Algebraic and topological indices of molecular pathway networks in human cancers.

2 years 1 month ago
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Algebraic and topological indices of molecular pathway networks in human cancers.

Math Biosci Eng. 2015 Dec;12(6):1289-302

Authors: Hinow P, Rietman EA, Omar SI, Tuszyński JA

Abstract
Protein-protein interaction networks associated with diseases have gained prominence as an area of research. We investigate algebraic and topological indices for protein-protein interaction networks of 11 human cancers derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. We find a strong correlation between relative automorphism group sizes and topological network complexities on the one hand and five year survival probabilities on the other hand. Moreover, we identify several protein families (e.g. PIK, ITG, AKT families) that are repeated motifs in many of the cancer pathways. Interestingly, these sources of symmetry are often central rather than peripheral. Our results can aide in identification of promising targets for anti-cancer drugs. Beyond that, we provide a unifying framework to study protein-protein interaction networks of families of related diseases (e.g. neurodegenerative diseases, viral diseases, substance abuse disorders).

PMID: 26775864 [PubMed - indexed for MEDLINE]

Synthesis, antiproliferative activity and molecular docking of Colchicine derivatives.

2 years 1 month ago
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Synthesis, antiproliferative activity and molecular docking of Colchicine derivatives.

Bioorg Chem. 2016 Feb;64:103-12

Authors: Huczyński A, Majcher U, Maj E, Wietrzyk J, Janczak J, Moshari M, Tuszynski JA, Bartl F

Abstract
In order to create more potent anticancer agents, a series of five structurally different derivatives of Colchicine have been synthesised. These compounds were characterised spectroscopically and structurally and their antiproliferative activity against four human tumour cell lines (HL-60, HL-60/vinc, LoVo, LoVo/DX) was evaluated. Additionally the activity of the studied compounds was calculated using computational methods involving molecular docking of the Colchicine derivatives to β-tubulin. The experimental and computational results are in very good agreement indicating that the antimitotic activity of Colchicine derivatives can be readily predicted using computational modeling methods.

PMID: 26794327 [PubMed - indexed for MEDLINE]

Characterization of the AXH domain of Ataxin-1 using enhanced sampling and functional mode analysis.

2 years 1 month ago
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Characterization of the AXH domain of Ataxin-1 using enhanced sampling and functional mode analysis.

Proteins. 2016 May;84(5):666-73

Authors: Deriu MA, Grasso G, Tuszynski JA, Massai D, Gallo D, Morbiducci U, Danani A

Abstract
Ataxin-1 is the protein responsible for the Spinocerebellar ataxia type 1, an incurable neurodegenerative disease caused by polyglutamine expansion. The AXH domain plays a pivotal role in physiological functions of Ataxin-1. In Spinocerebellar ataxia 1, the AXH domain is involved in the misfolding and aggregation pathway. Here molecular modeling is applied to investigate the protein-protein interactions contributing to the AXH dimer stability. Particular attention is focused on: (i) the characterization of AXH monomer-monomer interface; (ii) the molecular description of the AXH monomer-monomer interaction dynamics. Technically, an approach based on functional mode analysis, here applied to replica exchange molecular dynamics trajectories, was employed. The findings of this study are consistent with previous experimental results and elucidate the pivotal role of the I580 residue in mediating the AXH monomer-monomer interaction dynamics.

PMID: 26879337 [PubMed - indexed for MEDLINE]

Toward precision medicine of breast cancer.

2 years 1 month ago
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Toward precision medicine of breast cancer.

Theor Biol Med Model. 2016 Feb 29;13:7

Authors: Carels N, Spinassé LB, Tilli TM, Tuszynski JA

Abstract
In this review, we report on breast cancer's molecular features and on how high throughput technologies are helping in understanding the dynamics of tumorigenesis and cancer progression with the aim of developing precision medicine methods. We first address the current state of the art in breast cancer therapies and challenges in order to progress towards its cure. Then, we show how the interaction of high-throughput technologies with in silico modeling has led to set up useful inferences for promising strategies of target-specific therapies with low secondary effect incidence for patients. Finally, we discuss the challenge of pharmacogenetics in the clinical practice of cancer therapy. All these issues are explored within the context of precision medicine.

PMID: 26925829 [PubMed - indexed for MEDLINE]

New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy.

2 years 1 month ago
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New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy.

J Mol Graph Model. 2016 Apr;65:71-82

Authors: Gentile F, Tuszynski JA, Barakat KH

Abstract
Many cancer chemotherapy agents act by targeting the DNA of cancer cells, causing substantial damage within their genome and causing them to undergo apoptosis. An effective DNA repair pathway in cancer cells can act in a reverse way by removing these drug-induced DNA lesions, allowing cancer cells to survive, grow and proliferate. In this context, DNA repair inhibitors opened a new avenue in cancer treatment, by blocking the DNA repair mechanisms from removing the chemotherapy-mediated DNA damage. In particular, the nucleotide excision repair (NER) involves more than thirty protein-protein interactions and removes DNA adducts caused by platinum-based chemotherapy. The excision repair cross-complementation group 1 (ERCC1)-xeroderma pigmentosum, complementation group A (XPA) protein (XPA-ERCC1) complex seems to be one of the most promising targets in this pathway. ERCC1 is over expressed in cancer cells and the only known cellular function so far for XPA is to recruit ERCC1 to the damaged point. Here, we build upon our recent advances in identifying inhibitors for this interaction and continue our efforts to rationally design more effective and potent regulators for the NER pathway. We employed in silico drug design techniques to: (1) identify compounds similar to the recently discovered inhibitors, but more effective at inhibiting the XPA-ERCC1 interactions, and (2) identify different scaffolds to develop novel lead compounds. Two known inhibitor structures have been used as starting points for two ligand/structure-hybrid virtual screening approaches. The findings described here form a milestone in discovering novel inhibitors for the NER pathway aiming at improving the efficacy of current platinum-based therapy, by modulating the XPA-ERCC1 interaction.

PMID: 26939044 [PubMed - indexed for MEDLINE]

A physiologically-based flow network model for hepatic drug elimination III: 2D/3D DLA lobule models.

2 years 1 month ago
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A physiologically-based flow network model for hepatic drug elimination III: 2D/3D DLA lobule models.

Theor Biol Med Model. 2016 Mar 03;13:9

Authors: Rezania V, Coombe D, Tuszynski JA

Abstract
BACKGROUND: One of the major issues in current pharmaceutical development is potential hepatotoxicity and drug-induced liver damage. This is due to the unique metabolic processes performed in the liver to prevent accumulation of a wide range of chemicals in the blood. Recently, we developed a physiologically-based lattice model to address the transport and metabolism of drugs in the liver lobule (liver functional unit).
METHOD: In this paper, we extend our idealized model to consider structural and spatial variability in two and three dimensions. We introduce a hexagonal-based model with one input (portal vein) and six outputs (hepatic veins) to represent a typical liver lobule. To capture even more realistic structures, we implement a novel sequential diffusion-limited aggregation (DLA) method to construct a morphological sinusoid network in the lobule. A 3D model constructed with stacks of multiple 2D sinusoid realizations is explored to study the effects of 3D structural variations. The role of liver zonation on drug metabolism in the lobule is also addressed, based on flow-based predicted steady-state O2 profiles used as a zonation indicator.
RESULTS: With this model, we analyze predicted drug concentration levels observed exiting the lobule with their detailed distribution inside the lobule, and compare with our earlier idealized models. In 2D, due to randomness of the sinusoidal structure, individual hepatic veins respond differently (i.e. at different times) to injected drug. In 3D, however, the variation of response to the injected drug is observed to be less extreme. Also, the production curves show more diffusive behavior in 3D than in 2D.
CONCLUSION: Although, the individual producing ports respond differently, the average lobule production summed over all hepatic veins is more diffuse. Thus the net effect of all these variations makes the overall response smoother. We also show that, in 3D, the effect of zonation on drug production characteristics appears quite small. Our new biophysical structural analysis of a physiologically-based 3D lobule can therefore form the basis for a quantitative assessment of liver function and performance both in health and disease.

PMID: 26939615 [PubMed - indexed for MEDLINE]

Screening Anti-Cancer Drugs against Tubulin using Catch-and-Release Electrospray Ionization Mass Spectrometry.

2 years 1 month ago
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Screening Anti-Cancer Drugs against Tubulin using Catch-and-Release Electrospray Ionization Mass Spectrometry.

J Am Soc Mass Spectrom. 2016 May;27(5):876-85

Authors: Rezaei Darestani R, Winter P, Kitova EN, Tuszynski JA, Klassen JS

Abstract
Tubulin, which is the building block of microtubules, plays an important role in cell division. This critical role makes tubulin an attractive target for the development of chemotherapeutic drugs to treat cancer. Currently, there is no general binding assay for tubulin-drug interactions. The present work describes the application of the catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay to investigate the binding of colchicinoid drugs to αβ-tubulin dimers extracted from porcine brain. Proof-of-concept experiments using positive (ligands with known affinities) and negative (non-binders) controls were performed to establish the reliability of the assay. The assay was then used to screen a library of seven colchicinoid analogues to test their binding to tubulin and to rank their affinities.

PMID: 26944280 [PubMed - indexed for MEDLINE]

The Physical Mechanism for Retinal Discrete Dark Noise: Thermal Activation or Cellular Ultraweak Photon Emission?

2 years 1 month ago
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The Physical Mechanism for Retinal Discrete Dark Noise: Thermal Activation or Cellular Ultraweak Photon Emission?

PLoS One. 2016;11(3):e0148336

Authors: Salari V, Scholkmann F, Bokkon I, Shahbazi F, Tuszynski J

Abstract
For several decades the physical mechanism underlying discrete dark noise of photoreceptors in the eye has remained highly controversial and poorly understood. It is known that the Arrhenius equation, which is based on the Boltzmann distribution for thermal activation, can model only a part (e.g. half of the activation energy) of the retinal dark noise experimentally observed for vertebrate rod and cone pigments. Using the Hinshelwood distribution instead of the Boltzmann distribution in the Arrhenius equation has been proposed as a solution to the problem. Here, we show that the using the Hinshelwood distribution does not solve the problem completely. As the discrete components of noise are indistinguishable in shape and duration from those produced by real photon induced photo-isomerization, the retinal discrete dark noise is most likely due to 'internal photons' inside cells and not due to thermal activation of visual pigments. Indeed, all living cells exhibit spontaneous ultraweak photon emission (UPE), mainly in the optical wavelength range, i.e., 350-700 nm. We show here that the retinal discrete dark noise has a similar rate as UPE and therefore dark noise is most likely due to spontaneous cellular UPE and not due to thermal activation.

PMID: 26950936 [PubMed - indexed for MEDLINE]

Thermodynamic measures of cancer: Gibbs free energy and entropy of protein-protein interactions.

2 years 1 month ago
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Thermodynamic measures of cancer: Gibbs free energy and entropy of protein-protein interactions.

J Biol Phys. 2016 Jun;42(3):339-50

Authors: Rietman EA, Platig J, Tuszynski JA, Lakka Klement G

Abstract
Thermodynamics is an important driving factor for chemical processes and for life. Earlier work has shown that each cancer has its own molecular signaling network that supports its life cycle and that different cancers have different thermodynamic entropies characterizing their signaling networks. The respective thermodynamic entropies correlate with 5-year survival for each cancer. We now show that by overlaying mRNA transcription data from a specific tumor type onto a human protein-protein interaction network, we can derive the Gibbs free energy for the specific cancer. The Gibbs free energy correlates with 5-year survival (Pearson correlation of -0.7181, p value of 0.0294). Using an expression relating entropy and Gibbs free energy to enthalpy, we derive an empirical relation for cancer network enthalpy. Combining this with previously published results, we now show a complete set of extensive thermodynamic properties and cancer type with 5-year survival.

PMID: 27012959 [PubMed - indexed for MEDLINE]

Modelling DNA Repair Pathways: Recent Advances and Future Directions.

2 years 1 month ago
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Modelling DNA Repair Pathways: Recent Advances and Future Directions.

Curr Pharm Des. 2016;22(23):3527-46

Authors: Gentile F, Tuszynski JA, Barakat KH

Abstract
BACKGROUND: A major class of chemotherapy drugs targets the genome of cancer cells. These DNA damaging agents induce damage to the DNA helix, resulting in the programmed death of cancer cells. An overactivated DNA repair mechanism in cancer cells can reduce the efficacy of these drugs, thereby eliminating their therapeutic benefit and developing an acquired resistance to these otherwise effective drugs. A promising approach to enhance the therapeutic window of DNA damaging agents is to target the DNA repair pathways causing this type of resistance.
METHODS: Computational approaches have been applied successfully to study many of these DNA repair mechanisms at different scales and focusing on various aspects. The ultimate goal of these studies has been to identify the key players in developing resistance to DNA damaging agents and to design regulators for their activities. This review covers the most important and recent computational efforts toward this goal. This includes modelling the mechanisms involved in DNA repair and identifying novel pharmacological inhibitors for their activities.
RESULTS: We focus here mainly on the pathways associated with an acquired drug resistance to DNA damaging agents, concentrating on the recent advances in modelling the key mechanisms and foreseeing the future directions in this field.
CONCLUSION: We hope that this short, yet comprehensive review can help in discovering novel strategies to overcome the resistance effects inherent in various cancer treatments.

PMID: 27093954 [PubMed - indexed for MEDLINE]

Chemical synthesis, pharmacological evaluation and in silico analysis of new 2,3,3a,4,5,6-hexahydrocyclopenta[c]pyrazole derivatives as potential anti-mitotic agents.

2 years 1 month ago
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Chemical synthesis, pharmacological evaluation and in silico analysis of new 2,3,3a,4,5,6-hexahydrocyclopenta[c]pyrazole derivatives as potential anti-mitotic agents.

Bioorg Med Chem Lett. 2016 Aug 15;26(16):3855-61

Authors: Minu M, Singh D, Mahaddalkar T, Lopus M, Winter P, Ayoub AT, Missiaen K, Tilli TM, Pasdar M, Tuszynski J

Abstract
We have synthesized new, biologically active mono- and di-substituted 2,3,3a,4,5,6-hexahydrocyclopenta[c]pyrazole derivatives bearing electron withdrawing groups and electron donating groups. These derivative structures were characterized by their spectral and analytical data. The newly synthesized hexahydropyrazole analogues were evaluated for their in vitro anticancer activity against breast and lung cancer cell lines using a cytotoxicity bioassay. To understand their mechanism of action, tubulin binding assays were performed which pointed to their binding to microtubules in a mode similar to but not identical to colchicine, as evidenced by their KD value evaluation. Computational docking studies also suggested binding near the colchicine binding site on tubulin. These results were further confirmed by colchicine-binding assays on the most active compounds, which indicated that they bound to tubulin near but not at the colchicine site. The moderate cytotoxic effects of these compounds may be due to the presence of electron donating groups on the para-position of the phenyl ring, along with the hexahydropyrazole core nucleus. The observed anti-cancer activity based on inhibition of microtubule formation may be helpful in designing more potent compounds with a hexahydropyrazole moiety.

PMID: 27449957 [PubMed - indexed for MEDLINE]

A strategy to identify housekeeping genes suitable for analysis in breast cancer diseases.

2 years 1 month ago
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A strategy to identify housekeeping genes suitable for analysis in breast cancer diseases.

BMC Genomics. 2016 Aug 15;17(1):639

Authors: Tilli TM, Castro Cda S, Tuszynski JA, Carels N

Abstract
BACKGROUND: The selection of suitable internal control genes is crucial for proper interpretation of real-time PCR data. Here we outline a strategy to identify housekeeping genes that could serve as suitable internal control for comparative analyses of gene expression data in breast cancer cell lines and tissues obtained by high throughput sequencing and quantitative real-time PCR (qRT-PCR).
METHODS: The strategy proposed includes the large-scale screening of potential candidate reference genes from RNA-seq data as well as their validation by qRT-PCR, and careful examination of reference data from the International Cancer Genome Consortium, The Cancer Genome Atlas and Gene Expression Omnibus repositories.
RESULTS: The identified set of reference genes, also called novel housekeeping genes that includes CCSER2, SYMPK, ANKRD17 and PUM1, proved to be less variable and thus potentially more accurate for research and clinical analyses of breast cell lines and tissue samples compared to the traditional housekeeping genes used to this end.
DISCUSSION: These results highlight the importance of a massive evaluation of housekeeping genes for their relevance as internal control for optimized intra- and inter-assay comparison of gene expression.
CONCLUSION: We developed a strategy to identify and evaluate the significance of housekeeping genes as internal control for the intra- and inter-assay comparison of gene expression in breast cancer that could be applied to other tumor types and diseases.

PMID: 27526934 [PubMed - indexed for MEDLINE]

Validation of a network-based strategy for the optimization of combinatorial target selection in breast cancer therapy: siRNA knockdown of network targets in MDA-MB-231 cells as an in vitro model for inhibition of tumor development.

2 years 1 month ago
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Validation of a network-based strategy for the optimization of combinatorial target selection in breast cancer therapy: siRNA knockdown of network targets in MDA-MB-231 cells as an in vitro model for inhibition of tumor development.

Oncotarget. 2016 Sep 27;7(39):63189-63203

Authors: Tilli TM, Carels N, Tuszynski JA, Pasdar M

Abstract
Network-based strategies provided by systems biology are attractive tools for cancer therapy. Modulation of cancer networks by anticancer drugs may alter the response of malignant cells and/or drive network re-organization into the inhibition of cancer progression. Previously, using systems biology approach and cancer signaling networks, we identified top-5 highly expressed and connected proteins (HSP90AB1, CSNK2B, TK1, YWHAB and VIM) in the invasive MDA-MB-231 breast cancer cell line. Here, we have knocked down the expression of these proteins, individually or together using siRNAs. The transfected cell lines were assessed for in vitro cell growth, colony formation, migration and invasion relative to control transfected MDA-MB-231, the non-invasive MCF-7 breast carcinoma cell line and the non-tumoral mammary epithelial cell line MCF-10A. The knockdown of the top-5 upregulated connectivity hubs successfully inhibited the in vitro proliferation, colony formation, anchorage independence, migration and invasion in MDA-MB-231 cells; with minimal effects in the control transfected MDA-MB-231 cells or MCF-7 and MCF-10A cells. The in vitro validation of bioinformatics predictions regarding optimized multi-target selection for therapy suggests that protein expression levels together with protein-protein interaction network analysis may provide an optimized combinatorial target selection for a highly effective anti-metastatic precision therapy in triple-negative breast cancer. This approach increases the ability to identify not only druggable hubs as essential targets for cancer survival, but also interactions most susceptible to synergistic drug action. The data provided in this report constitute a preliminary step toward the personalized clinical application of our strategy to optimize the therapeutic use of anti-cancer drugs.

PMID: 27527857 [PubMed - indexed for MEDLINE]

Aurintricarboxylic acid structure modifications lead to reduction of inhibitory properties against virulence factor YopH and higher cytotoxicity.

2 years 1 month ago
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Aurintricarboxylic acid structure modifications lead to reduction of inhibitory properties against virulence factor YopH and higher cytotoxicity.

World J Microbiol Biotechnol. 2016 Oct;32(10):163

Authors: Kuban-Jankowska A, Sahu KK, Gorska M, Niedzialkowski P, Tuszynski JA, Ossowski T, Wozniak M

Abstract
Yersinia sp. bacteria owe their viability and pathogenic virulence to the YopH factor, which is a highly active bacterial protein tyrosine phosphatase. Inhibition of YopH phosphatase results in the lack of Yersinia sp. pathogenicity. We have previously described that aurintricarboxylic acid inhibits the activity of YopH at nanomolar concentrations and represents a unique mechanism of YopH inactivation due to a redox process. This work is a continuation of our previous studies. Here we show that modifications of the structure of aurintricarboxylic acid reduce the ability to inactivate YopH and lead to higher cytotoxicity. In the present paper we examine the inhibitory properties of aurintricarboxylic acid analogues, such as eriochrome cyanine R (ECR) and pararosaniline. Computational docking studies we report here indicate that ATA analogues are not precluded to bind in the YopH active site and in all obtained binding conformations ECR and pararosaniline bind to YopH active site. The free binding energy calculations show that ECR has a stronger binding affinity to YopH than pararosaniline, which was confirmed by experimental YopH enzymatic activity studies. We found that ATA analogues can reversibly reduce the enzymatic activity of YopH, but possess weaker inhibitory properties than ATA. The ATA analogues induced inactivation of YopH is probably due to oxidative mechanism, as pretreatment with catalase prevents from inhibition. We also found that ATA analogues significantly decrease the viability of macrophage cells, especially pararosaniline, while ATA reveals only slight effect on cell viability.

PMID: 27562597 [PubMed - indexed for MEDLINE]

Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s.

2 years 1 month ago
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Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s.

Sci Rep. 2016 09 12;6:33099

Authors: Parvez M, Qhanya LB, Mthakathi NT, Kgosiemang IK, Bamal HD, Pagadala NS, Xie T, Yang H, Chen H, Theron CW, Monyaki R, Raselemane SC, Salewe V, Mongale BL, Matowane RG, Abdalla SM, Booi WI, van Wyk M, Olivier D, Boucher CE, Nelson DR, Tuszynski JA, Blackburn JM, Yu JH, Mashele SS, Chen W, Syed K

Abstract
Since the initial identification of cytochrome P450 monooxygenases (CYPs/P450s), great progress has been made in understanding their structure-function relationship, diversity and application in producing compounds beneficial to humans. However, the molecular evolution of P450s in terms of their dynamics both at protein and DNA levels and functional conservation across kingdoms still needs investigation. In this study, we analyzed 17 598 P450s belonging to 113 P450 families (bacteria -42; fungi -19; plant -28; animal -22; plant and animal -1 and common P450 family -1) and found highly conserved and rapidly evolving P450 families. Results suggested that bacterial P450s, particularly P450s belonging to mycobacteria, are highly conserved both at protein and DNA levels. Mycobacteria possess the highest P450 diversity percentage compared to other microbes and have a high coverage of P450s (≥1%) in their genomes, as found in fungi and plants. Phylogenetic and functional analyses revealed the functional conservation of P450s despite belonging to different biological kingdoms, suggesting the adherence of P450s to their innate function such as their involvement in either generation or oxidation of steroids and structurally related molecules, fatty acids and terpenoids. This study's results offer new understanding of the dynamic structural nature of P450s.

PMID: 27616185 [PubMed - indexed for MEDLINE]

Relationship between intelligence and spectral characteristics of brain biophoton emission: Correlation does not automatically imply causation.

2 years 1 month ago
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Relationship between intelligence and spectral characteristics of brain biophoton emission: Correlation does not automatically imply causation.

Proc Natl Acad Sci U S A. 2016 09 20;113(38):E5540-1

Authors: Salari V, Bókkon I, Ghobadi R, Scholkmann F, Tuszynski JA

PMID: 27621479 [PubMed - indexed for MEDLINE]

Building a 3D Virtual Liver: Methods for Simulating Blood Flow and Hepatic Clearance on 3D Structures.

2 years 1 month ago
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Building a 3D Virtual Liver: Methods for Simulating Blood Flow and Hepatic Clearance on 3D Structures.

PLoS One. 2016;11(9):e0162215

Authors: White D, Coombe D, Rezania V, Tuszynski J

Abstract
In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver.

PMID: 27649537 [PubMed - indexed for MEDLINE]

Antitumor Activity of Lankacidin Group Antibiotics Is Due to Microtubule Stabilization via a Paclitaxel-like Mechanism.

2 years 1 month ago
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Antitumor Activity of Lankacidin Group Antibiotics Is Due to Microtubule Stabilization via a Paclitaxel-like Mechanism.

J Med Chem. 2016 Oct 27;59(20):9532-9540

Authors: Ayoub AT, Abou El-Magd RM, Xiao J, Lewis CW, Tilli TM, Arakawa K, Nindita Y, Chan G, Sun L, Glover M, Klobukowski M, Tuszynski J

Abstract
Lankacidin group antibiotics show strong antimicrobial activity against various Gram-positive bacteria. In addition, they were shown to have considerable antitumor activity against certain cell line models. For decades, the antitumor activity of lankacidin was associated with the mechanism of its antimicrobial action, which is interference with peptide bond formation during protein synthesis. This, however, was never confirmed experimentally. Due to significant similarity to paclitaxel-like hits in a previous computational virtual screening study, we suggested that the cytotoxic effect of lankacidin is due to a paclitaxel-like action. In this study, we tested this hypothesis computationally and experimentally and confirmed that lankacidin is a microtubule stabilizer that enhances tubulin assembly and displaces taxoids from their binding site. This study serves as a starting point for optimization of lankacidin derivatives for better antitumor activities. It also highlights the power of computational predictions and their aid in guiding experiments and formulating rigorous hypotheses.

PMID: 27718573 [PubMed - indexed for MEDLINE]

A new antiproliferative noscapine analogue: chemical synthesis and biological evaluation.

2 years 1 month ago
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A new antiproliferative noscapine analogue: chemical synthesis and biological evaluation.

Oncotarget. 2016 Jun 28;7(26):40518-40530

Authors: Ghaly PE, Abou El-Magd RM, Churchill CD, Tuszynski JA, West FG

Abstract
Noscapine, a naturally occurring opium alkaloid, is a widely used antitussive medication. Noscapine has low toxicity and recently it was also found to possess cytotoxic activity which led to the development of many noscapine analogues. In this paper we report on the synthesis and testing of a novel noscapine analogue. Cytotoxicity was assessed by MTT colorimetric assay using SKBR-3 and paclitaxel-resistant SKBR-3 breast cancer cell lines using different concentrations for both noscapine and the novel compound. Microtubule polymerization assay was used to determine the effect of the new compound on microtubules. To compare the binding affinity of noscapine and the novel compound to tubulin, we have done a fluorescence quenching assay. Finally, in silico methods using docking calculations were used to illustrate the binding mode of the new compound to α,β-tubulin. Our cytotoxicity results show that the new compound is more cytotoxic than noscapine on both SKBR-3 cell lines. This was confirmed by the stronger binding affinity of the new compound, compared to noscapine, to tubulin. Surprisingly, our new compound was found to have strong microtubule-destabilizing properties, while noscapine is shown to slightly stabilize microtubules. Our calculation indicated that the new compound has more binding affinity to the colchicine-binding site than to the noscapine site. This novel compound has a more potent cytotoxic effect on cancer cell lines than its parent, noscapine, and hence should be of interest as a potential anti-cancer drug.

PMID: 27777381 [PubMed - indexed for MEDLINE]

Personalized anticancer therapy selection using molecular landscape topology and thermodynamics.

2 years 1 month ago
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Personalized anticancer therapy selection using molecular landscape topology and thermodynamics.

Oncotarget. 2017 Mar 21;8(12):18735-18745

Authors: Rietman EA, Scott JG, Tuszynski JA, Klement GL

Abstract
Personalized anticancer therapy requires continuous consolidation of emerging bioinformatics data into meaningful and accurate information streams. The use of novel mathematical and physical approaches, namely topology and thermodynamics can enable merging differing data types for improved accuracy in selecting therapeutic targets. We describe a method that uses chemical thermodynamics and two topology measures to link RNA-seq data from individual patients with academically curated protein-protein interaction networks to select clinically relevant targets for treatment of low-grade glioma (LGG). We show that while these three histologically distinct tumor types (astrocytoma, oligoastrocytoma, and oligodendroglioma) may share potential therapeutic targets, the majority of patients would benefit from more individualized therapies. The method involves computing Gibbs free energy of the protein-protein interaction network and applying a topological filtration on the energy landscape to produce a subnetwork known as persistent homology. We then determine the most likely best target for therapeutic intervention using a topological measure of the network known as Betti number. We describe the algorithm and discuss its application to several patients.

PMID: 27793055 [PubMed - indexed for MEDLINE]