Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution

Abstract The inside of a cell is highly crowded with proteins and other biomolecules. How proteins express their specific functions together with many off-target proteins in crowded cellular environments is largely unknown. Here, we investigate an inhibitor binding with c-Src kinase using atomistic molecular dynamics (MD) simulations in dilute as well as crowded protein solution. The populations of the inhibitor, PP1, in bulk solution and on the surface of c-Src kinase are reduced as the concentration of crowder bovine serum albumins (BSAs) increases. This observation is consistent with the reduced PP1 inhibitor efficacy in experimental c-Src kinase assays in addition with BSAs. The crowded environment changes the major binding pathway of PP1 toward c-Src kinase compared to that in dilute solution. This change is explained based on the population shift mechanism of local conformations near the inhibitor binding site in c-Src kinase. Protein functions in a living cell could be examined using atomistic MD simulations with realistic cellular environments.

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Activation of Src kinase Lyn by the Kaposi sarcoma–associated herpesvirus K1 protein: implications for lymphomagenesis

Blood ◽

10.1182/blood-2004-07-2781 ◽

2005 ◽

Vol 105 (10) ◽

pp. 3987-3994 ◽

Cited By ~ 59

Author(s):

Om Prakash ◽

O. Rama Swamy ◽

Xiochang Peng ◽

Zhen-Ya Tang ◽

Li Li ◽

...

Keyword(s):

Kinase Activity ◽

Kinase Inhibitor ◽

Src Kinase ◽

Kaposi Sarcoma ◽

B Cell Lymphoma ◽

Proliferation Index ◽

Kinase Activation ◽

Transmembrane Glycoprotein ◽

Lyn Kinase ◽

A Cell

AbstractThe K1 gene of Kaposi sarcoma–associated herpesvirus (KSHV) encodes a transmembrane glycoprotein bearing a functional immunoreceptor tyrosine-based activation motif (ITAM). Previously, we reported that the K1 protein induced plasmablastic lymphomas in K1 transgenic mice, and that these lymphomas showed enhanced Lyn kinase activity. Here, we report that systemic administration of the nuclear factor kappa B (NF-κB) inhibitor Bay 11-7085 or an anti–vascular endothelial growth factor (VEGF) antibody significantly reduced K1 lymphoma growth in nude mice. Furthermore, in KVL-1 cells, a cell line derived from a K1 lymphoma, inhibition of Lyn kinase activity by the Src kinase inhibitor PP2 decreased VEGF induction, NF-κB activity, and the cell proliferation index by 50% to 75%. In contrast, human B-cell lymphoma BJAB cells expressing K1, but not the ITAM sequence–deleted mutant K1, showed a marked increase in Lyn kinase activity with concomitant VEGF induction and NF-κB activation, indicating that ITAM sequences were required for the Lyn kinase–mediated activation of these factors. Our results suggested that K1-mediated constitutive Lyn kinase activation in K1 lymphoma cells is crucial for the production of VEGF and NF-κB activation, both strongly implicated in the development of KSHV-induced lymphoproliferative disorders.

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Faculty Opinions recommendation of 2-aminothiazole as a novel kinase inhibitor template. Structure-activity relationship studies toward the discovery of N-(2-chloro-6-methylphenyl)-2-[[6-[4-(2-hydroxyethyl)-1- piperazinyl)]-2-methyl-4-pyrimidinyl]amino)]-1,3-thiazole-5-carboxamide (dasatinib, BMS-354825) as a potent pan-Src kinase inhibitor.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1085984.538933 ◽

2007 ◽

Author(s):

Andrew Combs

Keyword(s):

Kinase Inhibitor ◽

Src Kinase ◽

Structure Activity Relationship ◽

Activity Relationship ◽

Structure Activity ◽

Template Structure

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A phase II trial of the Src-kinase inhibitor saracatinib after four cycles of chemotherapy for patients with extensive stage small cell lung cancer: NCCTG trial N-0621

Lung Cancer ◽

10.1016/j.lungcan.2014.03.004 ◽

2014 ◽

Vol 85 (2) ◽

pp. 245-250 ◽

Cited By ~ 26

Author(s):

Julian R. Molina ◽

Nathan R. Foster ◽

Thanyanan Reungwetwattana ◽

Garth D. Nelson ◽

Andrew V. Grainger ◽

...

Keyword(s):

Lung Cancer ◽

Small Cell Lung Cancer ◽

Phase Ii ◽

Cell Lung Cancer ◽

Kinase Inhibitor ◽

Phase Ii Trial ◽

Src Kinase ◽

Small Cell ◽

Small Cell Lung ◽

Extensive Stage

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The mammalian Cut homeodomain protein functions as a cell-cycle-dependent transcriptional repressor which downmodulates p21WAF1/CIP1/SDI1 in S phase

The EMBO Journal ◽

10.1093/emboj/17.16.4680 ◽

1998 ◽

Vol 17 (16) ◽

pp. 4680-4694 ◽

Cited By ~ 103

Author(s):

O. Coqueret

Keyword(s):

Cell Cycle ◽

Transcriptional Repressor ◽

S Phase ◽

Homeodomain Protein ◽

Protein Functions ◽

A Cell ◽

Cycle Dependent

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Insight into Inhibitor Binding in the Eukaryotic Proteasome: Computations of the 20S CP

International Journal of Molecular Sciences ◽

10.3390/ijms19123858 ◽

2018 ◽

Vol 19 (12) ◽

pp. 3858

Author(s):

Milan Hodošček ◽

Nadia Elghobashi-Meinhardt

Keyword(s):

Electrostatic Interactions ◽

Active Sites ◽

Sampling Period ◽

Md Simulations ◽

Structural Features ◽

Relaxation Dynamics ◽

Inhibitor Binding ◽

Computational Analyses ◽

Insight Into ◽

Proteolytic Chamber

A combination of molecular dynamics (MD) simulations and computational analyses uncovers structural features that may influence substrate passage and exposure to the active sites within the proteolytic chamber of the 20S proteasome core particle (CP). MD simulations of the CP reveal relaxation dynamics in which the CP slowly contracts over the 54 ns sampling period. MD simulations of the SyringolinA (SylA) inhibitor within the proteolytic B 1 ring chamber of the CP indicate that favorable van der Waals and electrostatic interactions account for the predominant association of the inhibitor with the walls of the proteolytic chamber. The time scale required for the inhibitor to travel from the center of the proteolytic chamber to the chamber wall is on the order of 4 ns, accompanied by an average energetic stabilization of approximately −20 kcal/mol.

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Dynamical Behavior and Conformational Selection Mechanism of the Intrinsically Disordered Sic1 Kinase-Inhibitor Domain

Life ◽

10.3390/life10070110 ◽

2020 ◽

Vol 10 (7) ◽

pp. 110 ◽

Cited By ~ 1

Author(s):

Davide Sala ◽

Ugo Cosentino ◽

Anna Ranaudo ◽

Claudio Greco ◽

Giorgio Moro

Keyword(s):

Kinase Inhibitor ◽

Dynamical Behavior ◽

Md Simulations ◽

Molecular Shape ◽

Conformational Space ◽

Coarse Grained ◽

Conformational Ensemble ◽

Selection Mechanism ◽

Conformational Selection ◽

Intrinsically Disordered

Intrinsically Disordered Peptides and Proteins (IDPs) in solution can span a broad range of conformations that often are hard to characterize by both experimental and computational methods. However, obtaining a significant representation of the conformational space is important to understand mechanisms underlying protein functions such as partner recognition. In this work, we investigated the behavior of the Sic1 Kinase-Inhibitor Domain (KID) in solution by Molecular Dynamics (MD) simulations. Our results point out that application of common descriptors of molecular shape such as Solvent Accessible Surface (SAS) area can lead to misleading outcomes. Instead, more appropriate molecular descriptors can be used to define 3D structures. In particular, we exploited Weighted Holistic Invariant Molecular (WHIM) descriptors to get a coarse-grained but accurate definition of the variegated Sic1 KID conformational ensemble. We found that Sic1 is able to form a variable amount of folded structures even in absence of partners. Among them, there were some conformations very close to the structure that Sic1 is supposed to assume in the binding with its physiological complexes. Therefore, our results support the hypothesis that this protein relies on the conformational selection mechanism to recognize the correct molecular partners.

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