4.6 Article

Targeting Conformational Plasticity of Protein Kinases

期刊

ACS CHEMICAL BIOLOGY
卷 10, 期 1, 页码 190-200

出版社

AMER CHEMICAL SOC
DOI: 10.1021/cb500870a

关键词

-

向作者/读者索取更多资源

The quest for ever more selective kinase inhibitors as potential future drugs has yielded a large repertoire of chemical probes that are selective for specific kinase conformations. These probes have been useful tools to obtain structural snapshots of kinase conformational plasticity. Similarly, kinetic and thermodynamic inhibitor binding experiments provide glimpses at the time scales and energetics of conformational interconversions. These experimental insights are complemented by computational predictions of conformational energy landscapes and simulations of conformational transitions and of the process of inhibitors binding to the protein kinase domain. A picture emerges in which highly selective inhibitors capitalize on the dynamic nature of kinases.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.6
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Biochemistry & Molecular Biology

An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression

Steven K. Albanese, Daniel L. Parton, Mehtap Isik, Lucelenie Rodriguez-Laureano, Sonya M. Hanson, Julie M. Behr, Scott Gradia, Chris Jeans, Nicholas M. Levinson, Markus A. Seeliger, John D. Chodera

BIOCHEMISTRY (2018)

Article Genetics & Heredity

Prolyl isomerization of FAAP20 catalyzed by PIN1 regulates the Fanconi anemia pathway

Jingming Wang, Bryan Chan, Michael Tong, YiTing Paung, Ukhyun Jo, Dwight Martin, Markus Seeliger, John Haley, Hyungjin Kim

PLOS GENETICS (2019)

Article Biochemistry & Molecular Biology

Substrate-selective inhibitors that reprogram the activity of insulin-degrading enzyme

Juan Pablo Maianti, Grace A. Tan, Amedeo Vetere, Arnie J. Welsh, Bridget K. Wagner, Markus A. Seeliger, David R. Liu

NATURE CHEMICAL BIOLOGY (2019)

Article Cell Biology

IRE1β negatively regulates IRE1α signaling in response to endoplasmic reticulum stress

Michael J. Grey, Eva Cloots, Mariska S. Simpson, Nicole LeDuc, Yevgeniy Serebrenik, Heidi De Luca, DeLphine De Sutter, Phi Luong, Jay R. Thiagarajah, Adrienne W. Paton, James C. Paton, Markus A. Seeliger, Sven Eyckerman, Sophie Janssens, Wayne Lencer

JOURNAL OF CELL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture

Linglan Fang, Jessica Vilas-Boas, Sujata Chakraborty, Zachary E. Potter, Ames C. Register, Markus A. Seeliger, Dustin J. Maly

ACS CHEMICAL BIOLOGY (2020)

Article Chemistry, Multidisciplinary

Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset of Resistance Mutations in Kinases

Mrinal Shekhar, Zachary Smith, Markus A. Seeliger, Pratyush Tiwary

Summary: Understanding how mutations cause drug resistance is important. In this study, we demonstrate how molecular dynamics simulations can provide a detailed mechanistic explanation for the differences in drug dissociation pathway caused by a mutation. We found that a point mutation in a protein leads to changes in its flexibility, resulting in a faster drug dissociation pathway. We believe that this approach can efficiently explain resistance mutations that are hard to understand from a structural perspective.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

Review Biochemistry & Molecular Biology

Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome

Aziz M. Rangwala, Victoria R. Mingione, George Georghiou, Markus A. Seeliger

Summary: Phosphorylation plays a vital role in regulating biological processes, and protein kinases have been extensively studied for their involvement in human health and disease. Some kinases possess additional catalytic functions in addition to phosphotransferase activity, while others have lost their catalytic activity completely. In this study, we analyzed the UniProtKB database for bifunctional protein kinases and focused on those crucial for bacterial and human cellular homeostasis. These kinases have diverse functional roles in environmental sensing, metabolic regulation, immune-host defense, and cell cycle control. This article explores their dual catalytic activities and their contributions to disease pathogenesis.

BIOMOLECULES (2022)

Article Biochemistry & Molecular Biology

Extended DNA-binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks

Alexandra S. Weinheimer, YiTing Paung, Julie Rageul, Arafat Khan, Natalie Lo, Brian Ho, Michael Tong, Sebastien Alphonse, Hyungjin Kim, Markus A. Seeliger

Summary: Elevated DNA replication stress can lead to instability of the DNA replication fork and DNA mutations, which are involved in tumorigenesis. Our study characterizes a new DNA-binding motif in SDE2, called SAP domain, that prefers single-stranded DNA. We also find that SDE2 plays a role in preserving replication fork integrity by regulating the fork protection complex.

JOURNAL OF BIOLOGICAL CHEMISTRY (2022)

Article Biochemistry & Molecular Biology

Discovery and molecular basis of subtype-selective cyclophilin inhibitors

Alexander A. Peterson, Aziz M. Rangwala, Manish K. Thakur, Patrick S. Ward, Christie Hung, Ian R. Outhwaite, Alix Chan, Dmitry L. Usanov, Vamsi K. Mootha, Markus A. Seeliger, David R. Liu

Summary: Novel and selective cyclophilin inhibitors have been discovered through in vitro screening, which show high selectivity towards specific subtypes of cyclophilin and can inhibit mitochondrial function. The development of the first inhibitor for a specific cyclophilin subtype further advances the understanding and potential therapeutic applications of these proteins.

NATURE CHEMICAL BIOLOGY (2022)

Review Biochemistry & Molecular Biology

Allosteric regulation and inhibition of protein kinases

Victoria R. Mingione, YiTing Paung, Ian R. Outhwaite, Markus A. Seeliger

Summary: The human genome contains over 500 different protein kinases that have tightly regulated activity as signaling enzymes. The enzymatic activity of the conserved kinase domain is influenced by various regulatory inputs, including the binding of regulatory domains, substrates, and post-translational modifications such as autophosphorylation. This review focuses on the allosteric regulation of protein kinases and highlights recent advances in this field.

BIOCHEMICAL SOCIETY TRANSACTIONS (2023)

Article Biochemistry & Molecular Biology

Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk

Yagmur Kan, YiTing Paung, Yunyoung Kim, Markus A. Seeliger, W. Todd Miller

Summary: Tyrosine kinases (TKs) are important for regulating cell processes and their dysregulation is linked to various diseases. In this study, novel mutations in the nonreceptor tyrosine kinases Ack1 and Brk were identified in systemic lupus erythematosus (SLE) patients. These mutations resulted in loss of catalytic activity, and their structural impact was further investigated.

BIOCHEMISTRY (2023)

Article Multidisciplinary Sciences

Structural mechanism of a drug-binding process involving a large conformational change of the protein target

Pelin Ayaz, Agatha Lyczek, YiTing Paung, Victoria R. Mingione, Roxana E. Iacob, Parker W. de Waal, John R. Engen, Markus A. Seeliger, Yibing Shan, David E. Shaw

Summary: The authors used molecular dynamics simulations to study the binding process of Abl kinase with the cancer drug imatinib. The simulations revealed that imatinib induces a large conformational change of the protein and identified a region in Abl kinase that is structurally unstable during binding. Mutations in this region confer imatinib resistance by exacerbating structural instability.

NATURE COMMUNICATIONS (2023)

Review Cell Biology

Domain Architecture of the Nonreceptor Tyrosine Kinase Ack1

Yagmur Kan, YiTing Paung, Markus A. Seeliger, W. Todd Miller

Summary: The nonreceptor tyrosine kinase Ack1 has a unique arrangement of non-catalytic modules, including an SH3 domain located at the C-terminal of the kinase domain (SH1), which differs from the typical layout in NRTKs. Ack1 shares a region of high homology with the tumor suppressor protein Mig6. It is the only tyrosine kinase family known to carry a UBA domain. The GTPase binding and SAM domains are also uncommon in the NRTKs. Ack1 acts as a downstream effector of receptor tyrosine kinases and integrins, as well as an epigenetic regulator and mediator of drug resistance and hormone-sensitive tumor progression.
Article Multidisciplinary Sciences

Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance

Agatha Lyczek, Benedict-Tilman Berger, Aziz M. Rangwala, YiTing Paung, Jessica Tom, Hannah Philipose, Jiaye Guo, Steven K. Albanese, Matthew B. Robers, Stefan Knapp, John D. Chodera, Markus A. Seeliger

Summary: Protein kinase inhibitors are potent anticancer drugs, but some patients develop resistance to these inhibitors, leading to suboptimal treatment outcomes. Mutations in the Bcr-Abl kinase domain contribute to resistance, with some altering drug-protein interactions and others located far from the drug-binding site still conferring resistance.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemistry & Molecular Biology

What Makes a Kinase Promiscuous for Inhibitors?

Sonya M. Hanson, George Georghiou, Manish K. Thakur, W. Todd Miller, Joshua S. Rest, John D. Chodera, Markus A. Seeliger

CELL CHEMICAL BIOLOGY (2019)

暂无数据