scholarly journals Theoretical Evaluation of Potential Anti-Alanine Dehydrogenase Activities of Acetamide Derivatives

2021 ◽  
Vol 12 (6) ◽  
pp. 7469-7477
Keyword(s):  
Quantum Chemical ◽  
Causes Of Death ◽  
The Other ◽  
Log P ◽  
Theoretical Evaluation ◽  
Ability To Act ◽  
Docking Method ◽  
Molecular Compounds ◽  
Better Than ◽  
Molecular Docking Method

Tuberculosis is an airborne communicable syndrome, which has been observed to be among the top ten (10) causes of death worldwide. This work studied eleven molecular compounds via quantum chemical calculations, molecular docking method, and ADMET (absorption, distribution, metabolism, excretion, and toxicity). The selected obtained descriptors (Log P, HBA, HBD, and molecular weight) showed that the studied compounds have the ability to act drug-like. Compound D inhibited far better than the other studied ligands as well as the standard. ADMET properties of compound D proved that the predicted ADMET level was closer to the ADMET properties of the referenced drug (Isoniazid).

scholarly journals In-Silico Investigation on Chloroquine Derivatives: A Potential Anti-COVID-19 Main Protease

2021 ◽  
Vol 12 (6) ◽  
pp. 8492-8501
Keyword(s):  
Molecular Weight ◽  
Molecular Docking ◽  
Quantum Chemical ◽  
The Other ◽  
Log P ◽  
Ability To Act ◽  
Main Protease ◽  
The Common ◽  
Molecular Compounds ◽  
Better Than

SARS-CoV-2 (Covid 19) continues to be a great threat to lives globally as it causes illnesses such as the common cold, severe acute respiratory syndrome and spreads easily among people. In this work, thirteen molecular compounds were studied via quantum chemical calculations, molecular docking, and dynamic simulation, and ADMET (absorption, distribution, metabolism, excretion, and toxicity). The obtained descriptors (Log P, HBA, HBD, and molecular weight) showed that the studied compounds have the ability to act as a drug. Thus, it was detected that all the studied selected compounds possess a better tendency to inhibit main coronavirus protease; however, compound C1 has a higher tendency to inhibit main coronavirus protease than the other compounds, including the standard (Chloroquine). ADMET properties of compound C1 proved that the predicted ADMET level was better than the ADMET properties of the referenced drug.

scholarly journals Discovery of alliin as a putative inhibitor of the main protease of SARS-CoV-2 by molecular docking

BioTechniques ◽  
2020 ◽  
Vol 69 (2) ◽  
pp. 108-112 ◽  
Author(s):  
Bijun Cheng ◽  
Tianjiao Li
Keyword(s):  
Molecular Docking ◽  
Pharmaceutical Compounds ◽  
The Novel ◽  
Important Target ◽  
Main Protease ◽  
Docking Method ◽  
Life Threatening ◽  
Novel Coronavirus ◽  
Better Than ◽  
Molecular Docking Method

The outbreak of viral pneumonia caused by the novel coronavirus SARS-CoV-2 that began in December 2019 caused high mortality. It has been suggested that the main protease (Mpro) of SARS-CoV-2 may be an important target to discover pharmaceutical compounds for the therapy of this life-threatening disease. Remdesivir, ritonavir and chloroquine have all been reported to play a role in suppressing SARS-CoV-2. Here, we applied a molecular docking method to study the binding stability of these drugs with SARS-CoV-2 Mpro. It appeared that the ligand–protein binding stability of the alliin and SARS-CoV-2 Mpro complex was better than others. The results suggested that alliin may serve as a good candidate as an inhibitor of SARS-CoV-2 Mpro. Therefore, the present research may provide some meaningful guidance for the prevention and treatment of SARS-CoV-2.

scholarly journals Trigonella foenum-graecum Derived Phytochemicals against Cough

2020 ◽  
pp. 96-99
Author(s):  
Bidyashree Tripathy ◽  
Elina Sahoo ◽  
Sunil Jha ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Plant Extract ◽  
The Other ◽  
Discovery Studio ◽  
Trigonella Foenum Graecum ◽  
Other Hand ◽  
Docking Method ◽  
Molecular Docking Method

Phytochemicals from Trigonella foenum-graecum plant extract are traditionally used to cure Cough. There are many reasons for cough. It has been reported that cough can be caused as a result of Bordetella sp. infection. The objective of the study is to identify the phytochemical of Trigonella foenum-graecum capable of curing Cough.  Molecular docking method applied using “Biovia Discovery Studio”. The research clearly indicates that choline, arginine, and gentianine cannot effectively deactivate the enzyme histidinekinase of the microbe. On the other hand, carpaine and diosgenin failed to deactivate the enzyme. Thus, none of these phytochemicals can effectively deactivate the histidinekinase enzyme of Bordetella sp. and thus cannot be used to treat cough caused by this particular microbe.

Closing the GAP—A 5Å Scanning Microscope

1969 ◽  
Vol 27 ◽  
pp. 6-7
Author(s):  
A. V. Crewe
Keyword(s):  
Normal Form ◽  
The Other ◽  
Resolving Power ◽  
Scanning Microscope ◽  
Conventional Microscope ◽  
Other Hand ◽  
Closing The Gap ◽  
Thermal Sources ◽  
Better Than ◽  
Transmission Microscope

We have become accustomed to differentiating between the scanning microscope and the conventional transmission microscope according to the resolving power which the two instruments offer. The conventional microscope is capable of a point resolution of a few angstroms and line resolutions of periodic objects of about 1Å. On the other hand, the scanning microscope, in its normal form, is not ordinarily capable of a point resolution better than 100Å. Upon examining reasons for the 100Å limitation, it becomes clear that this is based more on tradition than reason, and in particular, it is a condition imposed upon the microscope by adherence to thermal sources of electrons.

MUNDANE MIRACLES IN AWADH. ENCOUNTERS WITH THE REVEALED AND THE HIDDEN

2020 ◽  
pp. 130-140
Author(s):  
Maxim B. Demchenko ◽  
Keyword(s):  
The Other ◽  
Local People ◽  
Natural Phenomena ◽  
Mughal Empire ◽  
The Public ◽  
British Raj ◽  
The Subject ◽  
Other World ◽  
Better Than

The sphere of the unknown, supernatural and miraculous is one of the most popular subjects for everyday discussions in Ayodhya – the last of the provinces of the Mughal Empire, which entered the British Raj in 1859, and in the distant past – the space of many legendary and mythological events. Mostly they concern encounters with inhabitants of the “other world” – spirits, ghosts, jinns as well as miraculous healings following magic rituals or meetings with the so-called saints of different religions (Hindu sadhus, Sufi dervishes),with incomprehensible and frightening natural phenomena. According to the author’s observations ideas of the unknown in Avadh are codified and structured in Avadh better than in other parts of India. Local people can clearly define if they witness a bhut or a jinn and whether the disease is caused by some witchcraft or other reasons. Perhaps that is due to the presence in the holy town of a persistent tradition of katha, the public presentation of plots from the Ramayana epic in both the narrative and poetic as well as performative forms. But are the events and phenomena in question a miracle for the Avadhvasis, residents of Ayodhya and its environs, or are they so commonplace that they do not surprise or fascinate? That exactly is the subject of the essay, written on the basis of materials collected by the author in Ayodhya during the period of 2010 – 2019. The author would like to express his appreciation to Mr. Alok Sharma (Faizabad) for his advice and cooperation.

Temperature Effects during Endodormancy Induction on Subsequent Anthesis and Growth of Peach Trees

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 452c-452 ◽  
Author(s):  
Schuyler D. Seeley ◽  
Raymundo Rojas-Martinez ◽  
James Frisby
Keyword(s):  
Temperature Effects ◽  
Shoot Length ◽  
The Other ◽  
Nighttime Temperatures ◽  
Peach Trees ◽  
Better Than

Mature peach trees in pots were treated with nighttime temperatures of –3, 6, 12, and 18 °C for 16 h and a daytime temperature of 20 °C for 8 h until the leaves abscised in the colder treatments. The trees were then chilled at 6 °C for 40 to 70 days. Trees were removed from chilling at 40, 50, 60, and 70 days and placed in a 20 °C greenhouse under increasing daylength, spring conditions. Anthesis was faster and shoot length increased with longer chilling treatments. Trees exposed to –3 °C pretreatment flowered and grew best with 40 days of chilling. However, they did not flower faster or grow better than the other treatments with longer chilling times. There was no difference in flowering or growth between the 6 and 12 °C pretreatments. The 18 °C pretreatment resulted in slower flowering and very little growth after 40 and 50 days of chilling, but growth was comparable to other treatments after 70 days of chilling.

Nglyc: A Random Forest Method for Prediction of N-Glycosylation Sites in Eukaryotic Protein Sequence

2020 ◽  
Vol 27 (3) ◽  
pp. 178-186 ◽  
Author(s):  
Ganesan Pugalenthi ◽  
Varadharaju Nithya ◽  
Kuo-Chen Chou ◽  
Govindaraju Archunan
Keyword(s):  
Random Forest ◽  
Protein Sequence ◽  
Glycosylation Site ◽  
Computational Method ◽  
The Other ◽  
Eukaryotic Protein ◽  
Random Forest Method ◽  
Glycosylation Sites ◽  
Human And Mouse ◽  
Better Than

Background: N-Glycosylation is one of the most important post-translational mechanisms in eukaryotes. N-glycosylation predominantly occurs in N-X-[S/T] sequon where X is any amino acid other than proline. However, not all N-X-[S/T] sequons in proteins are glycosylated. Therefore, accurate prediction of N-glycosylation sites is essential to understand Nglycosylation mechanism. Objective: In this article, our motivation is to develop a computational method to predict Nglycosylation sites in eukaryotic protein sequences. Methods: In this article, we report a random forest method, Nglyc, to predict N-glycosylation site from protein sequence, using 315 sequence features. The method was trained using a dataset of 600 N-glycosylation sites and 600 non-glycosylation sites and tested on the dataset containing 295 Nglycosylation sites and 253 non-glycosylation sites. Nglyc prediction was compared with NetNGlyc, EnsembleGly and GPP methods. Further, the performance of Nglyc was evaluated using human and mouse N-glycosylation sites. Results: Nglyc method achieved an overall training accuracy of 0.8033 with all 315 features. Performance comparison with NetNGlyc, EnsembleGly and GPP methods shows that Nglyc performs better than the other methods with high sensitivity and specificity rate. Conclusion: Our method achieved an overall accuracy of 0.8248 with 0.8305 sensitivity and 0.8182 specificity. Comparison study shows that our method performs better than the other methods. Applicability and success of our method was further evaluated using human and mouse N-glycosylation sites. Nglyc method is freely available at https://github.com/bioinformaticsML/ Ngly.

pLoc_bal-mEuk: Predict Subcellular Localization of Eukaryotic Proteins by General PseAAC and Quasi-balancing Training Dataset

2019 ◽  
Vol 15 (5) ◽  
pp. 472-485 ◽  
Author(s):  
Kuo-Chen Chou ◽  
Xiang Cheng ◽  
Xuan Xiao
Keyword(s):  
Drug Development ◽  
Subcellular Localization ◽  
Basic Research ◽  
The Other ◽  
Training Dataset ◽  
Sequence Information ◽  
Eukaryotic Proteins ◽  
Validation Tests ◽  
User Friendly ◽  
Better Than

<P>Background/Objective: Information of protein subcellular localization is crucially important for both basic research and drug development. With the explosive growth of protein sequences discovered in the post-genomic age, it is highly demanded to develop powerful bioinformatics tools for timely and effectively identifying their subcellular localization purely based on the sequence information alone. Recently, a predictor called “pLoc-mEuk” was developed for identifying the subcellular localization of eukaryotic proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with multi-label systems where many proteins, called “multiplex proteins”, may simultaneously occur in two or more subcellular locations. Although it is indeed a very powerful predictor, more efforts are definitely needed to further improve it. This is because pLoc-mEuk was trained by an extremely skewed dataset where some subset was about 200 times the size of the other subsets. Accordingly, it cannot avoid the biased consequence caused by such an uneven training dataset. </P><P> Methods: To alleviate such bias, we have developed a new predictor called pLoc_bal-mEuk by quasi-balancing the training dataset. Cross-validation tests on exactly the same experimentconfirmed dataset have indicated that the proposed new predictor is remarkably superior to pLocmEuk, the existing state-of-the-art predictor in identifying the subcellular localization of eukaryotic proteins. It has not escaped our notice that the quasi-balancing treatment can also be used to deal with many other biological systems. </P><P> Results: To maximize the convenience for most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc_bal-mEuk/. </P><P> Conclusion: It is anticipated that the pLoc_bal-Euk predictor holds very high potential to become a useful high throughput tool in identifying the subcellular localization of eukaryotic proteins, particularly for finding multi-target drugs that is currently a very hot trend trend in drug development.</P>

scholarly journals Chance or Necessity—The Fungi Co−Occurring with Formica polyctena Ants

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 204
Author(s):  
Igor Siedlecki ◽  
Michał Gorczak ◽  
Alicja Okrasińska ◽  
Marta Wrzosek
Keyword(s):  
Molecular Identification ◽  
High Frequency ◽  
Its Rdna ◽  
The Other ◽  
Formica Polyctena ◽  
Ant Nests ◽  
Mutualistic Fungi ◽  
The Tropics ◽  
High Diversity ◽  
Better Than

Studies on carton nesting ants and domatia−dwelling ants have shown that ant–fungi interactions may be much more common and widespread than previously thought. Until now, studies focused predominantly on parasitic and mutualistic fungi–ant interactions occurring mostly in the tropics, neglecting less−obvious interactions involving the fungi common in ants’ surroundings in temperate climates. In our study, we characterized the mycobiota of the surroundings of Formica polyctena ants by identifying nearly 600 fungal colonies that were isolated externally from the bodies of F. polyctena workers. The ants were collected from mounds found in northern and central Poland. Isolated fungi were assigned to 20 genera via molecular identification (ITS rDNA barcoding). Among these, Penicillium strains were the most frequent, belonging to eight different taxonomic sections. Other common and widespread members of Eurotiales, such as Aspergillus spp., were isolated very rarely. In our study, we managed to characterize the genera of fungi commonly present on F. polyctena workers. Our results suggest that Penicillium, Trichoderma, Mucor, Schwanniomyces and Entomortierella are commonly present in F. polyctena surroundings. Additionally, the high diversity and high frequency of Penicillium colonies isolated from ants in this study suggest that representatives of this genus may be adapted to survive in ant nests environment better than the other fungal groups, or that they are preferentially sustained by the insects in nests.

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