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Home > Screening of Natural Product Libraries to Identify the Novel Tnf- a Inhibitors by Employing in Silico Methods

Screening of Natural Product Libraries to Identify the Novel Tnf- a Inhibitors by Employing in Silico Methods

Thesis Info

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Author

Zaka, Mehreen

Program

PhD

Institute

Quaid-I-Azam University

City

Islamabad

Province

Islamabad.

Country

Pakistan

Thesis Completing Year

2020

Thesis Completion Status

Completed

Subject

Biotechnology

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/14424/1/Mehreen%20Zaka%20biotechnology%202020%20qau%20isb%20prr.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676727141351

Similar


Rheumatoid arthritis (RA) is a chronic, polyarticular and symmetric disease that affects around 2.5 million people in the United States of America (USA). The disease seems to have a special predilection for small proximal joints, although virtually all of the peripheral joints in our body may be involved. Rheumatoid arthritis strikes women usually in childbearing age, 3 times more than men. Its main manifestation is inflammation in the joints, but many extra-articular organ systems can be affected. Due to the chronic systemic nature of the disease, the quality of life of patients decreases significantly. Until now, no single therapeutic agent has been found that is universally effective for rheumatoid arthritis, so it has become a rule to apply a combination drug regimen. Recently, several new agents have been introduced with unique mechanisms of action and have been found to produce different degrees of clinical benefit. Among these agents are folate and purine antagonists, alkylating agents and antipyridamines. The much safer treatment for RA would be herbal drugs. We explored the anti-inflammatory natural products through computer-aided drug design by applying virtual screening and molecular docking techniques. In literature, there are many reports about the role of metals in Ayurveda and herbal medicines. We synthesized the metal nanoparticles from Cannabis sativa by the green synthesis approach. Cannabis sativa is an important plant from the family Cannabaceae and has important anti-inflammatory compounds in it to treat the RA. The main idea of this research is to explore all possible means to treat the RA by using medicinal plants. In the first experiment an extensive literature review was done on medicinal plants and three important medicinal plants (Cannabis sativa, Prunella vulgaris and Withania somnifera) were chosen for further studies. These plants possess antiinflammatory, anti-arthritic and anti-rheumatic properties. Virtual screening was done by using different plants related databases to explore the anti-inflammatory compounds. Later, the 13 chosen compounds were characterized and filtered out from medicinal plant species and analyzed for RA by targeting Tumor necrosis factor-α (TNF-α) through in silico analyses. Ligand-based pharmacophore was generated by using the selected compounds and the pharmacophore was used to screen the natural products libraries and we retrieved twenty unique molecules that displayed utmost binding affinity, least binding energies, and effective drug properties. The docking analyses revealed that Ala-22, Glu-23, Ser-65, Gln-67, Tyr-141, Leu-142, Asp-143, Phe-144 and Ala-145 were critical interacting residues for receptor-ligand interactions. It is proposed that the RA patients should use reported compounds for the prescription of RA by targeting TNF-α. This report is opening new dimensions for designing innovative therapeutic targets to cure RA. In the second experiment, the research was further expanded, and we targeted the TNF-α protein, an important receptor protein involved in the RA pathway. TNF-α is a multifunctional cytokine that acts as a central biological mediator for critical immune functions, including inflammation, infection, and antitumor responses. The biologics used to treat RA causes serious side effects such as triggering an autoimmune anti-antibody response or the weakening of the body’s immune defenses. Consequently, there is a dire need to find alternative small-molecule based therapies for TNF-α inhibition. In literature, the small molecules are reported which can inhibit the TNF-α, indirectly. In this study, we found the direct inhibitors of TNF-α by applying the combined in silico approaches. High throughput structure-based and ligand-based virtual screening methods are applied to identify TNF-α inhibitors from 3 different small molecule databases (~256.000 molecules from Otava drug-like green chemical collection, ~500.000 molecules from Otava Tangible database, ~2.500.000 Enamine small molecule database) and ~240.000 molecules from ZINC natural products libraries. Moreover, therapeutic activity prediction, as well as pharmacokinetic and toxicity profiles are also investigated using the MetaCore/MetaDrug platform which is based on a manually curated database of molecular interactions, molecular pathways, gene-disease associations, chemical metabolism, and toxicity information, uses binary QSAR models. Molecular Dynamics (MD) simulations were also performed for selected hits to investigate their detailed structural and dynamical analysis beyond docking studies. As a result, at least one hit from each database was identified as novel TNF-α inhibitors after the comprehensive virtual screening, multiple docking, e- Pharmacophore modeling (structure-based pharmacophore modeling), MD simulations, and MetaCore/MetaDrug analysis. Identified hits show predicted the promising anti-arthritic activity and no toxicity. In the third experiment, a novel method is applied to develop energetically optimized, structure-based pharmacophore models for rapid in silico drug screening. Fragment-based docking results were used in the construction of universal e-pharmacophore model development. As target protein, both homodimer and homotrimer forms of TNF-α were considered. The developed pharmacophore was used to screen the small-molecule library Specs-screening compounds (Specs- SC) which includes more than 200.000 drug-like molecules. In another approach, binary QSAR-based models were used to screen Specs-SC, as well as Specs-natural products (NP) which have around 750 compounds, and a library of drugs registered or approved for use in humans NIH''s NCGC pharmaceutical collection (NPC) which has around 7500 molecules. The MetaCore/MetaDrug platform was used for binary QSAR models for therapeutic activity prediction as well as pharmacokinetic and toxicity profile predictions of screening molecules. This platform is constructed based on a manually curated database of molecular interactions, molecular pathways, gene-disease associations, chemical metabolism, and toxicity information. Molecular docking and molecular dynamics (MD) simulations were performed for the selected hit molecules. In the fourth experiment, green synthesis of gold (Au), silver (Ag) and bimetallic alloy Au–Ag nanoparticles (NPs) from aqueous solutions using Cannabis sativa as reducing and stabilizing agent has been presented. The UV-visible spectroscopy was performed for the confirmation of NPs synthesis. Fourier transform-infrared (FTIR) spectroscopy was utilized to identify the possible biomolecules responsible for the reduction and stabilization of the NPs. The composition of elements in the NPs was confirmed by energy-dispersive X-ray spectroscopy analysis. The size and morphology of the synthesized metallic and bimetallic NPs were investigated using X-ray diffraction and scanning electron microscopy. Biological applicability of biosynthesized NPs was tested against five bacterial strains namely Klebsiella pneumonia, Bacillus subtilis (B. subtilis), Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa (P. aeruginosa) and Leishmania major promastigotes. The results showed considerable antibacterial and anti-leishmanial activity. The Au–Ag bimetallic NPs showed improved antibacterial activity against B. subtilis and P. aeruginosa as compared to Au and Ag alone, while maximum anti-leishmanial activity was observed at 250 μg ml−1 NP concentration. These results suggest that biosynthesized NPs can be used as a potent antibiotic and antileishmanial agents. So, these nanoparticles are safer to use as drug delivery vehicles in RA and may also be effective to reduce inflammation.
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القراءة الحداثية للسنة النبوية عرض ونقد لأطروحة محمد شحرور

تعدّ إشكالية تجديد الفكر الاسلامي أحد المواضيع الخلافية بين النخب الاسلامية المعاصرة لتجاوز تبعات الفجوة الحضارية بين العالم الاسلامي والعالم الغربي. وقد تعددت مناهج نقد التراث الاسلامي بين تياراتٍ ارتأى أصحابها استلهام التجربة النقدية الغربية وبين تياراتٍ أخرى اختارت التجديد من داخل المنظومة التراثية. وتهدف هذه المقالة إلى محاولة فهم مشروع من المشاريع الحداثية المهمة التي برزت مطلع القرن الحادي والعشرين الميلادي، رافعة لواء تجديد الفكر الاسلامي من خلال إعادة قراءة الأصول الاسلامية وفهمها فهما معاصرا على ضوء الأرضية المعرفية الغربية. وقد أحدثت أطروحة الدكتور محمد شحرور في السنة النبوية رجت كبيرة في مجال الدراسات الفكرية المعاصرة، من حيث جدة الطرح وجمالية العرض التي أعادت من خلالهما تشكيل تصورنا لمنزلة السنة واختزال دورها في التشريع الاسلامي وبالتالي اختزال دورها في الحياة اليومية للمسلم المعاصر. اخترنا الوقوف مع هذه الأطروحة من حيث عرض وجهة نظر صاحبها وتتبعها تتبعا نقديا بتفكيك بنيتها الداخلية وأصولها الاستدلالية من جهة أولى(تحليل ونقد براديغم الكتاب والقرآن)، ومن جهة ثانية: سعينا إلى رصد مواطن الخلل والتناقض في نسيجها(ضعف الاستقراء التام للنص المؤسس). أما من حيث البنيةُ الخارجية فقد أوضحنا الجذور النقدية التي اعتمدها محمد شحرور في تفكيك السنة، ساعيا إلى استلهام التطبيقات الاسلامية المعاصرة المعمول بها في النقد الاستشراقي للتراث الاسلامي، مستعينا بجملة من مناهج النقد الغربية المادية كالفيلولوجيا والتاريخانية وغيرها. كما عملنا على بيان موقف علماء الاسلام مما كان محل نقد جذري في نظرية محمد شحرور، مؤكدين على أن المسلمين الأوائل كانوا على وعي متقدم بتلكم الإشكالات وقدموا فيها حلولا مبتكرة.

A Study of Polluted Eco-System of Industrial Areas Caused by the Industrial Effluents

The adverse effects of industrial pollution are becoming a challenge for scientists and environmentalists around the globe. The management of the pollution is imperative to improve the human health, economy, aquatic life and to protect from further deterioration of the environment. The leading intend of the present work was to evaluate trace elemental contaminations in agricultural soil, crops and vegetables being irrigated with industrial effluents and their treatment to reduce the pollution. This research will be beneficial to decrease the industrial pollution by the immobilization of the toxic constituents in the effluents and will provide database pertaining to the concentration of metals in the industrial effluents and their accumulation in soil, crops and vegetables. The data will assist to identify the trends, nature, and sources of pollution and will aid in the formulation of legislation related to the controlled release of industrial effluents into the environment. Moreover, present data for nutrition can be useful for nutritionists and food technologists for the formulation of diet menu for the inhabitants of the respective regions with adequacy/ safety viewpoint for balance intake of essential and toxic trace elements. For this research, more than 500 samples of vegetables (brinjal, baffle gourd, ridged gourd, tomato, pumpkin, bitter gourd, cabbage, mustard, spinach, potato, turnip, radish & carrot), crops (millet, maize, rice & wheat), effluents (ceramics, pulp/paper & textile/yarn industries) and soils (top & sub-surfaces) have been collected from the vicinity of industrial zones of Faisalabad and Gujranwala areas. Each species of vegetable and crop plants was separated into its fruits (edible portion), flowers, leaves, stems and roots to evaluate the bio-distribution of trace elements, in each portion. Neutron Activation Analysis (NAA) and Atomic Absorption Spectroscopic (AAS) techniques have been utilized to analyze the selected samples for the quantitative determination of more than 36 trace and toxic elements. Accuracy and precision have been ensured by comparing with five different certified reference materials (CRMs) and by making replicate measurements for each sample. Moreover, the Z-score method was also applied to assess the discrepancy between the measured and the certified values. Ultra-filtration membrane therapy (UFMT), which is a separation technique, was used for the reduction of toxic level in industrial effluents. Various runs have been conducted on samples of the effluents by using a lab-scale UFMT unit, which was fitted VIIwith a Polyethylene tere phthalate (PETP) membrane. This filtration technique is very effective, reliable and economical for the quantitative separation of suspended particles from the effluents. The effects of temperature and pressure on flow rates of the effluents have been investigated. The parameters such as flux, temperature, applied pressure, filtration velocity, density, concentration of the effluents and their relationships have been illustrated. Spectro-photometric analyses prove the effectiveness of UFMT system in removing dissolved coloured species and chromate ions also. The pollution parameters such as colour/ dyes, biochemical oxygen demand (BOD), total suspended solids (TSS), total dissolved solids (TDS), turbidity, oil/ grease/ fat etc., have been reduced quantitatively up to 96% in the post filtration effluents. Moreover, in the absence of other electrolytes, the chromate removal up to 98.9% from effluents has also been achieved. Arsenic, chromium and iron metals have also been successfully removed from the industrial effluents, on laboratory scale, by using husk of sweet peanut. In this regard, optimize experimental parameters have been established for smooth/reliable performance. The analytical results for the concentrations of 36 minor, major, rare earth and toxic elements in each sample of vegetables, cereal, soil and effluents are presented in tables 6.1 to 6.12. Moreover, the evaluated concentrations of some selected trace elements have been presented in figures 7.4 ¾ 7.41 for their comparison patterns with each other. The results of physico-chemical analysis and trace elemental concentrations showed that all untreated effluents were un-fit for irrigation purposes due to the higher values of metals as compared to the NEQS values. Effluents vary in quality for textile, pulp, and ceramics industries and are specific for each industry. The effluent contamination has been decreased in the following pattern. Textile/ Yarn > Pulp/ Paper > Ceramics Faisalabad industrial area was divided into four zones (i.e. F-1, F-2, F-3 & F-4). Zone F-1 represents the area of Industrial Estate, F-2 represents the area of Ghulam Muhammad abad, F-3 represents the area of Peoples Colony and F-4 represents the area of Sitara Colony. According to the high concentration of the elements, the intensity of toxicity in the specified soils of Faisalabad is decreased in the following order. F-1 > F-2 > F-3 > F-4 VIIISimilarly, Gujranwala industrial area was divided into four zones (i.e. G-1, G-2, G-3 & G-4). Zone G-1 represents the area of Dhula, G -2 represents the area of Garjakh, G -3 represents the area of Small Industrial Estate and G-4 represents the area of Muhammad Nagar. Moreover, due to the high concentration values of concerned elements, the intensity of the toxicity in the specified soils of Gujranwala shows the following decreasing sequence. G-4 < G-3 < G-2 < G-1 Leaching tendency of some selected trace elements was observed for Faisalabad and Gujranwala soils. The elements (i.e. Ba, Cr, As, Na, Cl, K, Br & Mg) move from topsoil (S t ) to sub-soil (S s ) very easily as compared to other elements (i.e. Mn, Sb, Sc, Co, Se, Fe & Zn) due to high leaching tendency. The same behaviour was observed in both soils of Faisalabad and Gujranwala. Therefore, the quantities of the elements (i.e Ba, Cr, As, Na, Cl, K, Br & Mg) are higher in sub-soils as compared to the topsoil. This behavior was also confirmed by the evidence of observed high electrical conductivity (EC) values (5.6-4.3 mS cm -1 ) at sub-soil as compared to topsoil (4.1-3.1 mS cm -1 ) values. According to the concentrations of the trace elements, the industrial (Gujranwala & Faisalabad) and non-industrial (Rawalpindi & Islamabad) national soils are arranged in the following descending series. Gujranwala > Faisalabad > Rawalpindi > Islamabad A comparison was made among the national soils (i.e. Faisalabad & Gujranwala) and international soils (i.e. Norway & India). All soils samples were analyzed using NAA technique. According to the high concentrations of the trace elements, generally all zones are arranged in the following sequence. Gujranwala > Faisalabad > Norway > India Vegetables are staple part of food and are widely consumed in all over the world. The determination of metal contents in vegetables is significant from the viewpoint of crop-yield technology, food nutrition and health impacts. The differences for the accumulation of mineral/ metal contents in the edible portions of vegetables depend upon the soil compositions and the rate of uptake of minerals/ metals by each plant. Results showed that different vegetables had different abilities to take up heavy metals. IXHowever, the general trend shows that the maximum concentration of the trace elements is accumulated in roots while their least concentration is found in fruits i.e. edible part of the vegetables and are arranged in the following decrasing sequence. Roots > Stems > Leave > Fruits (Edible portion of vegetables/ crops) All over the world, about 70% of human diet consists of cereals and legumes. In case of edible portion of cereals the toxic activity decreases in the following sequence, which indicates that wheat crop is the least affected by the industrial effluents as compared to other cereal crops. Millet > Maize > Rice > Wheat It was observed that the concentrations of all elements are high in the wheat of Faisalabad and low in the wheat of Kashmir. The order of toxicity decreases as following: Faisalabad > Gujranwala > Islamabad > Kashmir The concentrations for majority of elements are high in the rice of Faisalabad and low in Kashmir. The order of toxicity decreases in the following sequence. Faisalabad > Islamabad > Gujranwala > Kashmir Similarly, the concentrations for majority of elements are high in the vegetables of Faisalabad and low in Islamabad. The order of toxicity decreases as under: Faisalabad > Gujranwala > Kashmir > Islamabad Regular monitoring for further assessment as to ascertain the quality of the foodstuffs and the origin of trace metal distribution is a pre-requisite. In order to obtain consolidate achievements numerous analyses of various species are required where seasonal and regional variations need to be studied in detail." xml:lang="en_US