of dysregulated BCR signaling has been explored by development of inhibitors of downstream mediators. Discovery of the biological function of BTK and the development of covalent inhibitors for clinical use, ibrutinib as the lead agent and acalabrutinib as the second clinically approved BTK inhibitor, have revolutionized the treatment options for B-cell malignancies. Currently, ibrutinib is approved for mantle cell lymphoma, chronic lymphocytic leukemia, lymphoplasmacytic lymphoma/Waldenström macroglobulinemia, small lymphocytic lymphoma, marginal zone lymphoma and chronic graft versus host disease, while acalabrutinib is approved for mantle cell lymphoma. Potential expansion of indications in other diseases is under investigation in several clinical trials, while combination of BTK inhibitors with either chemoimmunotherapy or other targeted agents is being systematically explored in B-cell malignancies.
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Wang S, Mondal S, Zhao C, Berishaj M, Ghanakota P, Batlevi CL, Dogan A, Seshan VE, Abel R, Green MR, Younes A, Wendel HG. Noncovalent inhibitors reveal BTK gatekeeper and auto-inhibitory residues that control its transforming activity. JCI Insight 2019; 4:127566. [PMID: 31217352 DOI: 10.1172/jci.insight.127566] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/16/2019] [Indexed: 12/13/2022] Open
Abstract
Inhibition of Bruton tyrosine kinase (BTK) is a breakthrough therapy for certain B cell lymphomas and B cell chronic lymphatic leukemia. Covalent BTK inhibitors (e.g., ibrutinib) bind to cysteine C481, and mutations of this residue confer clinical resistance. This has led to the development of noncovalent BTK inhibitors that do not require binding to cysteine C481. These new compounds are now entering clinical trials. In a systematic BTK mutagenesis screen, we identify residues that are critical for the activity of noncovalent inhibitors. These include a gatekeeper residue (T474) and mutations in the kinase domain. Strikingly, co-occurrence of gatekeeper and kinase domain lesions (L512M, E513G, F517L, L547P) in cis results in a 10- to 15-fold gain of BTK kinase activity and de novo transforming potential in vitro and in vivo. Computational BTK structure analyses reveal how these lesions disrupt an intramolecular mechanism that attenuates BTK activation. Our findings anticipate clinical resistance mechanisms to a new class of noncovalent BTK inhibitors and reveal intramolecular mechanisms that constrain BTK's transforming potential.
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Affiliation(s)
- Shenqiu Wang
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York USA
| | | | - Chunying Zhao
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York USA
| | - Marjan Berishaj
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York USA
| | | | | | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, and
| | - Venkatraman E Seshan
- Department of Epidemiology-Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | | | - Michael R Green
- Department of Lymphoma and Myeloma and Department of Genomic Medicine, University of Texas MD Anderson Cancer, Houston, Texas, USA
| | | | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York USA
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43
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Sharma A, Thelma BK. Pharmacophore modeling and virtual screening in search of novel Bruton's tyrosine kinase inhibitors. J Mol Model 2019; 25:179. [PMID: 31172362 DOI: 10.1007/s00894-019-4047-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/23/2019] [Indexed: 12/11/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a known drug target for B cell malignancies and autoimmune diseases like rheumatoid arthritis. Consequently, efforts to develop BTK inhibitors have gained momentum in the last decade, resulting in a number of potential inhibitory molecules. However, to date, there are only two FDA approved drugs for B cell malignancies (Ibrutinib and Acalabrutinib), thus continued efforts are warranted. A large number of molecular scaffolds with potential BTK inhibitory activity are already available from these studies, and therefore we employed a ligand-based approach towards computer-aided drug design to develop a pharmacophore model for BTK inhibitors. Using over 400 molecules with known half maximal inhibitory concentrations (IC50) for BTK, a four-point pharmacophore hypothesis was derived, with two aromatic rings (R), one hydrogen bond acceptor (A) and one hydrogen bond donor (D). Screening of two small-molecule databases against this pharmacophore returned 620 hits with matching chemical features. Docking these against the ATP-binding site of the BTK kinase domain through a virtual screening workflow yielded 30 hits from which ultimately two natural compounds (two best scoring poses for each) were prioritized. Molecular dynamics simulations of these four docked complexes confirmed the stability of protein-ligand binding over a 200 ns time period, and thus their suitability for lead molecule development with further optimization and experimental testing. Of note, the pharmacophore model developed in this study would also be further useful for de novo drug design and virtual screening efforts on a larger scale. Graphical abstract Pharmacophore modeling and virtual screening in search of novel Bruton's tyrosine kinase inhibitors.
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Affiliation(s)
- Aditya Sharma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India.
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Hopkins BT, Bame E, Bell N, Bohnert T, Bowden-Verhoek JK, Bui M, Cancilla MT, Conlon P, Cullen P, Erlanson DA, Fan J, Fuchs-Knotts T, Hansen S, Heumann S, Jenkins TJ, Marcotte D, McDowell B, Mertsching E, Negrou E, Otipoby KL, Poreci U, Romanowski MJ, Scott D, Silvian L, Yang W, Zhong M. Optimization of novel reversible Bruton's tyrosine kinase inhibitors identified using Tethering-fragment-based screens. Bioorg Med Chem 2019; 27:2905-2913. [PMID: 31138459 DOI: 10.1016/j.bmc.2019.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 01/06/2023]
Abstract
Since the approval of ibrutinib for the treatment of B-cell malignancies in 2012, numerous clinical trials have been reported using covalent inhibitors to target Bruton's tyrosine kinase (BTK) for oncology indications. However, a formidable challenge for the pharmaceutical industry has been the identification of reversible, selective, potent molecules for inhibition of BTK. Herein, we report application of Tethering-fragment-based screens to identify low molecular weight fragments which were further optimized to improve on-target potency and ADME properties leading to the discovery of reversible, selective, potent BTK inhibitors suitable for pre-clinical proof-of-concept studies.
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Affiliation(s)
- Brian T Hopkins
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States.
| | - Eris Bame
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Noah Bell
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Tonika Bohnert
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | | | - Minna Bui
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Mark T Cancilla
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Patrick Conlon
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Patrick Cullen
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Daniel A Erlanson
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Junfa Fan
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Tarra Fuchs-Knotts
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Stig Hansen
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Stacey Heumann
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Tracy J Jenkins
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Douglas Marcotte
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Bob McDowell
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | | | - Ella Negrou
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Kevin L Otipoby
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Urjana Poreci
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Michael J Romanowski
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Daniel Scott
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Laura Silvian
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Wenjin Yang
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Min Zhong
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
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Design, synthesis and evaluation of novel 7H-pyrrolo[2,3-d]pyrimidin-4-amine derivatives as potent, selective and reversible Bruton's tyrosine kinase (BTK) inhibitors for the treatment of rheumatoid arthritis. Eur J Med Chem 2019; 169:121-143. [DOI: 10.1016/j.ejmech.2019.02.077] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 01/29/2023]
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46
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Damm-Ganamet KL, Arora N, Becart S, Edwards JP, Lebsack AD, McAllister HM, Nelen MI, Rao NL, Westover L, Wiener JJM, Mirzadegan T. Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry. J Chem Inf Model 2019; 59:2046-2062. [DOI: 10.1021/acs.jcim.8b00941] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | | | | | | | - Marina I. Nelen
- Discovery Sciences, Janssen Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477, United States
| | | | - Lori Westover
- Discovery Sciences, Janssen Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477, United States
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47
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Leroux AE, Gross LZF, Sacerdoti M, Biondi RM. Allosteric Regulation of Protein Kinases Downstream of PI3-Kinase Signalling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:279-311. [PMID: 31707708 DOI: 10.1007/978-981-13-8719-7_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a basic principle that enables proteins to process and transmit cellular information. Protein kinases evolved allosteric mechanisms to transduce cellular signals to downstream signalling components or effector molecules. Protein kinases catalyse the transfer of the terminal phosphate from ATP to protein substrates upon specific stimuli. Protein kinases are targets for the development of small molecule inhibitors for the treatment of human diseases. Drug development has focussed on ATP-binding site, while there is increase interest in the development of drugs targeting alternative sites, i.e. allosteric sites. Here, we review the mechanism of regulation of protein kinases, which often involve the allosteric modulation of the ATP-binding site, enhancing or inhibiting activity. We exemplify the molecular mechanism of allostery in protein kinases downstream of PI3-kinase signalling with a focus on phosphoinositide-dependent protein kinase 1 (PDK1), a model kinase where small compounds can allosterically modulate the conformation of the kinase bidirectionally.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Lissy Z F Gross
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Mariana Sacerdoti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Frankfurt, Germany.
- DKTK German Cancer Consortium (DKTK), Frankfurt, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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48
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Wang C, Li S, Meng Q, Sun X, Li H, Shu X, Sun H, Liu K, Liu Z, Ma X. Novel amino acid-substituted diphenylpyrimidine derivatives as potent BTK inhibitors against B cell lymphoma cell lines. Bioorg Med Chem 2018; 26:4179-4186. [DOI: 10.1016/j.bmc.2018.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
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Balaji S, Ahmed M, Lorence E, Yan F, Nomie K, Wang M. NF-κB signaling and its relevance to the treatment of mantle cell lymphoma. J Hematol Oncol 2018; 11:83. [PMID: 29907126 PMCID: PMC6002979 DOI: 10.1186/s13045-018-0621-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/28/2018] [Indexed: 02/07/2023] Open
Abstract
Mantle cell lymphoma is an aggressive subtype of non-Hodgkin B cell lymphoma that is characterized by a poor prognosis determined by Ki67 and Mantle Cell International Prognostic Index scores, but it is becoming increasingly treatable. The majority of patients, especially if young, achieve a progression-free survival of at least 5 years. Mantle cell lymphoma can initially be treated with an anti-CD20 antibody in combination with a chemotherapy backbone, such as VR-CAP (the anti-CD20 monoclonal antibody rituximab administered with cyclophosphamide, doxorubicin, and prednisone) or R-CHOP (the anti-CD20 monoclonal antibody rituximab administered with cyclophosphamide, doxorubicin, vincristine, and prednisone). While initial treatment can facilitate recovery and complete remission in a few patients, many patients experience relapsed or refractory mantle cell lymphoma within 2 to 3 years after initial treatment. Targeted agents such as ibrutinib, an inhibitor of Bruton’s tyrosine kinase, which has been approved only in the relapsed setting, can be used to treat patients with relapsed or refractory mantle cell lymphoma. However, mantle cell lymphoma cells often acquire resistance to such targeted agents and continue to survive by activating alternate signaling pathways such as the PI3K-Akt pathway or the NF-κB pathways. NF-κB is a transcription factor family that regulates the growth and survival of B cells; mantle cell lymphoma cells depend on NF-κB signaling for continued growth and proliferation. The NF-κB signaling pathways are categorized into canonical and non-canonical types, wherein the canonical pathway prompts inflammatory responses, immune regulation, and cell proliferation, while the non-canonical leads to B cell maturation and lymphoid organogenesis. Since these pathways upregulate survival genes and tumor-promoting cytokines, they can be activated to overcome the inhibitory effects of targeted agents, thereby having profound effects on tumorigenesis. The NF-κB pathways are also highly targetable in that they are interconnected with numerous other pathways, including B cell receptor signaling, PI3K/Akt/mTOR signaling, and toll-like receptor signaling pathways. Additionally, elements of the non-canonical NF- κB pathway, such as NF-κB-inducing kinase, can be targeted to overcome resistance to targeting of the canonical NF- κB pathway. Targeting the molecular mechanisms of the NF-κB pathways can facilitate the development of novel agents to treat malignancies and overcome drug resistance in patients with relapsed or refractory mantle cell lymphoma.
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Affiliation(s)
- Swathi Balaji
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0429, Houston, TX, 77030-4009, USA
| | - Makhdum Ahmed
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0429, Houston, TX, 77030-4009, USA
| | - Elizabeth Lorence
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0429, Houston, TX, 77030-4009, USA
| | - Fangfang Yan
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0429, Houston, TX, 77030-4009, USA
| | - Krystle Nomie
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0429, Houston, TX, 77030-4009, USA
| | - Michael Wang
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0429, Houston, TX, 77030-4009, USA.
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50
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Zhang Z, Zhang D, Liu Y, Yang D, Ran F, Wang ML, Zhao G. Targeting Bruton's tyrosine kinase for the treatment of B cell associated malignancies and autoimmune diseases: Preclinical and clinical developments of small molecule inhibitors. Arch Pharm (Weinheim) 2018; 351:e1700369. [DOI: 10.1002/ardp.201700369] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Zhen Zhang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Daoguang Zhang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Yang Liu
- The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Dezhi Yang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Fansheng Ran
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
| | - Michael L. Wang
- The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Guisen Zhao
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences; Shandong University; Jinan Shandong P.R. China
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