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Kinase Inhibitors

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (15 July 2017) | Viewed by 109108

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Prof. Dr. Pierre Koch

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Department of Pharmaceutical and Medicinal Chemistry II, Institute of Pharmacy, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
Interests: protein kinase inhibitors; CNS diseases; synthetic organic chemistry; natural products
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Prof. Dr. Stefan Laufer

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Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
Interests: academic drug discovery; anti-inflammatories; anti-cancer; autoimmune; protein kinases; protein-protein interaction
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Dear Colleagues,

Kinases are a large and diverse multi-gene family of enzymes that catalyze the transfer of γ-phosphate of ATP onto hydroxyl groups of substrates. They are involved in numerous cell-signaling pathways. Disease might arise when deregulation or mutation of a kinase takes place. Therefore, kinases are promising drug targets for the treatment of a number of disorders, e.g., cancer, autoimmune diseases, inflammation, neurodegenerative diseases and diabetes. To date, more than 30 protein kinase inhibitors are approved, two-thirds of which were launched onto the market within the last five years. Most of them are tyrosine kinase inhibitors with low selectivity used for treatment of cancer. The design of highly selective kinase inhibitors both as tools and probes, and as potential therapeutics, remains still challenging for medicinal chemists.

This Special Issue aims to attract all researchers working in this research field and will collect new findings and recent advances on the development, synthesis and structure-activity relationships of novel kinase inhibitors. Research manuscripts, as well as a limited number of review manuscripts, are welcome.

Prof. Dr. Pierre Koch
Prof. Dr. Stefan Laufer
Guest Editors

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Keywords

Kinase inhibitors
Medicinal chemistry
Drug discovery
Rational design
Structure-based design
Selectivity
Reversible inhibitors
Covalent inhibitors

Published Papers (13 papers)

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Editorial

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3 pages, 152 KiB

Open AccessEditorial

Special Issue: Kinase inhibitors

by Pierre Koch and Stefan Laufer

Molecules 2018, 23(7), 1818; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules23071818 - 22 Jul 2018

Cited by 3 | Viewed by 3365

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(This article belongs to the Special Issue Kinase Inhibitors)

Research

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18 pages, 29645 KiB

Open AccessArticle

PKIDB: A Curated, Annotated and Updated Database of Protein Kinase Inhibitors in Clinical Trials

by Fabrice Carles, Stéphane Bourg, Christophe Meyer and Pascal Bonnet

Molecules 2018, 23(4), 908; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules23040908 - 15 Apr 2018

Cited by 122 | Viewed by 12013

Abstract

The number of protein kinase inhibitors (PKIs) approved worldwide continues to grow steadily, with 39 drugs approved in the period between 2001 and January 2018. PKIs on the market have been the subject of many reviews, and structure-property relationships specific to this class of drugs have been inferred. However, the large number of PKIs under development is often overlooked. In this paper, we present PKIDB (Protein Kinase Inhibitor Database), a monthly-updated database gathering approved PKIs as well as PKIs currently in clinical trials. The database compiles currently 180 inhibitors ranging from phase 0 to 4 clinical trials along with annotations extracted from seven public resources. The distribution and property ranges of standard physicochemical properties are presented. They can be used as filters to better prioritize compound selection for future screening campaigns. Interestingly, more than one-third of the kinase inhibitors violate at least one Lipinski’s rule. A Principal Component Analysis (PCA) reveals that Type-II inhibitors are mapped to a distinct chemical space as compared to orally administrated drugs as well as to other types of kinase inhibitors. Using a Principal Moment of Inertia (PMI) analysis, we show that PKIs under development tend to explore new shape territories as compared to approved PKIs. In order to facilitate the analysis of the protein space, the kinome tree has been annotated with all protein kinases being targeted by PKIs. Finally, we analyzed the pipeline of the pharmaceutical companies having PKIs on the market or still under development. We hope that this work will assist researchers in the kinase field in identifying and designing the next generation of kinase inhibitors for still untargeted kinases. The PKIDB database is freely accessible from a website at http://www.icoa.fr/pkidb and can be easily browsed through a user-friendly spreadsheet-like interface. Full article

(This article belongs to the Special Issue Kinase Inhibitors)

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1554 KiB

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From 2-Alkylsulfanylimidazoles to 2-Alkylimidazoles: An Approach towards Metabolically More Stable p38α MAP Kinase Inhibitors

by Fabian Heider, Urs Haun, Eva Döring, Mark Kudolo, Catharina Sessler, Wolfgang Albrecht, Stefan Laufer and Pierre Koch

Molecules 2017, 22(10), 1729; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22101729 - 14 Oct 2017

Cited by 10 | Viewed by 5581

Abstract

In vitro and in vivo metabolism studies revealed that 2-alkylsulfanylimidazole ML3403 (4-(5-(4-fluorophenyl)-2-(methylthio)-1H-imidazol-4-yl)-N-(1-phenylethyl)pyridin-2-amine) undergoes rapid oxidation to the sulfoxide. Replacing the sulfur atom present in the two potent p38α mitogen-activated protein (MAP) kinase inhibitors ML3403 and LN950 (2-((5-(4-fluorophenyl)-4-(2-((3-methylbutan-2-yl)amino)pyridin-4-yl)-1H-imidazol-2-yl)thio)ethan-1-ol) by a methylene group resulted in 2-alkylimidazole derivatives 1 and 2, respectively, having a remarkably improved metabolic stability. The 2-alkylimidazole analogs 1 and 2 showed 20% and 10% biotransformation after 4 h of incubation with human liver microsomes, respectively. They display a 4-fold increased binding affinity towards the target kinase as well as similar in vitro potency and ex vivo efficacy relative to their 2-alkylsulfanylimidazole counterparts ML3403 and LN950. For example, 2-alkylimidazole 2, the analog of LN950, inhibits both the p38α MAP kinase as well as the LPS-stimulated tumor necrosis factor-α release from human whole blood in the low double-digit nanomolar range. Full article

(This article belongs to the Special Issue Kinase Inhibitors)

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Methylisoindigo and Its Bromo-Derivatives Are Selective Tyrosine Kinase Inhibitors, Repressing Cellular Stat3 Activity, and Target CD133+ Cancer Stem Cells in PDAC

by Jana Tegethoff, Roland Bischoff, Sawsan Saleh, Biljana Blagojevic, Karl-Heinz Merz and Xinlai Cheng

Molecules 2017, 22(9), 1546; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22091546 - 13 Sep 2017

Cited by 3 | Viewed by 5446

Abstract

Indirubin is an active component of the herbal ingredient ‘Danggui Longhui wan’, which was used for the treatment of inflammation and chronic myeloid leukemia in China. The recent study showed its derivative methylisoindigo (also known as meisoindigo) preferentially targeting cancer stem cells (CSCs) in interference with AMPK and LKB1, the cellular metabolic sensors. In this study, we screened the effect of meisoindigo on a panel of 300 protein kinases and found that it selectively inhibited Stat3-associated tyrosine kinases and further confirmed its activity in cell based assays. To gain a deeper insight into the structure–activity relationship we produced 7 bromo-derivatives exhausting the accessible positions on the bisindole backbone except for in the 4-position due to the space limitation. We compared their anti-proliferative effects on tumor cells. We found that 6-bromomeisoindigo showed improved toxicity in company with increased Stat3 inhibition. Moreover, we detected that 6-bromomeisoindigo induced apoptosis of 95% of CD133+ pancreatic cancer cells. Considering that CD133 is a common marker highly expressed in a range of CSCs, our results imply the potential application of 6-bromomeisoindigo for the treatment of CSCs in different types of cancers. Full article

(This article belongs to the Special Issue Kinase Inhibitors)

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Synthesis and Evaluation of Novel 2-Pyrrolidone-Fused (2-Oxoindolin-3-ylidene)methylpyrrole Derivatives as Potential Multi-Target Tyrosine Kinase Receptor Inhibitors

by Ting-Hsuan Yang, Chun-I Lee, Wen-Hsin Huang and An-Rong Lee

Molecules 2017, 22(6), 913; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22060913 - 31 May 2017

Cited by 22 | Viewed by 6630

Abstract

Signaling pathways of VEGFs and PDGFs are crucial in tumor angiogenesis, which is essential in solid tumor progression and metastasis. This study reports our strategy for designing and synthesizing a series of novel 2-pyrrolidone-fused (2-oxoindolin-3-ylidene)methylpyrrole derivatives as potential multi-target tyrosine kinase receptor inhibitors. The target compounds were obtained by condensation of 5-substituted oxindoles with N-substituted 2-pyrrolidone aldehyde 7 in satisfactory yields. Of these, 11 and 12 had the highest potency and, compared to sunitinib, showed: (1) significant increase in anti-proliferation of various cancer cells with a favorable selective index (SI); (2) higher inhibitory potency against both VEGFR-2 and PDGFRβ. The molecular modeling results showed that, in terms of VEGFR-2 binding, the synthesized products had a similar binding mode to sunitinib but with tighter interaction. Full article

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1141 KiB

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Assessing Scaffold Diversity of Kinase Inhibitors Using Alternative Scaffold Concepts and Estimating the Scaffold Hopping Potential for Different Kinases

by Dilyana Dimova and Jürgen Bajorath

Molecules 2017, 22(5), 730; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22050730 - 03 May 2017

Cited by 14 | Viewed by 6442

Abstract

Publicly available kinase inhibitors provide a large source of information for structure–activity relationship analysis and kinase drug design. In this study, publicly available inhibitors of the human kinome were collected and analog series formed by kinase inhibitors systematically identified. Then, alternative scaffold concepts were applied to assess diversity and promiscuity of kinase inhibitors. Over the past two years, the number of publicly available kinase inhibitors with high-confidence activity data more than doubled, but coverage of the human kinome only slightly increased. Approximately 70% of current kinase inhibitors belonged to analog series. However, the detectable degree of promiscuity among these kinase inhibitors remained low. Approximately 76% of all inhibitors were only annotated with a single kinase, compared to ~70% two years ago. For many kinases, the assessment of scaffold diversity among their inhibitors and the distribution of differently defined scaffolds over analog series made it possible to assess scaffold hopping potential. Our analysis revealed that the consideration of conventional compound-based scaffolds most likely leads to an overestimation of scaffold hopping frequency, at least for compounds forming analog series. Full article

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Discovery and Biological Evaluation of a Series of Pyrrolo[2,3-b]pyrazines as Novel FGFR Inhibitors

by Yan Zhang, Hongchun Liu, Zhen Zhang, Ruifeng Wang, Tongchao Liu, Chaoyun Wang, Yuchi Ma, Jing Ai, Dongmei Zhao, Jingkang Shen and Bing Xiong

Molecules 2017, 22(4), 583; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22040583 - 05 Apr 2017

Cited by 9 | Viewed by 5125

Abstract

Abnormality of fibroblast growth factor receptor (FGFR)-mediated signaling pathways were frequently found in various human malignancies, making FGFRs hot targets for cancer treatment. To address the consistent need for a new chemotype of FGFR inhibitors, here, we started with a hit structure identified from our internal hepatocyte growth factor receptor (also called c-Met) inhibitor project, and conducted a chemical optimization. After exploring three parts of the hit compound, we finally discovered a new series of pyrrolo[2,3-b]pyrazine FGFR inhibitors, which contain a novel scaffold and unique molecular shape. We believe that our findings can help others to further develop selective FGFR inhibitors. Full article

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Optimized 4,5-Diarylimidazoles as Potent/Selective Inhibitors of Protein Kinase CK1δ and Their Structural Relation to p38α MAPK

by Jakob Halekotte, Lydia Witt, Chiara Ianes, Marc Krüger, Mike Bührmann, Daniel Rauh, Christian Pichlo, Elena Brunstein, Andreas Luxenburger, Ulrich Baumann, Uwe Knippschild, Joachim Bischof and Christian Peifer

Molecules 2017, 22(4), 522; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22040522 - 24 Mar 2017

Cited by 35 | Viewed by 7972

Abstract

The involvement of protein kinase CK1δ in the pathogenesis of severe disorders such as Alzheimer’s disease, amyotrophic lateral sclerosis, familial advanced sleep phase syndrome, and cancer has dramatically increased interest in the development of effective small molecule inhibitors for both therapeutic application and basic research. Unfortunately, the design of CK1 isoform-specific compounds has proved to be highly complicated due to the existence of six evolutionarily conserved human CK1 members that possess similar, different, or even opposite physiological and pathophysiological implications. Consequently, only few potent and selective CK1δ inhibitors have been reported so far and structurally divergent approaches are urgently needed in order to establish SAR that might enable complete discrimination of CK1 isoforms and related p38α MAPK. In this study we report on design and characterization of optimized 4,5-diarylimidazoles as highly effective ATP-competitive inhibitors of CK1δ with compounds 11b (IC₅₀ CK1δ = 4 nM, IC₅₀ CK1ε = 25 nM), 12a (IC₅₀ CK1δ = 19 nM, IC₅₀ CK1ε = 227 nM), and 16b (IC₅₀ CK1δ = 8 nM, IC₅₀ CK1ε = 81 nM) being among the most potent CK1δ-targeting agents published to date. Inhibitor compound 11b, displaying potential as a pharmacological tool, has further been profiled over a panel of 321 protein kinases exhibiting high selectivity. Cellular efficacy has been evaluated in human pancreatic cancer cell lines Colo357 (EC₅₀ = 3.5 µM) and Panc89 (EC₅₀ = 1.5 µM). SAR is substantiated by X-ray crystallographic analysis of 16b in CK1δ and 11b in p38α. Full article

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CDC25 Inhibition in Acute Myeloid Leukemia–A Study of Patient Heterogeneity and the Effects of Different Inhibitors

by Annette K. Brenner, Håkon Reikvam, Kristin Paulsen Rye, Karen Marie Hagen, Antonio Lavecchia and Øystein Bruserud

Molecules 2017, 22(3), 446; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22030446 - 11 Mar 2017

Cited by 12 | Viewed by 4876

Abstract

Cell division cycle 25 (CDC25) protein phosphatases regulate cell cycle progression through the activation of cyclin-dependent kinases (CDKs), but they are also involved in chromatin modulation and transcriptional regulation. CDC25 inhibition is regarded as a possible therapeutic strategy for the treatment of human malignancies, including acute myeloid leukemia (AML). We investigated the in vitro effects of CDC25 inhibitors on primary human AML cells derived from 79 unselected patients in suspension cultures. Both the previously well-characterized CDC25 inhibitor NSC95397, as well as five other inhibitors (BN82002 and the novel small molecular compounds ALX1, ALX2, ALX3, and ALX4), only exhibited antiproliferative effects for a subset of patients when tested alone. These antiproliferative effects showed associations with differences in genetic abnormalities and/or AML cell differentiation. However, the responders to CDC25 inhibition could be identified by analysis of global gene expression profiles. The differentially expressed genes were associated with the cytoskeleton, microtubules, and cell signaling. The constitutive release of 28 soluble mediators showed a wide variation among patients and this variation was maintained in the presence of CDC25 inhibition. Finally, NSC95397 had no or only minimal effects on AML cell viability. In conclusion, CDC25 inhibition has antiproliferative effects on primary human AML cells for a subset of patients, and these patients can be identified by gene expression profiling. Full article

(This article belongs to the Special Issue Kinase Inhibitors)

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Review

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Regulation of G2/M Transition by Inhibition of WEE1 and PKMYT1 Kinases

by Matthias Schmidt, Alexander Rohe, Charlott Platzer, Abdulkarim Najjar, Frank Erdmann and Wolfgang Sippl

Molecules 2017, 22(12), 2045; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22122045 - 23 Nov 2017

Cited by 122 | Viewed by 16326

Abstract

In the cell cycle, there are two checkpoint arrests that allow cells to repair damaged DNA in order to maintain genomic integrity. Many cancer cells have defective G1 checkpoint mechanisms, thus depending on the G2 checkpoint far more than normal cells. G2 checkpoint abrogation is therefore a promising concept to preferably damage cancerous cells over normal cells. The main factor influencing the decision to enter mitosis is a complex composed of Cdk1 and cyclin B. Cdk1/CycB is regulated by various feedback mechanisms, in particular inhibitory phosphorylations at Thr14 and Tyr15 of Cdk1. In fact, Cdk1/CycB activity is restricted by the balance between WEE family kinases and Cdc25 phosphatases. The WEE kinase family consists of three proteins: WEE1, PKMYT1, and the less important WEE1B. WEE1 exclusively mediates phosphorylation at Tyr15, whereas PKMYT1 is dual-specific for Tyr15 as well as Thr14. Inhibition by a small molecule inhibitor is therefore proposed to be a promising option since WEE kinases bind Cdk1, altering equilibria and thus affecting G2/M transition. Full article

(This article belongs to the Special Issue Kinase Inhibitors)

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Current Development Status of MEK Inhibitors

by Ying Cheng and Hongqi Tian

Molecules 2017, 22(10), 1551; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22101551 - 26 Sep 2017

Cited by 170 | Viewed by 10387

Abstract

The current development status of mitogen-activated protein kinase kinase (MEK) inhibitors, including the preclinical data and clinical study progress, has been summarized in this review. Different MEK inhibitors, possessing specific physicochemical properties and bioactivity characteristics, may provide different options for patients seeking treatment for cancer. Moreover, the combination of the MEK inhibitors with other therapies—such as chemotherapy, targeted therapy, and immunotherapy—may be a promising approach for clinical use. Full article

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The Role of Kinase Modulators in Cellular Senescence for Use in Cancer Treatment

by Chang Sup Lee, Juhwa Baek and Sun-Young Han

Molecules 2017, 22(9), 1411; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22091411 - 25 Aug 2017

Cited by 23 | Viewed by 7396

Abstract

Recently, more than 30 small molecules and eight monoclonal antibodies that modulate kinase signaling have been approved for the treatment of several pathological conditions, including cancer, idiopathic pulmonary fibrosis, and rheumatoid arthritis. Among them, kinase modulators have been a primary focus for use in cancer treatment. Cellular senescence is believed to protect cells from tumorigenesis by irreversibly halting cell cycle progression and avoiding the growth of damaged cells and tissues. Senescence can also contribute to tumor suppression and be utilized as a mechanism by anti-cancer agents. Although the role of kinase modulators in cancer treatment and their effects on senescence in tumor development have been extensively studied, the relationship between kinase modulators for cancer treatment and senescence has not been fully discussed. In this review, we discuss the pro- and anti-tumorigenesis functions of senescence and summarize the key roles of kinase modulators in the regulation of senescence against tumors. Full article

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Recent Advances in the Inhibition of p38 MAPK as a Potential Strategy for the Treatment of Alzheimer’s Disease

by Jong Kil Lee and Nam-Jung Kim

Molecules 2017, 22(8), 1287; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules22081287 - 02 Aug 2017

Cited by 236 | Viewed by 16525

Abstract

P38 mitogen-activated protein kinase (MAPK) is a crucial target for chronic inflammatory diseases. Alzheimer’s disease (AD) is characterized by the presence of amyloid plaques and neurofibrillary tangles in the brain, as well as neurodegeneration, and there is no known cure. Recent studies on the underlying biology of AD in cellular and animal models have indicated that p38 MAPK is capable of orchestrating diverse events related to AD, such as tau phosphorylation, neurotoxicity, neuroinflammation and synaptic dysfunction. Thus, the inhibition of p38 MAPK is considered a promising strategy for the treatment of AD. In this review, we summarize recent advances in the targeting of p38 MAPK as a potential strategy for the treatment of AD and envision possibilities of p38 MAPK inhibitors as a fundamental therapeutics for AD. Full article

(This article belongs to the Special Issue Kinase Inhibitors)

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