Personalized therapy design for systemic lupus erythematosus based on the analysis of protein-protein interaction networks.

2 weeks 3 days ago
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Personalized therapy design for systemic lupus erythematosus based on the analysis of protein-protein interaction networks.

PLoS One. 2020;15(3):e0226883

Authors: Brant EJ, Rietman EA, Klement GL, Cavaglia M, Tuszynski JA

Abstract
We analyzed protein expression data for Lupus patients, which have been obtained from publicly available databases. A combination of systems biology and statistical thermodynamics approaches was used to extract topological properties of the associated protein-protein interaction networks for each of the 291 patients whose samples were used to provide the molecular data. We have concluded that among the many proteins that appear to play critical roles in this pathology, most of them are either ribosomal proteins, ubiquitination pathway proteins or heat shock proteins. We propose some of the proteins identified in this study to be considered for drug targeting.

PMID: 32191711 [PubMed - in process]

In silico Investigations of the Mode of Action of Novel Colchicine Derivatives Targeting β-Tubulin Isotypes: A Search for a Selective and Specific β-III Tubulin Ligand.

3 weeks 6 days ago
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In silico Investigations of the Mode of Action of Novel Colchicine Derivatives Targeting β-Tubulin Isotypes: A Search for a Selective and Specific β-III Tubulin Ligand.

Front Chem. 2020;8:108

Authors: Pallante L, Rocca A, Klejborowska G, Huczynski A, Grasso G, Tuszynski JA, Deriu MA

Abstract
The cardinal role of microtubules in cell mitosis makes them interesting drug targets for many pharmacological treatments, including those against cancer. Moreover, different expression patterns between cell types for several tubulin isotypes represent a great opportunity to improve the selectivity and specificity of the employed drugs and to design novel compounds with higher activity only on cells of interest. In this context, tubulin isotype βIII represents an excellent target for anti-tumoral therapies since it is overexpressed in most cancer cells and correlated with drug resistance. Colchicine is a well-known antimitotic agent, which is able to bind the tubulin dimer and to halt the mitotic process. However, it shows high toxicity also on normal cells and it is not specific for isotype βIII. In this context, the search for colchicine derivatives is a matter of great importance in cancer research. In this study, homology modeling techniques, molecular docking, and molecular dynamics simulations have been employed to characterize the interaction between 55 new promising colchicine derivatives and tubulin isotype βIII. These compounds were screened and ranked based on their binding affinity and conformational stability in the colchicine binding site of tubulin βIII. Results from this study point the attention on an amide of 4-chlorine thiocolchicine. This colchicine-derivative is characterized by a unique mode of interaction with tubulin, compared to all other compounds considered, which is primarily characterized by the involvement of the α-T5 loop, a key player in the colchicine binding site. Information provided by the present study may be particularly important in the rational design of colchicine-derivatives targeting drug resistant cancer phenotypes.

PMID: 32154219 [PubMed]

Liver Bioreactor Design Issues of Fluid Flow and Zonation, Fibrosis, and Mechanics: A Computational Perspective.

1 month ago
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Liver Bioreactor Design Issues of Fluid Flow and Zonation, Fibrosis, and Mechanics: A Computational Perspective.

J Funct Biomater. 2020 Feb 28;11(1):

Authors: Rezania V, Coombe D, Tuszynski J

Abstract
Tissue engineering, with the goal of repairing or replacing damaged tissue and organs, has continued to make dramatic science-based advances since its origins in the late 1980's and early 1990's. Such advances are always multi-disciplinary in nature, from basic biology and chemistry through physics and mathematics to various engineering and computer fields. This review will focus its attention on two topics critical for tissue engineering liver development: (a) fluid flow, zonation, and drug screening, and (b) biomechanics, tissue stiffness, and fibrosis, all within the context of 3D structures. First, a general overview of various bioreactor designs developed to investigate fluid transport and tissue biomechanics is given. This includes a mention of computational fluid dynamic methods used to optimize and validate these designs. Thereafter, the perspective provided by computer simulations of flow, reactive transport, and biomechanics responses at the scale of the liver lobule and liver tissue is outlined, in addition to how bioreactor-measured properties can be utilized in these models. Here, the fundamental issues of tortuosity and upscaling are highlighted, as well as the role of disease and fibrosis in these issues. Some idealized simulations of the effects of fibrosis on lobule drug transport and mechanics responses are provided to further illustrate these concepts. This review concludes with an outline of some practical applications of tissue engineering advances and how efficient computational upscaling techniques, such as dual continuum modeling, might be used to quantify the transition of bioreactor results to the full liver scale.

PMID: 32121053 [PubMed]

Synthesis, biological evaluation and molecular docking studies of new amides of 4-chlorothiocolchicine as anticancer agents.

1 month 1 week ago
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Synthesis, biological evaluation and molecular docking studies of new amides of 4-chlorothiocolchicine as anticancer agents.

Bioorg Chem. 2020 Feb 13;97:103664

Authors: Klejborowska G, Urbaniak A, Maj E, Preto J, Moshari M, Wietrzyk J, Tuszynski JA, Chambers TC, Huczyński A

Abstract
Colchicine belongs to a large group of microtubule polymerization inhibitors. Although the anti-cancer activity of colchicine and its derivatives has been established, none of them has found commercial application in cancer treatment due to side effects. Therefore, we designed and synthesized a series of six triple-modified 4-chlorothiocolchicine analogues with amide moieties and one urea derivative. These novel derivatives were tested against several different cancer cell lines (A549, MCF-7, LoVo, LoVo/DX) and primary acute lymphoblastic leukemia (ALL) cells and they showed activity in the nanomolar range. The obtained IC50 values for novel derivatives were lower than those obtained for unmodified colchicine and common anticancer drugs such as doxorubicin and cisplatin. Further studies of colchicine and selected analogues were undertaken to indicate that they induced apoptotic cell death in ALL-5 cells. We also performed in silico studies to predict binding modes of the 4-chlorothiocolchicine derivatives to different β tubulin isotypes. The results indicate that select triple-modified 4-chlorothiocolchicine derivatives represent highly promising novel cancer chemotherapeutics.

PMID: 32106039 [PubMed - as supplied by publisher]

Using the Gibbs Function as a Measure of Human Brain Development Trends from Fetal Stage to Advanced Age.

1 month 3 weeks ago
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Using the Gibbs Function as a Measure of Human Brain Development Trends from Fetal Stage to Advanced Age.

Int J Mol Sci. 2020 Feb 07;21(3):

Authors: Rietman EA, Taylor S, Siegelmann HT, Deriu MA, Cavaglia M, Tuszynski JA

Abstract
We propose to use a Gibbs free energy function as a measure of the human brain development. We adopt this approach to the development of the human brain over the human lifespan: from a prenatal stage to advanced age. We used proteomic expression data with the Gibbs free energy to quantify human brain's protein-protein interaction networks. The data, obtained from BioGRID, comprised tissue samples from the 16 main brain areas, at different ages, of 57 post-mortem human brains. We found a consistent functional dependence of the Gibbs free energies on age for most of the areas and both sexes. A significant upward trend in the Gibbs function was found during the fetal stages, which is followed by a sharp drop at birth with a subsequent period of relative stability and a final upward trend toward advanced age. We interpret these data in terms of structure formation followed by its stabilization and eventual deterioration. Furthermore, gender data analysis has uncovered the existence of functional differences, showing male Gibbs function values lower than female at prenatal and neonatal ages, which become higher at ages 8 to 40 and finally converging at late adulthood with the corresponding female Gibbs functions.

PMID: 32046179 [PubMed - in process]

Investigation of the Electrical Properties of Microtubule Ensembles under Cell-Like Conditions.

1 month 3 weeks ago
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Investigation of the Electrical Properties of Microtubule Ensembles under Cell-Like Conditions.

Nanomaterials (Basel). 2020 Feb 05;10(2):

Authors: Kalra AP, Patel SD, Bhuiyan AF, Preto J, Scheuer KG, Mohammed U, Lewis JD, Rezania V, Shankar K, Tuszynski JA

Abstract
Microtubules are hollow cylindrical polymers composed of the highly negatively-charged (~23e), high dipole moment (1750 D) protein α, β- tubulin. While the roles of microtubules in chromosomal segregation, macromolecular transport, and cell migration are relatively well-understood, studies on the electrical properties of microtubules have only recently gained strong interest. Here, we show that while microtubules at physiological concentrations increase solution capacitance, free tubulin has no appreciable effect. Further, we observed a decrease in electrical resistance of solution, with charge transport peaking between 20-60 Hz in the presence of microtubules, consistent with recent findings that microtubules exhibit electric oscillations at such low frequencies. We were able to quantify the capacitance and resistance of the microtubules (MT) network at physiological tubulin concentrations to be 1.27 × 10-5 F and 9.74 × 104 Ω. Our results show that in addition to macromolecular transport, microtubules also act as charge storage devices through counterionic condensation across a broad frequency spectrum. We conclude with a hypothesis of an electrically tunable cytoskeleton where the dielectric properties of tubulin are polymerisation-state dependent.

PMID: 32033331 [PubMed]

Microtubules as Sub-Cellular Memristors.

1 month 3 weeks ago
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Microtubules as Sub-Cellular Memristors.

Sci Rep. 2020 Feb 07;10(1):2108

Authors: Tuszynski JA, Friesen D, Freedman H, Sbitnev VI, Kim H, Santelices I, Kalra AP, Patel SD, Shankar K, Chua LO

Abstract
Memristors represent the fourth electrical circuit element complementing resistors, capacitors and inductors. Hallmarks of memristive behavior include pinched and frequency-dependent I-V hysteresis loops and most importantly a functional dependence of the magnetic flux passing through an ideal memristor on its electrical charge. Microtubules (MTs), cylindrical protein polymers composed of tubulin dimers are key components of the cytoskeleton. They have been shown to increase solution's ionic conductance and re-orient in the presence of electric fields. It has been hypothesized that MTs also possess intrinsic capacitive and inductive properties, leading to transistor-like behavior. Here, we show a theoretical basis and experimental support for the assertion that MTs under specific circumstances behave consistently with the definition of a memristor. Their biophysical properties lead to pinched hysteretic current-voltage dependence as well a classic dependence of magnetic flux on electric charge. Based on the information about the structure of MTs we provide an estimate of their memristance. We discuss its significance for biology, especially neuroscience, and potential for nanotechnology applications.

PMID: 32034179 [PubMed - in process]

Dataset on interactions of membrane active agents with lipid bilayers.

2 months ago
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Dataset on interactions of membrane active agents with lipid bilayers.

Data Brief. 2020 Apr;29:105138

Authors: Ashrafuzzaman M, Tseng CY, Tuszynski JA

Abstract
We address drug interactions with lipids using in silico simulations and in vitro experiments. The data article provides extended explanations on molecular mechanisms behind membrane action of membrane-active agents (MAAs): antimicrobial peptides and chemotherapy drugs. Complete interpretation of the data is found in the associated original article 'charge-based interactions of antimicrobial peptides and general drugs with lipid bilayers' [1]. Data on molecular dynamic simulations of the drug lipid complexes are provided. Additional data and information are provided here to explain the connectivity among various information and techniques used for understanding of the membrane action and/or binding of MAAs including aptamers. Brief explanation has been provided on the possibility of achieving a converted triangle from newly discovered quadrangle, sides of which explain four different phenomena: 'membrane effects', 'detection and quantification', 'origin of energetics' and 'structure stability' while drug effects occur. Triangle or quadrangle corners represent various techniques that were applied.

PMID: 32016146 [PubMed]

Computer-Aided Drug Design of Small Molecule Inhibitors of the ERCC1-XPF Protein-Protein Interaction.

3 months ago
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Computer-Aided Drug Design of Small Molecule Inhibitors of the ERCC1-XPF Protein-Protein Interaction.

Chem Biol Drug Des. 2019 Dec 31;:

Authors: Gentile F, Elmenoufy AH, Ciniero G, Jay D, Karimi-Busheri F, Barakat KH, Weinfeld M, West FG, Tuszynski JA

Abstract
The heterodimer of DNA excision repair protein ERCC-1 and DNA repair endonuclease XPF (ERCC1-XPF) is a 5´-3´ structure-specific endonuclease essential for the nucleotide excision repair (NER) pathway, and it is also involved in other DNA repair pathways. In cancer cells, ERCC1-XPF plays a central role in repairing DNA damage induced by chemotherapeutics including platinum-based and crosslinking agents, thus its inhibition is a promising strategy to enhance the effect of these therapies. In this study, we rationally modified the structure of F06, a small molecule inhibitor of the ERCC1-XPF interaction (Jordheim et al., 2013), to improve its binding to the target. We followed a multi-step computational approach to investigate potential modification sites of F06, rationally design and rank a library of analogues, and identify candidates for chemical synthesis and in vitro testing. Our top compound, B5, showed an improved half-maximum inhibitory concentration (IC50 ) value of 0.49 µM for the inhibition of ERCC1-XPF endonuclease activity, and lays the foundation for further testing and optimization. Also, the computational approach reported here can be used to develop DNA repair inhibitors targeting the ERCC1-XPF complex.

PMID: 31891209 [PubMed - as supplied by publisher]

Gibbs free energy of protein-protein interactions correlates with ATP production in cancer cells.

3 months 2 weeks ago
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Gibbs free energy of protein-protein interactions correlates with ATP production in cancer cells.

J Biol Phys. 2019 Dec;45(4):423-430

Authors: Golas SM, Nguyen AN, Rietman EA, Tuszynski JA

Abstract
In this paper, we analyze several cancer cell types from two seemingly independent angles: (a) the over-expression of various proteins participating in protein-protein interaction networks and (b) a metabolic shift from oxidative phosphorylation to glycolysis. We use large data sets to obtain a thermodynamic measure of the protein-protein interaction network, namely the associated Gibbs free energy. We find a strong inverse correlation between the percentage of energy production via oxidative phosphorylation and the Gibbs free energy of the protein networks. The latter is a measure of functional dysregulation within the cell. Our findings corroborate earlier indications that signaling pathway upregulation in cancer cells is linked to the metabolic shift known as the Warburg effect; hence, these two seemingly independent characteristics of cancer phenotype may be interconnected.

PMID: 31845118 [PubMed - in process]

Charge-based interactions of antimicrobial peptides and general drugs with lipid bilayers.

4 months ago
Related Articles

Charge-based interactions of antimicrobial peptides and general drugs with lipid bilayers.

J Mol Graph Model. 2019 Nov 27;95:107502

Authors: Ashrafuzzaman M, Tseng CY, Tuszynski JA

Abstract
Membrane-active agents (MAAs), such as antimicrobial peptides (AMPs) and chemotherapy drugs (CDs), induce ion pores/channels inside lipid bilayer membrane, as confirmed by standard electrophysiology experiments. A novel experimental method is described which detects agents directly at the membrane as confirmed for MAAs, CDs and aptamers. MAAs exhibit characteristic 'charge based' interactions with lipids. Electrostatic (ES) and van der Waals (vdW) contributions to the interaction energies have been estimated using molecular dynamics (MD) simulations. These results are consistent with the screened Coulomb interaction predictions recently developed for lipid bilayer binding of integral AMP channels. Energy- and distance-dependence of MAA-lipid interactions from MD simulations are represented by universal probability functions. A generalized model of MAA-lipid interactions is developed based on the charge and geometrical profiles of the participating lipids and AMPs. The corresponding driving force correlates directly with the stability of MAA-lipid structures as observed in electrophysiology experiments. We conclude that MAAs and similar agents that target lipid membranes exhibit physiological effects mainly due to ES and vdW interactions determined by their charge profiles.

PMID: 31805474 [PubMed - as supplied by publisher]

Brain and Human Body Modeling: Computational Human Modeling at EMBC 2018

4 months 3 weeks ago
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Brain and Human Body Modeling: Computational Human Modeling at EMBC 2018

Book. 2019

Authors: Makarov S, Horner M, Noetscher G

Abstract
This chapter presents an overview of electric conduction in living cells when viewed as a composition of bioelectric circuits. We review the cell’s components that are known to exhibit electric conduction properties and represent them as parts of a complex circuitry. In particular, we discuss conductivity of the membrane, ion channels, actin filaments, DNA, and microtubules, each of which play important roles in the biological functioning of the cell. A new picture emerges where electrical conduction within the cell is taking place in an integrated fashion and may explain synchronization and orchestration of the cell dynamics.


PMID: 31725231

Brain and Human Body Modeling: Computational Human Modeling at EMBC 2018

4 months 3 weeks ago
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Brain and Human Body Modeling: Computational Human Modeling at EMBC 2018

Book. 2019

Authors: Makarov S, Horner M, Noetscher G

Abstract
Our goal is to uncover the mechanism underlying tumour-treating fields’ efficacy in killing cancer cells. Modelling the effects of these 200 kHz alternating current electric fields on tumour cell sub-structures has led us to focus on the microtubules (MTs), C-termini and the motor protein kinesin, which are integral to the critical functions of MT transport of proteins during the delicate orchestration of cell division (mitosis). Leading hypotheses of the TTFields’ mechanism that we are modelling include disruption of mitosis functions (such as the ‘kinesin walk’ along MTs), C-termini state transitions and MT polymerization.


PMID: 31725240

Signaling Complexity Measured by Shannon Entropy and Its Application in Personalized Medicine.

4 months 4 weeks ago
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Signaling Complexity Measured by Shannon Entropy and Its Application in Personalized Medicine.

Front Genet. 2019;10:930

Authors: Conforte AJ, Tuszynski JA, da Silva FAB, Carels N

Abstract
Traditional approaches to cancer therapy seek common molecular targets in tumors from different patients. However, molecular profiles differ between patients, and most tumors exhibit inherent heterogeneity. Hence, imprecise targeting commonly results in side effects, reduced efficacy, and drug resistance. By contrast, personalized medicine aims to establish a molecular diagnosis specific to each patient, which is currently feasible due to the progress achieved with high-throughput technologies. In this report, we explored data from human RNA-seq and protein-protein interaction (PPI) networks using bioinformatics to investigate the relationship between tumor entropy and aggressiveness. To compare PPI subnetworks of different sizes, we calculated the Shannon entropy associated with vertex connections of differentially expressed genes comparing tumor samples with their paired control tissues. We found that the inhibition of up-regulated connectivity hubs led to a higher reduction of subnetwork entropy compared to that obtained with the inhibition of targets selected at random. Furthermore, these hubs were described to be participating in tumor processes. We also found a significant negative correlation between subnetwork entropies of tumors and the respective 5-year survival rates of the corresponding cancer types. This correlation was also observed considering patients with lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) based on the clinical data from The Cancer Genome Atlas database (TCGA). Thus, network entropy increases in parallel with tumor aggressiveness but does not correlate with PPI subnetwork size. This correlation is consistent with previous reports and allowed us to assess the number of hubs to be inhibited for therapy to be effective, in the context of precision medicine, by reference to the 100% patient survival rate 5 years after diagnosis. Large standard deviations of subnetwork entropies and variations in target numbers per patient among tumor types characterize tumor heterogeneity.

PMID: 31695721 [PubMed]

Tubulin: Structure, Functions and Roles in Disease.

5 months 1 week ago
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Tubulin: Structure, Functions and Roles in Disease.

Cells. 2019 Oct 22;8(10):

Authors: Binarová P, Tuszynski J

Abstract
Highly conserved α- and β-tubulin heterodimers assemble into dynamic microtubules and perform multiple important cellular functions such as structural support, pathway for transport and force generation in cell division. Tubulin exists in different forms of isotypes expressed by specific genes with spatially- and temporally-regulated expression levels. Some tubulin isotypes are differentially expressed in normal and neoplastic cells, providing a basis for cancer chemotherapy drug development. Moreover, specific tubulin isotypes are overexpressed and localized in the nuclei of cancer cells and/or show bioenergetic functions through the regulation of the permeability of mitochondrial ion channels. It has also become clear that tubulin isotypes are involved in multiple cellular functions without being incorporated into microtubule structures. Understanding the mutations of tubulin isotypes specifically expressed in tumors and their post-translational modifications might help to identify precise molecular targets for the design of novel anti-microtubular drugs. Knowledge of tubulin mutations present in tubulinopathies brings into focus cellular functions of tubulin in brain pathologies such as Alzheimer's disease. Uncovering signaling pathways which affect tubulin functions during antigen-mediated activation of mast cells presents a major challenge in developing new strategies for the treatment of inflammatory and allergic diseases. γ-tubulin, a conserved member of the eukaryotic tubulin superfamily specialized for microtubule nucleation is a target of cell cycle and stress signaling. Besides its microtubule nucleation role, γ-tubulin functions in nuclear and cell cycle related processes. This special issue "Tubulin: Structure, Functions and Roles in Disease" contains eight articles, five of which are original research papers and three are review papers that cover diverse areas of tubulin biology and functions under normal and pathological conditions.

PMID: 31652491 [PubMed - in process]

Docosahexaenoic Acid Inhibits PTP1B Phosphatase and the Viability of MCF-7 Breast Cancer Cells.

5 months 1 week ago
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Docosahexaenoic Acid Inhibits PTP1B Phosphatase and the Viability of MCF-7 Breast Cancer Cells.

Nutrients. 2019 Oct 23;11(11):

Authors: Kuban-Jankowska A, Gorska-Ponikowska M, Sahu KK, Kostrzewa T, Wozniak M, Tuszynski J

Abstract
BACKGROUND: Docosahexaenoic acid (DHA) is an essential polyunsaturated fatty acid compound present in deep water fishes and dietary supplements, with a wide spectrum of potential health benefits, ranging from neurological to anti-inflammatory.
METHODS: Due to the fact that DHA is considered a breast cancer risk reducer, we examined the impact of DHA on MCF-7 breast cancer cells' viability and its inhibitory properties on protein tyrosine phosphatase 1B (PTP1B), a pro-oncogenic phosphatase.
RESULTS: We found that DHA is able to lower both the enzymatic activity of PTP1B phosphatase and the viability of MCF-7 breast cancer cells. We showed that unsaturated DHA possesses a significantly higher inhibitory activity toward PTP1B in comparison to similar fatty acids. We also performed a computational analysis of DHA binding to PTP1B and discovered that it is able to bind to an allosteric binding site.
CONCLUSIONS: Utilizing both a recombinant enzyme and cellular models, we demonstrated that DHA can be considered a potential pharmacological agent for the prevention of breast cancer.

PMID: 31652764 [PubMed - indexed for MEDLINE]

Synthesis, biological evaluation and molecular docking studies of new amides of 4-bromothiocolchicine as anticancer agents.

5 months 1 week ago
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Synthesis, biological evaluation and molecular docking studies of new amides of 4-bromothiocolchicine as anticancer agents.

Bioorg Med Chem. 2019 Oct 08;:115144

Authors: Klejborowska G, Urbaniak A, Preto J, Maj E, Moshari M, Wietrzyk J, Tuszynski JA, Chambers TC, Huczyński A

Abstract
Colchicine is the major alkaloid isolated from the plant Colchicum autumnale, which shows strong therapeutic effects towards different types of cancer. However, due to the toxicity of colchicine towards normal cells its application is limited. To address this issue we synthesized a series of seven triple-modified 4-bromothiocolchicine analogues with amide moieties. These novel derivatives were active in the nanomolar range against several different cancer cell lines and primary acute lymphoblastic leukemia cells, specifically compounds: 5-9 against primary ALL-5 (IC50 = 5.3-14 nM), 5, 7-9 against A549 (IC50 = 10 nM), 5, 7-9 against MCF-7 (IC50 = 11 nM), 5-9 against LoVo (IC50 = 7-12 nM), and 5, 7-9 against LoVo/DX (IC50 = 48-87 nM). These IC50 values were lower than those obtained for unmodified colchicine and common anticancer drugs such as doxorubicin and cisplatin. Further studies revealed that colchicine and selected analogues induced characteristics of apoptotic cell death but manifested their effects in different phases of the cell cycle in MCF-7 versus ALL-5 cells. Specifically, while colchicine and the studied derivatives arrested MCF-7 cells in mitosis, very little mitotically arrested ALL-5 cells were observed, suggesting effects were manifest instead in interphase. We also developed an in silico model of the mode of binding of these compounds to their primary target, β-tubulin. We conducted a correlation analysis (linear regression) between the calculated binding energies of colchicine derivatives and their anti-proliferative activity, and determined that the obtained correlation coefficients strongly depend on the type of cells used.

PMID: 31653441 [PubMed - as supplied by publisher]

GLUT1 and TUBB4 in Glioblastoma Could be Efficacious Targets.

6 months 4 weeks ago
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GLUT1 and TUBB4 in Glioblastoma Could be Efficacious Targets.

Cancers (Basel). 2019 Sep 05;11(9):

Authors: Guda MR, Labak CM, Omar SI, Asuthkar S, Airala S, Tuszynski J, Tsung AJ, Velpula KK

Abstract
Glioblastoma multiforme (GBM) is the most aggressive and deadly brain tumor, portending a median 13-month survival even following gross total resection with adjuvant chemotherapy and radiotherapy. This prognosis necessitates improved therapies for the disease. A target of interest for novel chemotherapies is the Warburg Effect, which describes the tumor's shift away from oxidative phosphorylation towards glycolysis. Here, we elucidate GLUT1 (Glucose transporter 1) and one of its associated binding partners, TUBB4 (Tubulin 4), as potentially druggable targets in GBM. Using data mining approach, we demonstrate that GLUT1 is overexpressed as a function of tumor grade in astrocytoma's and that its overexpression is associated with poorer prognosis. Using both mass spectrometry performed on hGBM (human glioblastoma patient specimen) and in silico modeling, we show that GLUT1 interacts with TUBB4, and more accurately demonstrates GLUT1's binding with fasentin. Proximity ligation assay (PLA) and immunoprecipitation studies confirm GLUT1 interaction with TUBB4. Treatment of GSC33 and GSC28 cells with TUBB4 inhibitor, CR-42-24, reduces the expression of GLUT1 however, TUBB4 expression is unaltered upon fasentin treatment. Using human pluripotent stem cell antibody array, we demonstrate reduced levels of Oct3/4, Nanog, Sox2, Sox17, Snail and VEGFR2 (Vascular endothelial growth factor receptor 2) upon CR-42-24 treatment. Overall, our data confirm that silencing TUBB4 or GLUT1 reduce GSC tumorsphere formation, self-renewal and proliferation in vitro. These findings suggest GLUT1 and its binding partner TUBB4 as druggable targets that warrant further investigation in GBM.

PMID: 31491891 [PubMed]

Synthesis, antiproliferative activity and molecular docking studies of 4-chlorothiocolchicine analogues.

7 months ago
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Synthesis, antiproliferative activity and molecular docking studies of 4-chlorothiocolchicine analogues.

Chem Biol Drug Des. 2019 Sep 04;:

Authors: Klejborowska G, Moshari M, Maj E, Majcher U, Preto J, Wietrzyk J, Tuszynski JA, Huczyński A

Abstract
Colchicine is a therapeutic agent currently used in therapies of many diseases. It also shows antimitotic effects and its high cytotoxic activity against different cancer cell lines has been demonstrated many times. To overcome the limitations of colchicine use in anticancer therapy, we synthesized a series of novel triple-modified 4-chloro-7-carbamatethiocolchicines. All the synthesized compounds have been tested in vitro to evaluate their cytotoxicity towards A549, MCF-7, LoVo, LoVo/DX and BALB/3T3 cell lines. Additionally, their mode of binding to ß-tubulin was evaluated in silico. The majority of triple-modified colchicine derivatives exhibited significantly higher cytotoxicity than colchicine, doxorubicin and cisplatin against tested cancerous cell lines with much higher selectivity index values for four of them. This article is protected by copyright. All rights reserved.

PMID: 31483093 [PubMed - as supplied by publisher]

Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments.

7 months ago
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Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments.

Biophys J. 2019 Aug 16;:

Authors: Churchill CDM, Healey MA, Preto J, Tuszynski JA, Woodside MT

Abstract
Intrinsically disordered proteins often play an important role in protein aggregation. However, it is challenging to determine the structures and interactions that drive the early stages of aggregation because they are transient and obscured in a heterogeneous mixture of disordered states. Even computational methods are limited because the lack of ordered structure makes it difficult to ensure that the relevant conformations are sampled. We address these challenges by integrating atomistic simulations with high-resolution single-molecule measurements reported previously, using the measurements to help discern which parts of the disordered ensemble of structures in the simulations are most probable while using the simulations to identify residues and interactions that are important for oligomer stability. This approach was applied to α-synuclein, an intrinsically disordered protein that aggregates in the context of Parkinson's disease. We simulated single-molecule pulling experiments on dimers, the minimal oligomer, and compared them to force spectroscopy measurements. Force-extension curves were simulated starting from a set of 66 structures with substantial structured content selected from the ensemble of dimer structures generated at zero force via Monte Carlo simulations. The pattern of contour length changes as the structures unfolded through intermediate states was compared to the results from optical trapping measurements on the same dimer to discern likely structures occurring in the measurements. Simulated pulling curves were generally consistent with experimental data but with a larger number of transient intermediates. We identified an ensemble of β-rich dimer structures consistent with the experimental data from which dimer interfaces could be deduced. These results suggest specific druggable targets in the structural motifs of α-synuclein that may help prevent the earliest steps of oligomerization.

PMID: 31477241 [PubMed - as supplied by publisher]