scholarly journals Combining kinase inhibitors for optimally co‐targeting cancer and drug escape by exploitation of drug target promiscuities

2020 ◽  
Vol 82 (1) ◽  
pp. 133-142
Author(s):  
Shangying Chen ◽  
Sheng Yong Yang ◽  
Xian Zeng ◽  
Feng Zhu ◽  
Ying Tan ◽  
...  
Keyword(s):  
Drug Target ◽  
Kinase Inhibitors

Monitoring Drug-Target Interactions through Target Engagement-Mediated Amplification on Arrays and in situ

2021 ◽  
Author(s):  
Rasel Al-Amin ◽  
Lars Johansson ◽  
Eldar Abdurakhmanov ◽  
Nils Landegren ◽  
Liza Löf ◽  
...  
Keyword(s):  
Drug Target ◽  
Kinase Inhibitors ◽  
Expression Profiles ◽  
Clinical Samples ◽  
Target Engagement ◽  
Rolling Circle Replication ◽  
Target Proteins ◽  
Dna Conjugates

Abstract Drugs are designed to bind their target proteins in physiologically relevant tissues and organs to modulate biological functions and elicit desirable clinical outcomes. Information about target engagement at cellular and subcellular resolution is therefore critical for guiding compound optimization in drug discovery, and for probing resistance mechanisms to targeted therapies in clinical samples. We describe a target engagement-mediated amplification (TEMA) technology, where oligonucleotide-conjugated drugs are used to visualize and measure target engagement in situ, amplified via rolling-circle replication of circularized oligonucleotide probes. We illustrate the TEMA technique using dasatinib and gefitinib, two kinase inhibitors with distinct selectivity profiles. In vitro binding by dasatinib probe to arrays of displayed proteins accurately reproduced known selectivity profiles, while their differential binding to a panel of fixed adherent cells agreed with expectations from expression profiles of the cells. These findings were corroborated by competition experiments using kinase inhibitors with overlapping and non-overlapping target specificities, and translated to pathology tissue sections. We also introduce a proximity ligation variant of TEMA in which these drug-DNA conjugates are combined with antibody-DNA conjugates to selectively investigate binding to specific target proteins of interest. This form of the assay serves to improve resolution of binding to on- and off-target proteins. In conclusion, TEMA has the potential to aid in drug development and clinical routine by conferring valuable insights in drug-target interactions at spatial resolution in protein arrays, cells and tissues.

Rapid discovery of drug target engagement by isothermal shift assay

2019 ◽  
Author(s):  
Kristofor J. Webb ◽  
Kerri A. Ball ◽  
Stephen J. Coleman ◽  
Jeremy Jacobsen ◽  
Michael H.B. Stowell ◽  
...  
Keyword(s):  
Drug Target ◽  
Drug Targets ◽  
Kinase Inhibitors ◽  
Rapid Identification ◽  
Living Cells ◽  
Experimental Designs ◽  
Living Systems ◽  
Target Engagement ◽  
Protein Targets ◽  
Drug Molecules

Identifying protein targets directly bound by drug molecules within living systems remains challenging. Here we present the isothermal shift assay, iTSA, for rapid identification of drug targets. Compared with thermal proteome profiling, a prevailing method for target engagement, iTSA offers a simplified workflow, 4-fold higher throughput, and multiplexed experimental designs with higher replication. We demonstrate application of iTSA to identify targets for several kinase inhibitors in lysates and living cells.

scholarly journals Identification and validation of novel and more effective choline kinase inhibitors against Streptococcus pneumoniae

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tahl Zimmerman ◽  
Valerie Chasten ◽  
Juan Carlos Lacal ◽  
Salam A. Ibrahim
Keyword(s):  
Streptococcus Pneumoniae ◽  
Drug Target ◽  
Kinase Inhibitors ◽  
Teichoic Acid ◽  
Cellular Level ◽  
Choline Kinase ◽  
Potential Therapeutic Target ◽  
Enzymatic Assays ◽  
Induced Autolysis ◽  
Promising Avenue

Abstract Streptococcus pneumoniae choline kinase (sChoK) has previously been proposed as a drug target, yet the effectiveness of the first and only known inhibitor of sChoK, HC-3, is in the millimolar range. The aim of this study was thus to further validate sChoK as a potential therapeutic target by discovering more powerful sChoK inhibitors. LDH/PK and colorimetric enzymatic assays revealed two promising sChoK inhibitor leads RSM-932A and MN58b that were discovered with IC50 of 0.5 and 150 μM, respectively, and were shown to be 2–4 magnitudes more potent than the previously discovered inhibitor HC-3. Culture assays showed that the minimum inhibitory concentration (MIC) of RSM-932A and MN58b for S. pneumoniae was 0.4 μM and 10 μM, respectively, and the minimum lethal concentration (MLC) was 1.6 μM and 20 μM, respectively. Western blot monitoring of teichoic acid production revealed differential patterns in response to each inhibitor. In addition, both inhibitors possessed a bacteriostatic mechanism of action, and neither interfered with the autolytic effects of vancomycin. Cells treated with MN58b but not RSM-932A were more sensitive to a phosphate induced autolysis with respect to the untreated cells. SEM studies revealed that MN58b distorted the cell wall, a result consistent with the apparent teichoic acid changes. Two novel and more highly potent putative inhibitors of sChoK, MN58b and RSM-932A, were characterized in this study. However, the effects of sChoK inhibitors can vary at the cellular level. sChoK inhibition is a promising avenue to follow in the development of therapeutics for treatment of S. pneumoniae.

scholarly journals Targeting HER3, a Catalytically Defective Receptor Tyrosine Kinase, Prevents Resistance of Lung Cancer to a Third-Generation EGFR Kinase Inhibitor

Cancers ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2394
Author(s):  
Donatella Romaniello ◽  
Ilaria Marrocco ◽  
Nishanth Belugali Nataraj ◽  
Irene Ferrer ◽  
Diana Drago-Garcia ◽  
...  
Keyword(s):  
Drug Target ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Treatment Options ◽  
Acquired Resistance ◽  
Underlying Mechanism ◽  
Xenograft Models ◽  
Emergence Of Resistance ◽  
Egfr Kinase ◽  
Egfr Antibody

Although two growth factor receptors, EGFR and HER2, are amongst the best targets for cancer treatment, no agents targeting HER3, their kinase-defective family member, have so far been approved. Because emergence of resistance of lung tumors to EGFR kinase inhibitors (EGFRi) associates with compensatory up-regulation of HER3 and several secreted forms, we anticipated that blocking HER3 would prevent resistance. As demonstrated herein, a neutralizing anti-HER3 antibody we generated can clear HER3 from the cell surface, as well as reduce HER3 cleavage by ADAM10, a surface metalloproteinase. When combined with a kinase inhibitor and an anti-EGFR antibody, the antibody completely blocked patient-derived xenograft models that acquired resistance to EGFRi. We found that the underlying mechanism involves posttranslational downregulation of HER3, suppression of MET and AXL upregulation, as well as concomitant inhibition of AKT signaling and upregulation of BIM, which mediates apoptosis. Thus, although HER3 is nearly devoid of kinase activity, it can still serve as an effective drug target in the context of acquired resistance. Because this study simulated in animals the situation of patients who develop resistance to EGFRi and remain with no obvious treatment options, the observations presented herein may warrant clinical testing.

scholarly journals Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

2017 ◽  
Vol 13 (8) ◽  
pp. e1005678 ◽  
Author(s):  
Anna Cichonska ◽  
Balaguru Ravikumar ◽  
Elina Parri ◽  
Sanna Timonen ◽  
Tapio Pahikkala ◽  
...  
Keyword(s):  
Drug Target ◽  
Experimental Approach ◽  
Kinase Inhibitors ◽  
Target Interaction

scholarly journals Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

2021 ◽  
Author(s):  
Abhisek Dwivedy ◽  
Richard Mariadasse ◽  
Mohammed Ahmad ◽  
Sayan Chakraborty ◽  
Deepsikha Kar ◽  
...  
Keyword(s):  
Active Site ◽  
Drug Target ◽  
Kinase Inhibitors ◽  
3D Structure ◽  
Drug Repurposing ◽  
Lead Compounds ◽  
Nucleotidyl Transferase ◽  
Domain Organisation ◽  
First Time

AbstractApart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness as well as DFT properties. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, the proposed kinase inhibitors and a few of the predicted nucleotidyl transferase inhibitors significantly inhibited the aforementioned enzymatic activity. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

scholarly journals Structure-Unbinding Kinetics Relationship of p38α MAPK Inhibitors

2019 ◽  
Author(s):  
Xiaoxia Ge ◽  
Hepan Tan ◽  
Lei Xie
Keyword(s):  
Residence Time ◽  
Drug Target ◽  
Kinase Inhibitors ◽  
Drug Efficacy ◽  
Distinct Type ◽  
Rational Drug Design ◽  
Average Lifetime ◽  
Kinetics Of

AbstractRational Drug Design still faces a major hurdle for the prediction of drug efficacyin vivosolely based on its binding affinity for the targetin vitro. The traditional perspective has proven to be inadequate as it lacks the consideration of essential aspects such as pharmacokinetics and binding kinetics in determining drug efficacy and toxicity. Residence time, the average lifetime of drug-target complex, has gained broader recognition as a better predictor for lead optimization. Long residence time could contribute to sustained pharmacological effect and may mitigate off-target toxicity as well. To unravel the underlining mechanism for variation of residence time and determine the ligand features governing the unbinding kinetics, unbinding kinetics of two distinct type II inhibitors of p38α MAP kinase were investigated and compared by molecular dynamics and metadynamics simulation approaches. Free energy landscape of key motions associated with unbinding was constructed for both inhibitors. Multiple unbinding pathways and rebinding were revealed during the drug-target dissociation process of faster unbinder Lig3 and slower unbinder Lig8 respectively, suggesting a novel mechanism of unbinding kinetics. This comparative study implies that hydrophobic and hydrogen-bonding interactions in the R1 group of ligands are crucial for slow unbinding. Such kind of structure-kinetics relationship approaches could also be applied to predict unbinding pathways and kinetics of many other small molecules, and facilitate the design of efficient kinase inhibitors.

Adaptation to chronic mTOR inhibition in cancer and in aging

2013 ◽  
Vol 41 (4) ◽  
pp. 956-961 ◽  
Author(s):  
Rebecca Gilley ◽  
Kathryn Balmanno ◽  
Claire L. Cope ◽  
Simon J. Cook
Keyword(s):  
Drug Target ◽  
Kinase Inhibitors ◽  
Mtor Inhibitors ◽  
Allosteric Inhibitors ◽  
Mtor Inhibition ◽  
Cell Responses ◽  
Downstream Effector ◽  
Signalling Network ◽  
Effector Pathways ◽  
Mtor Complex 1

The mTOR [mammalian (or mechanistic) target of rapamycin] protein kinase co-ordinates catabolic and anabolic processes in response to growth factors and nutrients and is a validated anticancer drug target. Rapamycin and related allosteric inhibitors of mTORC1 (mTOR complex 1) have had some success in specific tumour types, but have not exhibited broad anticancer activity, prompting the development of new ATP-competitive mTOR kinase inhibitors that inhibit both mTORC1 and mTORC2. In common with other targeted kinase inhibitors, tumours are likely to adapt and acquire resistance to mTOR inhibitors. In the present article, we review studies that describe how tumour cells adapt to become resistant to mTOR inhibitors. mTOR is a central signalling hub which responds to an array of signalling inputs and activates a range of downstream effector pathways. Understanding how this signalling network is remodelled and which pathways are invoked to sustain survival and proliferation in the presence of mTOR inhibitors can provide new insights into the importance of the various mTOR effector pathways and may suggest targets for intervention to combine with mTOR inhibitors. Finally, since chronic mTOR inhibition by rapamycin can increase lifespan and healthspan in nematodes, fruitflies and mice, we contrast these studies with tumour cell responses to mTOR inhibition.

Tracking cancer drugs in living cells by thermal profiling of the proteome

Science ◽  
2014 ◽  
Vol 346 (6205) ◽  
pp. 1255784 ◽  
Author(s):  
Mikhail M. Savitski ◽  
Friedrich B. M. Reinhard ◽  
Holger Franken ◽  
Thilo Werner ◽  
Maria Fälth Savitski ◽  
...  
Keyword(s):  
Drug Target ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Drug Efficacy ◽  
Living Cells ◽  
Live Cells ◽  
Downstream Effectors ◽  
Small Molecule Ligands ◽  
Thermal Profiling ◽  
Thermal Stability Of

The thermal stability of proteins can be used to assess ligand binding in living cells. We have generalized this concept by determining the thermal profiles of more than 7000 proteins in human cells by means of mass spectrometry. Monitoring the effects of small-molecule ligands on the profiles delineated more than 50 targets for the kinase inhibitor staurosporine. We identified the heme biosynthesis enzyme ferrochelatase as a target of kinase inhibitors and suggest that its inhibition causes the phototoxicity observed with vemurafenib and alectinib. Thermal shifts were also observed for downstream effectors of drug treatment. In live cells, dasatinib induced shifts in BCR-ABL pathway proteins, including CRK/CRKL. Thermal proteome profiling provides an unbiased measure of drug-target engagement and facilitates identification of markers for drug efficacy and toxicity.

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