RNAi-based screening of the human kinome identifies Akt-cooperating kinases: a new approach to designing efficacious multitargeted kinase inhibitors

AbstractProtein kinases are critical drug targets for treating a large variety of human diseases. Type-I and type-II kinase inhibitors frequently exhibit off-target toxicity or lead to mutation acquired resistance. Two highly specific allosteric type-III MEK-targeted drugs, Trametinib and Cobimetinib, offer a new approach. Thus, understanding the binding mechanism of existing type-III kinase inhibitors will provide insights for designing new type-III kinase inhibitors. In this work we have systematically studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamics simulation. Our studies provide detailed sequence, structure, interaction-fingerprint, pharmacophore and binding-site information on the binding characteristics of MEK type-III kinase inhibitors. We propose that the helix-folding activation loop is a hallmark allosteric binding site for type-III inhibitors. Subsequently we screened and predicted allosteric binding sites across the human kinome, suggesting other kinases as potential targets suitable for type-III inhibitors. Our findings will provide new insights into the design of potent and selective kinases inhibitors.Author SummaryHuman protein kinases represent a large protein family relevant to many diseases, especially cancers, and have become important drug targets. However, developing the desired selective kinase-targeted inhibitors remain challenging. Kinase allosteric inhibitors provide that opportunity, but, to date, few have been designed other than MEK inhibitors. To more efficiently develop kinase allosteric inhibitors, we systematically studied the binding mode of the MEK type-III allosteric kinase inhibitors using structural system pharmacology and molecular dynamics approaches. New insights into the binding mode and mechanism of type-III inhibitors were revealed that may facilitate the design of new prospective type-III kinase inhibitors.

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Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome

PLoS ONE ◽

10.1371/journal.pone.0179936 ◽

2017 ◽

Vol 12 (6) ◽

pp. e0179936 ◽

Cited By ~ 18

Author(s):

Zheng Zhao ◽

Lei Xie ◽

Philip E. Bourne

Keyword(s):

Kinase Inhibitors ◽

Binding Mode ◽

Type Iii ◽

Human Kinome

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Technological advances for interrogating the human kinome

Biochemical Society Transactions ◽

10.1042/bst20160163 ◽

2017 ◽

Vol 45 (1) ◽

pp. 65-77 ◽

Cited By ~ 15

Author(s):

Akanksha Baharani ◽

Brett Trost ◽

Anthony Kusalik ◽

Scott Napper

Keyword(s):

High Throughput ◽

Therapeutic Intervention ◽

Therapeutic Efficacy ◽

Kinase Inhibitors ◽

Cost Effective ◽

Disease Prognosis ◽

Technological Advances ◽

Human Kinome ◽

High Throughput Manner

There is increasing appreciation among researchers and clinicians of the value of investigating biology and pathobiology at the level of cellular kinase (kinome) activity. Kinome analysis provides valuable opportunity to gain insights into complex biology (including disease pathology), identify biomarkers of critical phenotypes (including disease prognosis and evaluation of therapeutic efficacy), and identify targets for therapeutic intervention through kinase inhibitors. The growing interest in kinome analysis has fueled efforts to develop and optimize technologies that enable characterization of phosphorylation-mediated signaling events in a cost-effective, high-throughput manner. In this review, we highlight recent advances to the central technologies currently available for kinome profiling and offer our perspectives on the key challenges remaining to be addressed.

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Computational Analysis of Kinase Inhibitors Identifies Promiscuity Cliffs across the Human Kinome

ACS Omega ◽

10.1021/acsomega.8b02998 ◽

2018 ◽

Vol 3 (12) ◽

pp. 17295-17308 ◽

Cited By ~ 8

Author(s):

Filip Miljković ◽

Jürgen Bajorath

Keyword(s):

Computational Analysis ◽

Kinase Inhibitors ◽

Human Kinome ◽

Promiscuity Cliffs

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Neurotrophic tyrosine kinase inhibitors: A review of implications for patients, clinicians and healthcare services

Journal of Oncology Pharmacy Practice ◽

10.1177/1078155220959428 ◽

2020 ◽

Vol 26 (8) ◽

pp. 2015-2019

Author(s):

Andrew Walker

Keyword(s):

Targeted Therapies ◽

Kinase Inhibitors ◽

Treatment Options ◽

Healthcare Providers ◽

Healthcare Services ◽

New Approach ◽

Regulatory Bodies ◽

Targeted Agent ◽

Tyrosine Receptor Kinase ◽

To Receive

Neurotrophic tyrosine receptor kinase (NTRK) inhibitors represent the latest advancement as a treatment option in targeted therapies for malignant disease. NTRK gene fusions involving NTRK1, 2 or 3 are implicated as genetics drivers for a number of tumour types which arise within adult and paedatric patients. NTRK inhibitors (Larotrectinib and Entrectinib) are effective agents which have demonstrated clinical benefit in the treatment of NTRK fusion positive solid tumours. Larotrectinib represents the first targeted agent to receive approval from international authorisation and commissioning bodies for the treatment of a specific genetic expression indiscriminate of the site from which the tumour has arisen. As such NTRK inhibitors could pave the way for international healthcare bodies to adopt a similar approach for future targeted therapies thereby altering the manner in which healthcare providers and patients are able to access and utilise innovative, targeted treatment options in future. The potential implications of this new approach are likely to impact upon several aspects of the traditional authorisation and commissioning pathways with potential changes to the design of clinical trials, the review and approval process by regulatory bodies and immunohistopathology services.

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‘Up with the LRRK’: a phosphorylated Rab10 assay for evaluation of LRRK2 activity and inhibitor engagement

Biochemical Journal ◽

10.1042/bcj20160671c ◽

2016 ◽

Vol 473 (18) ◽

pp. 2757-2762 ◽

Cited By ~ 3

Author(s):

Patrick A. Eyers

Keyword(s):

Kinase Inhibitors ◽

Cell Types ◽

New Approach ◽

Chemical Genetic ◽

Biochemical Journal ◽

Compare And Contrast ◽

Generic Analysis ◽

Phosphate Groups

Protein kinases catalyse the addition of phosphate groups to Ser/Thr and Tyr residues in cognate substrates and are mutated or hyperactive in a variety of diseases, making them important targets for rationally designed drugs. A good example is the Parkinson's disease-associated kinase, leucine-rich repeat kinase 2 (LRRK2), which is mutated (and probably hyperactive) in a small, but significant, subset of patients. An exciting new approach for personalised therapy is the development of central nervous system (CNS)-active small-molecule kinase inhibitors, which could be employed to ‘normalise’ LRRK2 signalling in affected cell types. However, the development of such drugs requires validated assays for the analysis of target engagement and the assembly of a set of tools for interrogating LRRK2, and its substrates, both in vitro and in vivo. A new study published in the Biochemical Journal by Ito et al. establishes that a ‘Phos-tag’™-binding assay can be exploited to measure phosphorylation of a recently identified LRRK2 substrate (Ras-related protein in brain 10 (Rab10)), and to compare and contrast relative catalytic output from disease-associated LRRK2 mutants. Powerful in vivo chemical genetic approaches are also disclosed, in which the catalytic activity of LRRK2 is unequivocally linked to the extent of Rab10 phosphorylation and the effects of chemically distinct LRRK2 inhibitors are matched with on-target inhibition mechanisms mediated through LRRK2 and its substrate Rab10. These important findings should simplify the generic analysis of Rab10 phosphorylation in model biological systems and are likely to be applicable to other substrates of LRRK2 (or indeed other kinases) for which phospho-specific antibodies are either absent or unsatisfactory.

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Exploring the understudied human kinome for research and therapeutic opportunities

10.1101/2020.04.02.022277 ◽

2020 ◽

Author(s):

Nienke Moret ◽

Changchang Liu ◽

Benjamin M. Gyori ◽

John A. Bachman ◽

Albert Steppi ◽

...

Keyword(s):

Drug Targets ◽

Kinase Inhibitors ◽

The Cancer Genome Atlas ◽

Public Knowledge ◽

Substantial Fraction ◽

The Public ◽

Cancer Genome Atlas ◽

Automatic Reading ◽

Human Kinome ◽

Genome Atlas

ABSTRACTThe functions of protein kinases have been widely studied and many kinase inhibitors have been developed into FDA-approved therapeutics. A substantial fraction of the human kinome is nonetheless understudied. In this perspective, members of the NIH Understudied Kinome Consortium mine publicly available databases to assess the functionality of these understudied kinases as well as their potential to be therapeutic targets for drug discovery campaigns. We start with a re-analysis of the kinome as a whole and describe criteria for creating an inclusive set of 710 kinase domains as well as a curated set of 557 protein kinase like (PKL) domains. We define an understudied (‘dark’) kinome by quantifying the public knowledge on each kinase with a PKL domain using an automatic reading machine. We find a substantial number are essential in the Cancer Dependency Map and differentially expressed or mutated in disease databases such as The Cancer Genome Atlas. Based on this and other data, it seems likely that the dark kinome contains biologically important genes, a subset of which may be viable drug targets.

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