scholarly journals DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics

2020 ◽  
Vol 49 (D1) ◽  
pp. D288-D297 ◽  
Author(s):  
Malak Pirtskhalava ◽  
Anthony A Amstrong ◽  
Maia Grigolava ◽  
Mindia Chubinidze ◽  
Evgenia Alimbarashvili ◽  
...  
Keyword(s):  
De Novo ◽  
Biological Activities ◽  
Antimicrobial Properties ◽  
Md Simulations ◽  
Data Bank ◽  
Amino Acid Sequences ◽  
Production Costs ◽  
Web Browser ◽  
Initial Release ◽  
High Production

Abstract The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures, bioactivities and toxicities of peptides that possess antimicrobial properties. DBAASP is updated continuously, and at present, version 3.0 (DBAASP v3) contains >15 700 entries (8000 more than the previous version), including >14 500 monomers and nearly 400 homo- and hetero-multimers. Of the monomeric antimicrobial peptides (AMPs), >12 000 are synthetic, about 2700 are ribosomally synthesized, and about 170 are non-ribosomally synthesized. Approximately 3/4 of the entries were added after the initial release of the database in 2014 reflecting the recent sharp increase in interest in AMPs. Despite the increased interest, adoption of peptide antimicrobials in clinical practice is still limited as a consequence of several factors including side effects, problems with bioavailability and high production costs. To assist in developing and optimizing de novo peptides with desired biological activities, DBAASP offers several tools including a sophisticated multifactor analysis of relevant physicochemical properties. Furthermore, DBAASP has implemented a structure modelling pipeline that automates the setup, execution and upload of molecular dynamics (MD) simulations of database peptides. At present, >3200 peptides have been populated with MD trajectories and related analyses that are both viewable within the web browser and available for download. More than 400 DBAASP entries also have links to experimentally determined structures in the Protein Data Bank. DBAASP v3 is freely accessible at http://dbaasp.org.

scholarly journals Homology Modeling and Structural Dynamics of the Glucose Oxidase

2019 ◽  
Vol 20 (1) ◽  
pp. 43
Author(s):  
Farhan Azhwin Maulana ◽  
Laksmi Ambarsari ◽  
Setyanto Tri Wahyudi
Keyword(s):  
Homology Modeling ◽  
Glucose Oxidase ◽  
Md Simulations ◽  
Data Bank ◽  
Positive Control ◽  
Glucose Biosensor ◽  
Amino Acid Sequences ◽  
Enzyme Thermostability ◽  
Modeled Structure ◽  
Reliable Model

Glucose oxidase from Aspergillus niger IPBCC.08.610 (GOD_IPBCC) is a locally sourced flavoenzyme from Indonesia that can potentially be developed in a variety of industrial processes. Although this enzyme has a high activity in catalyzing the redox reactions, the use of this enzyme was still limited to be applied as glucose biosensor. Using information from the amino acid sequences, a computational structure of GOD_IPBCC was therefore designed by homology modeling method using two homologous structures of GOD from protein data bank (1CF3 and 5NIT) as the templates. The quality of the resulting structures was evaluated geometrically for selection of the best model, and subsequently, 50 ns of MD simulations were carried out for the selected model as well as the corresponding template. Results obtained from the validation analysis showed that the 1CF3 template-built structure was selected as the best reliable model. The structural comparison exhibited that the best-modeled structure consisted of two functional domains and three catalytic residues similarly to the corresponding experimental structure. The overall dynamic behavior of the 50 ns of the structure was structurally stable and comparable with that of the positive control both from globally and locally observations. Implications of these stable nature within the best-modeled structure unfold the possibilities in search of notable residues and their roles to enhance enzyme thermostability.

scholarly journals Single amino acid bionanozyme for environmental remediation

2020 ◽  
Author(s):  
Pandeeswar Makam ◽  
Sharma Yamijala ◽  
Linda Shimon ◽  
Bryan Wong ◽  
Ehud Gazit
Keyword(s):  
Amino Acid ◽  
Environmental Remediation ◽  
De Novo ◽  
Cost Effective ◽  
Production Costs ◽  
Single Amino Acid ◽  
Great Promise ◽  
Highly Active ◽  
High Production ◽  
Laccase Enzyme

Abstract Enzymes are extremely complex catalytic structures with immense biological and technological importance. Nevertheless, their widespread environmental implementation faces several challenges, including high production costs, low operational stability, and intricate recovery and reusability. Therefore, the de novo design of minimalistic biomolecular nanomaterials that can efficiently mimic the biocatalytic function (bionanozyme) and overcome the limitations of natural enzymes is a key goal in biomolecular engineering. Here, we report an exceptionally simple yet highly active and robust single amino acid bionanozyme that can catalyze the rapid oxidation of environmentally toxic phenolic contaminates and serves as an ultrasensitive tool to detect biologically important neurotransmitters, similar to the laccase enzyme. While inspired by the laccase catalytic site, the substantially simpler copper-coordinated bionanozyme is ∼5400-fold more cost-effective, 10-fold more efficient, and 36-fold more sensitive compared to the natural protein. Furthermore, the designed mimic is stable under extreme conditions (pH, ionic strength, temperature, storage time), markedly reusable for several cycles and display broad substrate specificity. These findings hold great promise in the development of efficient bionanozyme for analytical chemistry, environmental protection, and biotechnology.

AN ECONOMICAL STUDY TO MEASUREMENT OF MARKETING EFFICIENCY IN CALF FATTENING FIELDS IN NINEVEH GOVERNORATE(2018)

2020 ◽  
Vol 51 (4) ◽  
Author(s):  
Abdullah & Al-Taye
Keyword(s):  
Commodity Prices ◽  
Red Meat ◽  
Production Costs ◽  
Meat Production ◽  
Marketing Efficiency ◽  
Basic Source ◽  
Essential Nutrient ◽  
High Production ◽  
Marketing Costs ◽  
Marketing Margins

This study was aimed at assessing marketing efficiency in the main sites of meat production of calf fattening fields in the private sector due to the importance of meat, especially red meat, which has essential nutrient for human body growth and high commodity prices depending on the measurement indicators used to suit the nature of the research conducted in calves fattening production fields in Gogjali region- Nineveh  (2018). The basic source data of the study is obtained from sources on the ongoing ground- marketing questionnaire of three levels, the producer, the wholesaler, the retailer and two fields groups of caste random sample. The first group included (100) fields with imported calves class. The second included (51) fields with local calves class. Whereas, according to the production and marketing costs indicator, the average of marketing efficiency (ME1 ) of marketed meat in both groups of claves fattening fields amounted (92.47, 93.39%) respectively for a kilogram which is a sign of high production costs and, according to the marketing margins indicator, the average of marketing efficiency (ME2 ) of marketed meat in both groups of claves fattening fields amounted (86.89,79.13 %) for per kg which is a sign of high marketing margins. Thus the study concluded a high value of marketing efficiency using the first scale with the fattening period time for both groups while marketing efficiency by using the second scale was characterized by the gradual decline in the imported fattening fields and a gradual rise in the local fattening fields.  The study recommends supporting production inputs (fodder, treatment), unifying markets and limiting the    importation of red meat importation  in order to obtain a good production and currency policy by which the production costs could be reduced to the minimum .

Recent Advances of In-Silico Modeling of Potent Antagonists for the Adenosine Receptors

2019 ◽  
Vol 25 (7) ◽  
pp. 750-773 ◽  
Author(s):  
Pabitra Narayan Samanta ◽  
Supratik Kar ◽  
Jerzy Leszczynski
Keyword(s):  
Drug Targets ◽  
Biological Activities ◽  
Scoring Function ◽  
Md Simulations ◽  
Energy Calculation ◽  
Binding Modes ◽  
Macromolecular Systems ◽  
In Silico Modeling ◽  
Mathematical Algorithms ◽  
The Impact

The rapid advancement of computer architectures and development of mathematical algorithms offer a unique opportunity to leverage the simulation of macromolecular systems at physiologically relevant timescales. Herein, we discuss the impact of diverse structure-based and ligand-based molecular modeling techniques in designing potent and selective antagonists against each adenosine receptor (AR) subtype that constitutes multitude of drug targets. The efficiency and robustness of high-throughput empirical scoring function-based approaches for hit discovery and lead optimization in the AR family are assessed with the help of illustrative examples that have led to nanomolar to sub-micromolar inhibition activities. Recent progress in computer-aided drug discovery through homology modeling, quantitative structure-activity relation, pharmacophore models, and molecular docking coupled with more accurate free energy calculation methods are reported and critically analyzed within the framework of structure-based virtual screening of AR antagonists. Later, the potency and applicability of integrated molecular dynamics (MD) methods are addressed in the context of diligent inspection of intricated AR-antagonist binding processes. MD simulations are exposed to be competent for studying the role of the membrane as well as the receptor flexibility toward the precise evaluation of the biological activities of antagonistbound AR complexes such as ligand binding modes, inhibition affinity, and associated thermodynamic and kinetic parameters.

Preparation, spectral properties and biological activities of 5-bromo-6-methyl-2'-deoxyuridine and 5-iodo-6-methyl-2'-deoxyuridine

1980 ◽  
Vol 45 (8) ◽  
pp. 2364-2370 ◽  
Author(s):  
Antonín Holý ◽  
Erik De Clercq
Keyword(s):  
Antiviral Activity ◽  
Spectral Properties ◽  
De Novo ◽  
Biological Activities ◽  
Rabbit Kidney ◽  
Kidney Cells ◽  
Cd Spectra ◽  
Methyl Derivatives ◽  
Primary Rabbit

Reaction of 3',5'-di-O-benzoyl-6-methyl-2'-deoxyuridine (IIa) with elementary bromine or iodine afforded 5-halogeno derivatives IIc and IId which on methanolysis gave 5-bromo-6-methyl-2'-deoxyurine (Ic) and 5-iodo-6-methyl-2'-deoxyurine (Id), respectively. The CD spectra of Ic, Id and 6-methyl-2'-deoxyuridine (Ia) are compared and discussed with regard to determination of the nucleoside conformation. Unlike 5-bromo- and 5-iodo-2'-deoxyuridine, the 6-methyl derivatives Ic and Id exhibit neither antibacterial nor antiviral activity. Nor do they exert any antimetabolic effect on the de novo DNA synthesis in primary rabbit kidney cells.

Platelet-activating factor and the kidney

1986 ◽  
Vol 251 (1) ◽  
pp. F1-F11 ◽  
Author(s):  
D. Schlondorff ◽  
R. Neuwirth
Keyword(s):  
De Novo ◽  
Mesangial Cells ◽  
Biological Activities ◽  
Platelet Activating Factor ◽  
Calcium Ionophore ◽  
Initial Step ◽  
Renal Physiology ◽  
Dependent Manner ◽  
Glomerular Mesangial Cells ◽  
Isolated Kidney

Platelet-activating factor (PAF) represents a group of phospholipids with the basic structure of 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine. A number of different cells are capable of producing PAF in response to various stimuli. The initial step of PAF formation is activation of phospholipase A2 in a calcium-dependent manner, yielding lyso-PAF. During this step arachidonic acid is also released and can be converted to its respective cyclooxygenase and lipoxygenase products. The lyso-PAF generated is then acetylated in position 2 of the glycerol backbone by a coenzyme A (CoA)-dependent acetyltransferase. An additional pathway may exist whereby PAF is generated de novo from 1-alkyl-2-acetyl-sn-glycerol by phosphocholine transferase. PAF inactivation in cells and blood is by specific acetylhydrolases. PAF exhibits a variety of biological activities including platelet and leukocyte aggregation and activation, increased vascular permeability, respiratory distress, decreased cardiac output, and hypotension. In the kidney PAF can produce decreases in blood flow, glomerular filtration, and fluid and electrolyte excretion. Intrarenal artery injection of PAF may also result in glomerular accumulation of platelets and leukocytes and mild proteinuria. PAF increases prostaglandin formation in the isolated kidney and in cultured glomerular mesangial cells. PAF also causes contraction of mesangial cells. Upon stimulation with calcium ionophore the isolated kidney, isolated glomeruli and medullary cells, and cultured mesangial cells are capable of producing PAF. The potential role for PAF in renal physiology and pathophysiology requires further investigation that may be complicated by 1) the multiple interactions of PAF, prostaglandins, and leukotrienes and 2) the autocoid nature of PAF, which may restrict its action to its site of generation.

scholarly journals Economic and Sustainability of Biodiesel Production—A Systematic Literature Review

2021 ◽  
Vol 3 (1) ◽  
pp. 19-36
Author(s):  
Tamás Mizik ◽  
Gábor Gyarmati
Keyword(s):  
Literature Review ◽  
Systematic Literature Review ◽  
Volatile Fatty Acids ◽  
First Generation ◽  
Production Costs ◽  
Raw Material ◽  
Biodiesel Production ◽  
Important Research Topic ◽  
The Social ◽  
High Production

As Earth’s fossil energy resources are limited, there is a growing need for renewable resources such as biodiesel. That is the reason why the social, economic and environmental impacts of biofuels became an important research topic in the last decade. Depleted stocks of crude oil and the significant level of environmental pollution encourage researchers and professionals to seek and find solutions. The study aims to analyze the economic and sustainability issues of biodiesel production by a systematic literature review. During this process, 53 relevant studies were analyzed out of 13,069 identified articles. Every study agrees that there are several concerns about the first-generation technology; however, further generations cannot be price-competitive at this moment due to the immature technology and high production costs. However, there are promising alternatives, such as wastewater-based microalgae with up to 70% oil content, fat, oils and grease (FOG), when production cost is below 799 USD/gallon, and municipal solid waste-volatile fatty acids technology, where the raw material is free. Proper management of the co-products (mainly glycerol) is essential, especially at the currently low petroleum prices (0.29 USD/L), which can only be handled by the biorefineries. Sustainability is sometimes translated as cost efficiency, but the complex interpretation is becoming more common. Common elements of sustainability are environmental and social, as well as economic, issues.

scholarly journals Antimicrobial Efficiency of Aloe arborescens and Aloe barbadensis Natural and Commercial Products

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 92
Author(s):  
Kaja Kupnik ◽  
Mateja Primožič ◽  
Željko Knez ◽  
Maja Leitgeb
Keyword(s):  
Biological Activities ◽  
Antimicrobial Properties ◽  
Aloe Barbadensis ◽  
Commercial Products ◽  
Qualitative And Quantitative ◽  
Gram Positive Bacteria ◽  
Antimicrobial Efficiency ◽  
Aloe Arborescens ◽  
Pharmaceutical Industries

Nowadays, there are many commercial products from natural resources on the market, but they still have many additives to increase their biological activities. On the other hand, there is particular interest in natural sources that would have antimicrobial properties themselves and would inhibit the growth and the reproduction of opportunistic microorganisms. Therefore, a comparative antimicrobial study of natural samples of aloe and its commercial products was performed. Qualitative and quantitative determination of antimicrobial efficiency of Aloe arborescens and Aloe barbadensis and its commercial products on fungi, Gram-negative, and Gram-positive bacteria was performed. Samples exhibited antimicrobial activity and slowed down the growth of all tested microorganisms. Research has shown that natural juices and gels of A. arborescens and A. barbadensis are at higher added concentrations comparable to commercial aloe products, especially against microbial cultures of Bacillus cereus, Candida albicans, and Pseudomonas aeruginosa, whose growths were completely inhibited at a microbial concentration of 600 μg/mL. Of particular importance are the findings of the good antimicrobial efficacy of fresh juice and gel of A. arborescens on tested microorganisms, which is less known and less researched. These results show great potential of A. arborescens for further use in medicine, cosmetics, food, and pharmaceutical industries.

scholarly journals Bioreactor Operating Strategies for Improved Polyhydroxyalkanoate (PHA) Productivity

Polymers ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1197 ◽  
Author(s):  
Warren Blunt ◽  
David Levin ◽  
Nazim Cicek
Keyword(s):  
Production Costs ◽  
Scale Production ◽  
Fed Batch ◽  
Continuous Bioreactor ◽  
Carbon Substrates ◽  
Pure Cultures ◽  
High Production ◽  
Operating Strategies ◽  
Major Factors ◽  
Industrial Scale Production

Microbial polyhydroxyalkanoates (PHAs) are promising biodegradable polymers that may alleviate some of the environmental burden of petroleum-derived polymers. The requirements for carbon substrates and energy for bioreactor operations are major factors contributing to the high production costs and environmental impact of PHAs. Improving the process productivity is an important aspect of cost reduction, which has been attempted using a variety of fed-batch, continuous, and semi-continuous bioreactor systems, with variable results. The purpose of this review is to summarize the bioreactor operations targeting high PHA productivity using pure cultures. The highest volumetric PHA productivity was reported more than 20 years ago for poly(3-hydroxybutryate) (PHB) production from sucrose (5.1 g L−1 h−1). In the time since, similar results have not been achieved on a scale of more than 100 L. More recently, a number fed-batch and semi-continuous (cyclic) bioreactor operation strategies have reported reasonably high productivities (1 g L−1 h−1 to 2 g L−1 h−1) under more realistic conditions for pilot or industrial-scale production, including the utilization of lower-cost waste carbon substrates and atmospheric air as the aeration medium, as well as cultivation under non-sterile conditions. Little development has occurred in the area of fully continuously fed bioreactor systems over the last eight years.

scholarly journals Natural Compound Modulates the Cervical Cancer Microenvironment—A Pharmacophore Guided Molecular Modelling Approaches

2018 ◽  
Vol 7 (12) ◽  
pp. 551 ◽  
Author(s):  
Shailima Rampogu ◽  
Doneti Ravinder ◽  
Smita Pawar ◽  
Keun Lee
Keyword(s):  
Cervical Cancer ◽  
Md Simulations ◽  
Data Bank ◽  
Docking Studies ◽  
New Drugs ◽  
Binding Modes ◽  
Cervical Cancer Cells ◽  
Causative Agents ◽  
Nitric Oxide Synthase 2 ◽  
Oxide Synthase

Cervical cancer is regarded as one of the major burdens noticed in women next to breast cancer. Although, human papilloma viruses (HPVs) are regarded as the principal causative agents, they require certain other factors such as oestrogen hormone to induce cervical cancer. Aromatase is an enzyme that converts androgens into oestrogens and hindering this enzyme could subsequently hamper the formation of oestrogen thereby alleviating the disease. Accordingly, in the current investigation, a structure based pharmacophore was generated considering two proteins bearing the Protein Data Bank (PDB) codes 3EQM (pharm 1) and 3S7S (pharm 2), respectively. The two models were employed as the 3D query to screen the in-house built natural compounds database. The obtained 51 compounds were escalated to molecular docking studies to decipher on the binding affinities and to predict the quintessential binding modes which were affirmed by molecular dynamics (MD) simulations. The compound has induced dose-dependent down regulation of PP2B, Nitric oxide synthase-2 (NOS2), and Interleukin 6 (IL-6) genes in the HeLa cells and has modulated the expression of apoptotic genes such as Bax, Bcl2, and caspases-3 at different concentrations. These results guide us to comprehend that the identified aromatase inhibitor was effective against the cervical cancer cells and additionally could server as scaffolds in designing new drugs.

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