Computational approaches in cancer multidrug resistance research: Identification of potential biomarkers, drug targets and drug-target interactions.

Like physics in the 19th century, biology and molecular biology in particular, has been fertilized and enhanced like few other scientific fields, by the incorporation of mathematical methods. In the last decades, a whole new scientific field, bioinformatics, has developed with an output of over 30,000 papers a year (Pubmed search using the keyword "bioinformatics"). Huge databases of mass throughput data have been established, with ArrayExpress alone containing more than 2.7 million assays (October 2019). Computational methods have become indispensable tools in molecular biology, particularly in one of the most challenging areas of cancer research, multidrug resistance (MDR). However, confronted with a plethora of different algorithms, approaches, and methods, the average researcher faces key questions: Which methods do exist? Which methods can be used to tackle the aims of a given study? Or, more generally, how do I use computational biology/bioinformatics to bolster my research? The current review is aimed at providing guidance to existing methods with relevance to MDR research. In particular, we provide an overview on: a) the identification of potential biomarkers using expression data; b) the prediction of treatment response by machine learning methods; c) the employment of network approaches to identify gene/protein regulatory networks and potential key players; d) the identification of drug-target interactions; e) the use of bipartite networks to identify multidrug targets; f) the identification of cellular subpopulations with the MDR phenotype; and, finally, g) the use of molecular modeling methods to guide and enhance drug discovery. This review shall serve as a guide through some of the basic concepts useful in MDR research. It shall give the reader some ideas about the possibilities in MDR research by using computational tools, and, finally, it shall provide a short overview of relevant literature.

Atomistic Picture of Fluorescent Probes with Hydrocarbon Tails in Lipid Bilayer Membranes: An Investigation of Selective Affinities and Fluorescent Anisotropies in Different Environmental Phases.

By reverting to spectroscopy, changes in the biological environment of a fluorescent probe can be monitored and the presence of various phases of the surrounding lipid bilayer membranes can be detected. However, it is currently not always clear in which phase the probe resides. The well-known orange 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbo-cyanine perchlorate (DiI-C18(5)) fluorophore, for instance, and the new, blue BODIPY (4,4-difluoro-4-bora-3 a,4 a-diaza- s-indacene) derivative were experimentally seen to target and highlight identical parts of giant unilamellar vesicles of various compositions, comprising mixtures of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), sphingomyelin (SM), and cholesterol (Chol). However, it was not clear which of the coexisting membrane phases were visualized (Bacalum et al., Langmuir. 2016, 32, 3495). The present study addresses this issue by utilizing large-scale molecular dynamics simulations and the z-constraint method, which allows evaluating Gibbs free-energy profiles. The current calculations give an indication why, at room temperature, both BODIPY and DiI-C18(5) probes prefer the gel (So) phase in DOPC/DPPC (2:3 molar ratio) and the liquid-ordered (Lo) phase in DOPC/SM/Chol (1:2:1 molar ratio) mixtures. This study highlights the important differences in orientation and location and therefore in efficiency between the probes when they are used in fluorescence microscopy to screen various lipid bilayer membrane phases. Dependent on the lipid composition, the angle between the transition-state dipole moments of both probes and the normal to the membrane is found to deviate clearly from 90°. It is seen that the DiI-C18(5) probe is located in the headgroup region of the SM/Chol mixture, in close contact with water molecules. A fluorescence anisotropy study also indicates that DiI-C18(5) gives rise to a distinctive behavior in the SM/Chol membrane compared to the other considered membranes. The latter behavior has not been seen for the studied BODIPY probe, which is located deeper in the membrane.

Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms.

The ABCC4/MRP4 exporter has a clinical impact on membrane transport of a broad range of xenobiotics. It is expressed at key locations for drug disposition or effects such as in the liver, the kidney and blood cells. Several polymorphisms and mutations (e.g., p.Gly187Trp) leading to MRP4 dysfunction are associated with an increased risk of toxicity of some drugs. So far, no human MRP4 structure has been elucidated, precluding rationalization of these dysfunctions at a molecular level. We constructed an atomistic model of the wild type (WT) MRP4 and the p.Gly187Trp mutant embedded in different lipid bilayers and relaxed them for hundreds of nanoseconds by molecular dynamics simulations. The WT MRP4 molecular structure confirmed and ameliorated the general knowledge about the transmembrane helices and the two nucleotide binding domains. Moreover, our model elucidated positions of three generally unresolved domains: L1 (linker between the two halves of the exporter); L0 (N-terminal domain); and the zipper helices (between the two NBDs). Each domain was thoroughly described in view of its function. The p.Gly187Trp mutation induced a huge structural impact on MRP4, mainly affecting NBD 1 structure and flexibility. The structure of transporter enabled rationalization of known dysfunctions associated with polymorphism of MRP4. This model is available to the pharmacology community to decipher the impact of any other clinically observed polymorphism and mutation on drug transport, giving rise to in silico predictive pharmacogenetics.

Application of recent double-hybrid density functionals to low-lying singlet-singlet excitation energies of large organic compounds.

The present work assesses some recently developed double-hybrid density functionals (B2π-PLYP, PBE0-DH, and PBE0-2) using linear-response Tamm-Dancoff Time-Dependent Density Functional Theory. This assessment is achieved against experimentally derived low-lying excitation energies of large organic dyes of recent interest, including some excitations dominated by charge-transfer transitions. Comparisons are made with some of the best-performing methods established from the literature, such as PBE0 or B3LYP hybrid or the recently proposed B2-PLYP and B2GP-PLYP double-hybrid models, to ascertain their quality and robustness on equal footing. The accuracy of parameter-free or empirical forms of double-hybrid functionals is also briefly discussed. Generally speaking, it turns out that double-hybrid expressions always provide more accurate estimates than corresponding hybrid methods. Double-hybrid functionals actually reach averaged accuracies of 0.2 eV, that can be admittedly considered close to any intended accuracy limit within the present theoretical framework.

Mechanism of one-electron oxidation of metformin in aqueous solution.

Hydroxyl free radical-induced oxidation of metformin was studied in aqueous solution as a function of the pH. Hydroxyl free radicals were generated by gamma radiolysis of water and the oxidation end-products were quantified by high-performance liquid chromatography coupled to mass spectrometry (HPLC/MS), as a function of the radiation dose. This work is a joint experimental and theoretical (DFT) approach that has paved the way towards a comprehensive rationalization of the one-electron mechanisms of MTF oxidation, as a function of the pH.

New aspects of the antioxidant properties of phenolic acids: a combined theoretical and experimental approach.

Ferulic acid is widely distributed in the leaves and seeds of cereals as well as in coffee, apples, artichokes, peanuts, oranges and pineapples. Like numerous other natural polyphenols it exhibits antioxidant properties. It is known to act as a free radical scavenger by H atom transfer from the phenolic OH group. In the present joint experimental and theoretical studies we studied a new mechanism to explain such activities. Ferulic acid can indeed act by radical addition on the alpha,beta-double bond. On the basis of the identification of metabolites formed in an oxidative radiolytic solution and after DFT calculations, we studied the thermodynamic and kinetic aspects of this reaction. Addition and HAT reactions were treated as competitive reactions. The possibility of dimer formation was also investigated from a theoretical point of view; the high barriers we obtained contribute to explaining why we did not observe those compounds as major radiolytic compounds. The DPPH free radical scavenging capacity of ferulic acid and the oxidative products was measured and is discussed on the basis of DFT calculations (BDEs and spin densities).

Free radical scavenging properties of guaiacol oligomers: a combined experimental and quantum study of the guaiacyl-moiety role.

Natural polyphenols are known to exhibit a lot of different biological properties, including antioxidant activity. For some polyphenols these activities are attributed to the presence of a guaiacol moiety. In the present paper we focus on the role of this moiety. For this purpose nine different compounds were enzymatically synthesized from guaiacol. To elucidate the structure-activity relationship of these polyphenols, DFT-(PCM)B3P86/6-311+G(2d,3pd)//(PCM)B3P86/6-31+G(d,p) calculations supported the experimental DPPH free radical scavenging activities. The antioxidant activities were correlated to (i) O-H BDEs (bond dissociation enthalpies), (ii) BDE(D) (BDE of a second H atom abstraction from the phenoxyradicals), (iii) spin density, (iv) HOMO (highest occupied molecular orbital) distribution, (v) IPs (ionization potentials), (vi) DeltaG and DeltaG(#) free energies of HAT (H atom transfer), and (vii) HAT rate constants. BDE(D) appeared to be the most important descriptor to understand the free radical scavenging ability of these compounds.

Brain stem diffusion-weighted imaging lesion score: a potential marker of outcome in acute basilar artery occlusion.

BACKGROUND AND PURPOSE: The benefit of recanalization in basilar artery occlusion (BAO) has been established. The baseline extent of brain stem damage may also influence the outcome. We investigated whether a baseline diffusion-weighted imaging (DWI) score may provide additional prognostic value in BAO. MATERIALS AND METHODS: We analyzed baseline clinical and DWI parameters in consecutive patients treated with endovascular procedures for acute BAO. Brain stem DWI lesions were assessed by using a semiquantitative score based on arterial territory segmentation. Outcome at 3 months was dichotomized according to the modified Rankin Scale (mRS) as favorable (mRS, 0-2) or unfavorable (mRS, 3-6). Spearman rank correlation tests assessed the correlation between DWI and clinical variables. Univariate and multivariate logistic regression analyses were used to identify clinical and MR imaging predictors of outcome. RESULTS: Twenty-nine patients were included. The brain stem DWI score (median, 3; range, 0-14) was correlated with the baseline National Institutes of Health Stroke Scale (NIHSS) score and the presence and length of coma (r = 0.67, 0.49, and 0.53, respectively; P < .01). Recanalization was achieved in 76%. A higher baseline NIHSS score (P = .02) and brain stem DWI score (P = .03), a lower Glasgow Coma Scale score (P = .04), and the presence of coma (P = .05) were associated with poor outcome in univariate analysis. Multivariate analysis showed that the brain stem DWI score was the only independent baseline predictor for clinical outcome (P = .026). CONCLUSIONS: Baseline brain stem DWI lesion score is an independent marker of outcome in BAO.

Fibrinolyse Precoce Avec Elevation Des Produits De Degradation Du Fibrinogene Dans L/'hematome Intra Cerebral Spontane

Description. L'hematome intracerebral est essentiellement considere comme une maladie vasculaire; liee a la structure des vaisseaux. Un traitement recent; le facteur VII; a montre indirectement l'importance de l'hemostase dans cette affection.Objectif. Explorer certains aspects de l'hemostase dans une serie d'hematomes intra-cerebraux spontanes. Methode : Des tests d'hemostase ont ete realises chez des patients porteurs d'un hematome intra-cerebral spontane. Les taux de fibrinogene et des produits de degradation de fibrinogene (PDF) ont ete doses a l'entree; tandis que la numeration des thrombocytes; l'International Normalized Ratio (INR); le temps de cephaline activee (TCA) ont ete par ailleurs determines.Resultats.Treize patients successifs ont ete etudies. Chez 3 patients; une elevation des facteurs de degradation du fibrinogene a ete observee (3/13 soit 23). Un cas de thrombopenie associee a l'augmentation des PDF a ete note.Conclusion. Dans un sous-groupe non negligeable d'hematomes; il existe une fibrinolyse concomitante dans les 24 premieres heures. Ce phenomene est soit primitif; soit secondaire a la rupture vasculaire

[Long-term outcome in patients with symptomatic low-grade oligodendrogliomatous tumors treated by cytotoxic agents]. / Effets à long terme de la chimiothérapie chez 7 patients présentant un gliome de bas grade symptomatique.

INTRODUCTION: Whether aggressive treatment or no treatment is the optimal management for low-grade gliomas is controversial. However, symptomatic low-grade gliomas require prompt therapeutic intervention because of neurological impairment, uncontrolled seizures, and deterioration of life quality. METHODS: We report the long-term follow-up, 71 months, of seven patients treated by procarbazine, lomustine and vincristine (PCV) therapy for a symptomatic low-grade oligodendrogliomatous tumor. The mean age at diagnosis was 47 years, the mean time from first symptoms to initiation of PCV therapy was 62 months (range 15-147). RESULTS: All patients initially responded favorably, with improvement of the neurological symptoms and radiological response. Chemotherapy was clinically well tolerated, the main side effect being low hematological toxicity. During the follow-up, no progression was observed in two patients. For the five remaining patients, the time to progression after the PCV induction was 56+/-12 months (range 38 to 73). Four of these patients showed favorable response to a second line of treatment. CONCLUSION: PCV therapy is an interesting therapeutic option for progressively symptomatic low-grade gliomas, even in cases with large tumoral volume. This treatment, of moderate toxicity, improves the quality of life and can result in long-term tumor stabilization.

[Management of malignant gliomas diagnosed during pregnancy]. / Prise en charge des gliomes malins découverts au cours d'une grossesse.

INTRODUCTION: Glioma is seldom diagnosed during pregnancy. In this situation management presents difficult problems for both neuro-oncologists and obstetricians. We report four cases and discuss the management of this unusual situation. CASE REPORT: The first patient was admitted to hospital at 29 weeks' gestation because of a generalized seizure and a right hemiparesis. MRI showed a left fronto-insular lesion. A stereotactic biopsy was obtained and revealed an anaplastic oligodendroglioma. With corticosteroids the patient remained stable until cesarean delivery at 36 weeks. In post-partum additional treatment with chemotherapy was started. The second patient was hospitalized at 26 weeks' gestation because of cranial hypertension, right hemiparesis and aphasia. MRI showed an important left fronto-parietal lesion. Partial resection was performed at 28 weeks. Histology revealed a glioblastoma multiforme. With corticosteroids the patient remained stable until cesarean delivery at 33 weeks. In post-partum additional treatment with radiotherapy and chemotherapy was started. The third patient was admitted to the hospital at 12 weeks' gestation because of cranial hypertension. MRI showed a left frontal lesion. A subtotal resection was done at 13 weeks. Histology revealed a glioblastoma multiforme. Two weeks after surgery the patient's neurological condition worsened and in agreement with the patient a therapeutic abortion was decided. Afterwards additional treatment with radiotherapy and chemotherapy was started. The last patient received combined treatment with radiotherapy and chemotherapy for local recurrence of a mesencephalic high-grade glioma. A posteriori it was discovered that the patient was at 4 months' gestation during this treatment. Cesarean delivery was done at 36 weeks. The child was normal at birth and is still in good health 5 years later. CONCLUSION: The management of gliomas diagnosed during pregnancy should not be different from the standard management of gliomas in young non-pregnant adults. Pregnant women because of their young age can have a long survival. Their pregnancy should not prevent them from receiving the best treatment for their glioma. Treatment will depend upon clinico-radiological presentation, histology, gestational age and the patient's desires. Generally speaking, surgical resection of high-grade gliomas should not be delayed during pregnancy. Progress in anesthesia and neurosurgery have greatly reduced the risks for the foetus. After delivery, if the delay between surgery and delivery is too long it is possible to begin cerebral radiotherapy during pregnancy. After the first trimester of gestation this treatment can be given without any important risks for the child.

Hyperthyroidism and cerebral venous thrombosis.

The demonstration of an underlying prothrombotic condition in cerebral venous thrombosis (CVT) may have important practical consequences in terms of prevention. Thyrotoxicosis through a hypercoagulable state may be a predisposing factor for CVT. The authors present the cases of 4 patients who developed CVT and hyperthyroidism. At the acute stage, hyperthyroidism was associated with an increase in factor VIII (FVIII). At follow-up, FVIII level remained increased in 2 patients. Hyperthyroidism may have an impact on FVIII level. Accordingly in patients with hyperthyroidism and neurological symptoms, the diagnosis of CVT should be considered and an exhaustive coagulation screening may be appropriate.

Clinical and imaging predictors of intracerebral haemorrhage in stroke patients treated with intravenous tissue plasminogen activator.

OBJECTIVE: To evaluate clinical, biological, and pretreatment imaging variables for predictors of tissue plasminogen activator (tPA) related intracerebral haemorrhage (ICH) in stroke patients. METHODS: 48 consecutive patients with hemispheric stroke were given intravenous tPA within seven hours of symptom onset, after computed tomography (CT) and magnetic resonance imaging (MRI) of the brain. Baseline diffusion weighted (DWI) and perfusion weighted (PWI) imaging volumes, time to peak, mean transit time, regional cerebral blood flow index, and regional cerebral blood volume were evaluated. The distribution of apparent diffusion coefficient (ADC) values was determined within each DWI lesion. RESULTS: The symptomatic ICH rate was 8.3% (four of 48); the rate for any ICH was 43.8% (21 of 48). Univariate analysis showed that age, weight, history of hyperlipidaemia, baseline NIHSS score, glucose level, red blood cell count, and lacunar state on MRI were associated with ICH. However, mean 24 hour systolic blood pressure and a hyperdense artery sign on pretreatment CT were the only independent predictors of ICH. Patients with a hyperdense artery sign had larger pretreatment PWI and DWI lesion volumes and a higher NIHSS score. Analysis of the distribution of ADC values within DWI lesions showed that a greater percentage of pixels had lower ADCs (< 400 x 10(-6) mm(2)/s) in patients who experienced ICH than in those who did not. CONCLUSION: Key clinical and biological variables, pretreatment CT signs, and MRI indices are associated with tPA related intracerebral haemorrhage.

[Delayed post-anoxic leukoencephalopathy]. / Leucoencéphalopathie post-anoxique d'apparition retardée.

INTRODUCTION: The onset of post-anoxic encephalopathies can be delayed after the acute hypoxic injury. CASE REPORT: We present the case of a 45-year-old woman who achieved complete recovery from an episode of hypoxia related to a suicide attempt (ingestion of benzodiazepine). Three weeks later she developed a confusional state with akinetic mutism and parkinsonism. Brain CT-scan showed bilateral hemispheric white matter hypodensities. MRI showed extensive bilateral hyperintensities on T2-weighted and Flair sequences within the hemispheric white matter and the globus pallidus. EEG showed diffuse slow activity. All investigations for leukodystrophies were negative. Brain biopsy showed normal cortex and widespread demyelination with axonal sparing in the underlying white matter. The patient experienced a partial clinical recovery. CONCLUSION: The clinical course and the results of paraclinic investigations were consistent with the diagnosis of delayed post-anoxic leukoencephalopathy.