Search results for: shale inhibitor

Authors: Camilo A. Guerrero-Martin, Erik Montes Paez, Marcia C. K. Oliveira, Jonathan Campos, Elizabete F. Lucas

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Asphaltenes precipitation is considered as a formation damage problem, which can reduce the oil recovery factor. It fouls piping and surface installations, as well as cause serious flow assurance complications and decline oil well production. Therefore, researchers have shown an interest in chemical treatments to control this phenomenon. The aim of this paper is to assess the asphaltenes precipitation onset of crude oils in the presence of cardanol, by titrating the crude with n-heptane. Moreover, based on this results obtained at atmosphere pressure, the asphaltenes precipitation onset pressure were calculated to predict asphaltenes precipitation in the reservoir, by using differential liberation and refractive index data of the oils. The influence of cardanol concentrations in the asphaltenes stabilization of three Brazilian crude oils samples (with similar API densities) was studied. Therefore, four formulations of cardanol in toluene were prepared: 0, 3, 5, 10 and 15 m/m%. The formulations were added to the crude at 2:98 ratio. The petroleum samples were characterized by API density, elemental analysis and differential liberation test. The asphaltenes precipitation onset (APO) was determined by titrating with n-heptane and monitoring with near-infrared (NIR). UV-Vis spectroscopy experiments were also done to assess the precipitate asphaltenes content. The asphaltenes precipitation envelopes (APE) were also determined by numerical simulation (Multiflash). In addition, the adequate artificial lift systems (ALS) for the oils were selected. It was based on the downhole well profile and a screening methodology. Finally, the oil flowrates were modelling by NODAL analysis production system in the PIPESIM software. The results of this study show that the asphaltenes precipitation onset of the crude oils were 2.2, 2.3 and 6.0 mL of n-heptane/g of oil. The cardanol was an effective inhibitor of asphaltenes precipitation for the crude oils used in this study, since it displaces the precipitation pressure of the oil to lower values. This indicates that cardanol can increase the oil wells productivity.

Keywords: asphaltenes, NODAL analysis production system, precipitation pressure onset, inhibitory molecule

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Authors: Pedro Cabrales, Scott Caroen, Tony R. Reid, Bryan Oronsky

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Introduction and Purpose RRx-001 is an NLRP3 inhibitor and Nrf2 agonist in Phase 3 trials for the treatment of cancer. The purpose of this study was to examine whether treatment with RRx-001, given itsanti-inflammatory and antioxidant properties, improvedexercise and skeletal muscle oxidative capacity in mice on the generalpremiss that better health outcomes correlatewith more activity. Material and Methods Male and female adult mice (n=6 per group) were subjected to an endurance exercise capacity (EEC)test until exhaustion on a motorized treadmill after 3 once weekly doses of either RRx-001 5 mg/kg, RRx-001 2 mg/kg, or vehicle. The EEC protocol consisted of a treadmill velocity of 30meters per min at an uphill inclination (slope of 10%) until the mice reached fatigue, which was defined as the inability of the mice to maintain the appropriate pace despitecontinuous hand stimulation for 1 min. The concentration of malondialdehyde (MDA), an indicator of lipid peroxidation, and creatine kinase (CK), an indicator of muscle damage, in the blood samples collected immediately after the acute exercise was determined with a commercial ELISA assay kit. ResultsThe exhaustive exercise times of the RRx-001 groups were significantly longer than that of the vehicle group (p<0.05) by weeks 2 and 3. In addition, MDA levels in the gastrocnemius, soleus, and extensor digitorum longus muscles were significantly lower than those of the vehicle group were (p<0.05), as were the serum CK levels(p<0.05). ConclusionsIn conclusion, this study found that RRx-001 has anti-fatigue properties, as evidenced by an increase in exercise capacity with RRx-001 treatment, and protects against strenuous exercise-induced muscle damage and lipid peroxidation. This data potentially supports the use of RRx-001 in the clinic to improve exercise performance and reduce physical fatigue.

Keywords: RRx-001, anti-fatigue, muscle protection, increased exercise tolerance, lipid peroxidation

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Authors: Abouchouaib Belahmira, Joerg W. Schneider, Hafid Saber, Sara Akboub

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The lithofacies analyzed herein were reported from the interbedded fluvial and lacustrine deposits of the Oued Issene and El Menizla formations. These formations are part of the sedimentary fill of the Carboniferous (Stephanian) submontaneous Souss basin. The latter is situated in the western High Atlas Mountains, south-central Morocco, about 50km east of Agadir. The Souss basin started as a single basin but was separated into sub-basins called Ida Ou Zal and Ida Ou Ziki by sinistral displacement along the west branch of the Tizi N'Test Fault during the end of the Mauritanid phase of the Variscan orogeny in Morocco, after the early Stephanian (Kasimovian) and before the late middle Permian (Capitanian). The studied succession is a monotonous finning-upward sequence of 1800 m thick. It consists of fine-grained sandstone, finely bedded siltstone and thinly laminated claystone, and black shale. Herein we provide a detailed characterization of lithofacies of the upper El Menizla and Oued Issène formations, with a focus on the prevailing overbank to flood plain fine-grained lithofacies. The studied facies are capping the Stephanian alluvial fan basal clast-supported conglomerates that are intercalated bedded coarse-grained sandstones of Ikhourba Formation in the Ou Zal subbasin and Tajgaline Formation in the Ida Ou Ziki subbasin, respectively. Within the fluvial elements, only two main facies have been observed. It comprises channel-fill and channel-bar deposits, mostly occur as lenticular –shape sand bodies or sheet-like sand greenish to gray fine-to medium (Fm), massive internally structureless, or very locally exhibits a medium to large scale trough-cross bedding medium to coarse sandstone (St), observable in relatively thicker bed. These facies are laterally extensive, with a thickness varying from a few to several meters. Finer-grained sediments such as mud can be present as drapes over bedforms. Whilst the fluvial association FA1, the overbank elements are represented by a relatively wide range of 5 facies. This exhibit mostly a cm scale horizontally bedded greenish fine- to medium sand and silt, and mm scale fossiliferous thinly laminated dark gray- black Corganic-rich clays to siltstone associated with black shale. Thus, FA2 includes flood plain fines (Fh, R) associated with the paleosols and back swamp coaly clay facies (C). The floodplain lake element comprises only laminated organic-rich dark gray facies of claystone, black shale, and graded siltstone. Bedsets are dm to several meters thick (typically < 1 m thick). They are intercalated between several m-thick fluvial sandstone, extend over a few meters, and are poorly bioturbated. The lacustrine facies described in this study have been divided into two sub-facies (Fl, B) based on field observations that indicate differing environmental conditions of formation. Thus, the thorough analysis of the lithofacies of the Souss basin units allows us to reconstruct the original environment that was interpreted as a typical fluvial-dominated braided to anastomosing wide distributary channel system and surrounding deep to shallow freshwater floodplain lakes and back swamps.

Keywords: Souss, carboniferous, facies, depositional setting

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Authors: Milu T. Cherian, Sergio C. Chai, Morgan A. Casal, Taosheng Chen

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This study aims to use CINPA1, a recently discovered small-molecule inhibitor of the xenobiotic receptor CAR (constitutive androstane receptor) for understanding the binding modes of CAR and to guide CAR-mediated gene expression profiling studies in human primary hepatocytes. CAR and PXR are xenobiotic sensors that respond to drugs and endobiotics by modulating the expression of metabolic genes that enhance detoxification and elimination. Elevated levels of drug metabolizing enzymes and efflux transporters resulting from CAR activation promote the elimination of chemotherapeutic agents leading to reduced therapeutic effectiveness. Multidrug resistance in tumors after chemotherapy could be associated with errant CAR activity, as shown in the case of neuroblastoma. CAR inhibitors used in combination with existing chemotherapeutics could be utilized to attenuate multidrug resistance and resensitize chemo-resistant cancer cells. CAR and PXR have many overlapping modulating ligands as well as many overlapping target genes which confounded attempts to understand and regulate receptor-specific activity. Through a directed screening approach we previously identified a new CAR inhibitor, CINPA1, which is novel in its ability to inhibit CAR function without activating PXR. The cellular mechanisms by which CINPA1 inhibits CAR function were also extensively examined along with its pharmacokinetic properties. CINPA1 binding was shown to change CAR-coregulator interactions as well as modify CAR recruitment at DNA response elements of regulated genes. CINPA1 was shown to be broken down in the liver to form two, mostly inactive, metabolites. The structure-activity differences of CINPA1 and its metabolites were used to guide computational modeling using the CAR-LBD structure. To rationalize how ligand binding may lead to different CAR pharmacology, an analysis of the docked poses of human CAR bound to CITCO (a CAR activator) vs. CINPA1 or the metabolites was conducted. From our modeling, strong hydrogen bonding of CINPA1 with N165 and H203 in the CAR-LBD was predicted. These residues were validated to be important for CINPA1 binding using single amino-acid CAR mutants in a CAR-mediated functional reporter assay. Also predicted were residues making key hydrophobic interactions with CINPA1 but not the inactive metabolites. Some of these hydrophobic amino acids were also identified and additionally, the differential coregulator interactions of these mutants were determined in mammalian two-hybrid systems. CINPA1 represents an excellent starting point for future optimization into highly relevant probe molecules to study the function of the CAR receptor in normal- and pathophysiology, and possible development of therapeutics (for e.g. use for resensitizing chemoresistant neuroblastoma cells).

Keywords: antagonist, chemoresistance, constitutive androstane receptor (CAR), multi-drug resistance, structure activity relationship (SAR), xenobiotic resistance

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Authors: Ahmed Chetouani

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Corrosion is a natural occurring process where it can be defined as the deterioration of materials properties due to its interaction with its environment. Corrosion can lead to failures in plant infrastructure and machines which are usually costly to repair. In terms of loss of contaminated products which will cause environmental damage and possibly costly in terms of human health. The driving force that causes metals to corrode is due to the natural consequence of their temporary existence in metallic form. There is a growing trend in utilizing plant extracts and pharmaceutical compounds as corrosion inhibitors. Exquisite identification of the essential oil of aerial parts of Pelargonium was obtained using hydrodistillation and identification using GC (gas chromatography) and GC/MS (gas chromatography-mass spectrometry). The oil was predominated by Citronellol (22.8%). The inhibitory effect of essential oil and extract of Pelargonium was estimated on the corrosion of mild steel in 1M hydrochloric acid (HCl) using weight loss, Electrochemical Impedance Spectroscopy (EIS) and Tafel polarization curves. Inhibition was found to increase with increasing concentration of the essential oil and extract of Pelargonium. The effect of temperature on the corrosion behaviour of mild steel in 1M HCl with addition of essential oil and extract was also studied and the thermodynamic parameters were determined and discussed. Values of inhibition efficiency were calculated from weight loss, Tafel polarization curves, and EIS. All results are in good agreement. Polarization curves showed that essential oil and extract of Pelargonium behave as mixed type inhibitors in hydrochloric acid. The results obtained showed that the essential oil and extract of Pelargonium could serve as an effective inhibitor of the corrosion of mild steel in Hydrochloric acid solution. To avoid any surprise of toxicity, the majority compounds have been studied by using POM analyses.

Keywords: corrosion inhibition, mild steel, pelargonium oil, extract, electrochemical system, hydrodistillation, side effects, POM Analyses

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Authors: Xinxiu Li, Chuqian Zheng, Yanyan Qian, Hong Fan

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Objectives: In hepatocellular carcinoma (HCC), oncogenes are continuously and robustly transcribed due to aberrant expression of essential components of the trans-acting super-enhancers (SE) complex. Preclinical and clinical trials are now being conducted on small-molecule inhibitors that target core-transcriptional components, including as transcriptional bromodomain protein 4 (BRD4) and cyclin-dependent kinase 7 (CDK7), in a number of malignant tumors. This study aims to explore whether co-overexpression of BRD4 and CDK7 is a potential marker of worse prognosis and a combined therapeutic target in HCC. Methods: The expression pattern of BRD4 and CDK7 and their correlation with prognosis in HCC were analyzed by RNA sequencing data and survival data of HCC patients from TCGA and GEO datasets. The protein levels of BRD4 and CDK7 were determined by immunohistochemistry (IHC), and survival data of patients were analyzed using the Kaplan-Meier method. The mRNA expression levels of genes in HCC cell lines were evaluated by quantitative PCR (q-PCR). CCK-8 and colony formation assays were conducted to assess cell proliferation of HCC upon treatment with BRD4 inhibitor JQ1 or/and CDK7 inhibitor THZ1. Results: It was shown that BRD4 and CDK7 were often overexpressed in HCCs and were associated with poor prognosis of HCC by analyzing the TCGA and GEO datasets. BRD4 or CDK7 overexpression was related to a lower survival rate. It's interesting to note that co-overexpression of CDK7 and BRD4 was a worse prognostic factor in HCC. Treatment with JQ1 or THZ1 alone had an inhibitory effect on cell proliferation; however, when JQ1 and THZ1 were combined, there was a more notable suppression of cell growth. At the same time, the combined use of JQ1 and THZ1 synergistically suppresses the expression of HCC driver genes. Conclusion: Our research revealed that BRD4 and CDK7 coupled can be a useful biomarker in HCC prognosis and the combination of JQ1 and THZ1 can be a promising therapeutic therapy against HCC.

Keywords: BRD4, CDK7, cell proliferation, combined inhibition

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Authors: Yen-Hao Su, Wan-Chun Tang, Ya-Wen Cheng, Peik Sia, Chi-Chen Huang, Yi-Chao Lee, Hsin-Yi Jiang, Ming-Heng Wu, I-Lu Lai, Jun-Wei Lee, Kuen-Haur Lee

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There is a wide range of drugs and combinations under investigation and/or approved over the last decade to treat colorectal cancer (CRC), but the 5-year survival rate remains poor at stages II–IV. Therefore, new, more efficient drugs still need to be developed that will hopefully be included in first-line therapy or overcome resistance when it appears, as part of second- or third-line treatments in the near future. In this study, we revealed that heat shock protein 90 (Hsp90) inhibitors have high therapeutic potential in CRC according to combinative analysis of NCBI's Gene Expression Omnibus (GEO) repository and chemical genomic database of Connectivity Map (CMap). We found that second generation Hsp90 inhibitor, NVP-AUY922, significantly down regulated the activities of a broad spectrum of kinases involved in regulating cell growth arrest and death of NVPAUY922-sensitive CRC cells. To overcome NVP-AUY922-induced upregulation of survivin expression which causes drug insensitivity, we found that combining berberine (BBR), a herbal medicine with potency in inhibiting survivin expression, with NVP-AUY922 resulted in synergistic antiproliferative effects for NVP-AUY922-sensitive and -insensitive CRC cells. Furthermore, we demonstrated that treatment of NVP-AUY922-insensitive CRC cells with the combination of NVP-AUY922 and BBR caused cell growth arrest through inhibiting CDK4 expression and induction of microRNA-296-5p (miR-296-5p)-mediated suppression of Pin1–β-catenin–cyclin D1 signaling pathway. Finally, we found that the expression level of Hsp90 in tumor tissues of CRC was positively correlated with CDK4 and Pin1 expression levels. Taken together, these results indicate that combination of NVP-AUY922 and BBR therapy can inhibit multiple oncogenic signaling pathways of CRC.

Keywords: berberine, colorectal cancer, connectivity map, heat shock protein 90 inhibitor

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Authors: Diana Larisa Vladoiu, Vasile Ostafe, Adriana Isvoran

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Molecular docking calculations reveal that pesticides provide favorable interactions with the bacterial chitinases. Pesticides interact with both hydrophilic and aromatic residues involved in the active site of the enzymes, their positions partially overlapping the substrate and the inhibitors locations. Molecular docking outcomes, in correlation with experimental literature data, suggest that the pesticides may be degraded or having an inhibitor effect on the activity of these enzymes, depending of the application dose and rate.

Keywords: chitinases, inhibition, molecular docking, pesticides

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Authors: Sadeg M. Ghnia, Mahmud Alghattawi

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The NC-210 study area is located in Atshan Saddle between both Ghadamis and Murzuq basins, west Libya. The preserved Palaeozoic successions are predominantly clastics reaching thickness of more than 20,000 ft in northern Ghadamis Basin depocenter. The Carboniferous series consist of interbedded sandstone, siltstone, shale, claystone and minor limestone deposited in a fluctuating shallow marine to brackish lacustrine/fluviatile environment which attain maximum thickness of over 5,000ft in the area of Atshan Saddle and recorded 3,500 ft. in outcrops of Murzuq Basin flanks. The Carboniferous strata was uplifted and eroded during Late Paleozoic and early Mesozoic time in northern Ghadamis Basin and Atshan Saddle. The M'rar Formation age is Tournaisian to Late Serpukhovian based on palynological markers and contains about 12 cycles of sandstone and shale deposited in shallow to outer neritic deltaic settings. The hydrocarbons in the M'rar reservoirs possibly sourced from the Lower Silurian and possibly Frasinian radioactive hot shales. The M'rar Formation lateral, vertical and thickness distribution is possibly influenced by the reactivation of Tumarline Strik-Slip fault and its conjugate faults. A pronounced structural paleohighs and paleolows, trending SE & NW through the Gargaf Saddle, is possibly indicative of the present of two sub-basins in the area of Atshan Saddle. A number of identified seismic reflectors from existing 2D seismic covering Atshan Saddle reflect M’rar deltaic 12 sandstone cycles. M’rar7, M’rar9, M’rar10 and M’rar12 are characterized by high amplitude reflectors, while M’rar2 and M’rar6 are characterized by medium amplitude reflectors. These horizons are productive reservoirs in the study area. Available seismic data in the study area contributed significantly to the identification of M’rar potential traps, which are prominently 3- way dip closure against fault zone. Also seismic data indicates the presence of a significant strikeslip component with the development of flower-structure. The M'rar Formation hydrocarbon discoveries are concentrated mainly in the Atshan Saddle located in southern Ghadamis Basin, Libya and Illizi Basin in southeast of Algeria. Significant additional hydrocarbons may be present in areas adjacent to the Gargaf Uplift, along structural highs and fringing the Hoggar Uplift, providing suitable migration pathways.

Keywords: hydrocarbon potential, stratigraphy, Ghadamis basin, seismic, well data integration

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Terahertz time-domain spectroscopy (THz-TDS) was used to observe the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different average molecular weights (10,000 g/mol, 40,000 g/mol, 360,000 g/mol). Distinct footprints of phase transition in the THz region (0.4 - 2.2 THz) were analyzed and absorption coefficients and complex refractive indices are obtained and compared in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz, polyvinylpyrrolidone (PVP), THz-TDS, inhibitor

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Authors: Zahoor Hussain

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Creasing is a physiological disorder of rind in sweet orange [Citrus sinensis (L.) Osbeck] fruit and causes serious economic losses in various countries of the world. The reversible inhibitor of ethylene, aminoethoxyvinylglycine (AVG) with the effects of different concentrations (0, 20, 40 and 60 mgL⁻¹) AVG with 0.05% ‘Tween 20’ as a surfactant applied at the fruit set, the golf ball or at the colour break stage on controlling creasing, rheological properties of fruit and rind as well as fruit quality in of Washington Navel and Lane Late sweet orange was investigated. Creasing was substantially reduced and fruit quality was improved with the exogenous application of AVG depending upon its concentration and stage of application in both cultivars. The spray application of AVG (60 mgL⁻¹) at the golf ball stage was effective in reducing creasing (27.86% and 24.29%) compared to the control (52.14 and 51.53%) in cv. Washington Navel during 2011 and 2012, respectively. Whilst, in cv. Lane Late lowest creasing was observed When AVG was applied at fruit set stage (22.86%) compared to the control (51.43%) during 2012. In cv. Washington Navel, AVG treatment (60 mgL⁻¹) was more effective to increase the fruit firmness (318.97 N) and rind hardness (25.94 N) when applied at fruit set stage. However, rind tensile strength was higher, when AVG was applied at the golf ball stage (54.13 N). In cv. Lane Late, the rind harness (28.61 N), rind tensile strength (78.82 N) was also higher when AVG was sprayed at fruit set stage. Whilst, the fruit compression force (369.68 N) was higher when AVG was applied at the golf ball stage. Similarly, the treatment AVG (60 mgL⁻¹) was more effective in improving fruit weight (281.00 and 298.50 g) and fruit diameter (87.30 and 82.69 mm), rind thickness (5.56 and 5.38 mm) and total sugars (15.27 mg.100ml⁻¹) when AVG was applied at the fruit golf ball stage in cv. Washington Navel and Lane Late, respectively. Similarly, rind harness (25.94 and 28.61 N), total antioxidants (45.30 and 46.48 mM trolox 100ml⁻¹), total sugars (13.64 and 15.27 mg.100ml⁻¹), citric acid (1.66 and 1.32 mg100ml⁻¹), malic acid (0.36 and 0.63 mg.100ml⁻¹) and succinic acid (0.35 and 0.38 mg100ml⁻¹) were also higher, when AVG was applied at the fruit set stage in both cultivars. In conclusion, the exogenous applications of AVG substantially reduces the creasing incidence, improves rheological properties of fruit and rind as well as fruit quality in Washington Navel and Lane Late sweet orange fruit.

Keywords: AVG, creasing, ethylene inhibitor, sweet orange

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Authors: Salma A. El-Marasy, Rehab F. Abdel-Rahman, Reham M. Abd-Elsalam

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The burden of stroke is intensely increasing worldwide. Brain injury following transient or permanent focal cerebral ischemia develops ischemic stroke as a consequence of a complex series of pathophysiological events. The aim of this study is to evaluate the possible neuroprotective effect of a dipeptidyl peptidase-4 inhibitor, vildagliptin, independent on its insulinotropic properties in non-diabetic rats subjected to cerebral ischemia. Anaesthetized Wistar rats were subjected to either left middle cerebral artery occlusion (MCAO) or sham operation followed by reperfusion after 30 min of MCAO. The other three groups were orally administered vildagliptin at 3 dose levels (2.5, 5, 10 mg/kg) for 3 successive weeks before subjected to left focal cerebral ischemia/reperfusion and till the end of the study. Neurological deficit scores and motor activity were assessed 24h following reperfusion. 48h following reperfusion, rats were euthanized and their left brain hemispheres were harvested and used in the biochemical, histopathological, and immunohistochemical investigations. Vildagliptin pretreatment improved neurological score deficit, locomotor activity and motor coordination in MCAO rats. Moreover, vildagliptin reduced malondialdehyde (MDA), elevated reduced glutathione (GSH), phosphotylinosital 3 kinase (PI3K), phosphorylated of protein kinase B (p-AKT), and mechanistic target of rapamycin (mTOR) brain contents in addition to reducing protein expression of caspase-3. Also, vildagliptin showed a dose-dependent attenuation in neuronal cell loss and histopathological alterations in MCAO rats. This study proves that vildagliptin exerted the neuroprotective effect in a dose-dependent manner as shown in amelioration of neuronal cell loss and histopathological damage in MCAO rats, which may be mediated by attenuating neuronal and motor deficits, it’s anti-oxidant property, activation of PI3K/AKT/mTOR pathway and its anti-apoptotic effect.

Keywords: caspase-3, cerebral ischemia, dipeptidyl peptidase-4 inhibitor, oxidative stress, PI3K/AKT/mTOR pathway, rats, vildagliptin

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Authors: Margarita S. Tikhonova, Alireza Baniasad, Anton G. Kalmykov, Georgy A. Kalmykov, Ralf Littke

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There is a high complexity in the pore structure of organic-rich rocks caused by the combination of inter-particle porosity from inorganic mineral matter and ultrafine intra-particle porosity from both organic matter and clay minerals. Fluids are retained in that pore space, but there are major uncertainties in how and where the fluids are stored and to what extent they are accessible or trapped in 'closed' pores. A large degree of tortuosity may lead to fractionation of organic matter so that the lighter and flexible compounds would diffuse to the reservoir whereas more complicated compounds may be locked in place. Additionally, parts of hydrocarbons could be bound to solid organic matter –kerogen– and mineral matrix during expulsion and migration. Larger compounds can occupy thin channels so that clogging or oil and gas entrapment will occur. Sequential extraction of applying different solvents is a powerful tool to provide more information about the characteristics of trapped organic matter distribution. The Upper Jurassic – Lower Cretaceous Bazhenov shale is one of the most petroliferous source rock extended in West Siberia, Russia. Concerning the variable mineral composition, pore space distribution and thermal maturation, there are high uncertainties in distribution and composition of organic matter in this formation. In order to address this issue geological and geochemical properties of 30 samples including mineral composition (XRD and XRF), structure and texture (thin-section microscopy), organic matter contents, type and thermal maturity (Rock-Eval) as well as molecular composition (GC-FID and GC-MS) of different extracted materials during sequential extraction were considered. Sequential extraction was performed by a Soxhlet apparatus using different solvents, i.e., n-hexane, chloroform and ethanol-benzene (1:1 v:v) first on core plugs and later on pulverized materials. The results indicate that the studied samples are mainly composed of type II kerogen with TOC contents varied from 5 to 25%. The thermal maturity ranged from immature to late oil window. Whereas clay contents decreased with increasing maturity, the amount of silica increased in the studied samples. According to molecular geochemistry, stored hydrocarbons in open and closed pore space reveal different geochemical fingerprints. The results improve our understanding of hydrocarbon expulsion and migration in the organic-rich Bazhenov shale and therefore better estimation of hydrocarbon potential for this formation.

Keywords: Bazhenov formation, bitumen, molecular geochemistry, sequential extraction

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Authors: Esther Friedlander, Philip Friedlander

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The use of immunotherapy that inhibits programmed death-1 (PD-1) or its ligand PD-L1 confers survival benefits in patients with non-small cell lung cancer (NSCLC). However, approximately 45% of patients experience primary treatment resistance, necessitating the development of strategies to improve efficacy. While the renin-angiotensin system (RAS) has systemic hemodynamic effects, tissue-specific regulation exists along with modulation of immune activity in part through regulation of myeloid cell activity, leading to the hypothesis that RAS inhibition may improve anti-PD-1/L-1 efficacy. A retrospective analysis was conducted that included 173 advanced solid tumor cancer patients treated at Valley Hospital, a community Hospital in New Jersey, USA, who were treated with a PD-1/L-1 inhibitor in a defined time period showing a statistically significant relationship between RAS pathway inhibition (RASi through concomitant treatment with an ACE inhibitor or angiotensin receptor blocker) and positive efficacy to the immunotherapy that was independent of age, gender and cancer type. Subset analysis revealed strong numerical benefit for efficacy in both patients with squamous and nonsquamous NSCLC as determined by documented clinician assessment of efficacy and by duration of therapy. A PUBMED literature search was now conducted to identify studies assessing the effect of RAS pathway inhibition on anti-PD-1/L1 efficacy in advanced solid tumor patients and compare these findings to those seen in the Valley Hospital retrospective study with a focus on NSCLC specifically. A total of 11 articles were identified assessing the effects of RAS pathway inhibition on the efficacy of checkpoint inhibitor immunotherapy in advanced cancer patients. Of the 11 studies, 10 assessed the effect on survival of RASi in the context of treatment with anti-PD-1/PD-L1, while one assessed the effect on CTLA-4 inhibition. Eight of the studies included patients with NSCLC, while the remaining 2 were specific to genitourinary malignancies. Of the 8 studies, two were specific to NSCLC patients, with the remaining 6 studies including a range of cancer types, of which NSCLC was one. Of these 6 studies, only 2 reported specific survival data for the NSCLC subpopulation. Patient characteristics, multivariate analysis data and efficacy data seen in the 2 NSLCLC specific studies and in the 2 basket studies, which provided data on the NSCLC subpopulation, were compared to that seen in the Valley Hospital retrospective study supporting a broader effect of RASi on anti-PD-1/L1 efficacy in advanced NSLCLC with the majority of studies showing statistically significant benefit or strong statistical trends but with one study demonstrating worsened outcomes. This comparison of studies extends published findings to the community hospital setting and supports prospective assessment through randomized clinical trials of efficacy in NSCLC patients with pharmacodynamic components to determine the effect on immune cell activity in tumors and on the composition of the tumor microenvironment.

Keywords: immunotherapy, cancer, angiotensin, efficacy, PD-1, lung cancer, NSCLC

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Authors: Barbora Svechova, Monika Licbinska

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Geochemical modeling of mineralogical changes of various materials in contact with an aqueous solution is an important tool for predicting the processes and development of given materials at the site. The modeling focused on the mutual interaction of groundwater at the contact with the rock mass and its subsequent influence on concrete structures. The studied locality is located in Slovakia in the area of the Liptov Basin, which is a significant inter-mountain lowland, which is bordered on the north and south by the core mountains belt of the Tatras, where in the center the crystalline rises to the surface accompanied by Mesozoic cover. Groundwater in the area is bound to structures with complicated geological structures. From the hydrogeological point of view, it is an environment with a crack-fracture character. The area is characterized by a shallow surface circulation of groundwater without a significant collector structure, and from a chemical point of view, groundwater in the area has been classified as calcium bicarbonate with a high content of CO2 and SO4 ions. According to the European standard EN 206-1, these are waters with medium aggression towards the concrete. Three rock samples were taken from the area. Based on petrographic and mineralogical research, they were evaluated as calcareous shale, micritic limestone and crystalline shale. These three rock samples were placed in demineralized water for one month and the change in the chemical composition of the water was monitored. During the solution-rock interaction there was an increase in the concentrations of all major ions, except nitrates. There was an increase in concentration after a week, but at the end of the experiment, the concentration was lower than the initial value. Another experiment was the interaction of groundwater from the studied locality with a concrete structure. The concrete sample was also left in the water for 1 month. The results of the experiment confirmed the assumption of a reduction in the concentrations of calcium and bicarbonate ions in water due to the precipitation of amorphous forms of CaCO3 on the surface of the sample.Vice versa, it was surprising to increase the concentration of sulphates, sodium, iron and aluminum due to the leaching of concrete. Chemical analyzes from these experiments were performed in the PHREEQc program, which calculated the probability of the formation of amorphous forms of minerals. From the results of chemical analyses and hydrochemical modeling of water collected in situ and water from experiments, it was found: groundwater at the site is unsaturated and shows moderate aggression towards reinforced concrete structures according to EN 206-1a, which will affect the homogeneity and integrity of concrete structures; from the rocks in the given area, Ca, Na, Fe, HCO3 and SO4. Unsaturated waters will dissolve everything as soon as they come into contact with the solid matrix. The speed of this process then depends on the physicochemical parameters of the environment (T, ORP, p, n, water retention time in the environment, etc.).

Keywords: geochemical modeling, concrete , dissolution , PHREEQc

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Authors: Sachin Mulmi Shrestha, Xin Fang, Hui Ye, Lihua Ren, Qinghua Ji, Ruihua Shi

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Background: Esophageal squamous cell carcinoma (ESCC) is a tumor arising from esophageal epithelial cells and is one of the major disease subtype in Asian countries, including China. Esophageal cancer is the 7th highest incidence based on the 2020 data of GLOBOCAN. The pathogenesis of cancer is still not well understood as many molecular and genetic basis of esophageal carcinogenesis has yet to be clearly elucidated. Circular RNAs are RNA molecules that are formed by back-splicing covalently joined 3′- and 5′-endsrather than canonical splicing, and recent data suggest circular RNAs could sponge miRNAs and are enriched with functional miRNA binding sites. Hence, we studied the mechanism of circular RNA, its biological function, and the relationship between microRNA in the carcinogenesis of ESCC. Methods: 4 pairs of normal and esophageal cancer tissues were collected in Zhongda hospital, affiliated to Southeast University, and high-throughput RNA sequencing was done. The result revealed that circ_0032746 was upregulated, and thus we selected circ_0032746 for further study. The backsplice junction of circRNA was validated by sanger sequence, and stability was determined by RNASE R assay. The binding site of circRNA and microRNA was predicted by circinteractome,mirandaand RNAhybrid database. Furthermore, circRNA was silenced by siRNA and then by lentivirus. The regulatory axis of circ0032746/miR4270 was validated by shRNA, mimic, and inhibitor transfection. Then, in vitro experiments were performed to assess the role of circ0032746 on proliferation (CCK-8 assay and colon formation assay), migration and invasion (Transewell assay), and apoptosis of ESCC. Results: The upregulated circ0032746 was validated in 9 pairs of tissues and 5 types of cell lines by qPCR, which showed high expression and was statistically significant (P<0.005) ). Upregulated circ0032746 was silenced by shRNA, which showed significant knockdown in KYSE 30 and TE-1 cell lines expression compared to control. Nuclear and cytoplasmic mRNA fraction experiment displayed the cytoplasmic location of circ0032746. The sponging of miR4270 was validated by co-transfection of sh-circ0032746 and mimic or inhibitor. Transfection with mimic showed the decreased expression of circ_0032746, whereas inhibitor inhibited the result. In vitro experiments showed that silencing of circ_0032746 inhibited the proliferation, migration, and invasion compared to the negative control group. The apoptosis was seen higher in a knockdown group than in the control group. Furthermore, 11 common mircoRNA target mRNAs were predicted by Targetscan, MirTarbase, and miRanda database, which may further play role in the pathogenesis. Conclusion: Our results showed that novel circ_0032746 is upregulated in ESCC and plays role in itsoncogenicity. Silencing of circ_0032746 inhibits the proliferation and migration of ESCC whereas increases the apoptosis of cancer cells. Hence, circ0032746 acts as an oncogene in ESCC by sponging with miR4270 and could be a potential biomarker in the diagnosis of ESCC in the future.

Keywords: circRNA, esophageal squamous cell carcinoma, microRNA, upregulated

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Authors: Arpit Kumar Shrivastava, Subrat Kumar, Rajani Kanta Mohapatra, Priyadarshi Soumyaranjan Sahu

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Computational approaches to predict structure, function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are not effective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines. We identified a unique hypothetical epitopic protein in C. hominis genome through BLASTP analysis. A 3D model of the hypothetical protein was generated using I-Tasser server through threading methodology. The quality of the model was validated through Ramachandran plot by PROCHECK server. The functional annotation of the hypothetical protein through DALI server revealed structural similarity with human Transportin 3. Phylogenetic analysis for this hypothetical protein also showed C. hominis hypothetical protein (CUV04613) was the closely related to human transportin 3 protein. The 3D protein model is further subjected to virtual screening study with inhibitors from the Zinc Database by using Dock Blaster software. Docking study reported N-(3-chlorobenzyl) ethane-1,2-diamine as the best inhibitor in terms of docking score. Docking analysis elucidated that Leu 525, Ile 526, Glu 528, Glu 529 are critical residues for ligand–receptor interactions. The molecular dynamic simulation was done to access the reliability of the binding pose of inhibitor and protein complex using GROMACS software at 10ns time point. Trajectories were analyzed at each 2.5 ns time interval, among which, H-bond with LEU-525 and GLY- 530 are significantly present in MD trajectories. Furthermore, antigenic determinants of the protein were determined with the help of DNA Star software. Our study findings showed a great potential in order to provide insights in the development of new drug(s) or vaccine(s) for control as well as prevention of cryptosporidiosis among humans and animals.

Keywords: cryptosporidium hominis, hypothetical protein, molecular docking, molecular dynamics simulation

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Authors: Nader Mohamed

Abstract:

The Late Cretaceous deposits are well developed through-out Egypt. This is due to a ‎transgression phase associated with the subsidence caused by the neo-Tethyan rift event that ‎took place across the northern margin of Africa, resulting in a period of dominantly marine ‎deposits in the Gulf of Suez. The Late Cretaceous Nezzazat Group represents the Cenomanian, ‎Turonian and clastic sediments of the Lower Senonian. The Nezzazat Group has been divided ‎into four formations namely, from base to top, the Raha Formation, the Abu Qada Formation, ‎the Wata Formation and the Matulla Formation. The Cenomanian Raha and the Lower Senonian ‎Matulla formations are the most important clastic sequence in the Nezzazat Group because they ‎provide the highest net reservoir thickness and the highest net/gross ratio. This study emphasis ‎on Matulla formation located in the eastern part of the Gulf of Suez. The three stratigraphic ‎surface sections (Wadi Sudr, Wadi Matulla and Gabal Nezzazat) which represent the exposed ‎Coniacian-Santonian sediments in Sinai are used for correlating Matulla sediments of Ras ‎Budran field. Cutting description, petrographic examination, log behaviors, biostratigraphy with ‎outcrops are used to identify the reservoir characteristics, lithology, facies environment logs and ‎subdivide the Matulla formation into three units. The lower unit is believed to be the main ‎reservoir where it consists mainly of sands with shale and sandy carbonates, while the other ‎units are mainly carbonate with some streaks of shale and sand. Reservoir modeling is an ‎effective technique that assists in reservoir management as decisions concerning development ‎and depletion of hydrocarbon reserves, So It was essential to model the Matulla reservoir as ‎accurately as possible in order to better evaluate, calculate the reserves and to determine the ‎most effective way of recovering as much of the petroleum economically as possible. All ‎available data on Matulla formation are used to build the reservoir structure model, lithofacies, ‎porosity, permeability and water saturation models which are the main parameters that describe ‎the reservoirs and provide information on effective evaluation of the need to develop the oil ‎potentiality of the reservoir. This study has shown the effectiveness of; 1) the integration of ‎geological data to evaluate and subdivide Matulla formation into three units. 2) Lithology and ‎facies environment interpretation which helped in defining the nature of deposition of Matulla ‎formation. 3) The 3D reservoir modeling technology as a tool for adequate understanding of the ‎spatial distribution of property and in addition evaluating the unlocked new reservoir areas of ‎Matulla formation which have to be drilled to investigate and exploit the un-drained oil. 4) This ‎study led to adding a new room of production and additional reserves to Ras Budran field. ‎

Keywords: geology, oil and gas, geoscience, sequence stratigraphy

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Authors: Safwat E. Musa, Nuha E. Mohamed, Nuha A. Bagi

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In this study, several crossplots of the P-impedance with the lithology logs (gamma ray, neutron porosity, deep resistivity, water saturation and Vp/Vs curves) were made in three available wells, which were drilled in central part of the Blue Nile basin in depths varies from 1460 m to 1600 m. These crossplots were successful to discriminate between sand and shale when using P-Impedance values, and between the wet sand and the pay sand when using both P-impedance and Vp/Vs together. Also, some impedance sections were converted to porosity sections using linear formula to characterize the reservoir in terms of porosity. The used crossplots were created on log resolution, while the seismic resolution can identify only the reservoir, unless a 3D seismic angle stacks were available; then it would be easier to identify the pay sand with great confidence; through high resolution seismic inversion and geostatistical approach when using P-impedance and Vp/Vs volumes.

Keywords: basin, Blue Nile, inversion, seismic

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Authors: Aussara Panya, Nunghathai Sawasdee, Mutita Junking, Chatchawan Srisawat, Kiattawee Choowongkomon, Pa-Thai Yenchitsomanus

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Dengue virus (DENV) infection is a global public health problem with approximately 100 million infected cases a year. Presently, there is no approved vaccine or effective drug available; therefore, the development of anti-DENV drug is urgently needed. The clinical reports revealing the positive association between the disease severity and viral titer has been reported previously suggesting that the anti-DENV drug therapy can possibly ameliorate the disease severity. Although several anti-DENV agents showed inhibitory activities against DENV infection, to date none of them accomplishes clinical use in the patients. The surface envelope (E) protein of DENV is critical for the viral entry step, which includes attachment and membrane fusion; thus, the blocking of envelope protein is an attractive strategy for anti-DENV drug development. To search the safe anti-DENV agent, this study aimed to search for novel peptide inhibitors to counter DENV infection through the targeting of E protein using a structure-based in silico design. Two selected strategies has been used including to identify the peptide inhibitor which interfere the membrane fusion process whereby the hydrophobic pocket on the E protein was the target, the destabilization of virion structure organization through the disruption of the interaction between the envelope and membrane proteins, respectively. The molecular docking technique has been used in the first strategy to search for the peptide inhibitors that specifically bind to the hydrophobic pocket. The second strategy, the peptide inhibitor has been designed to mimic the ectodomain portion of membrane protein to disrupt the protein-protein interaction. The designed peptides were tested for the effects on cell viability to measure the toxic to peptide to the cells and their inhibitory assay to inhibit the DENV infection in Vero cells. Furthermore, their antiviral effects on viral replication, intracellular protein level and viral production have been observed by using the qPCR, cell-based flavivirus immunodetection and immunofluorescence assay. None of tested peptides showed the significant effect on cell viability. The small peptide inhibitors achieved from molecular docking, Glu-Phe (EF), effectively inhibited DENV infection in cell culture system. Its most potential effect was observed for DENV2 with a half maximal inhibition concentration (IC50) of 96 μM, but it partially inhibited other serotypes. Treatment of EF at 200 µM on infected cells also significantly reduced the viral genome and protein to 83.47% and 84.15%, respectively, corresponding to the reduction of infected cell numbers. An additional approach was carried out by using peptide mimicking membrane (M) protein, namely MLH40. Treatment of MLH40 caused the reduction of foci formation in four individual DENV serotype (DENV1-4) with IC50 of 24-31 μM. Further characterization suggested that the MLH40 specifically blocked viral attachment to host membrane, and treatment with 100 μM could diminish 80% of viral attachment. In summary, targeting the hydrophobic pocket and M-binding site on the E protein by using the peptide inhibitors could inhibit DENV infection. The results provide proof of-concept for the development of antiviral therapeutic peptide inhibitors to counter DENV infection through the use of a structure-based design targeting conserved viral protein.

Keywords: dengue virus, dengue virus infection, drug design, peptide inhibitor

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Authors: M. A. Deyab

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The effect of zwitterionic surfactant (ZS) on erosion-corrosion of API X52 steel in oil sands slurry was studied using Tafel polarization and anodic polarization measurements. The surface morphology of API X52 steel was examined with scanning electron microscopy (SEM) and atomic force microscopy (AFM). ZS inhibited the erosion-corrosion of API X52 steel in oil sands' slurry, and the inhibition efficiency increased with increasing ZS concentration but decreased with increasing temperature. Polarization curves indicate that ZS act as a mixed type of inhibitor. Inhibition efficiencies of ZS in the dynamic condition are not as effective as that obtained in the static condition.

Keywords: corrosion, surfactant, oil sands slurry, erosion-corrosion

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Authors: M. Yavuz Hüseyinca, Şuayip Küpeli

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The Chemical Index of Alteration (CIA) values of Late Eocene-Oligocene aged sandstones that exposed on the eastern edge of Tuz Lake (Central Anatolia, Turkey) range from 49 to 59 with an average of 51. The A-CN-K diagram indicates that sandstones underwent post-depositional K-metasomatism. The original average CIA value before the K-metasomatism is calculated as 55. This value is lower than that of Post Archean Australian Shale (PAAS) and defines a low intense chemical weathering in the source-area. Extrapolation of sandstones back to the plagioclase-alkali feldspar line in the A-CN-K diagram suggests a high average plagioclase to alkali feldspar ratio in the provenance and a composition close to granodiorite. The Zr/Sc and Th/Sc ratios with the Al₂O₃-Zr-TiO₂ space do not show zircon addition that refuse both recycling of sediments and sorting effect. All these data suggest direct and rapid transportation from the source due to topographic uplift and probably arid to semi-arid climate conditions for the sandstones.

Keywords: central Anatolia, sandstone, sorting, weathering

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Authors: Malvina Hoxha, Valerie Capra, Carola Buccellati, Angelo Sala, Clara Cena, Roberta Fruttero, Massimo Bertinaria, G. Enrico Rovati

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Today COXIBs are used in the treatment of arthritis and many other painful conditions in selected patients with high gastrointestinal risk and low CV risk. Previously we found a new mechanism of action of a traditional NSAID (diclofenac) and a COXIB (lumiracoxib) that possess weak competitive antagonism at the TP receptor. We hypothesize that modifying the structure of a known specific inhibitor of cyclooxygenase-2 (COXIB), so that it becomes also a more potent thromboxane antagonist will preserve the anti-inflammatory and gastrointestinal safety typical of COXIBs and prevent the cardiovascular risk associated with long term therapy.

Keywords: cyclooxygenase, inflammation, lumiracoxib, thromboxane A2

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Authors: Agnieszka Krzemińska, Katarzyna Świderek, Vicente Molinier, Piotr Paneth

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In order to understand in details the interactions between ligands and the enzyme isotope effects were studied between clinically used drugs that bind in the active site of Human Immunodeficiency Virus Reverse Transcriptase, HIV-1 RT, as well as triazole-based inhibitor that binds in the allosteric pocket of this enzyme. The magnitudes and origins of the resulting binding isotope effects were analyzed. Subsequently, binding isotope effect of the same triazole-based inhibitor bound in the active site were analyzed and compared. Together, these results show differences in binding origins in two sites of the enzyme and allow to analyze binding mode and place of newly synthesized inhibitors. Typical protocol is described below on the example of triazole ligand in the allosteric pocket. Triazole was docked into allosteric cavity of HIV-1 RT with Glide using extra-precision mode as implemented in Schroedinger software. The structure of HIV-1 RT was obtained from Protein Data Bank as structure of PDB ID 2RKI. The pKa for titratable amino acids was calculated using PROPKA software, and in order to neutralize the system 15 Cl- were added using tLEaP package implemented in AMBERTools ver.1.5. Also N-terminals and C-terminals were build using tLEaP. The system was placed in 144x160x144Å3 orthorhombic box of water molecules using NAMD program. Missing parameters for triazole were obtained at the AM1 level using Antechamber software implemented in AMBERTools. The energy minimizations were carried out by means of a conjugate gradient algorithm using NAMD. Then system was heated from 0 to 300 K with temperature increment 0.001 K. Subsequently 2 ns Langevin−Verlet (NVT) MM MD simulation with AMBER force field implemented in NAMD was carried out. Periodic Boundary Conditions and cut-offs for the nonbonding interactions, range radius from 14.5 to 16 Å, are used. After 2 ns relaxation 200 ps of QM/MM MD at 300 K were simulated. The triazole was treated quantum mechanically at the AM1 level, protein was described using AMBER and water molecules were described using TIP3P, as implemented in fDynamo library. Molecules 20 Å apart from the triazole were kept frozen, with cut-offs established on range radius from 14.5 to 16 Å. In order to describe interactions between triazole and RT free energy of binding using Free Energy Perturbation method was done. The change in frequencies from ligand in solution to ligand bounded in enzyme was used to calculate binding isotope effects.

Keywords: binding isotope effects, molecular dynamics, HIV, reverse transcriptase

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Authors: Almas Rajguru

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The Oligocene succession of the Tapti- Daman area is one of the established petroleum plays in Tapti-Daman block of the Mumbai Offshore Basin. Despite good control and production history, the sand geometry and continuity of reservoir character of these sediments are less understood as most reservoirs are thin and fall below seismic resolution. The present work focuses on a detailed analysis of the Early Oligocene Mahuva Formation at the reservoir scale through laboratory studies (sedimentology and biostratigraphy) of core and sidewall cores in integration with electro logs for firming up facies’ distribution, micro-depositional environment and sequence stratigraphy, diagenesis and reservoir characterization from seventeen wells from North Tapti-C-37 area in Tapti Daman Block, WOB. The thick shale/claystone with thin interbeds of sandstone and siltstones of deeper marine in the lower part of Mahuva Fm represents deposition in a transgressive regime. The overlying interbedded sandstone, glauconitic-siltstone/fine-grained sandstone, and thin beds of packstone/grainstone within highly fissile shale were deposited in a prograding tide-dominated delta during late-rise normal regression. Nine litho facies (F1-F9) representing deposition in various microenvironments of the tide-dominated delta are identified based on their characteristic sediment texture, structure and microfacies. Massive, gritty sandstone (F1) with poorly sorted sands lithic fragments with calcareous and Fe-rich matrix represents channel fill sediments. High-angle cross-stratified sandstone (F2) deposited in rapidly shifting/migrating bars under strong tidal currents. F3 records the laterally accreted tidal-channel point bars. F3 (low-angle cross-stratified to parallel bedded sandstone) and F4 (Clean sandstone) are often associated with F2 in a tidal bar complex. F5 (interbedded thin sand and mud) and F6 (bioturbated sandstone) represent tidal flat deposits. High energy open marine carbonate shoals (F8) and fossiliferous sandstone in offshore bars (F7) represent deepening up facies. Shallow marine standstill conditions facilitated the deposition of thick shale (F9) beds. The reservoir facies (F1-F6) are commonly poorly to moderately sorted; bimodal, immature sandstone represented by quartz-wacke. The framework grains are sub-angular to sub-rounded, medium to coarse-grained (occasionally gritty) embedded within argillaceous (kaolinite/chlorite/chamosite) to highly Fe-rich matrix (sideritic). The facies F7 and F8, representing the sandy packstone and grainstone facies, respectively, exhibit poor reservoir characteristics due to sanitization, diagenetic compaction and matrix-filled intergranular spaces. The various diagenetic features such as the presence of authigenic clays (kaolinite/dickite/smectite); ferruginous minerals like siderite, pyrite, hematite and other iron oxides; bioturbations; glauconite; calcite and quartz cementation, precipitation of gypsum, pressure solution and other compaction effects are identified. These diagenetic features, wherever present, have reduced porosity and permeability thereby adversely affecting reservoir quality. Tidal bar sandstones possess good reservoir characteristics such as moderate to good sorting, fair to good porosity and geometry that facilitates efficient lateral extension and vertical thickness of reservoir. The sand bodies of F2, F3 and F4 facies of Well L, M and Q deposited in a tidal bar complex exhibit good reservoir quality represented by relatively cleaner, poorly burrowed, loose, friable sandstone with good porosity. Sandstone facies around these wells could prove a potential hydrocarbon reservoir and could be considered for further exploration.

Keywords: reservoir sedimentology, facies analysis, HST, tide dominated delta, tidal bars

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Authors: Bello Yusuf Idi

Abstract:

The Gongola arm of the Upper Banue Trough, Northeastern Nigeria is predominantly covered by the outcrops of Limestone-bearing rocks in form of Sandstone with intercalation of carbonate clay, shale, basaltic, felsphatic and migmatide rocks at subpixel dimension. In this work, subpixel classification algorithm was used to classify the data acquired from landsat 7 Enhance Thematic Mapper (ETM+) satellite system with the aim of producing fractional distribution image for three most economically important solid minerals of the area: Limestone, Basalt and Migmatide. Linear Spectral Unmixing (LSU) algorithm was used to produce fractional distribution image of abundance of the three mineral resources within a 100Km2 portion of the area. The results show that the minerals occur at different proportion all over the area. The fractional map could therefore serve as a guide to the ongoing reconnaissance for the economic potentiality of the formation.

Keywords: linear spectral un-mixing, upper benue trough, gongola arm, geological engineering

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Authors: Agnieszka E. Laudy, Karolina Stępien, Sergiusz Lulinski, Krzysztof Durka, Stefan Tyski

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1,3-dihydro-1-hydroxy-2,1-benzoxaborole and its derivatives are a particularly interesting group of synthetic agents and were successfully employed in supramolecular chemistry medicine. The first important compounds, 5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole and 5-chloro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole were identified as potent antifungal agents. In contrast, (S)-3-(aminomethyl)-7-(3-hydroxypropoxy)-1-hydroxy-1,3-dihydro-2,1-benzoxaborole hydrochloride is in the second phase of clinical trials as a drug for the treatment of Gram-negative bacterial infections of the Enterobacteriaceae family and Pseudomonas aeruginosa. Equally important and difficult task is to search for compounds active against Gram-negative bacilli, which have multi-drug-resistance efflux pumps actively removing many of the antibiotics from bacterial cells. We have examined whether halogen-substituted benzoxaborole-based derivatives and their analogues possess antibacterial activity and are substrates for multi-drug-resistance efflux pumps. The antibacterial activity of 1,3-dihydro-3-hydroxy-1,1-dimethyl-1,2,3-benzosiloxaborole and 10 halogen-substituted its derivatives, as well as 1,2-phenylenediboronic acid and 3 synthesised fluoro-substituted its analogs, were evaluated. The activity against the reference strains of Gram-positive (n=5) and Gram-negative bacteria (n=10) was screened by the disc-diffusion test (0.4 mg of tested compounds was applied onto paper disc). The minimal inhibitory concentration values and the minimal bactericidal concentration values were estimated according to The Clinical and Laboratory Standards Institute and The European Committee on Antimicrobial Susceptibility Testing recommendations. During the minimal inhibitory concentration values determination with or without phenylalanine-arginine beta-naphthylamide (50 mg/L) efflux pump inhibitor, the concentrations of tested compounds ranged 0.39-400 mg/L in the broth medium supplemented with 1 mM magnesium sulfate. Generally, the studied benzosiloxaboroles and benzoxadiboroles showed a higher activity against Gram-positive cocci than against Gram-negative rods. Moreover, benzosiloxaboroles have the higher activity than benzoxadiboroles compounds. In this study, we demonstrated that substitution (mono-, di- or tetra-) of 1,3-dihydro-3-hydroxy-1,1-dimethyl-1,2,3-benzosiloxaborole with halogen groups resulted in an increase in antimicrobial activity as compared to the parent substance. Interestingly, the 6,7-dichloro-substituted parent substance was found to be the most potent against Gram-positive cocci: Staphylococcus sp. (minimal inhibitory concentration 6.25 mg/L) and Enterococcus sp. (minimal inhibitory concentration 25 mg/L). On the other hand, mono- and dichloro-substituted compounds were the most actively removed by efflux pumps present in Gram-negative bacteria mainly from Enterobacteriaceae family. In the presence of efflux pump inhibitor the minimal inhibitory concentration values of chloro-substituted benzosiloxaboroles decreased from 400 mg/L to 3.12 mg/L. Of note, the highest increase in bacterial susceptibility to tested compounds in the presence of phenylalanine-arginine beta-naphthylamide was observed for 6-chloro-, 6,7-dichloro- and 6,7-difluoro-substituted benzosiloxaboroles. In the case of Escherichia coli, Enterobacter cloacae and P. aeruginosa strains at least a 32-fold decrease in the minimal inhibitory concentration values of these agents were observed. These data demonstrate structure-activity relationships of the tested derivatives and highlight the need for further search for benzoxaboroles and related compounds with significant antimicrobial properties. Moreover, the influence of phenylalanine-arginine beta-naphthylamide on the susceptibility of Gram-negative rods to studied benzosiloxaboroles indicate that some tested agents are substrates for efflux pumps in Gram-negative rods.

Keywords: antibacterial activity, benzosiloxaboroles, efflux pumps, phenylalanine-arginine beta-naphthylamide

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Authors: Md. Fazlul Karim, Ashik Sharfaraz, Aysha Ferdoushi

Abstract:

Background: Computational medicinal chemistry approaches are used for designing and identifying new drug-like molecules, predicting properties and pharmacological activities, and optimizing lead compounds in drug development. SIRT7, a nicotinamide adenine dinucleotide (NAD+)-dependent deacylase which regulates aging, is an emerging target for cancer therapy with mounting evidence that SIRT7 downregulation plays important roles in reversing cancer phenotypes and suppressing tumor growth. Activation or altered expression of SIRT7 is associated with the progression and invasion of various cancers, including liver, breast, gastric, prostate, and non-small cell lung cancer. Objectives: The goal of this work was to identify potent and selective bioactive candidate inhibitors of SIRT7 by in silico screening of small molecule compounds obtained from Nigella sativa (N. sativa). Methods: SIRT7 structure was retrieved from The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), and its active site was identified using CASTp and metaPocket. Molecular docking simulation was performed with PyRx 0.8 virtual screening software. Drug-likeness properties were tested using SwissADME and pkCSM. In silico toxicity was evaluated by Osiris Property Explorer. Bioactivity was predicted by Molinspiration software. Antitumor activity was screened for Prediction of Activity Spectra for Substances (PASS) using Way2Drug web server. Molecular dynamics (MD) simulation was carried out by Desmond v3.6 package. Results: A total of 159 bioactive compounds from the N. Sativa were screened against the SIRT7 enzyme. Five bioactive compounds: chrysin (CID:5281607), pinocembrin (CID:68071), nigellidine (CID:136828302), nigellicine (CID:11402337), and epicatechin (CID:72276) were identified as potent SIRT7 anti-cancer candidates after docking score evaluation and applying Lipinski's Rule of Five. Finally, MD simulation identified Chrysin as the top SIRT7 anti-cancer candidate molecule. Conclusion: Chrysin, which shows a potential inhibitory effect against SIRT7, can act as a possible anti-cancer drug candidate. This inhibitor warrants further evaluation to check its pharmacokinetics and pharmacodynamics properties both in vitro and in vivo.

Keywords: SIRT7, antitumor, molecular docking, molecular dynamics simulation

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Authors: Manohar Salla, Mark S. Butler, Ruby Pelingon, Geraldine Kaeslin, Daniel E. Croker, Janet C. Reid, Jong Min Baek, Paul V. Bernhardt, Elizabeth M. J. Gillam, Matthew A. Cooper, Avril A. B. Robertson

Abstract:

MCC950 is a potent and selective inhibitor of the NOD-like receptor pyrin domain-containing protein 3 (NLRP3) inflammasome that shows early promise for treatment of inflammatory diseases. The identification of major metabolites of lead molecule is an important step during drug development process. It provides an information about the metabolically labile sites in the molecule and thereby helping medicinal chemists to design metabolically stable molecules. To identify major metabolites of MCC950, the compound was incubated with human liver microsomes and subsequent analysis by (+)- and (−)-QTOF-ESI-MS/MS revealed a major metabolite formed due to hydroxylation on 1,2,3,5,6,7-hexahydro-s-indacene moiety of MCC950. This major metabolite can lose two water molecules and three possible regioisomers were synthesized. Co-elution of major metabolite with each of the synthesized compounds using HPLC-ESI-SRM-MS/MS revealed the structure of the metabolite (±) N-((1-hydroxy-1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl)-4-(2-hydroxypropan-2-yl)furan-2-sulfonamide. Subsequent synthesis of individual enantiomers and coelution in HPLC-ESI-SRM-MS/MS using a chiral column revealed the metabolite was R-(+)- N-((1-hydroxy-1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl)-4-(2-hydroxypropan-2-yl)furan-2-sulfonamide. To study the possible cytochrome P450 enzyme(s) responsible for the formation of major metabolite, MCC950 was incubated with a panel of cytochrome P450 enzymes. The result indicated that CYP1A2, CYP2A6, CYP2B6, CYP2C9, CYP2C18, CYP2C19, CYP2J2 and CYP3A4 are most likely responsible for the formation of the major metabolite. The biological activity of the major metabolite and the other synthesized regioisomers was also investigated by screening for for NLRP3 inflammasome inhibitory activity and cytotoxicity. The major metabolite had 170-fold less inhibitory activity (IC50-1238 nM) than MCC950 (IC50-7.5 nM). Interestingly, one regioisomer had shown nanomolar inhibitory activity (IC50-232 nM). However, no evidence of cytotoxicity was observed with any of these synthesized compounds when tested in human embryonic kidney 293 cells (HEK293) and human liver hepatocellular carcinoma G2 cells (HepG2). These key findings give an insight into the SAR of the hexahydroindacene moiety of MCC950 and reveal a metabolic soft spot which could be blocked by chemical modification.

Keywords: Cytochrome P450, inflammasome, MCC950, metabolite, microsome, NLRP3

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Authors: Michio Kurosu

Abstract:

Alterations in glycosylation not only directly impact cell growth and survival but also facilitate tumor-induced immunomodulation and eventual metastasis. Identification of cell type-specific glycoconjugates (tumor markers) has led to the discovery of new assay systems for certain cancers via immunodetection reagents. N- and O-linked glycans are the most abundant forms of glycoproteins. Recent studies of cancer immunotherapy are based on the immunogenicity of truncated O-glycan chains (e.g., Tn, sTn, T, and sLea/x). The prevalence of N-linked glycan changes in the development of tumor cells is known; however, therapeutic antibodies against N-glycans have not yet been developed. This is due to the lack of specificity of N-linked glycans between normal/healthy and cancer cells. Abnormal branching of N-linked glycans has been observed, particularly in solid cancer cells. While the discovery of drug-like glycosyltransferase inhibitors that block the biosynthesis of specific branching has a very low likelihood of success, altered glycosylation levels can be exploited by suppressing N-glycan biosynthesis through the inhibition of dolichyl-phosphate N-acetylglucosaminephosphotransferase1 (DPAGT1) activity. Inhibition of DPAGT1 function leads to changes of O-glycosylation on proteins associated with mitochondria and zinc finger binding proteins (indirect effects). On the basis of dynamic crosstalk between DPAGT1 and Snail/Slung/ZEB1 (a family of transcription factors that promote the repression of the adhesion molecules), we have developed pharmacologically acceptable selective DPAGT1 inhibitors. Tunicamycin kills a wide range of cancer and healthy cells in a non-selective manner. In sharp contrast, our DPAGT1 inhibitors display strong cytostatic effects against 16 solid cancers, which require the overexpression of DPAGT1 in their progression but do not affect the cell viability of healthy cells. The identified DPAGT1 inhibitors possess impressive anti-metastatic ability in various solid cancer cell lines and induce their mitochondrial structural changes, resulting in apoptosis. A prototype DPAGT1 inhibitor, APPB has already been proven to shrink solid tumors (e.g., pancreatic cancers, triple-negative breast cancers) in vivo while suppressing metastases and has strong synergistic effects when combined with current cytotoxic drugs (e.g., paclitaxel). At this conference, our discovery of selective DPAGT1 inhibitors with drug-like properties and proof-of-pharmaceutical concept studies of a novel DPAGT1 inhibitor are presented.

Keywords: DPAGT1 inhibitors, anti-metastatic drugs, natural product based drug designs, cytostatic effects

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