scholarly journals Structure-based virtual screening of bioherbicide candidates for weeds in sugarcane plantation using in silico approaches

2020 ◽  
Vol 88 (2) ◽  
Author(s):  
Galuh Wening PERMATASARI ◽  
Riza Arief PUTRANTO ◽  
Happy WIDIASTUTI
Keyword(s):  
Biological Activity ◽  
Binding Affinity ◽  
Potential Candidate ◽  
Activity Prediction ◽  
Important Species ◽  
Discovery Studio ◽  
Negative Effect ◽  
Amino Acid Interaction ◽  
And Control ◽  
Affinity Score

Weeds in sugarcane have negatively affected the sugar yield rate. Several approaches have been carried out to overcome the weeds, including the usage of diuron as synthetic herbicide. However, the long-term usage of diuron is known to have a negative effect leads to the production of 3,4- Dichloroaniline responsible for soil leach and bioaccumulation. Therefore, this study aimed to find a potential natural herbicide. By mimicking the diuron's mode of action which inhibits the process of photosynthesis through blocking the Photosystem II protein D1 (psbA) of the weeds, fourteen compounds as potential candidate bioherbicides were virtually docked by PyRx v0.9.5 software to the specific site. Three important species of the weeds were chosen including Eleusine indica, Praxelis clematidea, and Momordica charantia. The binding affinity score was further calculated and ranked to screen the top six compounds as bioherbicide candidates. Interaction of each complex and the biological activity prediction were then performed by Discovery Studio software and PASS server, respectively. Aurachin P, Aurachin A, and Cyanobacterin were placed in the top ranked compounds with high binding affinity score around -6 to -9 kcal mol-1 toward the psbA. The amino acid interaction involved in the complex shows 50-90% similar to the control, psbA and diuron complex. Besides, the biological activity prediction of Aurachin P, Aurachin A, and Cyanobacterin exhibits the terms related to the inhibition of photosynthesis process via enzymatic pathway. Thus, the active compounds might have inhibition action in the photosynthesis process and control  the weeds in sugarcane.

Binding affinity and biological activity of gonadotropin-releasing hormone analogs in the African catfish, Clarias gariepinus

Aquaculture ◽  
1988 ◽  
Vol 71 (1-2) ◽  
pp. 119-131 ◽  
Author(s):  
R. De Leeuw ◽  
C. Van 't Veer ◽  
W. Smit-Van Dijk ◽  
H.J.Th. Goos ◽  
P.G.W.J. Van Oordt
Keyword(s):  
Biological Activity ◽  
Binding Affinity ◽  
Clarias Gariepinus ◽  
Gonadotropin Releasing Hormone ◽  
African Catfish ◽  
Releasing Hormone ◽  
Hormone Analogs

scholarly journals Remix’s retreat? Content moderation, copyright law and mashup music

2021 ◽  
pp. 146144482110260
Author(s):  
Ragnhild Brøvig-Hanssen ◽  
Ellis Jones
Keyword(s):  
Online Survey ◽  
Copyright Infringement ◽  
Copyright Law ◽  
Online Media ◽  
Economic Power ◽  
Grey Zone ◽  
Negative Effect ◽  
State Of Affairs ◽  
Political Economic ◽  
And Control

Many online media platforms currently utilise algorithmically driven content moderation to prevent copyright infringement. This article explores content moderation’s effect on mashup music – a form of remix which relies primarily on the unauthorised combining of pre-existing, recognisable recordings. Drawing on interviews ( n = 30) and an online survey ( n = 92) with mashup producers, we show that content moderation affects producers’ creative decisions and distribution strategies, and has a strong negative effect on their overall motivation to create mashups. The objections that producers hold to this state of affairs often strongly resonate with current copyright exceptions. However, we argue that these exceptions, which form a legal ‘grey zone’, are currently unsatisfactorily accommodated for by platforms. Platforms’ political-economic power allows them, in effect, to ‘occupy’ and control this zone. Consequently, the practical efficacy of copyright law’s exceptions in this setting is significantly reduced.

scholarly journals Automatic Promotion and Student Dropout: Evidence from Uganda, Using Propensity Score in Difference in Differences Model

2018 ◽  
Vol 7 (2) ◽  
pp. 191 ◽  
Author(s):  
Jeje Moses Okurut
Keyword(s):  
Propensity Score ◽  
Dropping Out ◽  
Probit Regression ◽  
Difference In Differences ◽  
Student Dropout ◽  
Analysis Technique ◽  
Analysis Strategy ◽  
Negative Effect ◽  
And Control ◽  
The Impact

The impact of automatic promotion practice on students dropping out of Uganda’s primary education was assessed using propensity score in difference in differences analysis technique. The analysis strategy was instrumental in addressing the selection bias problem, as well as biases arising from common trends over time, and permanent latent differences between the treated and control groups. Probit regression results indicate a negative effect on the probability of students dropping out, but only at P3. There seems to be no policy effect at P6. Decomposing the effect incidence along school location shows the policy as having had an effect only on P3 students studying in urban schools; otherwise, there is no effect among students at P3 rural, P6 rural or P6 Urban. In terms of the gender component, automatic promotion appears to have had an effect on P3 male and female students and no effect on either sex at P6.

scholarly journals DESIGN AND ANTICANCER ACTIVITY PREDICTION OF DIHYROPYRIMIDINONE BASED NOVEL INHIBITORS OF P53-MDM2 INTERACTION

2017 ◽  
Vol 10 (16) ◽  
pp. 110
Author(s):  
Surendra Kumar Nayak ◽  
Gopal Lal Khatik ◽  
Rakesh Narang ◽  
Harish Kumar Chopra
Keyword(s):  
Anticancer Activity ◽  
Binding Affinity ◽  
Anticancer Agents ◽  
P53 Protein ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Activity Prediction ◽  
Cycle Regulation ◽  
Mdm2 Inhibitor ◽  
Better Than

  Objective: P53 protein is well known for its role in cell cycle regulation and induction of apoptosis. This protein is degraded by MDM2 mediated proteolysis. Inhibition of interaction between p53 and MDM2 has been recognized as a most potential and selective target for development of novel anticancer agents. Recently, several molecules entered in the clinical trial study for the treatment of various types of cancers are based on inhibition of interaction between p53-MDM2. Therefore, in this study, a novel dihydropyridine based molecules were designed as p53-MDM2 inhibitor, and their anticancer activity (including reference) was determined in comparison with most active anticancer agent and inactive anticancer agents in National Cancer Institute database using “Cancer IN” server.Methods: In this work, a novel dihydropyrimidinone based lead (L11) on the basis of molecular docking study, predicted IC50, anticancer activity, and toxicity profile were designed. Lead L11 was obtained after sequential isosteric replacement of functional groups for optimization in compound L0.Results: The docking scores of L3-L11 found to be in range of 21-25 close to docking score 25 of SAR405838 and better than nutlin-3a. MDM2 binding affinity values (37-78 Kcal/mol) of all ligands were also found to better than that of nutlin-3a (37 Kcal/mol). Surprisingly, MDM2 binding affinity of L11 (78 Kcal/mol) found to be equal to that of SAR405838 and 2-fold greater than nutlin-3a.Conclusion: These data indicating that L11 as a potential lead from dihydropyrimidinones for inhibition of p53-MDM2 interaction.

scholarly journals Analysis and control of flow at suction connection in high-speed centrifugal pump

2017 ◽  
Vol 9 (1) ◽  
pp. 168781401668529 ◽  
Author(s):  
Wen-wu Song ◽  
Li-chao Wei ◽  
Jie Fu ◽  
Jian-wei Shi ◽  
Xiu-xin Yang ◽  
...  
Keyword(s):  
Flow Field ◽  
Centrifugal Pump ◽  
High Speed ◽  
Internal Flow ◽  
Orifice Plate ◽  
Centrifugal Pumps ◽  
Pressure Area ◽  
Negative Effect ◽  
And Control ◽  
Experimental Data Analysis

The backflow vortexes at the suction connection in high-speed centrifugal pumps have negative effect on the flow field. Setting an orifice plate in front of the inducer is able to decrease the negative effect caused by backflow vortexes. The traditional plate is able to partially control the backflow vortexes, but a small part of the vortex is still in the inlet and the inducer. Four new types of orifice plates were created, and the control effects on backflow vortexes were analyzed. The ANSYS-CFX software was used to numerically simulate a high-speed centrifugal pump. The variations of streamline and velocity vectors at the suction connection were analyzed. Meanwhile, the effects of these plates on the impeller pressure and the internal flow field of the inducer were analyzed. Numerically, simulation and experimental data analysis methods were used to compare the head and efficiency of the high-speed pumps. The results show that the C-type orifice plate can improve the backflow vortex, reduce the low-pressure area, and improve the hydraulic performance of the high-speed pump.

scholarly journals Molecular Docking Senyawa Gingerol dan Zingiberol pada Tanaman Jahe sebagai Penanganan COVID-19

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Belinda D. P. M. Ratu ◽  
Widdhi Bodhi ◽  
Fona Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Docking Method ◽  
Pubmed Database ◽  
Almost All ◽  
The Impact

Abstract: COVID-19 is a new disease. Many people feel the impact of this disease. There is no definite cure for COVID-19, so many people use traditional medicine to ward off COVID-19, including ginger. This study aims to determine whether there is an interaction between compounds in ginger (gingerol and zingiberol) and the COVID-19’s main protease (6LU7). This study uses a molecular docking method using 4 main applications, namely Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, and Open Babel GUI. The samples used were gingerol and zingiberol compounds in ginger plants downloaded from Pubchem. The data used in this study used Mendeley, Clinical Key, and PubMed database. The study showed that almost all of the amino acid residues in the gingerol compound acted on the 6LU7 active site, whereas the zingiberol did not. The results of the binding affinity of ginger compounds, both gingerol and zingiberol, do not exceed the binding affinity of remdesivir, a drug that is widely researched as a COVID-19 handling drug. In conclusion, gingerol and zingiberol compounds in ginger can’t be considered as COVID-19’s treatment.Keywords: molecular docking, gingerol, zingiberol Abstrak: COVID-19 merupakan sebuah penyakit yang baru. Banyak masyarakat yang merasakan dampak dari penyakit ini. Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat yang menggunakan pengobatan tradisional untuk menangkal COVID-19, termasuk jahe. Penelitian ini bertujuan untuk mengetahui apakah ada interaksi antara senyawa pada jahe (gingerol dan zingiberol) dengan main protease COVID-19 (6LU7). Penelitian ini menggunakan metode molecular docking dengan menggunakan 4 aplikasi utama, yaitu Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, dan Open Babel GUI. Sampel yang digunakan yaitu senyawa gingerol dan zingiberol pada tanaman jahe yang diunduh di Pubchem. Data yang digunakan dalam penelitian ini menggunakan database Mendeley, Clinical Key, dan PubMed. Penelitian menunjukkan bahwa hampir semua residu asam amino pada senyawa gingerol bekerja pada sisi aktif 6LU7, sedangkan tidak demikian pada zingiberol. Hasil binding affinity senyawa jahe, baik gingerol maupun zingiberol tidak  melebihi binding affinity remdesivir, obat yang banyak diteliti sebagai obat penanganan COVID-19. Sebagai simpulan, senyawa gingerol dan zingiberol pada tanaman jahe tidak dapat dipertimbangkan sebagai penanganan COVID-19Kata Kunci: molecular docking, gingerol, zingiberol

scholarly journals Insights into Cross-species Evolution of Novel Human Coronavirus 2019-nCoV and Defining Immune Determinants for Vaccine Development

2020 ◽  
Author(s):  
Arunachalam Ramaiah ◽  
Vaithilingaraja Arumugaswami
Keyword(s):  
Binding Affinity ◽  
Vaccine Development ◽  
Asia Pacific ◽  
Potential Candidate ◽  
T Cell Epitopes ◽  
Live Animal ◽  
Synonymous Mutations ◽  
Wide Range ◽  
Novel Coronavirus ◽  
N Proteins

ABSTRACTNovel Coronavirus (nCoV) outbreak in the city of Wuhan, China during December 2019, has now spread to various countries across the globe triggering a heightened containment effort. This human pathogen is a member of betacoronavirus genus carrying 30 kilobase of single positive-sense RNA genome. Understanding the evolution, zoonotic transmission, and source of this novel virus would help accelerating containment and prevention efforts. The present study reported detailed analysis of 2019-nCoV genome evolution and potential candidate peptides for vaccine development. This nCoV genotype might have been evolved from a bat-CoV by accumulating non-synonymous mutations, indels, and recombination events. Structural proteins Spike (S), and Membrane (M) had extensive mutational changes, whereas Envelope (E) and Nucleocapsid (N) proteins were very conserved suggesting differential selection pressures exerted on 2019-nCoV during evolution. Interestingly, 2019-nCoV Spike protein contains a 39 nucleotide sequence insertion relative to SARS-like bat-SL-CoVZC45/2017. Furthermore, we identified eight high binding affinity (HBA) CD4 T-cell epitopes in the S, E, M and N proteins, which can be commonly recognized by HLA-DR alleles of Asia and Asia-Pacific Region population. These immunodominant epitopes can be incorporated in universal subunit CoV vaccine. Diverse HLA types and variations in the epitope binding affinity may contribute to the wide range of immunopathological outcomes of circulating virus in humans. Our findings emphasize the requirement for continuous surveillance of CoV strains in live animal markets to better understand the viral adaptation to human host and to develop practical solutions to prevent the emergence of novel pathogenic CoV strains.

scholarly journals Pharmacophore Modelling-Based Drug Repurposing Approaches for SARS-CoV-2 Therapeutics

2021 ◽  
Vol 9 ◽  
Author(s):  
Shailima Rampogu ◽  
Keun Woo Lee
Keyword(s):  
Effective Treatment ◽  
Pharmacophore Model ◽  
Drug Repurposing ◽  
Binding Pocket ◽  
Binding Mode ◽  
Computational Method ◽  
Dynamics Simulation ◽  
Potential Candidate ◽  
Pharmacophore Modelling ◽  
Discovery Studio

The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating effect globally with no effective treatment. The swift strategy to find effective treatment against coronavirus disease 2019 (COVID-19) is to repurpose the approved drugs. In this pursuit, an exhaustive computational method has been used on the DrugBank compounds targeting nsp16/nsp10 complex (PDB code: 6W4H). A structure-based pharmacophore model was generated, and the selected model was escalated to screen DrugBank database, resulting in three compounds. These compounds were subjected to molecular docking studies at the protein-binding pocket employing the CDOCKER module available with the Discovery Studio v18. In order to discover potential candidate compounds, the co-crystallized compound S-adenosyl methionine (SAM) was used as the reference compound. Additionally, the compounds remdesivir and hydroxycholoroquine were employed for comparative docking. The results have shown that the three compounds have demonstrated a higher dock score than the reference compounds and were upgraded to molecular dynamics simulation (MDS) studies. The MDS results demonstrated that the three compounds, framycetin, kanamycin, and tobramycin, are promising candidate compounds. They have represented a stable binding mode at the targets binding pocket with an average protein backbone root mean square deviation below 0.3 nm. Additionally, they have prompted the hydrogen bonds during the entire simulations, inferring that the compounds have occupied the active site firmly. Taken together, our findings propose framycetin, kanamycin, and tobramycin as potent putative inhibitors for COVID-19 therapeutics.

scholarly journals Analysis of Financial Ratios for Predicting Bankruptcy in SMEs Listed on PEFINDO25

2020 ◽  
Vol 19 (2) ◽  
Author(s):  
Vitalia Fina Carla Rettobjaan
Keyword(s):  
Logistic Regression ◽  
Data Analysis ◽  
Activity Ratio ◽  
Significant Positive Effect ◽  
Debt Structure ◽  
Financial Ratio ◽  
Independent Variables ◽  
Negative Effect ◽  
And Control ◽  
Positive Effect

This study aims to analyze the Financial Ratio for Predicting Bankruptcy. The sample used in this study are SMEs according PEFINDO25 period 2013 to 2017. The independent variables in this study is liquidity, profitability, debt structure, solvency and activity ratio; and control variables is size and age, as well as the dependent variable is bankruptcy. The amount of sample in this study 32 companies PEFINDO25 by using purposive sampling. The method of data analysis is done by using logistic regression with SPSS version 23. The result of this research showed that liquidity, profitability and age has significant negative effect on bankruptcy. Debt structure has significant positive effect on bankruptcy. While solvency, activity ratio and size does not significantly effect on bankruptcy

scholarly journals Regulation of Escherichia coli RelA Requires Oligomerization of the C-Terminal Domain

2001 ◽  
Vol 183 (2) ◽  
pp. 570-579 ◽  
Author(s):  
Michal Gropp ◽  
Yael Strausz ◽  
Miriam Gross ◽  
Gad Glaser
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Catalytic Domain ◽  
Mutational Analysis ◽  
Amino Acid Starvation ◽  
E Coli ◽  
Terminal Domain ◽  
Negative Effect ◽  
And Control ◽  
Two Hybrid

ABSTRACT The E. coli RelA protein is a ribosome-dependent (p)ppGpp synthetase that is activated in response to amino acid starvation. RelA can be dissected both functionally and physically into two domains: The N-terminal domain (NTD) (amino acids [aa] 1 to 455) contains the catalytic domain of RelA, and the C-terminal domain (CTD) (aa 455 to 744) is involved in regulating RelA activity. We used mutational analysis to localize sites important for RelA activity and control in these two domains. We inserted two separate mutations into the NTD, which resulted in mutated RelA proteins that were impaired in their ability to synthesize (p)ppGpp. When we caused the CTD inrelA + cells to be overexpressed, (p)ppGpp accumulation during amino acid starvation was negatively affected. Mutational analysis showed that Cys-612, Asp-637, and Cys-638, found in a conserved amino acid sequence (aa 612 to 638), are essential for this negative effect of the CTD. When mutations corresponding to these residues were inserted into the full-length relA gene, the mutated RelA proteins were impaired in their regulation. In attempting to clarify the mechanism through which the CTD regulates RelA activity, we found no evidence for competition for ribosomal binding between the normal RelA and the overexpressed CTD. Results from CyaA complementation experiments of the bacterial two-hybrid system fusion plasmids (G. Karimova, J. Pidoux, A. Ullmann, and D. Ladant, Proc. Natl. Acad. Sci. USA 95:5752–5756, 1998) indicated that the CTD (aa 564 to 744) is involved in RelA-RelA interactions. Our findings support a model in which RelA activation is regulated by its oligomerization state.

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