1
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Wang X, DeFilippis RA, Yan W, Shah NP, Li HY. Overcoming Secondary Mutations of Type II Kinase Inhibitors. J Med Chem 2024; 67:9776-9788. [PMID: 38837951 DOI: 10.1021/acs.jmedchem.3c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Type II kinase inhibitors bind in the "DFG-out" kinase conformation and are generally considered to be more potent and selective than type I inhibitors, which target a DFG-in conformation. Nine type II inhibitors are currently clinically approved, with more undergoing clinical development. Resistance-conferring secondary mutations emerged with the first series of type II inhibitors, most commonly at residues within the kinase activation loop and at the "gatekeeper" position. Recently, new inhibitors have been developed to overcome such mutations; however, mutations activating other pathways (and/or other targets) have subsequently emerged on occasion. Here, we systematically summarize the secondary mutations that confer resistance to type II inhibitors, the structural basis for resistance, newer inhibitors designed to overcome resistance, as well as the challenges and opportunities for the development of new inhibitors to overcome secondary kinase domain mutations.
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Affiliation(s)
- Xiuqi Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rosa Anna DeFilippis
- Division of Hematology/Oncology, University of California, San Francisco, California 94143, United States
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Department of Pharmacology, School of Medicine, The University of Texas Health San Antonio, San Antonio, Texas 78229, United States
| | - Neil P Shah
- Division of Hematology/Oncology, University of California, San Francisco, California 94143, United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Department of Pharmacology, School of Medicine, The University of Texas Health San Antonio, San Antonio, Texas 78229, United States
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2
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Yu G, Zhang W, Basyal M, Nishida Y, Mizumo H, Ly C, Zhang H, Rice WG, Andreeff M. The multi-kinase inhibitor CG-806 exerts anti-cancer activity against acute myeloid leukemia by co-targeting FLT3, BTK, and aurora kinases. Leuk Lymphoma 2024:1-16. [PMID: 38871487 DOI: 10.1080/10428194.2024.2364839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/01/2024] [Indexed: 06/15/2024]
Abstract
Despite the development of several Fms-like tyrosine kinase 3 (FLT3) inhibitors that have improved outcomes in patients with FLT3-mutant acute myeloid leukemia (AML), drug resistance is frequently observed, which may be associated with the activation of additional pro-survival pathways, such as those regulated by BTK, aurora kinases (AuroK), and potentially others, in addition to acquired tyrosine kinase domain (TKD) mutations of FLT3 gene. FLT3 may not always be a driver mutation. We evaluated the anti-leukemia efficacy of the novel multi-kinase inhibitor CG-806, which targets FLT3 and other kinases, to circumvent drug resistance and target FLT3 wild-type (WT) cells. The anti-leukemia activity of CG-806 was investigated by measuring apoptosis induction and analyzing the cell cycle using flow cytometry in vitro. CG-806 demonstrated superior anti-leukemia efficacy compared to commercially available FLT3 inhibitors, both in vitro and in vivo, regardless of FLT3 mutational status. The mechanism of action of CG-806 may involve its broad inhibitory profile against FLT3, BTK, and AuroK. In FLT3 mutant cells, CG-806 induced G1 phase blockage, whereas in FLT3 WT cells, it resulted in G2/M phase arrest. Targeting FLT3 and Bcl-2 and/or Mcl-1 simultaneously results in a synergistic pro-apoptotic effect in FLT3 mutant leukemia cells. The results of this study suggest that CG-806 is a promising multi-kinase inhibitor with anti-leukemic efficacy regardless of FLT3 mutational status. A phase 1 clinical trial of CG-806 for the treatment of AML has been initiated (NCT04477291).Key pointsThe multi-kinase inhibitor CG-806 exerts superior anti-leukemic activity in AML, regardless of its FLT3 status.CG-806 triggered G1 arrest in FLT3 mutated cells and G2/M arrest in FLT3 WT cells through the suppression of FLT3/BTK and aurora kinases.Concomitantly targeting FLT3 and Bcl-2 and/or Mcl-1 exerted synergistic pro-apoptotic effects on both FLT3 WT and mutated AML cells.
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Affiliation(s)
- Guopan Yu
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weiguo Zhang
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mahesh Basyal
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuki Nishida
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hideaki Mizumo
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charlie Ly
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Michael Andreeff
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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3
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Khan ZR, Welsby PJ, Stasik I, Hayes JM. Discovery of Potent Multikinase Type-II Inhibitors Targeting CDK5 in the DFG-out Inactive State with Promising Potential against Glioblastoma. J Med Chem 2024. [PMID: 38686637 DOI: 10.1021/acs.jmedchem.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Kinases have proven valuable targets in successful cancer drug discovery projects, but not yet for malignant brain tumors where type-II inhibition of cyclin-dependent kinase 5 (CDK5) stabilizing the DFG-out inactive state has potential for design of selective and clinically efficient drug candidates. In the absence of crystallographic evidence for a CDK5 DFG-out inactive state protein-ligand complex, for the first time, a model was designed using metadynamics/molecular dynamics simulations. Glide docking of the ZINC15 biogenic database identified [pyrimidin-2-yl]amino-furo[3,2-b]-furyl-urea/amide hit chemical scaffolds. For four selected analogues (4, 27, 36, and 42), potent effects on glioblastoma cell viability in U87-MG, T98G, and U251-MG cell lines and patient-derived cultures were generally observed (IC50s ∼ 10-40 μM at 72 h). Selectivity profiling against 11 homologous kinases revealed multikinase inhibition (CDK2, CDK5, CDK9, and GSK-3α/β), most potent for GSK-3α in the nanomolar range (IC50s ∼ 0.23-0.98 μM). These compounds may therefore have diverse anticancer mechanisms of action and are of considerable interest for lead optimization.
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Affiliation(s)
- Zahra R Khan
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Philip J Welsby
- Education Directorate, Royal College of Physicians, Liverpool L7 3FA, United Kingdom
| | - Izabela Stasik
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Joseph M Hayes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
- Biomedical Evidence-Based Transdisciplinary (BEST) Health Research Institute, University of Central Lancashire, Preston PR1 2HE, United Kingdom
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4
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Daoud S, Taha M. Protein characteristics substantially influence the propensity of activity cliffs among kinase inhibitors. Sci Rep 2024; 14:9058. [PMID: 38643174 PMCID: PMC11032345 DOI: 10.1038/s41598-024-59501-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/11/2024] [Indexed: 04/22/2024] Open
Abstract
Activity cliffs (ACs) are pairs of structurally similar molecules with significantly different affinities for a biotarget, posing a challenge in computer-assisted drug discovery. This study focuses on protein kinases, significant therapeutic targets, with some exhibiting ACs while others do not despite numerous inhibitors. The hypothesis that the presence of ACs is dependent on the target protein and its complete structural context is explored. Machine learning models were developed to link protein properties to ACs, revealing specific tripeptide sequences and overall protein properties as critical factors in ACs occurrence. The study highlights the importance of considering the entire protein matrix rather than just the binding site in understanding ACs. This research provides valuable insights for drug discovery and design, paving the way for addressing ACs-related challenges in modern computational approaches.
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Affiliation(s)
- Safa Daoud
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Sciences Private University, Amman, Jordan.
| | - Mutasem Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan.
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5
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Veiga RN, de Azevedo ALK, de Oliveira JC, Gradia DF. Targeting EphA2: a promising strategy to overcome chemoresistance and drug resistance in cancer. J Mol Med (Berl) 2024; 102:479-493. [PMID: 38393661 DOI: 10.1007/s00109-024-02431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 01/24/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024]
Abstract
Erythropoietin-producing hepatocellular A2 (EphA2) is a vital member of the Eph tyrosine kinase receptor family and has been associated with developmental processes. However, it is often overexpressed in tumors and correlates with cancer progression and worse prognosis due to the activation of its noncanonical signaling pathway. Throughout cancer treatment, the emergence of drug-resistant tumor cells is relatively common. Since the early 2000s, researchers have focused on understanding the role of EphA2 in promoting drug resistance in different types of cancer, as well as finding efficient and secure EphA2 inhibitors. In this review, the current knowledge regarding induced resistance by EphA2 in cancer treatment is summarized, and the types of cancer that lead to the most cancer-related deaths are highlighted. Some EphA2 inhibitors were also investigated. Regardless of whether the cancer treatment has reached a drug-resistance stage in EphA2-overexpressing tumors, once EphA2 is involved in cancer progression and aggressiveness, targeting EphA2 is a promising therapeutic strategy, especially in combination with other target-drugs for synergistic effect. For that reason, monoclonal antibodies against EphA2 and inhibitors of this receptor should be investigated for efficacy and drug toxicity.
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Affiliation(s)
- Rafaela Nasser Veiga
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics. Department of Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Alexandre Luiz Korte de Azevedo
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics. Department of Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Jaqueline Carvalho de Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics. Department of Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics. Department of Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil.
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6
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Fouad MA, Osman AA, Abdelhamid NM, Rashad MW, Nabawy AY, El Kerdawy AM. Discovery of dual kinase inhibitors targeting VEGFR2 and FAK: structure-based pharmacophore modeling, virtual screening, and molecular docking studies. BMC Chem 2024; 18:29. [PMID: 38347617 PMCID: PMC10863211 DOI: 10.1186/s13065-024-01130-5] [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: 11/03/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
VEGFR2 and FAK signaling pathways are interconnected and have synergistic effects on tumor angiogenesis, growth, and metastasis. Thus, instead of the conventional targeting of each of these proteins individually with a specific inhibitor, the present work aimed to discover novel dual inhibitors targeting both VEGFR2 and FAK exploiting their association. To this end, receptor-based pharmacophore modeling technique was opted to generate 3D pharmacophore models for VEGFR2 and FAK type II kinase inhibitors. The generated pharmacophore models were validated by assessing their ability to discriminate between active and decoy compounds in a pre-compiled test set of VEGFR2 and FAK active compounds and decoys. ZINCPharmer web tool was then used to screen the ZINC database purchasable subset using the validated pharmacophore models retrieving 42,616 hits for VEGFR2 and 28,475 hits for FAK. Subsequently, they were filtered using various filters leaving 13,023 and 6,832 survived compounds for VEGFR2 and FAK, respectively, with 124 common compounds. Based on molecular docking simulations, thirteen compounds were found to satisfy all necessary interactions with VEGFR2 and FAK kinase domains. Thus, they are predicted to have a possible dual VEGFR2/FAK inhibitory activity. Finally, SwissADME web tool showed that compound ZINC09875266 is not only promising in terms of binding pattern to our target kinases, but also in terms of pharmacokinetic properties.
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Affiliation(s)
- Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo, 11562, Egypt.
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt.
| | - Alaa A Osman
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Noha M Abdelhamid
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Mai W Rashad
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Ashrakat Y Nabawy
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo, 11562, Egypt
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, Lincolnshire, UK
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7
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Bai Y, Qiao Y, Li M, Yang W, Chen H, Wu Y, Zhang H. RIPK1 inhibitors: A key to unlocking the potential of necroptosis in drug development. Eur J Med Chem 2024; 265:116123. [PMID: 38199165 DOI: 10.1016/j.ejmech.2024.116123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
Within the field of medical science, there is a great deal of interest in investigating cell death pathways in the hopes of discovering new drugs. Over the past two decades, pharmacological research has focused on necroptosis, a cell death process that has just been discovered. Receptor-interacting protein kinase 1 (RIPK1), an essential regulator in the cell death receptor signalling pathway, has been shown to be involved in the regulation of important events, including necrosis, inflammation, and apoptosis. Therefore, researching necroptosis inhibitors offers novel ways to treat a variety of disorders that are not well-treated by the therapeutic medications now on the market. The research and medicinal potential of RIPK1 inhibitors, a promising class of drugs, are thoroughly examined in this study. The journey from the discovery of Necrostatin-1 (Nec-1) to the recent advancements in RIPK1 inhibitors is marked by significant progress, highlighting the integration of traditional medicinal chemistry approaches with modern technologies like high-throughput screening and DNA-encoded library technology. This review presents a thorough exploration of the development and therapeutic potential of RIPK1 inhibitors, a promising class of compounds. Simultaneously, this review highlights the complex roles of RIPK1 in various pathological conditions and discusses potential inhibitors discovered through diverse pathways, emphasizing their efficacy against multiple disease models, providing significant guidance for the expansion of knowledge about RIPK1 and its inhibitors to develop more selective, potent, and safe therapeutic agents.
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Affiliation(s)
- Yinliang Bai
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, 730030, China; School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Yujun Qiao
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Mingming Li
- Department of Neurology, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Wenzhen Yang
- Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Haile Chen
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Yanqing Wu
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Honghua Zhang
- Department of Pharmacy, National University of Singapore, Singapore, 117544, Singapore.
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8
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Aboutaleb MH, El-Gohary NS, Ghabbour HA, El-Kerdawy MM. Design, synthesis, and evaluation of new benzimidazole thiourea derivatives as antitumor agents. Arch Pharm (Weinheim) 2023; 356:e2300269. [PMID: 37602810 DOI: 10.1002/ardp.202300269] [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: 05/15/2023] [Revised: 06/18/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
Novel benzimidazole thiourea derivatives were designed and synthesized based on sorafenib as a lead compound. The benzimidazole moiety was traded by the pyridine ring to enhance the hydrophobic interaction and retain hydrogen bonding in the hinge region, while lipophilic moieties with different bulkiness were employed in the deep hydrophobic pocket for better hydrophobic interactions. Thiourea as a urea bioisostere was also utilized. Substantial activity was demonstrated against a leukemia subpanel in an in vitro antitumor screening at the NCI. In the single-dose assay, compounds 7i, 7j, and 7l had a GI%) higher than sorafenib against most leukemia cell lines (GI% = 86.2%-137.1%), while in the five-dose assay, compound 7l outperformed sorafenib against the HL-60(TB) and SR leukemia cell lines in terms of GI50 , TGI, and LC50 . Compound 7l also caused cycle arrest at the G0-G1 and S phases in the HL-60(TB) leukemia cell line and induced apoptosis via elevating the Bax/Bcl-2 ratio and increasing caspases 3, 7, and 9 by 5.1-, 3.2-, and 5.2-fold, respectively. Compounds 7i, 7j, and 7l also inhibited the vascular endothelial growth factor receptor-2 (VEGFR-2), B-Raf(V600E) , and platelet-derived growth factor receptor beta (PDGFR-β) enzymes with an IC50 range of 0.063-0.44 μM. COMPARE analysis and a molecular docking study were also performed to predict the possible mechanism of action and binding mode, respectively.
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Affiliation(s)
- Mohamed H Aboutaleb
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University, New Damietta, Egypt
| | - Nadia S El-Gohary
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Hazem A Ghabbour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mohamed M El-Kerdawy
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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9
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Herrington NB, Stein D, Li YC, Pandey G, Schlessinger A. Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555779. [PMID: 37693436 PMCID: PMC10491245 DOI: 10.1101/2023.08.31.555779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Protein kinase function and interactions with drugs are controlled in part by the movement of the DFG and ɑC-Helix motifs, which enable kinases to adopt various conformational states. Small molecule ligands elicit therapeutic effects with distinct selectivity profiles and residence times that often depend on the kinase conformation(s) they bind. However, the limited availability of experimentally determined structural data for kinases in inactive states restricts drug discovery efforts for this major protein family. Modern AI-based structural modeling methods hold potential for exploring the previously experimentally uncharted druggable conformational space for kinases. Here, we first evaluated the currently explored conformational space of kinases in the PDB and models generated by AlphaFold2 (AF2) (1) and ESMFold (2), two prominent AI-based structure prediction methods. We then investigated AF2's ability to predict kinase structures in different conformations at various multiple sequence alignment (MSA) depths, based on this parameter's ability to explore conformational diversity. Our results showed a bias within the PDB and predicted structural models generated by AF2 and ESMFold toward structures of kinases in the active state over alternative conformations, particularly those conformations controlled by the DFG motif. Finally, we demonstrate that predicting kinase structures using AF2 at lower MSA depths allows the exploration of the space of these alternative conformations, including identifying previously unobserved conformations for 398 kinases. The results of our analysis of structural modeling by AF2 create a new avenue for the pursuit of new therapeutic agents against a notoriously difficult-to-target family of proteins. Significance Statement Greater abundance of kinase structural data in inactive conformations, currently lacking in structural databases, would improve our understanding of how protein kinases function and expand drug discovery and development for this family of therapeutic targets. Modern approaches utilizing artificial intelligence and machine learning have potential for efficiently capturing novel protein conformations. We provide evidence for a bias within AlphaFold2 and ESMFold to predict structures of kinases in their active states, similar to their overrepresentation in the PDB. We show that lowering the AlphaFold2 algorithm's multiple sequence alignment depth can help explore kinase conformational space more broadly. It can also enable the prediction of hundreds of kinase structures in novel conformations, many of whose models are likely viable for drug discovery.
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10
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Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH. How many kinases are druggable? A review of our current understanding. Biochem J 2023; 480:1331-1363. [PMID: 37642371 PMCID: PMC10586788 DOI: 10.1042/bcj20220217] [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: 05/04/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
There are over 500 human kinases ranging from very well-studied to almost completely ignored. Kinases are tractable and implicated in many diseases, making them ideal targets for medicinal chemistry campaigns, but is it possible to discover a drug for each individual kinase? For every human kinase, we gathered data on their citation count, availability of chemical probes, approved and investigational drugs, PDB structures, and biochemical and cellular assays. Analysis of these factors highlights which kinase groups have a wealth of information available, and which groups still have room for progress. The data suggest a disproportionate focus on the more well characterized kinases while much of the kinome remains comparatively understudied. It is noteworthy that tool compounds for understudied kinases have already been developed, and there is still untapped potential for further development in this chemical space. Finally, this review discusses many of the different strategies employed to generate selectivity between kinases. Given the large volume of information available and the progress made over the past 20 years when it comes to drugging kinases, we believe it is possible to develop a tool compound for every human kinase. We hope this review will prove to be both a useful resource as well as inspire the discovery of a tool for every kinase.
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Affiliation(s)
- Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Zachary W. Davis-Gilbert
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
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11
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Kwon EJ, Mashelkar KK, Seo J, Shin YZ, Sung K, Jang SC, Cheon SW, Lee H, Lee HW, Kim G, Han BW, Lee SK, Jeong LS, Cha HJ. In Silico Discovery of 5'-Modified 7-Deoxy-7-ethynyl-4'-thioadenosine as a HASPIN Inhibitor and Its Synergistic Anticancer Effect with the PLK1 Inhibitor. ACS CENTRAL SCIENCE 2023; 9:1140-1149. [PMID: 37396870 PMCID: PMC10311661 DOI: 10.1021/acscentsci.3c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Indexed: 07/04/2023]
Abstract
Despite genetic perturbations resulting in embryo lethality for most mitotic kinases, loss of the histone H3 mitotic kinase HASPIN reveals no adverse effect in mice models, establishing HASPIN as a promising target for anticancer therapy. However, developing a HASPIN inhibitor from conventional pharmacophores poses a technical challenge as this atypical kinase shares slight similarities with eukaryotic protein kinases. Chemically modifying a cytotoxic 4'-thioadenosine analogue through high genotoxicity yielded several novel nongenotoxic kinase inhibitors. In silico apporoaches utilizing transcriptomic and chemical similarities with known compounds and KINOMEscan profiles unveiled the HASPIN inhibitor LJ4827. LJ4827's specificity and potency as a HASPIN inhibitor were verified through in vitro kinase assay and X-ray crystallography. HASPIN inhibition by LJ4827 reduced histone H3 phosphorylation and impeded Aurora B recruitment in cancer cell centromeres but not in noncancer cells. Through transcriptome analysis of lung cancer patients, PLK1 was determined as a druggable synergistic partner to complement HASPIN inhibition. Chemical or genetic PLK1 perturbation with LJ4827 effectuated pronounced lung cancer cytotoxicity in vitro and in vivo. Therefore, LJ4827 is a novel anticancer therapeutic for selectively impeding cancer mitosis through potent HASPIN inhibition, and simultaneous HASPIN and PLK1 interference is a promising therapeutic strategy for lung cancer.
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Affiliation(s)
- Eun-Ji Kwon
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | | | - Juhee Seo
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoon-Ze Shin
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kisu Sung
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Natural Products
Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Won Cheon
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Haeseung Lee
- College
of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
- Research
Institute for Drug Development, Pusan National
University, Busan 46241, Republic
of Korea
| | - Hyuk Woo Lee
- Future
Medicine Company, Limited, Seongnam, Gyeonggi-do 13449, Republic of Korea
| | - Gyudong Kim
- College
of Pharmacy, and Research Institute of Drug Development, Chonnam National University, Gwangju 61469, Republic of Korea
| | - Byung Woo Han
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic
of Korea
| | - Sang Kook Lee
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Natural Products
Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Lak Shin Jeong
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic
of Korea
- Future
Medicine Company, Limited, Seongnam, Gyeonggi-do 13449, Republic of Korea
| | - Hyuk-Jin Cha
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic
of Korea
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12
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Kim D, Orr MJ, Kwong AJ, Deibler KK, Munshi HH, Bridges CS, Chen TJ, Zhang X, Lacorazza HD, Scheidt KA. Rational Design of Highly Potent and Selective Covalent MAP2K7 Inhibitors. ACS Med Chem Lett 2023; 14:606-613. [PMID: 37197477 PMCID: PMC10184151 DOI: 10.1021/acsmedchemlett.3c00029] [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: 01/24/2023] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
The mitogen-activated protein kinase signaling cascade is conserved across eukaryotes, where it plays a critical role in the regulation of activities including proliferation, differentiation, and stress responses. This pathway propagates external stimuli through a series of phosphorylation events, which allows external signals to influence metabolic and transcriptional activities. Within the cascade, MEK, or MAP2K, enzymes occupy a molecular crossroads immediately upstream to significant signal divergence and cross-talk. One such kinase, MAP2K7, also known as MEK7 and MKK7, is a protein of great interest in the molecular pathophysiology underlying pediatric T cell acute lymphoblastic leukemia (T-ALL). Herein, we describe the rational design, synthesis, evaluation, and optimization of a novel class of irreversible MAP2K7 inhibitors. With a streamlined one-pot synthesis, favorable in vitro potency and selectivity, and promising cellular activity, this novel class of compounds wields promise as a powerful tool in the study of pediatric T-ALL.
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Affiliation(s)
- Dalton
R. Kim
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Meghan J. Orr
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Ada J. Kwong
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kristine K. Deibler
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hasan H. Munshi
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Cory Seth Bridges
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Taylor Jie Chen
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Xiaoyu Zhang
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United
States
| | - H. Daniel Lacorazza
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Karl A. Scheidt
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United
States
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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13
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Hu J, Zhang D, Tian K, Ren C, Li H, Lin C, Huang X, Liu J, Mao W, Zhang J. Small-molecule LRRK2 inhibitors for PD therapy: Current achievements and future perspectives. Eur J Med Chem 2023; 256:115475. [PMID: 37201428 DOI: 10.1016/j.ejmech.2023.115475] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multifunctional protein that orchestrates a diverse array of cellular processes, including vesicle transport, autophagy, lysosome degradation, neurotransmission, and mitochondrial activity. Hyperactivation of LRRK2 triggers vesicle transport dysfunction, neuroinflammation, accumulation of α-synuclein, mitochondrial dysfunction, and the loss of cilia, ultimately leading to Parkinson's disease (PD). Therefore, targeting LRRK2 protein is a promising therapeutic strategy for PD. The clinical translation of LRRK2 inhibitors was historically impeded by issues surrounding tissue specificity. Recent studies have identified LRRK2 inhibitors that have no effect on peripheral tissues. Currently, there are four small-molecule LRRK2 inhibitors undergoing clinical trials. This review provides a summary of the structure and biological functions of LRRK2, along with an overview of the binding modes and structure-activity relationships (SARs) of small-molecule inhibitors targeting LRRK2. It offers valuable references for developing novel drugs targeting LRRK2.
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Affiliation(s)
- Jiarui Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Keyue Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Changyu Ren
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Heng Li
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Congcong Lin
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaoli Huang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wuyu Mao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China; Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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14
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Xiao ZP, Liao M, Huang XJ, Wang YT, Lan XC, Wang XY, Li XT. Design, synthesis and evaluation of a series of potential prodrugs of a Bruton’s tyrosine kinase (BTK) inhibitor. Front Pharmacol 2023; 14:1162216. [PMID: 36969836 PMCID: PMC10031131 DOI: 10.3389/fphar.2023.1162216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
BTK has become a particularly attractive therapeutic target in autoimmune diseases and B-cell malignancies, making BTK inhibitors a valuable and important therapeutic option. We present the design, synthesis, and evaluation of a series of prodrugs of a BTK inhibitor with an insoluble 2,5-diaminopyrimidine structure. Tails containing different solubilizing groups were added to the parent molecule via an ester linkage. Prodrug 5a showed good aqueous solubility and could be efficiently converted to the parent in a human plasma stability study. The rational prodrug design was supported by molecular studies and a dramatically reduced BTK kinase-inhibitory potential. Taken together, the chemical, biological, and molecular studies suggest that prodrug derivatization of the 2,5-diaminopyrimidine scaffold could be a potential strategy for advancing this series of BTK inhibitors into the therapeutic arena.
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Affiliation(s)
- Zhou-Peng Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Min Liao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xue-Juan Huang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yu-Tong Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xiao-Cui Lan
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xue-Ying Wang
- BayRay Innovative Center, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xi-Tao Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- *Correspondence: Xi-Tao Li,
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15
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Nojima Y, Aoki M, Re S, Hirano H, Abe Y, Narumi R, Muraoka S, Shoji H, Honda K, Tomonaga T, Mizuguchi K, Boku N, Adachi J. Integration of pharmacoproteomic and computational approaches reveals the cellular signal transduction pathways affected by apatinib in gastric cancer cell lines. Comput Struct Biotechnol J 2023; 21:2172-2187. [PMID: 37013003 PMCID: PMC10066531 DOI: 10.1016/j.csbj.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Apatinib is known to be a highly selective vascular endothelial growth factor receptor 2 (VEGFR2) inhibitor with anti-angiogenic and anti-tumor properties. In a phase III study, the objective response rate to apatinib was low. It remains unclear why the effectivity of apatinib varies among patients and what type of patients are candidates for the treatment. In this study, we investigated the anti-tumor efficacy of apatinib against 13 gastric cancer cell lines and found that it differed depending on the cell line. Using integrated wet and dry approaches, we showed that apatinib was a multi-kinase inhibitor of c-Kit, RAF1, VEGFR1, VEGFR2, and VEGFR3, predominantly inhibiting c-Kit. Notably, KATO-III, which was the most apatinib-sensitive among the gastric cancer cell lines investigated, was the only cell line expressing c-Kit, RAF1, VEGFR1, and VEGFR3 but not VEGFR2. Furthermore, we identified SNW1 as a molecule affected by apatinib that plays an important role in cell survival. Finally, we identified the molecular network related to SNW1 that was affected by treatment with apatinib. These results suggest that the mechanism of action of apatinib in KATO-III cells is independent of VEGFR2 and that the differential efficacy of apatinib was due to differences in expression patterns of receptor tyrosine kinases. Furthermore, our results suggest that the differential efficacy of apatinib in gastric cell lines may be attributed to SNW1 phosphorylation levels at a steady state. These findings contribute to a deeper understanding of the mechanism of action of apatinib in gastric cancer cells.
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Affiliation(s)
- Yosui Nojima
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Center for Mathematical Modeling and Data Science, Osaka University, Osaka 560–8531, Japan
| | - Masahiko Aoki
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Department of Early Clinical Development, Graduate School of Medicine, Kyoto University Hospital, Kyoto 606–8507, Japan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
| | - Hidekazu Hirano
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya 464–8681, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Satoshi Muraoka
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Hirokazu Shoji
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
| | - Kazufumi Honda
- Department of Biomarkers for Early Detection of Cancer, National Cancer Center Research Institute, Tokyo 104–0045, Japan
- Department of Bioregulation, Graduate School of Medicine, Nippon Medical School, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Proteobiologics Co., Ltd., Osaka 567–0085, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Institute for Protein Research, Osaka University, Osaka 565–0871, Japan
| | - Narikazu Boku
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, Tokyo 108–8639, Japan
- Correspondence to: Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, 4–6-1 Minato-ku, Shiroganedai, Tokyo 108–8639, Japan.
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Correspondence to: Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, 7–6-8 Saito-asagi, Ibaraki, Osaka 567–0085, Japan.
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16
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Molecular and Biological Investigation of Isolated Marine Fungal Metabolites as Anticancer Agents: A Multi-Target Approach. Metabolites 2023; 13:metabo13020162. [PMID: 36837781 PMCID: PMC9964656 DOI: 10.3390/metabo13020162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Cancer is the leading cause of death globally, with an increasing number of cases being annually reported. Nature-derived metabolites have been widely studied for their potential programmed necrosis, cytotoxicity, and anti-proliferation leading to enrichment for the modern medicine, particularly within the last couple of decades. At a more rapid pace, the concept of multi-target agents has evolved from being an innovative approach into a regular drug development procedure for hampering the multi-fashioned pathophysiology and high-resistance nature of cancer cells. With the advent of the Red Sea Penicillium chrysogenum strain S003-isolated indole-based alkaloids, we thoroughly investigated the molecular aspects for three major metabolites: meleagrin (MEL), roquefortine C (ROC), and isoroquefortine C (ISO) against three cancer-associated biological targets Cdc-25A, PTP-1B, and c-Met kinase. The study presented, for the first time, the detailed molecular insights and near-physiological affinity for these marine indole alkaloids against the assign targets through molecular docking-coupled all-atom dynamic simulation analysis. Findings highlighted the superiority of MEL's binding affinity/stability being quite in concordance with the in vitro anticancer activity profile conducted via sulforhodamine B bioassay on different cancerous cell lines reaching down to low micromolar or even nanomolar potencies. The advent of lengthy structural topologies via the metabolites' extended tetracyclic cores and aromatic imidazole arm permitted multi-pocket accommodation addressing the selectivity concerns. Additionally, the presence decorating polar functionalities on the core hydrophobic tetracyclic ring contributed compound's pharmacodynamic preferentiality. Introducing ionizable functionality with more lipophilic characters was highlighted to improve binding affinities which was also in concordance with the conducted drug-likeness/pharmacokinetic profiling for obtaining a balanced pharmacokinetic/dynamic profile. Our study adds to the knowledge regarding drug development and optimization of marine-isolated indole-based alkaloids for future iterative synthesis and pre-clinical investigations as multi-target anticancer agents.
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17
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Naik RR, Shakya AK. Exploring the chemotherapeutic potential of currently used kinase inhibitors: An update. Front Pharmacol 2023; 13:1064472. [PMID: 36699049 PMCID: PMC9868582 DOI: 10.3389/fphar.2022.1064472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/28/2022] [Indexed: 01/11/2023] Open
Abstract
Protein kinases are enzymes that transfer phosphate to protein, resulting in the modification of the protein. The human genome encodes approximately 538 kinases. Kinases play a role in maintaining a number of cellular processes, including control of the cell cycle, metabolism, survival, and differentiation. Protein kinase dysregulation causes several diseases, and it has been shown that numerous kinases are deregulated in cancer. The oncogenic potential of these kinases is increased by a number of processes, including overexpression, relocation, fusion point mutations, and the disruption of upstream signaling. Understanding of the mechanism or role played by kinases has led to the development of a large number of kinase inhibitors with promising clinical benefits. In this review, we discuss FDA-approved kinase inhibitors and their mechanism, clinical benefits, and side effects, as well as the challenges of overcoming some of their side effects and future prospects for new kinase inhibitor discovery.
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Affiliation(s)
- Rajashri R. Naik
- Faculty of Allied Medical Sciences, Pharmacological and Diagnostic Research Center, Al-Ahliyya Amman University, Amman, Jordan
| | - Ashok K. Shakya
- Faculty of Pharmacy, Pharmacological and Diagnostic Research Center, Al-Ahliyya Amman University, Amman, Jordan,*Correspondence: Ashok K. Shakya,
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18
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Lee PY, Yeoh Y, Low TY. A recent update on small‐molecule kinase inhibitors for targeted cancer therapy and their therapeutic insights from mass spectrometry‐based proteomic analysis. FEBS J 2022. [DOI: 10.1111/febs.16442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/21/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI) Universiti Kebangsaan Malaysia Kuala Lumpur Malaysia
| | - Yeelon Yeoh
- UKM Medical Molecular Biology Institute (UMBI) Universiti Kebangsaan Malaysia Kuala Lumpur Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI) Universiti Kebangsaan Malaysia Kuala Lumpur Malaysia
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19
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Design, synthesis and anticancer evaluation of 6,7-disubstituted-4-phenoxyquinoline derivatives bearing 1,8-naphthyridine-3-carboxamide moiety as novel multi-target TKIs. Bioorg Chem 2022; 121:105672. [PMID: 35202851 DOI: 10.1016/j.bioorg.2022.105672] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/01/2022] [Accepted: 02/07/2022] [Indexed: 12/20/2022]
Abstract
Giving the fact that the disorders of multiple receptor tyrosine kinases (RTKs) are characteristics of various cancers, we assumed that developing novel multi-target drugs might have an advantage in treating the complex cancers. Taking the multi-target c-Met inhibitor Foretinib as the leading compound, we discovered a novel series of 6,7-disubstituted-4-phenoxyquinoline derivatives bearing 1,8-naphthyridine-3-carboxamide moiety with the help of molecular docking. Among them, the most promising compound 33 showed a prominent activity against Hela (IC50 = 0.21 µM), A549 (IC50 = 0.39 µM), and MCF-7 (IC50 = 0.33 µM), which were 3.28-4.82 times more active than that of Foretinib. Additionally, compound 33 dose dependently induced apoptosis by arresting A549 cells at G1 phase. Enzymatic assays and docking analyses were further confirmed that compound 33 was a multi-target inhibitor with the strong potencies against c-Met (IC50 = 11.77 nM), MEK1 (IC50 = 10.71 nM), and Flt-3 (IC50 = 22.36 nM). In the A549 cells mediated xenograft mouse model, compound 33 inhibited the tumor growth (TGI = 64%) without obvious toxicity, establishing compound 33 as a promising candidate for cancer therapy.
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20
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Lešnik S, Bren U. Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking. Foods 2021; 11:67. [PMID: 35010191 PMCID: PMC8750736 DOI: 10.3390/foods11010067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 01/18/2023] Open
Abstract
Rosemary (Rosmarinus officinalis L.) represents a medicinal plant known for its various health-promoting properties. Its extracts and essential oils exhibit antioxidative, anti-inflammatory, anticarcinogenic, and antimicrobial activities. The main compounds responsible for these effects are the diterpenes carnosic acid, carnosol, and rosmanol, as well as the phenolic acid ester rosmarinic acid. However, surprisingly little is known about the molecular mechanisms responsible for the pharmacological activities of rosemary and its compounds. To discern these mechanisms, we performed a large-scale inverse molecular docking study to identify their potential protein targets. Listed compounds were separately docked into predicted binding sites of all non-redundant holo proteins from the Protein Data Bank and those with the top scores were further examined. We focused on proteins directly related to human health, including human and mammalian proteins as well as proteins from pathogenic bacteria, viruses, and parasites. The observed interactions of rosemary compounds indeed confirm the beforementioned activities, whereas we also identified their potential for anticoagulant and antiparasitic actions. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using both redocking procedures and retrospective metrics.
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Affiliation(s)
- Samo Lešnik
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia;
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia;
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
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21
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Turner LD, Trinh CH, Hubball RA, Orritt KM, Lin CC, Burns JE, Knowles MA, Fishwick CWG. From Fragment to Lead: De Novo Design and Development toward a Selective FGFR2 Inhibitor. J Med Chem 2021; 65:1481-1504. [PMID: 34780700 DOI: 10.1021/acs.jmedchem.1c01163] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fibroblast growth factor receptors (FGFRs) are implicated in a range of cancers with several pan-kinase and selective-FGFR inhibitors currently being evaluated in clinical trials. Pan-FGFR inhibitors often cause toxic side effects and few examples of subtype-selective inhibitors exist. Herein, we describe a structure-guided approach toward the development of a selective FGFR2 inhibitor. De novo design was carried out on an existing fragment series to yield compounds predicted to improve potency against the FGFRs. Subsequent iterative rounds of synthesis and biological evaluation led to an inhibitor with nanomolar potency that exhibited moderate selectivity for FGFR2 over FGFR1/3. Subtle changes to the lead inhibitor resulted in a complete loss of selectivity for FGFR2. X-ray crystallographic studies revealed inhibitor-specific morphological differences in the P-loop which were posited to be fundamental to the selectivity of these compounds. Additional docking studies have predicted an FGFR2-selective H-bond which could be utilized to design more selective FGFR2 inhibitors.
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Affiliation(s)
- Lewis D Turner
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
| | - Ryan A Hubball
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
| | - Kyle M Orritt
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
| | - Chi-Chuan Lin
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
| | - Julie E Burns
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, LS9 7TF, U.K
| | - Margaret A Knowles
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, LS9 7TF, U.K
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22
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Bauer S, George S, von Mehren M, Heinrich MC. Early and Next-Generation KIT/PDGFRA Kinase Inhibitors and the Future of Treatment for Advanced Gastrointestinal Stromal Tumor. Front Oncol 2021; 11:672500. [PMID: 34322383 PMCID: PMC8313277 DOI: 10.3389/fonc.2021.672500] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
The majority of gastrointestinal stromal tumors (GIST) harbor an activating mutation in either the KIT or PDGFRA receptor tyrosine kinases. Approval of imatinib, a KIT/PDGFRA tyrosine kinase inhibitor (TKI), meaningfully improved the treatment of advanced GIST. Other TKIs subsequently gained approval: sunitinib as a second-line therapy and regorafenib as a third-line therapy. However, resistance to each agent occurs in almost all patients over time, typically due to secondary kinase mutations. A major limitation of these 3 approved therapies is that they target the inactive conformation of KIT/PDGFRA; thus, their efficacy is blunted against secondary mutations in the kinase activation loop. Neither sunitinib nor regorafenib inhibit the full spectrum of KIT resistance mutations, and resistance is further complicated by extensive clonal heterogeneity, even within single patients. To combat these limitations, next-generation TKIs were developed and clinically tested, leading to 2 new USA FDA drug approvals in 2020. Ripretinib, a broad-spectrum KIT/PDGFRA inhibitor, was recently approved for the treatment of adult patients with advanced GIST who have received prior treatment with 3 or more kinase inhibitors, including imatinib. Avapritinib, a type I kinase inhibitor that targets active conformation, was approved for the treatment of adults with unresectable or metastatic GIST harboring a PDGFRA exon 18 mutation, including PDGFRA D842V mutations. In this review, we will discuss how resistance mutations have driven the need for newer treatment options for GIST and compare the original GIST TKIs with the next-generation KIT/PDGFRA kinase inhibitors, ripretinib and avapritinib, with a focus on their mechanisms of action.
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Affiliation(s)
- Sebastian Bauer
- Department of Medical Oncology, West German Cancer Center, Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Suzanne George
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Margaret von Mehren
- Department of Hematology and Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Michael C. Heinrich
- Department of Medicine, Portland VA Health Care System and OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
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Beeston HS, Klein T, Norman RA, Tucker JA, Anderson M, Ashcroft AE, Holdgate GA. Validation of ion mobility spectrometry - mass spectrometry as a screening tool to identify type II kinase inhibitors of FGFR1 kinase. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021:e9130. [PMID: 34038603 DOI: 10.1002/rcm.9130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/24/2021] [Indexed: 05/22/2023]
Abstract
RATIONALE The protein kinase FGFR1 regulates cellular processes in human development. As over-activity of FGFR1 is implicated with cancer, effective inhibitors are in demand. Type I inhibitors, which bind to the active form of FGFR1, are less effective than type II inhibitors, which bind to the inactive form. Screening to distinguish between type I and type II inhibitors is required. METHODS X-ray crystallography was used to indicate whether a range of potential inhibitors bind to the active or inactive FGFR1 kinase conformation. The binding affinity of each ligand to FGFR1 was measured using biochemical methods. Electrospray ionisation - ion mobility spectrometry - mass spectrometry (ESI-IMS-MS) in conjunction with collision-induced protein unfolding generated a conformational profile of each FGFR1-ligand complex. The results indicate that the protein's conformational profile depends on whether the inhibitor is type I or type II. RESULTS X-ray crystallography confirmed which of the kinase inhibitors bind to the active or inactive form of FGFR1 kinase. Collision-induced unfolding combined with ESI-IMS-MS showed distinct differences in the FGFR1 folding landscape for type I and type II inhibitors. Biochemical studies indicated a similar range of FGFR1 affinities for both types of inhibitors, thus providing confidence that the conformational variations detected using ESI-IMS-MS can be interpretated unequivocally and that this is an effective screening method. CONCLUSIONS A robust ESI-IMS-MS method has been implemented to distinguish between the binding mode of type I and type II inhibitors by monitoring the conformational unfolding profile of FGFR1. This rapid method requires low sample concentrations and could be used as a high-throughput screening technique for the characterisation of novel kinase inhibitors.
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Affiliation(s)
- Helen S Beeston
- Astbury Centre for Structural Molecular Biology & Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Tobias Klein
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Richard A Norman
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Julie A Tucker
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Malcolm Anderson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology & Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Geoffrey A Holdgate
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
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24
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A Special View of What Was Almost Forgotten: p38δ MAPK. Cancers (Basel) 2021; 13:cancers13092077. [PMID: 33923030 PMCID: PMC8123357 DOI: 10.3390/cancers13092077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary p38δ MAPK, as well as the other p38 isoforms, was proposed as a drug target for cancer therapy, owing to its critical roles in cellular signaling. However, herein, we show that p38δ inhibition may be therapeutically beneficial for treatment of specific cancer types, such as skin carcinoma, hepatocellular carcinoma (HCC), head and neck squamous cell carcinoma (HNSCC), cholangiocarcinoma (CC), and breast cancer. This review aims to discuss the roles of p38δ in cancer and summarize the findings of molecules with potential to inhibit p38δ in order to guide the search for new target cancer therapies based on p38δ inhibitors. Abstract The p38δ mitogen-activated protein kinase is an important signal transduction enzyme. p38δ has recently emerged as a drug target due to its tissue-specific expression patterns and its critical roles in regulation of cellular processes related to cancer and inflammatory diseases, such as cell proliferation, cell migration, apoptosis, and inflammatory responses. However, potent and specific p38δ inhibitors have not been defined so far. Moreover, in cancer disease, p38δ appears to act as a tumor suppressor or tumor promoter according to cancer and cell type studied. In this review, we outline the current understanding of p38δ roles in each cancer type, to define whether it is possible to delineate new cancer therapies based on small-molecule p38δ inhibitors. We also highlight recent advances made in the design of molecules with potential to inhibit p38 isoforms and discuss structural approaches to guide the search for p38δ inhibitors.
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25
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Cerchione C, Locatelli F, Martinelli G. Dasatinib in the Management of Pediatric Patients With Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia. Front Oncol 2021; 11:632231. [PMID: 33842339 PMCID: PMC8027101 DOI: 10.3389/fonc.2021.632231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Acute leukemia is the most common cancer in childhood; in particular, acute lymphoblastic leukemia (ALL) represents roughly up to 80% of all cases of acute leukemias in children. Survival of children with ALL has dramatically improved over the last few decades, and is now over 90% (versus 40% of adult patients) in developed countries, except for in infants (i.e., children < 1 year), where no significant improvement was registered. Philadelphia positive ALL (Ph+ALL) accounts for around 3% of cases of childhood ALL, its incidence increasing with patient's age. Before the era of tyrosine-kinase inhibitors (TKIs), pediatric Ph+ALL showed a worse prognosis in comparison to other forms of ALL, and was managed with intensive chemotherapy, followed, whenever possible, by allogenic hematopoietic stem cell transplantation (HSCT) in first morphological complete remission. TKIs have revolutionized the current clinical approach, which involves combinations of imatinib plus standard chemotherapy that can abrogate the negative prognostic impact conferred by the presence of BCR/ABL1 rearrangement, resulting in the probability of event-free survival (EFS) being significantly better than that recorded in the pre-TKI era. Long-term follow-up confirms these data, questioning the role of a real advantage offered by HSCT over intensive chemotherapy plus TKI in all Ph+ALL pediatric patients. Imatinib was the first generation TKI and the prototype of targeted therapy, but over the years second- (dasatinib, nilotinib, bosutinib) and third-generation (ponatinib) TKIs showed a capacity to overcome resistance to imatinib in Ph+ hematological neoplasms. Given the effectiveness of the first-in-class TKI, imatinib, also the second-generation TKI dasatinib was incorporated in the treatment regimens of Ph+ALL. In this manuscript, we will discuss the role of this drug in pediatric Ph+ALL, analyzing the available data published to date.
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Affiliation(s)
- Claudio Cerchione
- Hematology Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Department of Pediatrics, University of Rome, Sapienza, Rome, Italy
| | - Giovanni Martinelli
- Hematology Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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26
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Davies MP, Benitez R, Perez C, Jakupovic S, Welsby P, Rzepecka K, Alder J, Davidson C, Martinez A, Hayes JM. Structure-Based Design of Potent Selective Nanomolar Type-II Inhibitors of Glycogen Synthase Kinase-3β. J Med Chem 2021; 64:1497-1509. [PMID: 33499592 DOI: 10.1021/acs.jmedchem.0c01568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
For the first time, the in silico design, screening, and in vitro validation of potent GSK-3β type-II inhibitors are presented. In the absence of crystallographic evidence for a DFG-out GSK-3β activation loop conformation, computational models were designed using an adapted DOLPHIN approach and a method consisting of Prime loop refinement, induced-fit docking, and molecular dynamics. Virtual screening of the Biogenics subset from the ZINC database led to an initial selection of 20 Phase I compounds revealing two low micromolar inhibitors in an isolated enzyme assay. Twenty more analogues (Phase II compounds) related to the hit [pyrimidin-2-yl]amino-furo[3,2-b]furyl-urea scaffold were selected for structure-activity relationship analysis. The Phase II studies led to five highly potent nanomolar inhibitors, with compound 23 (IC50 =0.087 μM) > 100 times more potent than the best Phase I inhibitor, and selectivity for GSK-3β inhibition compared to homologous kinases was observed. Ex vivo experiments (SH-SY5Y cell lines) for tau hyperphosphorylation revealed promising neuroprotective effects at low micromolar concentrations. The type-II inhibitor design has been unraveled as a potential route toward more clinically effective GSK-3β inhibitors.
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Affiliation(s)
- Matthew P Davies
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Rocio Benitez
- Centro de Investigaciones Biologicas, CSIC, Avenida Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Concepción Perez
- Instituto de Quimica Medica, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Sven Jakupovic
- AnalytiCon Discovery GmbH, Hermannswerder Haus 17, 14473 Potsdam, Germany
| | - Philip Welsby
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Klaudia Rzepecka
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Jane Alder
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Colin Davidson
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Ana Martinez
- Centro de Investigaciones Biologicas, CSIC, Avenida Ramiro de Maeztu 9, 28040 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28031 Madrid, Spain
| | - Joseph M Hayes
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
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27
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Smith RHB, Khan ZM, Ung PMU, Scopton AP, Silber L, Mack SM, Real AM, Schlessinger A, Dar AC. Type II Binders Targeting the "GLR-Out" Conformation of the Pseudokinase STRADα. Biochemistry 2021; 60:289-302. [PMID: 33440120 DOI: 10.1021/acs.biochem.0c00714] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pseudokinases play important roles in signal transduction and cellular processes similar to those of catalytically competent kinases. However, pseudokinase pharmacological tractability and conformational space accessibility are poorly understood. Pseudokinases have only recently been suggested to adopt "inactive" conformations or interact with conformation-specific kinase inhibitors (e.g., type II compounds). In this work, the heavily substituted pseudokinase STRADα, which possesses a DFG → GLR substitution in the catalytic site that permits nucleotide binding while impairing divalent cation coordination, is used as a test case to demonstrate the potential applicability of conformation-specific, type II compounds to pseudokinase pharmacology. Integrated structural modeling is employed to generate a "GLR-out" conformational ensemble. Likely interacting type II compounds are identified through virtual screening against this ensemble model. Biophysical validation of compound binding is demonstrated through protein thermal stabilization and ATP competition. Localization of a top-performing compound through surface methylation strongly suggests that STRADα can adopt the "GLR-out" conformation and interact with compounds that comply with the standard type II pharmacophore. These results suggest that, despite a loss of catalytic function, some pseudokinases, including STRADα, may retain the conformational switching properties of conventional protein kinases.
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Affiliation(s)
- Ryan H B Smith
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Zaigham M Khan
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Peter Man-Un Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Alex P Scopton
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Lisa Silber
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Seshat M Mack
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Alexander M Real
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Arvin C Dar
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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28
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Ceramella J, Iacopetta D, Barbarossa A, Caruso A, Grande F, Bonomo MG, Mariconda A, Longo P, Carmela S, Sinicropi MS. Carbazole Derivatives as Kinase-Targeting Inhibitors for Cancer Treatment. Mini Rev Med Chem 2020; 20:444-465. [PMID: 31951166 DOI: 10.2174/1389557520666200117144701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/01/2019] [Accepted: 10/19/2019] [Indexed: 12/11/2022]
Abstract
Protein Kinases (PKs) are a heterogeneous family of enzymes that modulate several biological pathways, including cell division, cytoskeletal rearrangement, differentiation and apoptosis. In particular, due to their crucial role during human tumorigenesis and cancer progression, PKs are ideal targets for the design and development of effective and low toxic chemotherapeutics and represent the second group of drug targets after G-protein-coupled receptors. Nowadays, several compounds have been claimed to be PKs inhibitors, and some of them, such as imatinib, erlotinib and gefitinib, have already been approved for clinical use, whereas more than 30 others are in various phases of clinical trials. Among them, some natural or synthetic carbazole-based molecules represent promising PKs inhibitors due to their capability to interfere with PK activity by different mechanisms of action including the ability to act as DNA intercalating agents, interfere with the activity of enzymes involved in DNA duplication, such as topoisomerases and telomerases, and inhibit other proteins such as cyclindependent kinases or antagonize estrogen receptors. Thus, carbazoles can be considered a promising this class of compounds to be adopted in targeted therapy of different types of cancer.
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Affiliation(s)
- Jessica Ceramella
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Domenico Iacopetta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Alexia Barbarossa
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Anna Caruso
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Fedora Grande
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | | | | | - Pasquale Longo
- Department of Biology and Chemistry, University of Salerno, 84084 Fisciano, Italy
| | - Saturnino Carmela
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
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29
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Hepp Rehfeldt SC, Majolo F, Goettert MI, Laufer S. c-Jun N-Terminal Kinase Inhibitors as Potential Leads for New Therapeutics for Alzheimer's Diseases. Int J Mol Sci 2020; 21:E9677. [PMID: 33352989 PMCID: PMC7765872 DOI: 10.3390/ijms21249677] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's Disease (AD) is becoming more prevalent as the population lives longer. For individuals over 60 years of age, the prevalence of AD is estimated at 40.19% across the world. Regarding the cognitive decline caused by the disease, mitogen-activated protein kinases (MAPK) pathways such as the c-Jun N-terminal kinase (JNK) pathway are involved in the progressive loss of neurons and synapses, brain atrophy, and augmentation of the brain ventricles, being activated by synaptic dysfunction, oxidative stress, and excitotoxicity. Nowadays, AD symptoms are manageable, but the disease itself remains incurable, thus the inhibition of JNK3 has been explored as a possible therapeutic target, considering that JNK is best known for its involvement in propagating pro-apoptotic signals. This review aims to present biological aspects of JNK, focusing on JNK3 and how it relates to AD. It was also explored the recent development of inhibitors that could be used in AD treatment since several drugs/compounds in phase III clinical trials failed. General aspects of the MAPK family, therapeutic targets, and experimental treatment in models are described and discussed throughout this review.
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Affiliation(s)
- Stephanie Cristine Hepp Rehfeldt
- Graduate Program in Biotechnology, University of Vale do Taquari (Univates), Lajeado CEP 95914-014, Rio Grande do Sul, Brazil; (S.C.H.R.); (F.M.)
| | - Fernanda Majolo
- Graduate Program in Biotechnology, University of Vale do Taquari (Univates), Lajeado CEP 95914-014, Rio Grande do Sul, Brazil; (S.C.H.R.); (F.M.)
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre CEP 90619-900, Rio Grande do Sul, Brazil
| | - Márcia Inês Goettert
- Graduate Program in Biotechnology, University of Vale do Taquari (Univates), Lajeado CEP 95914-014, Rio Grande do Sul, Brazil; (S.C.H.R.); (F.M.)
| | - Stefan Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Faculty of Sciences, University of Tuebingen, D-72076 Tuebingen, Germany
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30
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Baier A, Szyszka R. Compounds from Natural Sources as Protein Kinase Inhibitors. Biomolecules 2020; 10:biom10111546. [PMID: 33198400 PMCID: PMC7698043 DOI: 10.3390/biom10111546] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
The advantage of natural compounds is their lower number of side-effects when compared to most synthetic substances. Therefore, over the past several decades, the interest in naturally occurring compounds is increasing in the search for new potent drugs. Natural compounds are playing an important role as a starting point when developing new selective compounds against different diseases. Protein kinases play a huge role in several diseases, like cancers, neurodegenerative diseases, microbial infections, or inflammations. In this review, we give a comprehensive view of natural compounds, which are/were the parent compounds in the development of more potent substances using computational analysis and SAR studies.
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Affiliation(s)
- Andrea Baier
- Department of Animal Physiology and Toxicology, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, 20-950 Lublin, Poland
- Correspondence:
| | - Ryszard Szyszka
- Department of Molecular Biology, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, 20-950 Lublin, Poland;
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31
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Iswandana R, Pham BT, Suriguga S, Luangmonkong T, van Wijk LA, Jansen YJM, Oosterhuis D, Mutsaers HAM, Olinga P. Murine Precision-cut Intestinal Slices as a Potential Screening Tool for Antifibrotic Drugs. Inflamm Bowel Dis 2020; 26:678-686. [PMID: 31943022 PMCID: PMC7150673 DOI: 10.1093/ibd/izz329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Intestinal fibrosis is a hallmark of Crohn's disease. Here, we investigated the impact of several putative antifibrotic compounds on the expression of fibrosis markers using murine precision-cut intestinal slices. METHODS Murine precision-cut intestinal slices were cultured for 48 hours in the presence of profibrotic and/or antifibrotic compounds. The fibrotic process was studied on gene and protein level using procollagen 1a1 (Col1α1), heat shock protein 47 (Hsp47), fibronectin (Fn2), and plasminogen activator inhibitor-1 (Pai-1). The effects of potential antifibrotic drugs mainly inhibiting the transforming growth factor β (TGF-β) pathway (eg, valproic acid, tetrandrine, pirfenidone, SB203580, and LY2109761) and compounds mainly acting on the platelet-derived growth factor (PDGF) pathway (eg, imatinib, sorafenib, and sunitinib) were assessed in the model at nontoxic concentrations. RESULTS Murine precision-cut intestinal slices remained viable for 48 hours, and an increased expression of fibrosis markers was observed during culture, including Hsp47, Fn2, and Pai-1. Furthermore, TGF-β1 stimulated fibrogenesis, whereas PDGF did not have an effect. Regarding the tested antifibrotics, pirfenidone, LY2109761, and sunitinib had the most pronounced impact on the expression of fibrosis markers, both in the absence and presence of profibrotic factors, as illustrated by reduced levels of Col1α1, Hsp47, Fn2, and Pai-1 after treatment. Moreover, sunitinib significantly reduced Hsp47 and Fn2 protein expression and the excretion of procollagen 1. CONCLUSIONS Precision-cut intestinal slices can successfully be used as a potential preclinical screening tool for antifibrotic drugs. We demonstrated that sunitinib reduced the expression of several fibrosis markers, warranting further evaluation of this compound for the treatment of intestinal fibrosis.
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Affiliation(s)
- Raditya Iswandana
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands,Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia
| | - Bao Tung Pham
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands,Department of Pharmaceutics, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Su Suriguga
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Theerut Luangmonkong
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands,Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Louise A van Wijk
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Yvette J M Jansen
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Dorenda Oosterhuis
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Henricus Antonius Maria Mutsaers
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Peter Olinga
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Groningen, the Netherlands,Address correspondence to: Professor Peter Olinga, Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, the Netherlands. E-mail:
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32
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Moccia M, Frett B, Zhang L, Lakkaniga NR, Briggs DC, Chauhan R, Brescia A, Federico G, Yan W, Santoro M, McDonald NQ, Li HY, Carlomagno F. Bioisosteric Discovery of NPA101.3, a Second-Generation RET/VEGFR2 Inhibitor Optimized for Single-Agent Polypharmacology. J Med Chem 2020; 63:4506-4516. [PMID: 32298114 PMCID: PMC7901654 DOI: 10.1021/acs.jmedchem.9b01336] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RET receptor tyrosine kinase is a driver oncogene in human cancer. We recently identified the clinical drug candidate Pz-1, which targets RET and VEGFR2. A key in vivo metabolite of Pz-1 is its less active demethylated pyrazole analogue. Using bioisosteric substitution methods, here, we report the identification of NPA101.3, lacking the structural liability for demethylation. NPA101.3 showed a selective inhibitory profile and an inhibitory concentration 50 (IC50) of <0.003 μM for both RET and VEGFR2. NPA101.3 inhibited phosphorylation of all tested RET oncoproteins as well as VEGFR2 and proliferation of cells transformed by RET. Oral administration of NPA101.3 (10 mg/kg/day) completely prevented formation of tumors induced by RET/C634Y-transformed cells, while it weakened, but did not abrogate, formation of tumors induced by a control oncogene (HRAS/G12V). The balanced synchronous inhibition of both RET and VEGFR2, as well the resistance to demethylation, renders NPA101.3 a potential clinical candidate for RET-driven cancers.
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Affiliation(s)
- Marialuisa Moccia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States.,Synactix Pharmaceuticals, Inc., Tucson, Arizona 85718, United States
| | - Lingtian Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - David C Briggs
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Rakhee Chauhan
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Annalisa Brescia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy
| | - Giorgia Federico
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Massimo Santoro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy
| | - Neil Q McDonald
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London WC1E 7HX, U.K
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States.,Synactix Pharmaceuticals, Inc., Tucson, Arizona 85718, United States
| | - Francesca Carlomagno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy.,Istituto di Endocrinologia ed Oncologia Sperimentale del CNR, 80131 Napoli, Italy
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Zhang F, Zhai T, Haider S, Liu Y, Huang ZJ. Synergistic Effect of Chlorogenic Acid and Caffeic Acid with Fosfomycin on Growth Inhibition of a Resistant Listeria monocytogenes Strain. ACS OMEGA 2020; 5:7537-7544. [PMID: 32280897 PMCID: PMC7144146 DOI: 10.1021/acsomega.0c00352] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/16/2020] [Indexed: 05/08/2023]
Abstract
Listeria monocytogenes, a human foodborne pathogen that causes listeriosis with high-rate mortality, has been reported to be resistant to commonly used antibiotics. New antibiotics or cocktails of existing antibiotics with synergistic compounds are in high demand for treating this multi-drug-resistant pathogen. Fosfomycin is one of the novel and promising therapeutic antibiotics for the treatment of listeriosis. However, some L. monocytogenes strains with the FosX gene were recently reported to survive from the fosfomycin treatment. This work aims to identify FosX inhibitors that can revive fosfomycin in treating resistant L. monocytogenes. Since structures and activities of the FosX protein in L. monocytogenes have been well studied, we used an integrated computational and experimental approach to identify FosX inhibitors that show synergistic effect with fosfomycin in treating resistant L. monocytogenes. Specifically, automated ligand docking was implemented to perform virtual screening of the Indofine natural-product database and FDA-approved drugs to identify potential inhibitors. An in vitro bacterial growth inhibition test was then utilized to verify the effectiveness of identified compounds combined with fosfomycin in inhibiting the resistant L. monocytogenes strains. Two phenolic acids, i.e., caffeic acid and chlorogenic acid, were predicted as high-affinity FosX inhibitors from the ligand-docking platform. Experiments with these compounds indicated that the cocktail of either caffeic acid (1.5 mg/mL) or chlorogenic acid (3 mg/mL) with fosfomycin (50 mg/L) was able to significantly inhibit the growth of the pathogen. The finding of this work implies that the combination of fosfomycin with either caffeic acid or chlorogenic acid is of potential to be used in the clinical treatment of Listeria infections.
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Affiliation(s)
- Fangyuan Zhang
- Department
of Chemical Engineering, Villanova University, 800 E Lancaster Avenue, Villanova, Pennsylvania 19085, United States
| | - Tianhua Zhai
- Department
of Chemical Engineering, Villanova University, 800 E Lancaster Avenue, Villanova, Pennsylvania 19085, United States
| | - Shozeb Haider
- School
of Pharmacy, University College London (UCL), London WC1E 6BT, U.K.
| | - Yanhong Liu
- Molecular
Characterization of Foodborne Pathogens Research Unit, Eastern Regional
Research Center, U.S. Department of Agriculture, Wyndmoor, Pennsylvania 19038, United States
| | - Zuyi Jacky Huang
- Department
of Chemical Engineering, Villanova University, 800 E Lancaster Avenue, Villanova, Pennsylvania 19085, United States
- . Tel: 1-610-519-4848
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34
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Ghione S, Mabrouk N, Paul C, Bettaieb A, Plenchette S. Protein kinase inhibitor-based cancer therapies: Considering the potential of nitric oxide (NO) to improve cancer treatment. Biochem Pharmacol 2020; 176:113855. [PMID: 32061562 DOI: 10.1016/j.bcp.2020.113855] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
The deregulation of a wide variety of protein kinases is associated with cancer cell initiation and tumor progression. Owing to their indispensable function in signaling pathways driving malignant cell features, protein kinases constitute major therapeutic targets in cancer. Over the past two decades, intense efforts in drug development have been dedicated to this field. The development of protein kinase inhibitors (PKIs) have been a real breakthrough in targeted cancer therapy. Despite obvious successes across patients with different types of cancer, the development of PKI resistance still prevails. Combination therapies are part of a comprehensive approach to address the problem of drug resistance. The therapeutic use of nitric oxide (NO) donors to bypass PKI resistance in cancer has never been tested in clinic yet but several arguments suggest that the combination of PKIs and NO donors may exert a potential anticancer effect. The present review summarized the current state of knowledge on common targets to both PKIs and NO. Herein, we attempt to provide the rationale underlying a potential combination of PKIs and NO donors for future directions and design of new combination therapies in cancer.
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Affiliation(s)
- Silvia Ghione
- Laboratoire d'Immunologie et Immunothérapie des Cancers, EPHE, PSL Research University, 75000 Paris, France; LIIC, EA7269, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Nesrine Mabrouk
- Laboratoire d'Immunologie et Immunothérapie des Cancers, EPHE, PSL Research University, 75000 Paris, France; LIIC, EA7269, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Catherine Paul
- Laboratoire d'Immunologie et Immunothérapie des Cancers, EPHE, PSL Research University, 75000 Paris, France; LIIC, EA7269, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Ali Bettaieb
- Laboratoire d'Immunologie et Immunothérapie des Cancers, EPHE, PSL Research University, 75000 Paris, France; LIIC, EA7269, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Stéphanie Plenchette
- Laboratoire d'Immunologie et Immunothérapie des Cancers, EPHE, PSL Research University, 75000 Paris, France; LIIC, EA7269, Université de Bourgogne Franche-Comté, 21000 Dijon, France.
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35
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Jaballah MY, Serya RAT, Saad N, Khojah SM, Ahmed M, Barakat K, Abouzid KAM. Towards discovery of novel scaffold with potent antiangiogenic activity; design, synthesis of pyridazine based compounds, impact of hinge interaction, and accessibility of their bioactive conformation on VEGFR-2 activities. J Enzyme Inhib Med Chem 2020; 34:1573-1589. [PMID: 31852269 PMCID: PMC6746272 DOI: 10.1080/14756366.2019.1651723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pyridazine scaffolds are considered privileged structures pertaining to its novelty, chemical stability, and synthetic feasibility. In our quest towards the development of novel scaffolds for effective vascular endothelial growth 2 (VEGFR-2) inhibition with antiangiogenic activity, four novel series of pyridazines were designed and synthesised. Five of the synthesised compounds; namely (8c, 8f, 15, 18b, and 18c) exhibited potent VEGFR-2 inhibitory potency (>80%); with IC50 values ranging from low micromolar to nanomolar range; namely compounds 8c, 8f, 15, 18c with (1.8 µM, 1.3 µM, 1.4 µM, 107 nM), respectively. Moreover, 3-[4-{(6-oxo-1,6-dihydropyridazin-3-yl)oxy}phenyl]urea derivative (18b) exhibited nanomolar potency towards VEGFR-2 (60.7 nM). In cellular assay, the above compounds showed excellent inhibition of VEGF-stimulated proliferation of human umbilical vein endothelial cells at 10 μM concentration. Finally, an extensive molecular simulation study was performed to investigate the probable interaction with VEGFR-2.
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Affiliation(s)
- Maiy Y Jaballah
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Abbassia, Cairo, Egypt
| | - Rabah A T Serya
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Abbassia, Cairo, Egypt
| | - Nasser Saad
- Faculty of Pharmaceutical Sciences and Pharmaceutical Industries, Pharmaceutical Chemistry Department, Future University in Egypt, Cairo, Egypt
| | - Sohair M Khojah
- Faculty of Science, Biochemistry Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.,Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, Canada
| | - Khaled A M Abouzid
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Abbassia, Cairo, Egypt.,Faculty of Pharmacy, Department of Organic and Medicinal Chemistry, University of Sadat City, Menoufia, Egypt
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36
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Exploring receptor tyrosine kinases-inhibitors in Cancer treatments. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0035-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AbstractBackgroundReceptor tyrosine kinases (RTKs) are signaling enzymes responsible for the transfer of Adenosine triphosphate (ATP) γ-phosphate to the tyrosine residues substrates. RTKs demonstrate essential roles in cellular growth, metabolism, differentiation, and motility. Anomalous expression of RTK customarily leads to cell growth dysfunction, which is connected to tumor takeover, angiogenesis, and metastasis. Understanding the structure, mechanisms of adaptive and acquired resistance, optimizing inhibition of RTKs, and eradicating cum minimizing the havocs of quiescence cancer cells is paramount.MainTextTyrosine kinase inhibitors (TKIs) vie with RTKs ATP-binding site for ATP and hitherto reduce tyrosine kinase phosphorylation, thus hampering the growth of cancer cells. TKIs can either be monoclonal antibodies that compete for the receptor’s extracellular domain or small molecules that inhibit the tyrosine kinase domain and prevent conformational changes that activate RTKs. Progression of cancer is related to aberrant activation of RTKs due to due to mutation, excessive expression, or autocrine stimulation.ConclusionsUnderstanding the modes of inhibition and structures of RTKs is germane to the design of novel and potent TKIs. This review shed light on the structures of tyrosine kinases, receptor tyrosine kinases, tyrosine kinase inhibitors, minimizing imatinib associated toxicities, optimization of tyrosine kinase inhibition in curtailing quiescence in cancer cells and the prospects of receptor tyrosine kinase based treatments.
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37
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The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from Leishmania major may be Involved in the Resistance to Drugs such as Paromomycin. Biomolecules 2019; 9:biom9110723. [PMID: 31718000 PMCID: PMC6920834 DOI: 10.3390/biom9110723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
The identification and clarification of the mechanisms of action of drugs used against leishmaniasis may improve their administration regimens and prevent the development of resistant strains. Herein, for the first time, we describe the structure of the putatively essential Ser/Thr kinase LmjF.22.0810 from Leishmania major. Molecular dynamics simulations were performed to assess the stability of the kinase model. The analysis of its sequence and structure revealed two druggable sites on the protein. Furthermore, in silico docking of small molecules showed that aminoglycosides preferentially bind to the phosphorylation site of the protein. Given that transgenic LmjF.22.0810-overexpressing parasites displayed less sensitivity to aminoglycosides such as paromomycin, our predicted models support the idea that the mechanism of drug resistance observed in those transgenic parasites is the tight binding of such compounds to LmjF.22.0810 associated with its overexpression. These results may be helpful to understand the complex machinery of drug response in Leishmania.
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38
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Ong BX, Yoo Y, Han MG, Park JB, Choi MK, Choi Y, Shin JS, Bahn YS, Cho HS. Structural analysis of fungal pathogenicity-related casein kinase α subunit, Cka1, in the human fungal pathogen Cryptococcus neoformans. Sci Rep 2019; 9:14398. [PMID: 31591414 PMCID: PMC6779870 DOI: 10.1038/s41598-019-50678-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 09/16/2019] [Indexed: 12/28/2022] Open
Abstract
CK2α is a constitutively active and highly conserved serine/threonine protein kinase that is involved in the regulation of key cellular metabolic pathways and associated with a variety of tumours and cancers. The most well-known CK2α inhibitor is the human clinical trial candidate CX-4945, which has recently shown to exhibit not only anti-cancer, but also anti-fungal properties. This prompted us to work on the CK2α orthologue, Cka1, from the pathogenic fungus Cryptococcus neoformans, which causes life-threatening systemic cryptococcosis and meningoencephalitis mainly in immunocompromised individuals. At present, treatment of cryptococcosis remains a challenge due to limited anti-cryptococcal therapeutic strategies. Hence, expanding therapeutic options for the treatment of the disease is highly clinically relevant. Herein, we report the structures of Cka1-AMPPNP-Mg2+ (2.40 Å) and Cka1-CX-4945 (2.09 Å). Structural comparisons of Cka1-AMPPNP-Mg2+ with other orthologues revealed the dynamic architecture of the N-lobe across species. This may explain for the difference in binding affinities and deviations in protein-inhibitor interactions between Cka1-CX-4945 and human CK2α-CX-4945. Supporting it, in vitro kinase assay demonstrated that CX-4945 inhibited human CK2α much more efficiently than Cka1. Our results provide structural insights into the design of more selective inhibitors against Cka1.
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Affiliation(s)
- Belinda X Ong
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Youngki Yoo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Myeong Gil Han
- Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jun Bae Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Myung Kyung Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yeseul Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jeon-Soo Shin
- Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Severance Biomedical Science Institute and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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39
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Vucicevic J, Nikolic K, Mitchell JB. Rational Drug Design of Antineoplastic Agents Using 3D-QSAR, Cheminformatic, and Virtual Screening Approaches. Curr Med Chem 2019; 26:3874-3889. [DOI: 10.2174/0929867324666170712115411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/07/2023]
Abstract
Background:Computer-Aided Drug Design has strongly accelerated the development of novel antineoplastic agents by helping in the hit identification, optimization, and evaluation.Results:Computational approaches such as cheminformatic search, virtual screening, pharmacophore modeling, molecular docking and dynamics have been developed and applied to explain the activity of bioactive molecules, design novel agents, increase the success rate of drug research, and decrease the total costs of drug discovery. Similarity, searches and virtual screening are used to identify molecules with an increased probability to interact with drug targets of interest, while the other computational approaches are applied for the design and evaluation of molecules with enhanced activity and improved safety profile.Conclusion:In this review are described the main in silico techniques used in rational drug design of antineoplastic agents and presented optimal combinations of computational methods for design of more efficient antineoplastic drugs.
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Affiliation(s)
- Jelica Vucicevic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - John B.O. Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, United Kingdom
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40
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Yuan X, Yang Q, Liu T, Li K, Liu Y, Zhu C, Zhang Z, Li L, Zhang C, Xie M, Lin J, Zhang J, Jin Y. Design, synthesis and in vitro evaluation of 6-amide-2-aryl benzoxazole/benzimidazole derivatives against tumor cells by inhibiting VEGFR-2 kinase. Eur J Med Chem 2019; 179:147-165. [PMID: 31252306 DOI: 10.1016/j.ejmech.2019.06.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 12/24/2022]
Abstract
Herein, we have carried out a structural optimization campaign to discover the novel anti-tumor agents with our previously screened YQY-26 as the hit compound. A library of thirty-seven 6-amide-2-aryl benzoxazole/benzimidazole derivatives has been designed and synthesized based on the highly conserved active site of VEGFR-2. Several title compounds exhibited selective inhibitory activities against VEGFR-2 than EGFR kinases, which also displayed selective anti-proliferation potency against the HUVEC and HepG2 than the A549 and MDA-MB-231 cancer cell lines. The newly synthesized compounds were evaluated for anti-angiogenesis capability by chick chorioallantoic membrane (CAM) assay. Among them, compounds 9d showed the most potent anti-angiogenesis ability (79% inhibition at 10 nM/eggs), the efficient cytotoxic activities (in vitro against the HUVEC and HepG2 cell lines with IC50 values of 1.47 and 2.57 μM, respectively), and excellent VEGFR-2 kinase inhibition (IC50 = 0.051 μM). The molecular docking analysis revealed that compound 9d is a Type II inhibitor of VEGFR-2 kinase. These results indicated that the 6-amide-2-arylbenzoxazole and 6-amide-2-aryl benzimidazole derivatives are promising inhibitors of VEGFR-2 kinase for the potential treatment of anti-angiogenesis.
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Affiliation(s)
- Xu Yuan
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China
| | - Qingyi Yang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China; School of Clinical Medicine, Dehong Vocational College, Mangshi, 678400, China
| | - Tongyan Liu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Ke Li
- Biomedical Department, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, PR China.
| | - Yuwen Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China
| | - Changcheng Zhu
- Institute of Drug Research and Development, Kunming Pharmaceutical Corporation, Kunming, 650100, PR China
| | - Zhiyun Zhang
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, 650011, PR China
| | - Linghua Li
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, 650011, PR China
| | - Conghai Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China
| | - Mingjin Xie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China
| | - Jun Lin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China.
| | - Jihong Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, 650500, PR China.
| | - Yi Jin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China.
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41
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Schwarz D, Merget B, Deane C, Fulle S. Modeling conformational flexibility of kinases in inactive states. Proteins 2019; 87:943-951. [PMID: 31168936 PMCID: PMC6852311 DOI: 10.1002/prot.25756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/26/2019] [Indexed: 02/02/2023]
Abstract
Kinase structures in the inactive "DFG-out" state provide a wealth of druggable binding site variants. The conformational plasticity of this state can be mainly described by different conformations of binding site-forming elements such as DFG motif, A-loop, P-loop, and αC-helix. Compared to DFG-in structures, DFG-out structures are largely underrepresented in the Protein Data Bank (PDB). Thus, structure-based drug design efforts for DFG-out inhibitors may benefit from an efficient approach to generate an ensemble of DFG-out structures. Accordingly, the presented modeling pipeline systematically generates homology models of kinases in several DFG-out conformations based on a sophisticated creation of template structures that represent the major states of the flexible structural elements. Eighteen template classes were initially selected from all available kinase structures in the PDB and subsequently employed for modeling the entire kinome in different DFG-out variants by fusing individual structural elements to multiple chimeric template structures. Molecular dynamics simulations revealed that conformational transitions between the different DFG-out states generally do not occur within trajectories of a few hundred nanoseconds length. This underlines the benefits of the presented homology modeling pipeline to generate relevant conformations of "DFG-out" kinase structures for subsequent in silico screening or binding site analysis studies.
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Affiliation(s)
- Dominik Schwarz
- BioMed X Innovation Center, Heidelberg, Germany.,Department of Statistics, University of Oxford, Oxford, UK
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42
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Ung PMU, Sonoshita M, Scopton AP, Dar AC, Cagan RL, Schlessinger A. Integrated computational and Drosophila cancer model platform captures previously unappreciated chemicals perturbing a kinase network. PLoS Comput Biol 2019; 15:e1006878. [PMID: 31026276 PMCID: PMC6506148 DOI: 10.1371/journal.pcbi.1006878] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 05/08/2019] [Accepted: 02/18/2019] [Indexed: 12/13/2022] Open
Abstract
Drosophila provides an inexpensive and quantitative platform for measuring whole animal drug response. A complementary approach is virtual screening, where chemical libraries can be efficiently screened against protein target(s). Here, we present a unique discovery platform integrating structure-based modeling with Drosophila biology and organic synthesis. We demonstrate this platform by developing chemicals targeting a Drosophila model of Medullary Thyroid Cancer (MTC) characterized by a transformation network activated by oncogenic dRetM955T. Structural models for kinases relevant to MTC were generated for virtual screening to identify unique preliminary hits that suppressed dRetM955T-induced transformation. We then combined features from our hits with those of known inhibitors to create a ‘hybrid’ molecule with improved suppression of dRetM955T transformation. Our platform provides a framework to efficiently explore novel kinase inhibitors outside of explored inhibitor chemical space that are effective in inhibiting cancer networks while minimizing whole body toxicity. Effective and safe treatment of multigenic diseases often involves drugs that address multiple points along disease networks, i.e., polypharmacology. Polypharmacology is increasingly appreciated as a potentially desirable property of kinase drugs. However, most known drugs that interact with multiple targets have been identified as such by chance and most polypharmacological compounds are not chemically unique, resembling structures of known kinase inhibitors. The fruit fly Drosophila provides an inexpensive, rapid, quantitative, whole animal screening platform that has the potential to complement computational approaches. We present a chemical genetics approach that efficiently combines Drosophila with structural prediction and virtual screening, creating a unique discovery platform. We demonstrate the utility of our approach by developing useful small molecules targeting a kinase network in a Drosophila model of Medullary Thyroid Cancer (MTC) driven by oncogenic dRetM955T.
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Affiliation(s)
- Peter M U Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Masahiro Sonoshita
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alex P Scopton
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Arvin C Dar
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ross L Cagan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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43
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Zhou T, Wang Q, Phan N, Ren J, Yang H, Feldman CC, Feltenberger JB, Ye Z, Wildman SA, Tang W, Liu B. Identification of a novel class of RIP1/RIP3 dual inhibitors that impede cell death and inflammation in mouse abdominal aortic aneurysm models. Cell Death Dis 2019; 10:226. [PMID: 30842407 PMCID: PMC6403222 DOI: 10.1038/s41419-019-1468-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/29/2018] [Accepted: 12/18/2018] [Indexed: 12/14/2022]
Abstract
Receptor interacting protein kinase-1 and -3 (RIP1 and RIP3) are essential mediators of cell death processes and participate in inflammatory responses. Our group recently demonstrated that gene deletion of Rip3 or pharmacological inhibition of RIP1 attenuated pathogenesis of abdominal aortic aneurysm (AAA), a life-threatening degenerative vascular disease characterized by depletion of smooth muscle cells (SMCs), inflammation, negative extracellular matrix remodeling, and progressive expansion of aorta. The goal of this study was to develop drug candidates for AAA and other disease conditions involving cell death and inflammation. We screened 1141 kinase inhibitors for their ability to block necroptosis using the RIP1 inhibitor Necrostatin-1s (Nec-1s) as a selection baseline. Positive compounds were further screened for cytotoxicity and virtual binding to RIP3. A cluster of top hits, represented by GSK2593074A (GSK'074), displayed structural similarity to the established RIP3 inhibitor GSK'843. In multiple cell types including mouse SMCs, fibroblasts (L929), bone marrow derived macrophages (BMDM), and human colon epithelial cells (HT29), GSK'074 inhibited necroptosis with an IC50 of ~3 nM. Furthermore, GSK'074, but not Nec-1s, blocked cytokine production by SMCs. Biochemical analyses identified both RIP1 and RIP3 as the biological targets of GSK'074. Unlike GSK'843 which causes profound apoptosis at high doses (>3 µM), GSK'074 showed no detectable cytotoxicity even at 20 µM. Daily intraperitoneal injection of GSK'074 at 0.93 mg/kg significantly attenuated aortic expansion in two mouse models of AAA (calcium phosphate: DMSO 66.06 ± 9.17% vs GSK'074 27.36 ± 8.25%, P < 0.05; Angiotensin II: DMSO 85.39 ± 15.76% vs GSK'074 36.28 ± 5.76%, P < 0.05). Histologically, GSK'074 treatment diminished cell death and macrophage infiltration in aneurysm-prone aortae. Together, our data suggest that GSK'074 represents a new class of necroptosis inhibitors with dual targeting ability to both RIP1 and RIP3. The high potency and minimum cytotoxicity make GSK'074 a desirable drug candidate of pharmacological therapies to attenuate AAA progression and other necroptosis related diseases.
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Affiliation(s)
- Ting Zhou
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Qiwei Wang
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Noel Phan
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Jun Ren
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Huan Yang
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Conner C Feldman
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - John B Feltenberger
- School of Pharmacy, Medicinal Chemistry Center, University of Wisconsin, Madison, WI, 53705, USA
| | - Zhengqing Ye
- School of Pharmacy, Medicinal Chemistry Center, University of Wisconsin, Madison, WI, 53705, USA
| | - Scott A Wildman
- UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Weiping Tang
- School of Pharmacy, Medicinal Chemistry Center, University of Wisconsin, Madison, WI, 53705, USA
| | - Bo Liu
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA.
- Department of Cellular and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA.
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Arrouchi H, Lakhlili W, Ibrahimi A. Re-positioning of known drugs for Pim-1 kinase target using molecular docking analysis. Bioinformation 2019; 15:116-120. [PMID: 31435157 PMCID: PMC6677905 DOI: 10.6026/97320630015116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 12/02/2022] Open
Abstract
The Concept of reusing existing drugs for new targets is gaining momentum in recent years because of cost-effectiveness as safety and
toxicology data are already available. Therefore, it is of interest to re-profile known drugs against the Pim-1 kinase target using molecular
docking analysis. Results show that known drugs such as nilotinib, vemurafenib, Idelalisib, and other small kinases inhibitors have high
binding ability with Pim-1 kinase for consideration as potential inhibitors.
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Affiliation(s)
- Housna Arrouchi
- Biotechnology Laboratory (Medbiotech),BioInova Research center,Rabat Medical and Pharmacy School,Mohammed V University in Rabat,Rabat,Morroco
| | - Wiame Lakhlili
- Biotechnology Laboratory (Medbiotech),BioInova Research center,Rabat Medical and Pharmacy School,Mohammed V University in Rabat,Rabat,Morroco
| | - Azeddine Ibrahimi
- Biotechnology Laboratory (Medbiotech),BioInova Research center,Rabat Medical and Pharmacy School,Mohammed V University in Rabat,Rabat,Morroco
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Ikegashira K, Ikenogami T, Yamasaki T, Oka T, Hase Y, Miyagawa N, Inagaki K, Kawahara I, Koga Y, Hashimoto H. Optimization of an azetidine series as inhibitors of colony stimulating factor-1 receptor (CSF-1R) Type II to lead to the clinical candidate JTE-952. Bioorg Med Chem Lett 2019; 29:873-877. [PMID: 30755337 DOI: 10.1016/j.bmcl.2019.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 12/20/2022]
Abstract
Optimization of novel azetidine compounds, which we had found as colony stimulating factor-1 receptor (CSF-1R) Type II inhibitors, provided JTE-952 as a clinical candidate with high cellular activity (IC50 = 20 nM) and good pharmacokinetics profile. JTE-952 was also effective against a mouse collagen-induced model of arthritis (mouse CIA-model). Additionally, the X-ray co-crystal structure of JTE-952 with CSF-1R protein was shown to be a Type II inhibitor, and the kinase panel assay indicated that JTE-952 had high kinase selectivity.
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Affiliation(s)
- Kazutaka Ikegashira
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Taku Ikenogami
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takayuki Yamasaki
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takahiro Oka
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yasunori Hase
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Naoki Miyagawa
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Koji Inagaki
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Iichiro Kawahara
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yoshihisa Koga
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Hiromasa Hashimoto
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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46
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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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47
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Discovery of a novel azetidine scaffold for colony stimulating factor-1 receptor (CSF-1R) Type II inhibitors by the use of docking models. Bioorg Med Chem Lett 2019; 29:115-118. [DOI: 10.1016/j.bmcl.2018.10.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 01/14/2023]
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48
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49
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Suplatov D, Kopylov K, Sharapova Y, Švedas V. Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod. J Biomol Struct Dyn 2018; 37:2049-2060. [PMID: 29749295 DOI: 10.1080/07391102.2018.1475260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the 'out' state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod's binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry Suplatov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Kirill Kopylov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Yana Sharapova
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Vytas Švedas
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
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50
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Yan W, Lakkaniga NR, Carlomagno F, Santoro M, McDonald NQ, Lv F, Gunaganti N, Frett B, Li HY. Insights into Current Tropomyosin Receptor Kinase (TRK) Inhibitors: Development and Clinical Application. J Med Chem 2018; 62:1731-1760. [PMID: 30188734 DOI: 10.1021/acs.jmedchem.8b01092] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The use of kinase-directed precision medicine has been heavily pursued since the discovery and development of imatinib. Annually, it is estimated that around ∼20 000 new cases of tropomyosin receptor kinase (TRK) cancers are diagnosed, with the majority of cases exhibiting a TRK genomic rearrangement. In this Perspective, we discuss current development and clinical applications for TRK precision medicine by providing the following: (1) the biological background and significance of the TRK kinase family, (2) a compilation of known TRK inhibitors and analysis of their cocrystal structures, (3) an overview of TRK clinical trials, and (4) future perspectives for drug discovery and development of TRK inhibitors.
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Affiliation(s)
- Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Francesca Carlomagno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università Federico II , Via S Pansini 5 , 80131 Naples , Italy.,Istituto di Endocrinologia e Oncologia Sperimentale del CNR , Via S Pansini 5 , 80131 Naples , Italy
| | - Massimo Santoro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università Federico II , Via S Pansini 5 , 80131 Naples , Italy
| | - Neil Q McDonald
- Signaling and Structural Biology Laboratory , The Francis Crick Institute , London NW1 1AT , U.K.,Institute of Structural and Molecular Biology, Department of Biological Sciences , Birkbeck College , Malet Street , London WC1E 7HX , U.K
| | - Fengping Lv
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Naresh Gunaganti
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
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