1
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Rizvi SFA, Zhang H, Fang Q. Engineering peptide drug therapeutics through chemical conjugation and implication in clinics. Med Res Rev 2024. [PMID: 38704826 DOI: 10.1002/med.22046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/21/2024] [Accepted: 04/21/2024] [Indexed: 05/07/2024]
Abstract
The development of peptide drugs has made tremendous progress in the past few decades because of the advancements in modification chemistry and analytical technologies. The novel-designed peptide drugs have been modified through various biochemical methods with improved diagnostic, therapeutic, and drug-delivery strategies. Researchers found it a helping hand to overcome the inherent limitations of peptides and bring continued advancements in their applications. Furthermore, the emergence of peptide-drug conjugates (PDCs)-utilizes target-oriented peptide moieties as a vehicle for cytotoxic payloads via conjugation with cleavable chemical agents, resulting in the key foundation of the new era of targeted peptide drugs. This review summarizes the various classifications of peptide drugs, suitable chemical modification strategies to improve the ADME (adsorption, distribution, metabolism, and excretion) features of peptide drugs, and recent (2015-early 2024) progress/achievements in peptide-based drug delivery systems as well as their fruitful implication in preclinical and clinical studies. Furthermore, we also summarized the brief description of other types of PDCs, including peptide-MOF conjugates and peptide-UCNP conjugates. The principal aim is to provide scattered and diversified knowledge in one place and to help researchers understand the pinching knots in the science of PDC development and progress toward a bright future of novel peptide drugs.
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Affiliation(s)
- Syed Faheem Askari Rizvi
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Haixia Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Quan Fang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
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2
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Rizvi SF, Zhang L, Zhang H, Fang Q. Peptide-Drug Conjugates: Design, Chemistry, and Drug Delivery System as a Novel Cancer Theranostic. ACS Pharmacol Transl Sci 2024; 7:309-334. [PMID: 38357281 PMCID: PMC10863443 DOI: 10.1021/acsptsci.3c00269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 02/16/2024]
Abstract
The emergence of peptide-drug conjugates (PDCs) that utilize target-oriented peptide moieties as carriers of cytotoxic payloads, interconnected with various cleavable/noncleavable linkers, resulted in the key-foundation of the new era of targeted therapeutics. They are capable of retaining the integrity of conjugates in the blood circulatory system as well as releasing the drugs at the tumor microenvironment. Other valuable advantages are specificity and selectivity toward targeted-receptors, higher penetration ability, and drug-loading capacity, making them a suitable candidate to play their vital role as promising carrier agents. In this review, we summarized the types of cell-targeting (CTPs) and cell-penetrating peptides (CPPs) that have broad applications in the advancement of targeted drug-delivery systems (DDS). Moreover, the techniques to overcome the limitations of peptide-chemistry for their extensive implementation to construct the PDCs. Besides this, the diversified breakthrough of linker chemistry, and ample knowledge of various cytotoxic payloads used in PDCs in recent years, as well as the mechanism of action of PDCs was critically discussed. The principal aim is to provide scattered and diversified knowledge in one place and to help researchers understand the pinching knots in the science of PDC development, also their progression toward a bright future for PDCs as novel theranostics in clinical practice.
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Affiliation(s)
- Syed Faheem
Askari Rizvi
- Key
Laboratory of Preclinical Study for New Drugs of Gansu Province, and
Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, Gansu P.R. China
- State
Key Laboratory of Applied Organic Chemistry, College of Chemistry
and Chemical Engineering, Lanzhou University, Lanzhou, 730000, Gansu P.R. China
- Institute
of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, 54000, Punjab Pakistan
| | - Linjie Zhang
- State
Key Laboratory of Applied Organic Chemistry, College of Chemistry
and Chemical Engineering, Lanzhou University, Lanzhou, 730000, Gansu P.R. China
| | - Haixia Zhang
- State
Key Laboratory of Applied Organic Chemistry, College of Chemistry
and Chemical Engineering, Lanzhou University, Lanzhou, 730000, Gansu P.R. China
| | - Quan Fang
- Key
Laboratory of Preclinical Study for New Drugs of Gansu Province, and
Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, Gansu P.R. China
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3
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Imoto H, Rauch N, Neve AJ, Khorsand F, Kreileder M, Alexopoulos LG, Rauch J, Okada M, Kholodenko BN, Rukhlenko OS. A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression. Biomolecules 2023; 13:1212. [PMID: 37627277 PMCID: PMC10452107 DOI: 10.3390/biom13081212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer cells often adapt to targeted therapies, yet the molecular mechanisms underlying adaptive resistance remain only partially understood. Here, we explore a mechanism of RAS/RAF/MEK/ERK (MAPK) pathway reactivation through the upregulation of RAF isoform (RAFs) abundance. Using computational modeling and in vitro experiments, we show that the upregulation of RAFs changes the concentration range of paradoxical pathway activation upon treatment with conformation-specific RAF inhibitors. Additionally, our data indicate that the signaling output upon loss or downregulation of one RAF isoform can be compensated by overexpression of other RAF isoforms. We furthermore demonstrate that, while single RAF inhibitors cannot efficiently inhibit ERK reactivation caused by RAF overexpression, a combination of two structurally distinct RAF inhibitors synergizes to robustly suppress pathway reactivation.
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Affiliation(s)
- Hiroaki Imoto
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ashish J. Neve
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Fahimeh Khorsand
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Martina Kreileder
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Leonidas G. Alexopoulos
- Protavio Ltd., Demokritos Science Park, 153 43 Athens, Greece
- Department of Mechanical Engineering, National Technical University of Athens, 106 82 Athens, Greece
| | - Jens Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Mariko Okada
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka 565-0871, Japan
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Oleksii S. Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
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4
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Soliman DH, Nafie MS. Design, synthesis, and docking studies of novel pyrazole-based scaffolds and their evaluation as VEGFR2 inhibitors in the treatment of prostate cancer. RSC Adv 2023; 13:20443-20456. [PMID: 37435371 PMCID: PMC10331375 DOI: 10.1039/d3ra02579a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023] Open
Abstract
Since VEGFR-2 plays a crucial role in tumor growth, angiogenesis, and metastasis, it is a prospective target for cancer treatment. In this work, a series of 3-phenyl-4-(2-substituted phenylhydrazono)-1H-pyrazol-5(4H)-ones (3a-l) were synthesized and investigated for their cytotoxicity against the PC-3 human cancer cell line compared to Doxorubicin and Sorafenib as reference drugs. Two compounds 3a and 3i showed comparable cytotoxic activity with IC50 values of 1.22 and 1.24 μM compared to the reference drugs (IC50 = 0.932, 1.13 μM). Compound 3i was found to be the most effective VEGFR-2 inhibitor using in vitro testing of the synthesized compounds, with nearly 3-fold higher activity than Sorafenib (30 nM), with IC50 8.93 nM. Compound 3i significantly stimulated total apoptotic prostate cancer cell death 55.2-fold (34.26% compared to 0.62% for the control) arresting the cell cycle at the S-phase. The genes involved in apoptosis were also impacted, with proapoptotic genes being upregulated and antiapoptotic Bcl-2 being downregulated. These results were supported by docking studies of these two compounds within the active site of the VEGFR2 enzyme. Finally, in vivo, the study revealed the potentiality of compound 3i to inhibit tumor proliferation by 49.8% reducing the tumor weight from 234.6 mg in untreated mice to 83.2 mg. Therefore, 3i could be a promising anti-prostate cancer agent.
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Affiliation(s)
- Dalia H Soliman
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University Badr City Cairo Egypt
| | - Mohamed S Nafie
- Department of Chemistry (Biochemistry Program), Faculty of Science, Suez Canal University Ismailia 41522 Egypt
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5
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Krishnan K, Tian H, Tao P, Verkhivker GM. Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials. J Chem Phys 2022; 157:245101. [PMID: 36586979 PMCID: PMC11184971 DOI: 10.1063/5.0133826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
In the current study, multiscale simulation approaches and dynamic network methods are employed to examine the dynamic and energetic details of conformational landscapes and allosteric interactions in the ABL kinase domain that determine the kinase functions. Using a plethora of synergistic computational approaches, we elucidate how conformational transitions between the active and inactive ABL states can employ allosteric regulatory switches to modulate intramolecular communication networks between the ATP site, the substrate binding region, and the allosteric binding pocket. A perturbation-based network approach that implements mutational profiling of allosteric residue propensities and communications in the ABL states is proposed. Consistent with biophysical experiments, the results reveal functionally significant shifts of the allosteric interaction networks in which preferential communication paths between the ATP binding site and substrate regions in the active ABL state become suppressed in the closed inactive ABL form, which in turn features favorable allosteric coupling between the ATP site and the allosteric binding pocket. By integrating the results of atomistic simulations with dimensionality reduction methods and Markov state models, we analyze the mechanistic role of macrostates and characterize kinetic transitions between the ABL conformational states. Using network-based mutational scanning of allosteric residue propensities, this study provides a comprehensive computational analysis of long-range communications in the ABL kinase domain and identifies conserved regulatory hotspots that modulate kinase activity and allosteric crosstalk between the allosteric pocket, ATP binding site, and substrate binding regions.
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Affiliation(s)
| | - Hao Tian
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, USA
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, USA
| | - Gennady M. Verkhivker
- Author to whom correspondence should be addressed: . Telephone: 714-516-4586. Fax: 714-532-6048
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Armanmehr A, Jafari Khamirani H, Zoghi S, Dianatpour M. Analysis of DYRK1B, PPARG, and CEBPB Expression Patterns in Adipose-Derived Stem Cells from Patients Carrying DYRK1B R102C and Healthy Individuals During Adipogenesis. Metab Syndr Relat Disord 2022; 20:576-583. [PMID: 36318489 DOI: 10.1089/met.2021.0140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background: Metabolic syndrome (MetS) is a group of signs and symptoms that are associated with a higher risk of type 2 diabetes mellitus and cardiovascular diseases. The major risk factor for developing MetS is abdominal obesity, which is caused by an increase in adipocyte size or quantity. Increased adipocyte quantity is a result of differentiation of stem cells into adipose tissue. Numerous studies have investigated the expression of key transcription factors, including PPARG and CEBPB during adipocyte differentiation in murine cells such as 3T3-L1 cell lines. To better understand the expression changes during the process of fat accumulation in adipose-derived stem cells (ASCs), we compared the expression of DYRK1B, PPARG, and ẟB in ASCs between the patient (harboring DYRK1B R102C) and control (healthy individuals) groups. Methods: Gene expression was evaluated on the eighth day before induction and days 1, 5, and 15 postinduction. The pluripotent capacity of ASCs and the potential for differentiation into adipocytes were confirmed by flow cytometry analysis of surface markers (CD34, CD44, CD105, and CD90), and Oil Red O staining, respectively. The Expression of DYRK1B, PPARG, and CEBPB were assessed by real-time-polymerase chain reaction in patients and normal individuals. The effects of AZ191, a potent small molecule inhibitor on DYRK1B and CEBPB expression in patients' samples were studied. Result: The expression of DYRK1B kinase and transcription factors (CEBPB and PPARG) are higher in ASCs harboring DYRK1B R102C compared with noncarriers on days 5 and 15 during adipocyte differentiation. These proteins may be helpful to elucidate the mechanisms underlying obesity and obesity-related disorders like MetS. Furthermore, the new compound AZ191 exhibited inhibitory activity toward DYRK1B and CEBPB. We suggest that AZ191 may be helpful in defining the potential roles of DYRK1B and CEBPB in adipogenesis.
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Affiliation(s)
- Azam Armanmehr
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Jafari Khamirani
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran.,Comprehensive Medical Genetic Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sina Zoghi
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Dianatpour
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran.,Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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7
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Castiblanco LL, García de Yébenes MJ, Martín Martín JM, Carmona L. Safety and efficacy in the nursing care of people with rheumatic diseases on janus kinase inhibitor therapy. Rheumatol Int 2022; 42:2125-2133. [PMID: 35982184 DOI: 10.1007/s00296-022-05185-2] [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: 07/04/2022] [Accepted: 08/06/2022] [Indexed: 11/29/2022]
Abstract
Nurses's support of patients needs an evidence base as much as that of specialists management. However, some more practical aspects need specific questions that are not addressed in medical societies' recommendations. Our objective was to investigate the effect of Janus kinase inhibitors (jakinibs) on efficacy, safety, infections, cardiovascular risk, vaccination, pregnancy and lactation, interactions, surgery, and switch in adult patients with rheumatic diseases. We used the methodology for rapid reviews. Medline was searched for systematic reviews of randomised clinical trials and longitudinal observational studies reporting on the target aspects, without limits, yielding 540 titles, of which 70 articles were selected for detailed reading after the screening of title and abstract. In the case of no systematic review being published on a specific question, we resorted to the information provided by primary studies. The efficacy and safety profiles are similar to that of TNF-inhibitors to which they are compared in most studies; however, there is an increased risk of herpes zoster infections with jakinibs. The evidence on pregnancy, surgery and switches between jakinibs is very limited, although, so far, there are no major issues to inform patients about or to implement specific measures. In general, evidence to support nursing management in patients being treated with jakinibs is of moderate quality and scarce, ought to the recent incursion of jakinibs as a treatment.
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Affiliation(s)
| | | | | | - Loreto Carmona
- Institute of Musculoskeletal Health (Inmusc), Calle de Méndez Álvaro, 20, 28045, Madrid, Spain.
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8
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Male contraceptive development: A medicinal chemistry perspective. Eur J Med Chem 2022; 243:114709. [DOI: 10.1016/j.ejmech.2022.114709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/20/2022] [Accepted: 08/21/2022] [Indexed: 11/21/2022]
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9
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Omar AM, Khayat MT, Ahmed F, Muhammad YA, Malebari AM, Ibrahim SM, Khan MI, Shah DK, Childers WE, El-Araby ME. SAR Probing of KX2-391 Provided Analogues With Juxtaposed Activity Profile Against Major Oncogenic Kinases. Front Oncol 2022; 12:879457. [PMID: 35669422 PMCID: PMC9166630 DOI: 10.3389/fonc.2022.879457] [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: 02/19/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Tirbanibulin (KX2-391, KX-01), a dual non-ATP (substrate site) Src kinase and tubulin-polymerization inhibitor, demonstrated a universal anti-cancer activity for variety of cancer types. The notion that KX2-391 is a highly selective Src kinase inhibitor have been challenged by recent reports on the activities of this drug against FLT3-ITD mutations in some leukemic cell lines. Therefore, we hypothesized that analogues of KX2-391 may inhibit oncogenic kinases other than Src. A set of 4-aroylaminophenyl-N-benzylacetamides were synthesized and found to be more active against leukemia cell lines compared to solid tumor cell lines. N-(4-(2-(benzylamino)-2-oxoethyl)phenyl)-4-chlorobenzamide (4e) exhibited activities at IC50 0.96 µM, 1.62 µM, 1.90 µM and 4.23 µM against NB4, HL60, MV4-11 and K562 leukemia cell lines, respectively. We found that underlying mechanisms of 4e did not include tubulin polymerization or Src inhibition. Such results interestingly suggested that scaffold-hopping of KX2-391 may change the two main underlying cytotoxic mechanisms (Src and tubulin). Kinase profiling using two methods revealed that 4e significantly reduces the activities of some other potent oncogenic kinases like the MAPK member ERK1/2 (>99%) and it also greatly upregulates the pro-apoptotic c-Jun kinase (84%). This research also underscores the importance of thorough investigation of total kinase activities as part of the structure-activity relationship studies.
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Affiliation(s)
- Abdelsattar M Omar
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, King Abdulaziz University, Jeddah, Saudi Arabia.,Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia.,Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Al-Azhar University, Cairo, Egypt
| | - Maan T Khayat
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Farid Ahmed
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yosra A Muhammad
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Azizah M Malebari
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sara M Ibrahim
- Faculty of Science, Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad I Khan
- Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia.,Faculty of Science, Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dhaval K Shah
- School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Wayne E Childers
- Moulder Center for Drug Discovery Research, School of Pharmacy, Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA, United States
| | - Moustafa E El-Araby
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, King Abdulaziz University, Jeddah, Saudi Arabia.,Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
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10
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Abstract
Proteolysis-targeting chimeras are a new modality of chemical tools and potential therapeutics involving the induction of protein degradation. Cyclin-dependent kinase (CDK) protein, which is involved in cycles and transcription cycles, participates in regulation of the cell cycle, transcription and splicing. Proteolysis-targeting chimeras targeting CDKs show several advantages over traditional CDK small-molecule inhibitors in potency, selectivity and drug resistance. In addition, the discovery of molecule glues promotes the development of CDK degraders. Herein, the authors describe the existing CDK degraders and focus on the discussion of the structural characteristics and design of these degraders.
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11
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Shen C, He Y, Chen Q, Feng H, Williams TM, Lu Y, He Z. Narrative review of emerging roles for AKT-mTOR signaling in cancer radioimmunotherapy. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1596. [PMID: 34790802 PMCID: PMC8576660 DOI: 10.21037/atm-21-4544] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022]
Abstract
Objective To summarize the roles of AKT-mTOR signaling in the regulation of the DNA damage response and PD-L1 expression in cancer cells, and propose a novel strategy of targeting AKT-mTOR signaling in combination with radioimmunotherapy in the era of cancer immunotherapy Background Immunotherapy has greatly improved the clinical outcomes of many cancer patients and has changed the landscape of cancer patient management. However, only a small subgroup of cancer patients (~20–30%) benefit from immune checkpoint blockade-based immunotherapy. The current challenge is to find biomarkers to predict the response of patients to immunotherapy and strategies to sensitize patients to immunotherapy. Methods Search and review the literature which were published in PUBMED from 2000–2021 with the key words mTOR, AKT, drug resistance, DNA damage response, immunotherapy, PD-L1, DNA repair, radioimmunotherapy. Conclusions More than 50% of cancer patients receive radiotherapy during their course of treatment. Radiotherapy has been shown to reduce the growth of locally irradiated tumors as well as metastatic non-irradiated tumors (abscopal effects) by affecting systemic immunity. Consistently, immunotherapy has been demonstrated to enhance radiotherapy with more than one hundred clinical trials of radiation in combination with immunotherapy (radioimmunotherapy) across cancer types. Nevertheless, current available data have shown limited efficacy of trials testing radioimmunotherapy. AKT-mTOR signaling is a major tumor growth-promoting pathway and is upregulated in most cancers. AKT-mTOR signaling is activated by growth factors as well as genotoxic stresses including radiotherapy. Importantly, recent advances have shown that AKT-mTOR is one of the main signaling pathways that regulate DNA damage repair as well as PD-L1 levels in cancers. These recent advances clearly suggest a novel cancer therapy strategy by targeting AKT-mTOR signaling in combination with radioimmunotherapy.
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Affiliation(s)
- Changxian Shen
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Yuqi He
- Monash School of Medicine, Monash University, Clayton, VIC, Australia
| | - Qiang Chen
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Haihua Feng
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Terence M Williams
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Yuanzhi Lu
- Department of Clinical Pathology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zhengfu He
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, College of Medicine Zhejiang University, Hangzhou, China
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12
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Chiurillo MA, Jensen BC, Docampo R. Drug Target Validation of the Protein Kinase AEK1, Essential for Proliferation, Host Cell Invasion, and Intracellular Replication of the Human Pathogen Trypanosoma cruzi. Microbiol Spectr 2021; 9:e0073821. [PMID: 34585973 PMCID: PMC8557885 DOI: 10.1128/spectrum.00738-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/31/2021] [Indexed: 12/02/2022] Open
Abstract
Protein phosphorylation is involved in several key biological roles in the complex life cycle of Trypanosoma cruzi, the etiological agent of Chagas disease, and protein kinases are potential drug targets. Here, we report that the AGC essential kinase 1 (TcAEK1) exhibits a cytosolic localization and a higher level of expression in the replicative stages of the parasite. A CRISPR/Cas9 editing technique was used to generate ATP analog-sensitive TcAEK1 gatekeeper residue mutants that were selectively and acutely inhibited by bumped kinase inhibitors (BKIs). Analysis of a single allele deletion cell line (TcAEK1-SKO), and gatekeeper mutants upon treatment with inhibitor, showed that epimastigote forms exhibited a severe defect in cytokinesis. Moreover, we also demonstrated that TcAEK1 is essential for epimastigote proliferation, trypomastigote host cell invasion, and amastigote replication. We suggest that TcAEK1 is a pleiotropic player involved in cytokinesis regulation in T. cruzi and thus validate TcAEK1 as a drug target for further exploration. The gene editing strategy we applied to construct the ATP analog-sensitive enzyme could be appropriate for the study of other proteins of the T. cruzi kinome. IMPORTANCE Chagas disease affects 6 to 7 million people in the Americas, and its treatment has been limited to drugs with relatively high toxicity and low efficacy in the chronic phase of the infection. New validated targets are needed to combat this disease. In this work, we report the chemical and genetic validation of the protein kinase AEK1, which is essential for cytokinesis and infectivity, using a novel gene editing strategy.
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Affiliation(s)
- Miguel A. Chiurillo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Bryan C. Jensen
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
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13
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Kaur P, Goyal N. Pathogenic role of mitogen activated protein kinases in protozoan parasites. Biochimie 2021; 193:78-89. [PMID: 34706251 DOI: 10.1016/j.biochi.2021.10.012] [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: 04/23/2021] [Revised: 09/29/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023]
Abstract
Protozoan parasites with complex life cycles have high mortality rates affecting billions of human lives. Available anti-parasitic drugs are inadequate due to variable efficacy, toxicity, poor patient compliance and drug-resistance. Hence, there is an urgent need for the development of safer and better chemotherapeutics. Mitogen Activated Protein Kinases (MAPKs) have drawn much attention as potential drug targets. This review summarizes unique structural and functional features of MAP kinases and their possible role in pathogenesis of obligate intracellular protozoan parasites namely, Leishmania, Trypanosoma, Plasmodium and Toxoplasma. It also provides an overview of available knowledge concerning the target proteins of parasite MAPKs and the need to understand and unravel unknown interaction network(s) of MAPK(s).
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Affiliation(s)
- Pavneet Kaur
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Neena Goyal
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India.
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14
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Fournier JCL, Evans JP, Zappacosta F, Thomas DA, Patel VK, White GV, Campos S, Tomkinson NCO. Acetylation of the Catalytic Lysine Inhibits Kinase Activity in PI3Kδ. ACS Chem Biol 2021; 16:1644-1653. [PMID: 34397208 DOI: 10.1021/acschembio.1c00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covalent inhibition is a powerful strategy to develop potent and selective small molecule kinase inhibitors. Targeting the conserved catalytic lysine is an attractive method for selective kinase inactivation. We have developed novel, selective inhibitors of phosphoinositide 3-kinase δ (PI3Kδ) which acylate the catalytic lysine, Lys779, using activated esters as the reactive electrophiles. The acylating agents were prepared by adding the activated ester motif to a known selective dihydroisobenzofuran PI3Kδ inhibitor. Three esters were designed, including an acetate ester which was the smallest lysine modification evaluated in this work. Covalent binding to the enzyme was characterized by intact protein mass spectrometry of the PI3Kδ-ester adducts. An enzymatic digest coupled with tandem mass spectrometry identified Lys779 as the covalent binding site, and a biochemical activity assay confirmed that PI3Kδ inhibition was a direct result of covalent lysine acylation. These results indicate that a simple chemical modification such as lysine acetylation is sufficient to inhibit kinase activity. The selectivity of the compounds was evaluated against lipid kinases in cell lysates using a chemoproteomic binding assay. Due to the conserved nature of the catalytic lysine across the kinome, we believe the covalent inhibition strategy presented here could be applicable to a broad range of clinically relevant targets.
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Affiliation(s)
- Julie C. L. Fournier
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - John P. Evans
- Arctoris, 120E Olympic Avenue, Milton Park, Oxford, OX14 4SA, United Kingdom
| | | | - Daniel A. Thomas
- Arctoris, 120E Olympic Avenue, Milton Park, Oxford, OX14 4SA, United Kingdom
| | - Vipulkumar K. Patel
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Gemma V. White
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Sebastien Campos
- Pharmaron, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, United Kingdom
| | - Nicholas C. O. Tomkinson
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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15
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Bunev AS, Khochenkov DA, Khochenkova YA, Machkova YS, Varakina EV, Gasanov RE, Troshina MA, Avdyakova OS. Synthesis and anticancer activity of novel 2-alkylthio-4-amino-5-(thiazol-2-YL)pyrimidines. SYNTHETIC COMMUN 2021. [DOI: 10.1080/00397911.2021.1939383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Alexander S. Bunev
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russian Federation
| | - Dmitry A. Khochenkov
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russian Federation
- Laboratory of Biomarkers and Mechanisms of Tumor Angiogenesis, N. N. Blokhin National Medical Research Center of Oncology, Moscow, Russian Federation
| | - Yulia A. Khochenkova
- Laboratory of Biomarkers and Mechanisms of Tumor Angiogenesis, N. N. Blokhin National Medical Research Center of Oncology, Moscow, Russian Federation
| | - Yulia S. Machkova
- Laboratory of Biomarkers and Mechanisms of Tumor Angiogenesis, N. N. Blokhin National Medical Research Center of Oncology, Moscow, Russian Federation
| | - Elena V. Varakina
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russian Federation
| | - Rovshan E. Gasanov
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russian Federation
| | - Marina A. Troshina
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russian Federation
| | - Olga S. Avdyakova
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russian Federation
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16
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Islam S, Wang S, Bowden N, Martin J, Head R. Repurposing existing therapeutics, its importance in oncology drug development: Kinases as a potential target. Br J Clin Pharmacol 2021; 88:64-74. [PMID: 34192364 PMCID: PMC9292808 DOI: 10.1111/bcp.14964] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/04/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022] Open
Abstract
Repurposing the large arsenal of existing non‐cancer drugs is an attractive proposition to expand the clinical pipelines for cancer therapeutics. The earlier successes in repurposing resulted primarily from serendipitous findings, but more recently, drug or target‐centric systematic identification of repurposing opportunities continues to rise. Kinases are one of the most sought‐after anti‐cancer drug targets over the last three decades. There are many non‐cancer approved drugs that can inhibit kinases as “off‐targets” as well as many existing kinase inhibitors that can target new additional kinases in cancer. Identifying cancer‐associated kinase inhibitors through mining commercial drug databases or new kinase targets for existing inhibitors through comprehensive kinome profiling can offer more effective trial‐ready options to rapidly advance drugs for clinical validation. In this review, we argue that drug repurposing is an important approach in modern drug development for cancer therapeutics. We have summarized the advantages of repurposing, the rationale behind this approach together with key barriers and opportunities in cancer drug development. We have also included examples of non‐cancer drugs that inhibit kinases or are associated with kinase signalling as a basis for their anti‐cancer action.
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Affiliation(s)
- Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
| | - Nikola Bowden
- Centre for Human Drug Repurposing and Medicines Research, University of Newcastle, NSW, 2305, Australia
| | - Jennifer Martin
- Centre for Human Drug Repurposing and Medicines Research, University of Newcastle, NSW, 2305, Australia
| | - Richard Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
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17
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Amarnath Jonniya N, Sk MF, Kar P. Elucidating specificity of an allosteric inhibitor WNK476 among With‐No‐Lysine kinase isoforms using molecular dynamic simulations. Chem Biol Drug Des 2021; 98:405-420. [DOI: 10.1111/cbdd.13863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/19/2021] [Accepted: 05/01/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
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18
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Knox J, Joly N, Linossi EM, Carmona-Negrón JA, Jura N, Pintard L, Zuercher W, Roy PJ. A survey of the kinome pharmacopeia reveals multiple scaffolds and targets for the development of novel anthelmintics. Sci Rep 2021; 11:9161. [PMID: 33911106 PMCID: PMC8080662 DOI: 10.1038/s41598-021-88150-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/08/2021] [Indexed: 11/10/2022] Open
Abstract
Over one billion people are currently infected with a parasitic nematode. Symptoms can include anemia, malnutrition, developmental delay, and in severe cases, death. Resistance is emerging to the anthelmintics currently used to treat nematode infection, prompting the need to develop new anthelmintics. Towards this end, we identified a set of kinases that may be targeted in a nematode-selective manner. We first screened 2040 inhibitors of vertebrate kinases for those that impair the model nematode Caenorhabditis elegans. By determining whether the terminal phenotype induced by each kinase inhibitor matched that of the predicted target mutant in C. elegans, we identified 17 druggable nematode kinase targets. Of these, we found that nematode EGFR, MEK1, and PLK1 kinases have diverged from vertebrates within their drug-binding pocket. For each of these targets, we identified small molecule scaffolds that may be further modified to develop nematode-selective inhibitors. Nematode EGFR, MEK1, and PLK1 therefore represent key targets for the development of new anthelmintic medicines.
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Affiliation(s)
- Jessica Knox
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Nicolas Joly
- Programme Équipe Labellisée Ligue Contre Le Cancer, Institut Jacques Monod, UMR7592, Université de Paris, CNRS, Paris, France
| | - Edmond M Linossi
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - José A Carmona-Negrón
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Lionel Pintard
- Programme Équipe Labellisée Ligue Contre Le Cancer, Institut Jacques Monod, UMR7592, Université de Paris, CNRS, Paris, France
| | - William Zuercher
- School of Pharmacy, UNC Eshelman, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Peter J Roy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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19
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Lippert LG, Ma N, Ritt M, Jain A, Vaidehi N, Sivaramakrishnan S. Kinase inhibitors allosterically disrupt a regulatory interaction to enhance PKCα membrane translocation. J Biol Chem 2021; 296:100339. [PMID: 33508318 PMCID: PMC7949123 DOI: 10.1016/j.jbc.2021.100339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 10/28/2022] Open
Abstract
The eukaryotic kinase domain has multiple intrinsically disordered regions whose conformation dictates kinase activity. Small molecule kinase inhibitors (SMKIs) rely on disrupting the active conformations of these disordered regions to inactivate the kinase. While SMKIs are selected for their ability to cause this disruption, the allosteric effects of conformational changes in disordered regions is limited by a lack of dynamic information provided by traditional structural techniques. In this study, we integrated multiscale molecular dynamics simulations with FRET sensors to characterize a novel allosteric mechanism that is selectively triggered by SMKI binding to the protein kinase Cα domain. The indole maleimide inhibitors BimI and sotrastaurin were found to displace the Gly-rich loop (G-loop) that normally shields the ATP-binding site. Displacement of the G-loop interferes with a newly identified, structurally conserved binding pocket for the C1a domain on the N lobe of the kinase domain. This binding pocket, in conjunction with the N-terminal regulatory sequence, masks a diacylglycerol (DAG) binding site on the C1a domain. SMKI-mediated displacement of the G-loop released C1a and exposed the DAG binding site, enhancing protein kinase Cα translocation both to synthetic lipid bilayers and to live cell membranes in the presence of DAG. Inhibitor chemotype determined the extent of the observed allosteric effects on the kinase domain and correlated with the extent of membrane recruitment. Our findings demonstrate the allosteric effects of SMKIs beyond the confines of kinase catalytic conformation and provide an integrated computational-experimental paradigm to investigate parallel mechanisms in other kinases.
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Affiliation(s)
- Lisa G Lippert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Michael Ritt
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Abhinandan Jain
- The Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA.
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA.
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20
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Umezawa K, Kii I. Druggable Transient Pockets in Protein Kinases. Molecules 2021; 26:molecules26030651. [PMID: 33513739 PMCID: PMC7865889 DOI: 10.3390/molecules26030651] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 12/29/2022] Open
Abstract
Drug discovery using small molecule inhibitors is reaching a stalemate due to low selectivity, adverse off-target effects and inevitable failures in clinical trials. Conventional chemical screening methods may miss potent small molecules because of their use of simple but outdated kits composed of recombinant enzyme proteins. Non-canonical inhibitors targeting a hidden pocket in a protein have received considerable research attention. Kii and colleagues identified an inhibitor targeting a transient pocket in the kinase DYRK1A during its folding process and termed it FINDY. FINDY exhibits a unique inhibitory profile; that is, FINDY does not inhibit the fully folded form of DYRK1A, indicating that the FINDY-binding pocket is hidden in the folded form. This intriguing pocket opens during the folding process and then closes upon completion of folding. In this review, we discuss previously established kinase inhibitors and their inhibitory mechanisms in comparison with FINDY. We also compare the inhibitory mechanisms with the growing concept of “cryptic inhibitor-binding sites.” These sites are buried on the inhibitor-unbound surface but become apparent when the inhibitor is bound. In addition, an alternative method based on cell-free protein synthesis of protein kinases may allow the discovery of small molecules that occupy these mysterious binding sites. Transitional folding intermediates would become alternative targets in drug discovery, enabling the efficient development of potent kinase inhibitors.
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Affiliation(s)
- Koji Umezawa
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-Minowa, Kami-ina, Nagano 399-4598, Japan;
| | - Isao Kii
- Laboratory for Drug Target Research, Faculty & Graduate School of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-ina, Nagano 399-4598, Japan
- Correspondence: ; Tel.: +81-265-77-1521
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21
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Xie Z, Yang X, Duan Y, Han J, Liao C. Small-Molecule Kinase Inhibitors for the Treatment of Nononcologic Diseases. J Med Chem 2021; 64:1283-1345. [PMID: 33481605 DOI: 10.1021/acs.jmedchem.0c01511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Great successes have been achieved in developing small-molecule kinase inhibitors as anticancer therapeutic agents. However, kinase deregulation plays essential roles not only in cancer but also in almost all major disease areas. Accumulating evidence has revealed that kinases are promising drug targets for different diseases, including cancer, autoimmune diseases, inflammatory diseases, cardiovascular diseases, central nervous system disorders, viral infections, and malaria. Indeed, the first small-molecule kinase inhibitor for treatment of a nononcologic disease was approved in 2011 by the U.S. FDA. To date, 10 such inhibitors have been approved, and more are in clinical trials for applications other than cancer. This Perspective discusses a number of kinases and their small-molecule inhibitors for the treatment of diseases in nononcologic therapeutic fields. The opportunities and challenges in developing such inhibitors are also highlighted.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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22
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Jonniya NA, Sk MF, Kar P. Characterizing an allosteric inhibitor-induced inactive state in with-no-lysine kinase 1 using Gaussian accelerated molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:7343-7358. [DOI: 10.1039/d0cp05733a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The binding of an allosteric inhibitor in WNK1 leads to the inactive state.
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Affiliation(s)
- Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, MP
- India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, MP
- India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, MP
- India
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23
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Nash P, Kerschbaumer A, Dörner T, Dougados M, Fleischmann RM, Geissler K, McInnes I, Pope JE, van der Heijde D, Stoffer-Marx M, Takeuchi T, Trauner M, Winthrop KL, de Wit M, Aletaha D, Baraliakos X, Boehncke WH, Emery P, Isaacs JD, Kremer J, Lee EB, Maksymowych WP, Voshaar M, Tam LS, Tanaka Y, van den Bosch F, Westhovens R, Xavier R, Smolen JS. Points to consider for the treatment of immune-mediated inflammatory diseases with Janus kinase inhibitors: a consensus statement. Ann Rheum Dis 2021; 80:71-87. [PMID: 33158881 PMCID: PMC7788060 DOI: 10.1136/annrheumdis-2020-218398] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Janus kinase inhibitors (JAKi) have been approved for use in various immune-mediated inflammatory diseases. With five agents licensed, it was timely to summarise the current understanding of JAKi use based on a systematic literature review (SLR) on efficacy and safety. METHODS Existing data were evaluated by a steering committee and subsequently reviewed by a 29 person expert committee leading to the formulation of a consensus statement that may assist the clinicians, patients and other stakeholders once the decision is made to commence a JAKi. The committee included patients, rheumatologists, a gastroenterologist, a haematologist, a dermatologist, an infectious disease specialist and a health professional. The SLR informed the Task Force on controlled and open clinical trials, registry data, phase 4 trials and meta-analyses. In addition, approval of new compounds by, and warnings from regulators that were issued after the end of the SLR search date were taken into consideration. RESULTS The Task Force agreed on and developed four general principles and a total of 26 points for consideration which were grouped into six areas addressing indications, treatment dose and comedication, contraindications, pretreatment screening and risks, laboratory and clinical follow-up examinations, and adverse events. Levels of evidence and strengths of recommendations were determined based on the SLR and levels of agreement were voted on for every point, reaching a range between 8.8 and 9.9 on a 10-point scale. CONCLUSION The consensus provides an assessment of evidence for efficacy and safety of an important therapeutic class with guidance on issues of practical management.
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Affiliation(s)
- Peter Nash
- School of Medicine, Griffith University, Brisbane, Queensland, Australia
| | - Andreas Kerschbaumer
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Dörner
- Dept. Med./Rheumatology and Clinical Immunology, Charite Univ. Hospital, Berlin, Germany
| | - Maxime Dougados
- Hopital Cochin, Rheumatology, Université Paris Descartes, Paris, France
| | - Roy M Fleischmann
- Department of Medicine, Southwestern University of Texas, Dallas, Texas, USA
| | | | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Janet E Pope
- Medicine, Division of Rheumatology, The University of Western Ontario, London, Ontario, Canada
| | | | - Michaela Stoffer-Marx
- Section for Outcomes Research, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | | | - Michael Trauner
- Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | | | - Maarten de Wit
- Medical Humanities, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Daniel Aletaha
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090 Vienna, Austria
| | | | | | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
| | - John D Isaacs
- Musculoskeletal Research Group, Newcastle University, Newcastle upon Tyne, UK
| | - Joel Kremer
- Rheumatology, Albany Medical College, Albany, New York, USA
| | - Eun Bong Lee
- Internal Medicine, Seoul National University College of Medicine, Seoul, Korea (the Republic of)
| | - Walter P Maksymowych
- Medicine, University of Alberta Faculty of Medicine and Dentistry, Edmonton, Alberta, Canada
| | - Marieke Voshaar
- Medical Humanities, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Lai-Shan Tam
- Department of Medicine & Therapeutics, Chinese University of Hong Kong Shaw College, New Territories, Hong Kong
| | - Yoshiya Tanaka
- First Department of Internal Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | | | | | - Ricardo Xavier
- Division of Rheumatology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Josef S Smolen
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090 Vienna, Austria
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24
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Nash P, Kerschbaumer A, Dörner T, Dougados M, Fleischmann RM, Geissler K, McInnes I, Pope JE, van der Heijde D, Stoffer-Marx M, Takeuchi T, Trauner M, Winthrop KL, de Wit M, Aletaha D, Baraliakos X, Boehncke WH, Emery P, Isaacs JD, Kremer J, Lee EB, Maksymowych WP, Voshaar M, Tam LS, Tanaka Y, van den Bosch F, Westhovens R, Xavier R, Smolen JS. Points to consider for the treatment of immune-mediated inflammatory diseases with Janus kinase inhibitors: a consensus statement. Ann Rheum Dis 2021. [PMID: 33158881 DOI: 10.1136/annrheumdis2020-218580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
OBJECTIVES Janus kinase inhibitors (JAKi) have been approved for use in various immune-mediated inflammatory diseases. With five agents licensed, it was timely to summarise the current understanding of JAKi use based on a systematic literature review (SLR) on efficacy and safety. METHODS Existing data were evaluated by a steering committee and subsequently reviewed by a 29 person expert committee leading to the formulation of a consensus statement that may assist the clinicians, patients and other stakeholders once the decision is made to commence a JAKi. The committee included patients, rheumatologists, a gastroenterologist, a haematologist, a dermatologist, an infectious disease specialist and a health professional. The SLR informed the Task Force on controlled and open clinical trials, registry data, phase 4 trials and meta-analyses. In addition, approval of new compounds by, and warnings from regulators that were issued after the end of the SLR search date were taken into consideration. RESULTS The Task Force agreed on and developed four general principles and a total of 26 points for consideration which were grouped into six areas addressing indications, treatment dose and comedication, contraindications, pretreatment screening and risks, laboratory and clinical follow-up examinations, and adverse events. Levels of evidence and strengths of recommendations were determined based on the SLR and levels of agreement were voted on for every point, reaching a range between 8.8 and 9.9 on a 10-point scale. CONCLUSION The consensus provides an assessment of evidence for efficacy and safety of an important therapeutic class with guidance on issues of practical management.
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Affiliation(s)
- Peter Nash
- School of Medicine, Griffith University, Brisbane, Queensland, Australia
| | - Andreas Kerschbaumer
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Dörner
- Dept. Med./Rheumatology and Clinical Immunology, Charite Univ. Hospital, Berlin, Germany
| | - Maxime Dougados
- Hopital Cochin, Rheumatology, Université Paris Descartes, Paris, France
| | - Roy M Fleischmann
- Department of Medicine, Southwestern University of Texas, Dallas, Texas, USA
| | | | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Janet E Pope
- Medicine, Division of Rheumatology, The University of Western Ontario, London, Ontario, Canada
| | | | - Michaela Stoffer-Marx
- Section for Outcomes Research, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | | | - Michael Trauner
- Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | | | - Maarten de Wit
- Medical Humanities, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Daniel Aletaha
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090 Vienna, Austria
| | | | | | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
| | - John D Isaacs
- Musculoskeletal Research Group, Newcastle University, Newcastle upon Tyne, UK
| | - Joel Kremer
- Rheumatology, Albany Medical College, Albany, New York, USA
| | - Eun Bong Lee
- Internal Medicine, Seoul National University College of Medicine, Seoul, Korea (the Republic of)
| | - Walter P Maksymowych
- Medicine, University of Alberta Faculty of Medicine and Dentistry, Edmonton, Alberta, Canada
| | - Marieke Voshaar
- Medical Humanities, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Lai-Shan Tam
- Department of Medicine & Therapeutics, Chinese University of Hong Kong Shaw College, New Territories, Hong Kong
| | - Yoshiya Tanaka
- First Department of Internal Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | | | | | - Ricardo Xavier
- Division of Rheumatology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Josef S Smolen
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090 Vienna, Austria
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25
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Kolarski D, Sugiyama A, Rodat T, Schulte A, Peifer C, Itami K, Hirota T, Feringa BL, Szymanski W. Reductive stability evaluation of 6-azopurine photoswitches for the regulation of CKIα activity and circadian rhythms. Org Biomol Chem 2021; 19:2312-2321. [DOI: 10.1039/d1ob00014d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
6-Azopurines were evaluated for their reductive stability, and the ability to modulate CKIα activity and cellular circadian rhythms, revealing key challenges for long-term activity modulation utilizing chronophotopharmacology.
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Affiliation(s)
- Dušan Kolarski
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Theo Rodat
- Department of Pharmaceutical and Medicinal Chemistry
- Christian-Albrechts-University of Kiel
- 24118 Kiel
- Germany
| | - Albert Schulte
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Christian Peifer
- Department of Pharmaceutical and Medicinal Chemistry
- Christian-Albrechts-University of Kiel
- 24118 Kiel
- Germany
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Ben L. Feringa
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
- Medical Imaging Center
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Synthesis and cytotoxic activity of novel 4-amino-5-cyano-2-sulfonylpyrimidines. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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The retinal tyrosine kinome of diabetic Akimba mice highlights potential for specific Src family kinase inhibition in retinal vascular disease. Exp Eye Res 2020; 197:108108. [PMID: 32590005 DOI: 10.1016/j.exer.2020.108108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/11/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022]
Abstract
Although anti-VEGF therapies have radically changed clinical practice, there is still an urgent demand for novel, integrative approaches for sight-threatening retinal vascular diseases. As we hypothesize that protein tyrosine kinases are key signaling mediators in retinal vascular disease, we performed a comprehensive activity-based tyrosine kinome profiling on retinal tissue of 12-week-old Akimba mice, a translational model displaying hallmarks of early and advanced diabetic retinopathy. Western blotting was used to confirm retinal tyrosine kinase activity in Akimba mice. HUVEC tube formation and murine organotypic choroidal sprouting assays were applied to compare tyrosine kinase inhibitors with different specificity profiles. HUVEC toxicity and proliferation were evaluated using the CellTox™ Green Cytotoxicity and PrestoBlue™ Assays. Our results indicate a shift of the Akimba retinal tyrosine kinome towards a hyperactive state. Functional network analysis of significantly hyperphosphorylated peptides and upstream kinase prediction revealed a central role for Src-FAK family kinases. Western blotting confirmed hyperactivity of this signaling node in the retina of Akimba mice. We demonstrated that not only Src but also FAK family kinase inhibitors with different selectivity profiles were able to suppress angiogenesis in vitro and ex vivo. In the latter model, the novel selective Src family kinase inhibitor eCF506 was able to achieve potent reduction of angiogenesis, comparable to the less specific inhibitor Dasatinib. None of the tested compounds demonstrated acute endothelial cell toxicity. Overall, the collected findings provide the first comprehensive overview of retinal tyrosine kinome changes in the Akimba model of diabetic retinopathy and for the first time highlight Src family kinase inhibition using highly specific inhibitors as an attractive therapeutic intervention for retinal vascular pathology.
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Wilde S, Queisser N, Sutter A. Image analysis of mechanistic protein biomarkers for the characterization of genotoxicants: Aneugens, clastogens, and reactive oxygen species inducers. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:534-550. [PMID: 32297368 DOI: 10.1002/em.22374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023]
Abstract
The early detection of genotoxicity contributes to cutting-edge drug discovery and development, requiring effective identification of genotoxic hazards posed by drugs while providing mode of action (MoA) information in a high throughput manner. In other words, there is a need to complement standard genotoxicity testing according to the test battery given in ICH S2(R1) with new in vitro tools, thereby contributing to a more in-depth analysis of genotoxic effects. Here, we report on a proof-of-concept MoA approach based on post-translational modifications of proteins (PTMs) indicative of clastogenic and aneugenic effects in TK6 cells using imaging technology (with automated analysis). Cells were exposed in a 96-well plate format with a panel of reference (geno)toxic compounds and subsequently analyzed at 4 and 24 hr to detect dose-dependent changes in PTMs, relevant for mechanistic analysis. All tested compounds that interfere with the spindle apparatus yielded a BubR1 (S640) (3/3) and phospho-histone H3 (S28) (7/9) positive dose-response reflecting aneugenicity, whereas compounds inducing DNA double-strand-breaks were associated with positive FANCD2 (S1404) and 53BP1 (S1778) responses pointing to clastogenicity (2/3). The biomarker p53 (K373) was able to distinguish genotoxicants from non-genotoxicants (2/4), while the induction of reactive oxygen species (ROS), potentially causing DNA damage, was associated with a positive Nrf2 (S40) response (2/2). This work demonstrates that genotoxicants and non-genotoxicants induce different biomarker responses in TK6 cells which can be used for reliable classification into MoA groups (aneugens/clastogens/non-genotoxicants/ROS inducers), supporting a more in-depth safety assessment of drug candidates.
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Affiliation(s)
- Sabrina Wilde
- Fraunhofer ITEM, Preclinical Pharmacology and In Vitro Toxicology, Hannover, Germany
- Bayer AG, Investigational Toxicology, Berlin, Germany
| | - Nina Queisser
- Bayer AG, Investigational Toxicology, Berlin, Germany
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Synthesis and evaluation of 7-azaindole derivatives bearing benzocycloalkanone motifs as protein kinase inhibitors. Bioorg Med Chem 2020; 28:115468. [DOI: 10.1016/j.bmc.2020.115468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022]
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30
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Xiong H, Zhang J, Zhang Q, Duan Y, Zhang H, Zheng P, Tang Q. Design, synthesis and biological evaluation of 4-(pyridin-4-yloxy)benzamide derivatives bearing a 5-methylpyridazin-3(2H)-one fragment. Bioorg Med Chem Lett 2020; 30:127076. [PMID: 32173195 DOI: 10.1016/j.bmcl.2020.127076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/27/2020] [Accepted: 03/01/2020] [Indexed: 02/02/2023]
Abstract
A series of 4-(pyridin-4-yloxy)benzamide derivatives bearing a 5-methylpyridazin-3(2H)-one fragment were designed, synthesized, and evaluated for their biological activity. Most compounds showed effective inhibitory activity against cancer cell lines of A549, HeLa and MCF-7. Among them, the most promising compound 40 showed excellent activity against A549, HeLa and MCF-7 cell lines with IC50 values of 1.03, 1.15 and 2.59 μM, respectively, which was 2.606.95 times more active than that of Golvatinib. The structure-activity relationships (SARs) showed that the introduction of 5-methylpyridazin-3(2H)-one to "5-atom linker" and the modification of the amide with morpholine group were beneficial for enhancing the inhibitory activity of compounds. In addition, the further research on compound 40 mainly include c-Met kinase activity, concentration dependence, apoptosis (acridine orange staining), and molecular docking.
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Affiliation(s)
- Hehua Xiong
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, PR China
| | - Jianqing Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, PR China
| | - Qian Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, PR China
| | - Yongli Duan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, PR China; School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, PR China
| | - Han Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, PR China
| | - Pengwu Zheng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, PR China.
| | - Qidong Tang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, PR China.
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Saleh NM, El-Gazzar MG, Aly HM, Othman RA. Novel Anticancer Fused Pyrazole Derivatives as EGFR and VEGFR-2 Dual TK Inhibitors. Front Chem 2020; 7:917. [PMID: 32039146 PMCID: PMC6993756 DOI: 10.3389/fchem.2019.00917] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
EGFR and VEGFR-2 represent promising targets for cancer treatment as they are very important in tumor development as well as in angiogenesis and metastasis. In this work, 6-amino-4-(2-bromophenyl)-3-methyl-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile 1 and (E)-4-(2-Bromobenzylidene)-5-methyl-2,4-dihydro-3H-pyrazol-3-one 11 were selected as starting materials to synthesize different fused pyrazole derivatives; dihydropyrano[2,3-c]pyrazole 1, 2, 7–9, and 15, pyrazolo[4′,3′:5,6]pyrano[2,3-d]pyrimidine 3–6, pyrazolo[3,4-d]pyrimidine 12 and 13, and pyrazolo[3,4-c]pyrazole 14 derivatives were synthesized to evaluate their anticancer activity against HEPG2 human cancer cell lines compared to erlotinib and sorafenib as reference drugs. Seven compounds 1, 2, 4, 8, 11, 12, and 15 showed nearly 10 fold higher activity than erlotinib (10.6 μM) with IC50 ranging from 0.31 to 0.71 μM. In vitro EGFR and VEGFR-2 inhibitory activity were performed for the synthesized compounds, and the results identified compound 3 as the most potent EGFR inhibitor (IC50 = 0.06 μM) and compound 9 as the most potent VEGFR-2 inhibitor (IC50 = 0.22 μM). Moreover, compounds 9 and 12 revealed potent dual EGFR and VEGFR-2 inhibition, and these results were supported by docking studies of these two compounds within the active sites of both enzymes.
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Affiliation(s)
- Nashwa M Saleh
- Department of Chemistry, Faculty of Science (Girl's), Al-Azhar University, Cairo, Egypt
| | - Marwa G El-Gazzar
- Department of Drug Radiation Research, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Hala M Aly
- Department of Chemistry, Faculty of Science (Girl's), Al-Azhar University, Cairo, Egypt
| | - Rana A Othman
- Department of Chemistry, Faculty of Science (Girl's), Al-Azhar University, Cairo, Egypt
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Haspin-dependent and independent effects of the kinase inhibitor 5-Iodotubercidin on self-renewal and differentiation. Sci Rep 2020; 10:232. [PMID: 31937797 PMCID: PMC6959359 DOI: 10.1038/s41598-019-54350-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023] Open
Abstract
The kinase Haspin phosphorylates histone H3 at threonine-3 (H3T3ph), creating a docking site for the Chromosomal Passenger Complex (CPC). CPC plays a pivotal role in preventing chromosome misalignment. Here, we have examined the effects of 5-Iodotubercidin (5-ITu), a commonly used Haspin inhibitor, on self-renewal and differentiation of mouse embryonic stem cells (ESCs). Treatment with low concentrations of 5-ITu eliminates the H3T3ph mark during mitosis, but does not affect the mode or the outcome of self-renewal divisions. Interestingly, 5-ITu causes sustained accumulation of p53, increases markedly the expression of histone genes and results in reversible upregulation of the pluripotency factor Klf4. However, the properties of 5-ITu treated cells are distinct from those observed in Haspin-knockout cells generated by CRISPR/Cas9 genome editing, suggesting “off-target” effects. Continuous exposure to 5-ITu allows modest expansion of the ESC population and growth of embryoid bodies, but release from the drug after an initial treatment aborts embryoid body or teratoma formation. The data reveal an unusual robustness of ESCs against mitotic perturbants and suggest that the lack of H3T3ph and the “off-target” effects of 5-ITu can be partially compensated by changes in expression program or accumulation of suppressor mutations.
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Lamore SD, Kohnken RA, Peters MF, Kolaja KL. Cardiovascular Toxicity Induced by Kinase Inhibitors: Mechanisms and Preclinical Approaches. Chem Res Toxicol 2019; 33:125-136. [DOI: 10.1021/acs.chemrestox.9b00387] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sarah D. Lamore
- Preclinical Development, Wave Life Sciences, Lexington, Massachusetts 02421, United States
| | - Rebecca A. Kohnken
- Preclinical Safety, Abbvie, North Chicago, Illinois 60064, United States
| | - Matthew F. Peters
- Oncology Safety, Clinical Pharmacology and Safety Sciences, AstraZeneca Pharmaceuticals, Waltham, Massachusetts 02451, United States
| | - Kyle L. Kolaja
- Investigative Toxicology and Cell Therapy Safety, Nonclinical Development, Celgene Corporation, Summit, New Jersey 07901, United States
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Murányi J, Varga A, Gyulavári P, Pénzes K, Németh CE, Csala M, Pethő L, Csámpai A, Halmos G, Peták I, Vályi-Nagy I. Novel Crizotinib-GnRH Conjugates Revealed the Significance of Lysosomal Trapping in GnRH-Based Drug Delivery Systems. Int J Mol Sci 2019; 20:ijms20225590. [PMID: 31717403 PMCID: PMC6888004 DOI: 10.3390/ijms20225590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022] Open
Abstract
Several promising anti-cancer drug–GnRH (gonadotropin-releasing hormone) conjugates have been developed in the last two decades, although none of them have been approved for clinical use yet. Crizotinib is an effective multi-target kinase inhibitor, approved against anaplastic lymphoma kinase (ALK)- or ROS proto-oncogene 1 (ROS-1)-positive non-small cell lung carcinoma (NSCLC); however, its application is accompanied by serious side effects. In order to deliver crizotinib selectively into the tumor cells, we synthesized novel crizotinib analogues and conjugated them to a [d-Lys6]–GnRH-I targeting peptide. Our most prominent crizotinib–GnRH conjugates, the amide-bond-containing [d-Lys6(crizotinib*)]–GnRH-I and the ester-bond-containing [d-Lys6(MJ55*)]–GnRH-I, were able to bind to GnRH-receptor (GnRHR) and exert a potent c-Met kinase inhibitory effect. The efficacy of compounds was tested on the MET-amplified and GnRHR-expressing EBC-1 NSCLC cells. In vitro pharmacological profiling led to the conclusion that that crizotinib–GnRH conjugates are transported directly into lysosomes, where the membrane permeability of crizotinib is diminished. As a consequence of GnRHR-mediated endocytosis, GnRH-conjugated crizotinib bypasses its molecular targets—the ATP-binding site of RTKs— and is sequestered in the lysosomes. These results explained the lower efficacy of crizotinib–GnRH conjugates in EBC-1 cells, and led to the conclusion that drug escape from the lysosomes is a major challenge in the development of clinically relevant anti-cancer drug–GnRH conjugates.
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Affiliation(s)
- József Murányi
- MTA-SE Pathobiochemistry Research Group, Tűzoltó St. 37-47, H1094 Budapest, Hungary; (A.V.); (P.G.); (K.P.)
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, H1094 Budapest, Hungary; (C.E.N.); (M.C.)
- Correspondence:
| | - Attila Varga
- MTA-SE Pathobiochemistry Research Group, Tűzoltó St. 37-47, H1094 Budapest, Hungary; (A.V.); (P.G.); (K.P.)
| | - Pál Gyulavári
- MTA-SE Pathobiochemistry Research Group, Tűzoltó St. 37-47, H1094 Budapest, Hungary; (A.V.); (P.G.); (K.P.)
| | - Kinga Pénzes
- MTA-SE Pathobiochemistry Research Group, Tűzoltó St. 37-47, H1094 Budapest, Hungary; (A.V.); (P.G.); (K.P.)
| | - Csilla E. Németh
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, H1094 Budapest, Hungary; (C.E.N.); (M.C.)
| | - Miklós Csala
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, H1094 Budapest, Hungary; (C.E.N.); (M.C.)
| | - Lilla Pethő
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, H1117 Budapest, Hungary
| | - Antal Csámpai
- Institute of Chemistry, Eötvös Loránd University, H1117 Budapest, Hungary;
| | - Gábor Halmos
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, H4032 Debrecen, Hungary;
| | - István Peták
- Oncompass Medicine Hungary Ltd., H1024 Budapest, Hungary;
| | - István Vályi-Nagy
- Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, H1097 Budapest, Hungary;
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Synthesis, Biological Activities and Docking Studies of Novel 4-(Arylaminomethyl)benzamide Derivatives as Potential Tyrosine Kinase Inhibitors. Molecules 2019; 24:molecules24193543. [PMID: 31574962 PMCID: PMC6804006 DOI: 10.3390/molecules24193543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 01/06/2023] Open
Abstract
A number of new compounds containing the 4-(aminomethyl)benzamide fragment as a linker were designed and synthesized, and their biological activities were evaluated as potential anticancer agents. The cytotoxicity activity of the designed compounds was studied in two hematological and five solid cell lines in comparison with the reference drugs. Targeted structures against eight receptor tyrosine kinases including EGFR, HER-2, HER-4, IGF1R, InsR, KDR, PDGFRa, and PDGFRb were investigated. The majority of the compounds showed a potent inhibitory activity against the tested kinases. The analogues 11 and 13 with the (trifluoromethyl)benzene ring in the amide or amine moiety of the molecule were proven to be highly potent against EGFR, with 91% and 92% inhibition at 10 nM, respectively. The docking of synthesized target compounds for nine protein kinases contained in the Protein Data Bank (PDB) database was carried out. The molecular modeling results for analogue 10 showed that the use of the 4-(aminomethyl)benzamide as a flexible linker leads to a favorable overall geometry of the molecule, which allows one to bypass the bulk isoleucine residue and provides the necessary binding to the active center of the T315I-mutant Abl (PDB: 3QRJ).
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36
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Wong WW, Jackson RK, Liew LP, Dickson BD, Cheng GJ, Lipert B, Gu Y, Hunter FW, Wilson WR, Hay MP. Hypoxia-selective radiosensitisation by SN38023, a bioreductive prodrug of DNA-dependent protein kinase inhibitor IC87361. Biochem Pharmacol 2019; 169:113641. [PMID: 31541630 DOI: 10.1016/j.bcp.2019.113641] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/16/2019] [Indexed: 02/06/2023]
Abstract
DNA-dependent protein kinase (DNA-PK) plays a key role in repair of radiation-induced DNA double strand breaks (DSB) by non-homologous end-joining. DNA-PK inhibitors (DNA-PKi) are therefore efficient radiosensitisers, but normal tissue radiosensitisation represents a risk for their use in radiation oncology. Here we describe a novel prodrug, SN38023, that is metabolised to a potent DNA-PKi (IC87361) selectively in radioresistant hypoxic cells. DNA-PK inhibitory potency of SN38023 was 24-fold lower than IC87361 in cell-free assays, consistent with molecular modelling studies suggesting that SN38023 is unable to occupy one of the predicted DNA-PK binding modes of IC87361. One-electron reduction of the prodrug by radiolysis of anoxic formate solutions, and by metabolic reduction in anoxic HCT116/POR cells that overexpress cytochrome P450 oxidoreductase (POR), generated IC87361 efficiently as assessed by LC-MS. SN38023 inhibited radiation-induced Ser2056 autophosphorylation of DNA-PK catalytic subunit and radiosensitised HCT116/POR and UT-SCC-54C cells selectively under anoxia. SN38023 was an effective radiosensitiser in anoxic HCT116 spheroids, demonstrating potential for penetration into hypoxic tumour tissue, but in spheroid co-cultures of high-POR and POR-null cells it showed no evidence of bystander effects resulting from local diffusion of IC87361. Pharmacokinetics of IC87361 and SN38023 at maximum achievable doses in NIH-III mice demonstrated sub-optimal exposure of UT-SCC-54C tumour xenografts and did not provide significant tumour radiosensitisation. In conclusion, SN38023 has potential for exploiting hypoxia for selective delivery of a potent DNA-PKi to the most radioresistant subpopulation of cells in tumours. However, prodrugs providing improved systemic pharmacokinetics and that release DNA-PKi that elicit bystander effects are needed to maximise therapeutic utility.
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Affiliation(s)
- Way Wua Wong
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand
| | - Rosanna K Jackson
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand
| | - Lydia P Liew
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Benjamin D Dickson
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand
| | - Gary J Cheng
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand
| | - Barbara Lipert
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand
| | - Yongchuan Gu
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Francis W Hunter
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - William R Wilson
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand.
| | - Michael P Hay
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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Systematic Meta-Analysis Identifies Co-Expressed Kinases and GPCRs in Ovarian Cancer Tissues Revealing a Potential for Targeted Kinase Inhibitor Delivery. Pharmaceutics 2019; 11:pharmaceutics11090454. [PMID: 31480803 PMCID: PMC6781325 DOI: 10.3390/pharmaceutics11090454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/12/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022] Open
Abstract
The use of many anticancer drugs is problematic due to severe adverse effects. While the recent clinical launch of several kinase inhibitors led to tremendous progress, these targeted agents tend to be of non-specific nature within the kinase target class. Moreover, target mediated adverse effects limit the exploitation of some very promising kinase targets, including mitotic kinases. A future strategy will be the development of nanocarrier-based systems for the active delivery of kinase inhibitors using cancer specific surface receptors. The G-protein-coupled-receptors (GPCRs) represent the largest cell surface receptor family and some members are known to be frequently overexpressed in various cancer types. In the presented study, we used ovarian cancer tissues as an example to systematically identify concurrently overexpressed GPCRs and kinases. The rationale of this approach will guide the future design of nanoparticles, which will dock to GPCRs on cancer cells via specific ligands and deliver anticancer compounds after receptor mediated internalization. In addition to this, the approach is expected to be most effective by matching the inhibitor profiles of the delivered kinase inhibitors to the observed kinase gene expression profiles. We validated the suggested strategy in a meta-analysis, revealing overexpression of selected GPCRs and kinases in individual samples of a large ovarian cancer data set. The presented data demonstrate a large untapped potential for personalized cancer therapy using high-end targeted nanopharmaceuticals with kinase inhibitors.
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Konze KD, Bos PH, Dahlgren MK, Leswing K, Tubert-Brohman I, Bortolato A, Robbason B, Abel R, Bhat S. Reaction-Based Enumeration, Active Learning, and Free Energy Calculations To Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin-Dependent Kinase 2 Inhibitors. J Chem Inf Model 2019; 59:3782-3793. [PMID: 31404495 DOI: 10.1021/acs.jcim.9b00367] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The hit-to-lead and lead optimization processes usually involve the design, synthesis, and profiling of thousands of analogs prior to clinical candidate nomination. A hit finding campaign may begin with a virtual screen that explores millions of compounds, if not more. However, this scale of computational profiling is not frequently performed in the hit-to-lead or lead optimization phases of drug discovery. This is likely due to the lack of appropriate computational tools to generate synthetically tractable lead-like compounds in silico, and a lack of computational methods to accurately profile compounds prospectively on a large scale. Recent advances in computational power and methods provide the ability to profile much larger libraries of ligands than previously possible. Herein, we report a new computational technique, referred to as "PathFinder", that uses retrosynthetic analysis followed by combinatorial synthesis to generate novel compounds in synthetically accessible chemical space. In this work, the integration of PathFinder-driven compound generation, cloud-based FEP simulations, and active learning are used to rapidly optimize R-groups, and generate new cores for inhibitors of cyclin-dependent kinase 2 (CDK2). Using this approach, we explored >300 000 ideas, performed >5000 FEP simulations, and identified >100 ligands with a predicted IC50 < 100 nM, including four unique cores. To our knowledge, this is the largest set of FEP calculations disclosed in the literature to date. The rapid turnaround time, and scale of chemical exploration, suggests that this is a useful approach to accelerate the discovery of novel chemical matter in drug discovery campaigns.
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Affiliation(s)
- Kyle D Konze
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
| | - Pieter H Bos
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
| | - Markus K Dahlgren
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
| | - Karl Leswing
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
| | - Ivan Tubert-Brohman
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
| | - Andrea Bortolato
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
| | - Braxton Robbason
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
| | - Robert Abel
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
| | - Sathesh Bhat
- Schrödinger Inc. , 120 West 45th Street, 17th floor , New York , New York 10036 , United States
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Abbas HAS, Abd El-Karim SS. Design, synthesis and anticervical cancer activity of new benzofuran–pyrazol-hydrazono- thiazolidin-4-one hybrids as potential EGFR inhibitors and apoptosis inducing agents. Bioorg Chem 2019; 89:103035. [DOI: 10.1016/j.bioorg.2019.103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/23/2019] [Accepted: 06/03/2019] [Indexed: 11/16/2022]
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40
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Bhatt AB, Gupta M, Hoang VT, Chakrabarty S, Wright TD, Elliot S, Chopra IK, Monlish D, Anna K, Burow ME, Cavanaugh JE, Flaherty PT. Novel Diphenylamine Analogs Induce Mesenchymal to Epithelial Transition in Triple Negative Breast Cancer. Front Oncol 2019; 9:672. [PMID: 31417863 PMCID: PMC6682674 DOI: 10.3389/fonc.2019.00672] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/09/2019] [Indexed: 12/31/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) is a cellular program that converts non-motile epithelial cells into invasive mesenchymal cells. EMT is implicated in cancer metastasis, chemo-resistance, cancer progression, and generation of cancer stem cells (CSCs). Inducing mesenchymal to epithelial transition (MET), the reverse phenomenon of EMT, is proposed as a novel strategy to target triple negative and tamoxifen-resistant breast cancer. Triple negative breast cancer (TNBC) is characterized by the loss of hormone receptors, a highly invasive mesenchymal phenotype, and a lack of targeted therapy. Estrogen receptor-positive breast cancer can be targeted by tamoxifen, an ER antagonist. However, these cells undergo EMT over the course of treatment and develop resistance. Thus, there is an urgent need to develop therapeutic interventions to target these aggressive cancers. In this study, we examined the role of novel diphenylamine analogs in converting the mesenchymal phenotype of MDA-MB-231 TNBC cells to a lesser aggressive epithelial phenotype. Using analog-based drug design, a series of diphenylamine analogs were synthesized and initially evaluated for their effect on E-cadherin protein expression and changes incell morphology, which was quantified by measuring the spindle index (SI) value. Selected compound 1 from this series increases the expression of E-cadherin, a primary marker for epithelial cells, and decreases the mesenchymal markers SOX2, ZEB1, Snail, and vimentin. The increase in epithelial markers and the decrease in mesenchymal markers are consistent with a phenotypic switch from spindle-like morphology to cobblestone-like morphology. Furthermore, Compound 1 decreases spheroid viability, cell migration, and cell proliferation in triple negative BT-549 and tamoxifen-resistant MCF-7 breast cancer cells.
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Affiliation(s)
- Akshita B Bhatt
- Division of Pharmacology, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Mohit Gupta
- Division of Medicinal Chemistry, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Van T Hoang
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, United States
| | - Suravi Chakrabarty
- Division of Medicinal Chemistry, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Thomas D Wright
- Division of Pharmacology, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Steven Elliot
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, United States
| | - Ishveen K Chopra
- Division of Medicinal Chemistry, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Darlene Monlish
- Division of Pharmacology, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Katie Anna
- Division of Pharmacology, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Matthew E Burow
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, United States
| | - Jane E Cavanaugh
- Division of Pharmacology, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Patrick T Flaherty
- Division of Medicinal Chemistry, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
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Astl L, Verkhivker GM. Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks. Biochim Biophys Acta Gen Subj 2019:S0304-4165(19)30179-5. [PMID: 31330173 DOI: 10.1016/j.bbagen.2019.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Computational studies of allosteric interactions have witnessed a recent renaissance fueled by the growing interest in modeling of the complex molecular assemblies and biological networks. Allosteric interactions in protein structures allow for molecular communication in signal transduction networks. METHODS In this work, we performed a large scale comprehensive and multi-faceted analysis of >300 diverse allosteric proteins and complexes with allosteric modulators. By modeling and exploring coarse-grained dynamics, residue coevolution, and residue interaction networks for allosteric proteins, we have determined unifying molecular signatures shared by allosteric systems. RESULTS The results of this study have suggested that allosteric inhibitors and allosteric activators may differentially affect global dynamics and network organization of protein systems, leading to diverse allosteric mechanisms. By using structural and functional data on protein kinases, we present a detailed case study that that included atomic-level analysis of coevolutionary networks in kinases bound with allosteric inhibitors and activators. CONCLUSIONS We have found that coevolutionary networks can form direct communication pathways connecting functional regions and can recapitulate key regulatory sites and interactions responsible for allosteric signaling in the studied protein systems. The results of this computational investigation are compared with the experimental studies and reveal molecular signatures of known regulatory hotspots in protein kinases. GENERAL SIGNIFICANCE This study has shown that allosteric inhibitors and allosteric activators can have a different effect on residue interaction networks and can exploit distinct regulatory mechanisms, which could open up opportunities for probing allostery and new drug combinations with broad range of activities.
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Affiliation(s)
- Lindy Astl
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States of America
| | - Gennady M Verkhivker
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States of America; Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States of America.
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42
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Lev S, Li C, Desmarini D, Sorrell TC, Saiardi A, Djordjevic JT. Fungal Kinases With a Sweet Tooth: Pleiotropic Roles of Their Phosphorylated Inositol Sugar Products in the Pathogenicity of Cryptococcus neoformans Present Novel Drug Targeting Opportunities. Front Cell Infect Microbiol 2019; 9:248. [PMID: 31380293 PMCID: PMC6660261 DOI: 10.3389/fcimb.2019.00248] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022] Open
Abstract
Invasive fungal pathogens cause more than 300 million serious human infections and 1.6 million deaths per year. A clearer understanding of the mechanisms by which these fungi cause disease is needed to identify novel targets for urgently needed therapies. Kinases are key components of the signaling and metabolic circuitry of eukaryotic cells, which include fungi, and kinase inhibition is currently being exploited for the treatment of human diseases. Inhibiting evolutionarily divergent kinases in fungal pathogens is a promising avenue for antifungal drug development. One such group of kinases is the phospholipase C1-dependent inositol polyphosphate kinases (IPKs), which act sequentially to transfer a phosphoryl group to a pre-phosphorylated inositol sugar (IP). This review focuses on the roles of fungal IPKs and their IP products in fungal pathogenicity, as determined predominantly from studies performed in the model fungal pathogen Cryptococcus neoformans, and compares them to what is known in non-pathogenic model fungi and mammalian cells to highlight potential drug targeting opportunities.
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Affiliation(s)
- Sophie Lev
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Sydney Medical School-Westmead, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - Cecilia Li
- Sydney Medical School-Westmead, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, NSW Health Pathology, Westmead Hospital, Sydney, NSW, Australia
| | - Desmarini Desmarini
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Sydney Medical School-Westmead, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Sydney Medical School-Westmead, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - Adolfo Saiardi
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Julianne T Djordjevic
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Sydney Medical School-Westmead, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
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43
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Kannan S, Fox SJ, Verma CS. Exploring Gatekeeper Mutations in EGFR through Computer Simulations. J Chem Inf Model 2019; 59:2850-2858. [PMID: 31099565 DOI: 10.1021/acs.jcim.9b00361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of resistance against drugs that inhibit a particular protein is a major problem in targeted therapy. There is a clear need for rigorous methods to predict the likelihood of specific drug-resistance mutations arising in response to the binding of a drug. In this work we attempt to develop a robust computational protocol for predicting drug resistant mutations at the gatekeeper position (T790) in EGFR. We explore how mutations at this site affects interactions with ATP and three drugs that are currently used in clinics. We found, as expected, that certain mutations are not tolerated structurally, while some other mutations interfere with the natural substrate and hence are unlikely to be selected for. However, we found five possible mutations that are well tolerated structurally and energetically. Two of these mutations were predicted to have increased affinity for the drugs over ATP, as has been reported earlier. By reproducing the trends in the experimental binding affinities of the data, the methods chosen here are able to correctly predict the effects of these mutations on the binding affinities of the drugs. However, the increased affinity does not always translate into increased efficacy, because the efficacy is affected by several other factors such as binding kinetics, competition with ATP, and residence times. The computational methods used in the current study are able to reproduce or predict the effects of mutations on the binding affinities. However, a different set of methods is required to predict the kinetics of drug binding.
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Affiliation(s)
- Srinivasaraghavan Kannan
- Bioinformatics Institute , Agency for Science Technology and Research (A*STAR) , 30 Biopolis Street , #07-01 Matrix, Singapore 138671 Singapore
| | - Stephen J Fox
- Bioinformatics Institute , Agency for Science Technology and Research (A*STAR) , 30 Biopolis Street , #07-01 Matrix, Singapore 138671 Singapore
| | - Chandra S Verma
- Bioinformatics Institute , Agency for Science Technology and Research (A*STAR) , 30 Biopolis Street , #07-01 Matrix, Singapore 138671 Singapore.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551 , Singapore.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
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44
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Ramurthy S, Taft BR, Aversa RJ, Barsanti PA, Burger MT, Lou Y, Nishiguchi GA, Rico A, Setti L, Smith A, Subramanian S, Tamez V, Tanner H, Wan L, Hu C, Appleton BA, Mamo M, Tandeske L, Tellew JE, Huang S, Yue Q, Chaudhary A, Tian H, Iyer R, Hassan AQ, Mathews Griner LA, La Bonte LR, Cooke VG, Van Abbema A, Merritt H, Gampa K, Feng F, Yuan J, Mishina Y, Wang Y, Haling JR, Vaziri S, Hekmat-Nejad M, Polyakov V, Zang R, Sethuraman V, Amiri P, Singh M, Sellers WR, Lees E, Shao W, Dillon MP, Stuart DD. Design and Discovery of N-(3-(2-(2-Hydroxyethoxy)-6-morpholinopyridin-4-yl)-4-methylphenyl)-2-(trifluoromethyl)isonicotinamide, a Selective, Efficacious, and Well-Tolerated RAF Inhibitor Targeting RAS Mutant Cancers: The Path to the Clinic. J Med Chem 2019; 63:2013-2027. [PMID: 31059256 DOI: 10.1021/acs.jmedchem.9b00161] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Direct pharmacological inhibition of RAS has remained elusive, and efforts to target CRAF have been challenging due to the complex nature of RAF signaling, downstream of activated RAS, and the poor overall kinase selectivity of putative RAF inhibitors. Herein, we describe 15 (LXH254, Aversa, R.; et al. Int. Patent WO2014151616A1, 2014), a selective B/C RAF inhibitor, which was developed by focusing on drug-like properties and selectivity. Our previous tool compound, 3 (RAF709; Nishiguchi, G. A.; et al. J. Med. Chem. 2017, 60, 4969), was potent, selective, efficacious, and well tolerated in preclinical models, but the high human intrinsic clearance precluded further development and prompted further investigation of close analogues. A structure-based approach led to a pyridine series with an alcohol side chain that could interact with the DFG loop and significantly improved cell potency. Further mitigation of human intrinsic clearance and time-dependent inhibition led to the discovery of 15. Due to its excellent properties, it was progressed through toxicology studies and is being tested in phase 1 clinical trials.
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Affiliation(s)
- Savithri Ramurthy
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Benjamin R Taft
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Robert J Aversa
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Paul A Barsanti
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Matthew T Burger
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yan Lou
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Gisele A Nishiguchi
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alice Rico
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lina Setti
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Aaron Smith
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sharadha Subramanian
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Victoriano Tamez
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Huw Tanner
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lifeng Wan
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cheng Hu
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brent A Appleton
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mulugeta Mamo
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Laura Tandeske
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - John E Tellew
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Shenlin Huang
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Qin Yue
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Apurva Chaudhary
- Process Research and Development, Chemical and Analytical Development, Novartis Institute for Biomedical Research, One Health Plaza, East Hanover, New Jersey 07936, United States
| | - Hung Tian
- Technical Research & Development, Global Drug Development, Novartis Pharmaceuticals Corp., One Health Plaza, East Hanover, New Jersey 07936, United States
| | - Raman Iyer
- Technical Research & Development, Global Drug Development, Novartis Pharmaceuticals Corp., One Health Plaza, East Hanover, New Jersey 07936, United States
| | - A Quamrul Hassan
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lesley A Mathews Griner
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Laura R La Bonte
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Vesselina G Cooke
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Anne Van Abbema
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Hanne Merritt
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kalyani Gampa
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Fei Feng
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jing Yuan
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yuji Mishina
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yingyun Wang
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jacob R Haling
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Sepideh Vaziri
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Mohammad Hekmat-Nejad
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Valery Polyakov
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Richard Zang
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Vijay Sethuraman
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Payman Amiri
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mallika Singh
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - William R Sellers
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Emma Lees
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenlin Shao
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael P Dillon
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Darrin D Stuart
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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45
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A class of highly selective inhibitors bind to an active state of PI3Kγ. Nat Chem Biol 2019; 15:348-357. [DOI: 10.1038/s41589-018-0215-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/12/2018] [Indexed: 12/20/2022]
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46
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Smith BE, Wang SL, Jaime-Figueroa S, Harbin A, Wang J, Hamman BD, Crews CM. Differential PROTAC substrate specificity dictated by orientation of recruited E3 ligase. Nat Commun 2019; 10:131. [PMID: 30631068 PMCID: PMC6328587 DOI: 10.1038/s41467-018-08027-7] [Citation(s) in RCA: 291] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/07/2018] [Indexed: 01/10/2023] Open
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) are hetero-bifunctional molecules that recruit an E3 ubiquitin ligase to a given substrate protein resulting in its targeted degradation. Many potent PROTACs with specificity for dissimilar targets have been developed; however, the factors governing degradation selectivity within closely-related protein families remain elusive. Here, we generate isoform-selective PROTACs for the p38 MAPK family using a single warhead (foretinib) and recruited E3 ligase (von Hippel-Lindau). Based on their distinct linker attachments and lengths, these two PROTACs differentially recruit VHL, resulting in degradation of p38α or p38δ. We characterize the role of ternary complex formation in driving selectivity, showing that it is necessary, but insufficient, for PROTAC-induced substrate ubiquitination. Lastly, we explore the p38δ:PROTAC:VHL complex to explain the different selectivity profiles of these PROTACs. Our work attributes the selective degradation of two closely-related proteins using the same warhead and E3 ligase to heretofore underappreciated aspects of the ternary complex model.
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Affiliation(s)
- Blake E Smith
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
| | - Stephen L Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
| | - Saul Jaime-Figueroa
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
| | - Alicia Harbin
- Arvinas, Inc., 5 Science Park, New Haven, CT, 06511, USA
| | - Jing Wang
- Arvinas, Inc., 5 Science Park, New Haven, CT, 06511, USA
| | - Brian D Hamman
- Arvinas, Inc., 5 Science Park, New Haven, CT, 06511, USA
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, New Haven, CT, 06511, USA. .,Department of Pharmacology, Yale University, New Haven, CT, 06511, USA.
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47
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A novel scaffold for EGFR inhibition: Introducing N-(3-(3-phenylureido)quinoxalin-6-yl) acrylamide derivatives. Sci Rep 2019; 9:14. [PMID: 30626888 PMCID: PMC6327040 DOI: 10.1038/s41598-018-36846-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/29/2018] [Indexed: 11/08/2022] Open
Abstract
Clinical data acquired over the last decade on non-small cell lung cancer (NSCLC) treatment with small molecular weight Epidermal Growth Factor Receptor (EGFR) inhibitors have shown significant influence of EGFR point mutations and in-frame deletions on clinical efficacy. Identification of small molecules capable of inhibiting the clinically relevant EGFR mutant forms is desirable, and novel chemical scaffolds might provide knowledge regarding selectivity among EGFR forms and shed light on new strategies to overcome current clinical limitations. Design, synthesis, docking studies and in vitro evaluation of N-(3-(3-phenylureido)quinoxalin-6-yl) acrylamide derivatives (7a-m) against EGFR mutant forms are described. Compounds 7h and 7l were biochemically active in the nanomolar range against EGFRwt and EGFRL858R. Molecular docking and reaction enthalpy calculations have shown the influence of the combination of reversible and covalent binding modes with EGFR on the inhibitory activity. The inhibitory profile of 7h against a panel of patient-derived tumor cell lines was established, demonstrating selective growth inhibition of EGFR related cells at 10 μM among a panel of 30 cell lines derived from colon, melanoma, breast, bladder, kidney, prostate, pancreas and ovary tumors.
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48
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Hanson SM, Georghiou G, Thakur MK, Miller WT, Rest JS, Chodera JD, Seeliger MA. What Makes a Kinase Promiscuous for Inhibitors? Cell Chem Biol 2019; 26:390-399.e5. [PMID: 30612951 DOI: 10.1016/j.chembiol.2018.11.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/13/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
ATP-competitive kinase inhibitors often bind several kinases due to the high conservation of the ATP binding pocket. Through clustering analysis of a large kinome profiling dataset, we found a cluster of eight promiscuous kinases that on average bind more than five times more kinase inhibitors than the other 398 kinases in the dataset. To understand the structural basis of promiscuous inhibitor binding, we determined the co-crystal structure of the receptor tyrosine kinase DDR1 with the type I inhibitors dasatinib and VX-680. Surprisingly, we find that DDR1 binds these type I inhibitors in an inactive conformation typically reserved for type II inhibitors. Our computational and biochemical studies show that DDR1 is unusually stable in this inactive conformation, giving a mechanistic explanation for inhibitor promiscuity. This phenotypic clustering analysis provides a strategy to obtain functional insights not available by sequence comparison alone.
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Affiliation(s)
- Sonya M Hanson
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065-1115, USA
| | - George Georghiou
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Manish K Thakur
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - John D Chodera
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065-1115, USA.
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA.
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49
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Astl L, Tse A, Verkhivker GM. Interrogating Regulatory Mechanisms in Signaling Proteins by Allosteric Inhibitors and Activators: A Dynamic View Through the Lens of Residue Interaction Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:187-223. [DOI: 10.1007/978-981-13-8719-7_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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50
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Imamura RM, Kumagai K, Nakano H, Okabe T, Nagano T, Kojima H. Inexpensive High-Throughput Screening of Kinase Inhibitors Using One-Step Enzyme-Coupled Fluorescence Assay for ADP Detection. SLAS DISCOVERY 2018; 24:284-294. [PMID: 30418800 DOI: 10.1177/2472555218810139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein kinases are attractive targets for both biological research and drug development. Several assay kits, especially for the detection of adenosine diphosphate (ADP), which is universally produced by kinases, are commercially available for high-throughput screening (HTS) of kinase inhibitors, but their cost is quite high for large-scale screening. Here, we report a new enzyme-coupled fluorescence assay for ADP detection, which uses just 10 inexpensive, commercially available components. The assay protocol is very simple, requiring only the mixing of test solutions with ADP detection solution and reading the fluorescence intensity of resorufin produced by coupling reaction. To validate the assay, we focused on CDC2-like kinase 1 (CLK1), a dual-specificity kinase that plays an important role in alternative splicing, and we used the optimized assay to screen an in-house chemical library of about 215,000 compounds for CLK1 inhibitors. We identified and validated 12 potent inhibitors of CLK1, including a novel inhibitory scaffold. The results demonstrate that this assay platform is not only simple and cost-effective, but also sufficiently robust, showing good reproducibility and giving similar results to those obtained with the widely used ADP-Glo bioluminescent assay.
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Affiliation(s)
| | - Kazuo Kumagai
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan.,2 Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hirofumi Nakano
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Okabe
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Nagano
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Hirotatsu Kojima
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
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