Relationship between soybean yield/quality and soil quality in a major soybean-producing area based on a 2D-QSAR model

Epidermal growth factor receptor (EGFR) is an important target for cancer therapy. In this study, EGFR inhibitors were investigated to build a two-dimensional quantitative structure-activity relationship (2D-QSAR) model and a three-dimensional quantitative structure-activity relationship (3D-QSAR) model. In the 2D-QSAR model, the support vector machine (SVM) classifier combined with the feature selection method was applied to predict whether a compound was an EGFR inhibitor. As a result, the prediction accuracy of the 2D-QSAR model was 98.99% by using tenfold cross-validation test and 97.67% by using independent set test. Then, in the 3D-QSAR model, the model with q2=0.565 (cross-validated correlation coefficient) and r2=0.888 (non-cross-validated correlation coefficient) was built to predict the activity of EGFR inhibitors. The mean absolute error (MAE) of the training set and test set was 0.308 log units and 0.526 log units, respectively. In addition, molecular docking was also employed to investigate the interaction between EGFR inhibitors and EGFR.

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Comprehensive data on a 2D-QSAR model for Heme Oxygenase isoform 1 inhibitors

Data in Brief ◽

10.1016/j.dib.2017.09.036 ◽

2017 ◽

Vol 15 ◽

pp. 281-299 ◽

Cited By ~ 23

Author(s):

Emanuele Amata ◽

Agostino Marrazzo ◽

Maria Dichiara ◽

Maria N. Modica ◽

Loredana Salerno ◽

...

Keyword(s):

Heme Oxygenase ◽

Qsar Model ◽

2D Qsar ◽

Comprehensive Data

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Generation of 2D-QSAR Model for Angiogenin Inhibitors: A Ligand-Based Approach for Cancer Drug Design

Trends in Bioinformatics ◽

10.3923/tb.2016.1.13 ◽

2016 ◽

Vol 9 (1) ◽

pp. 1-13 ◽

Cited By ~ 1

Author(s):

Krishnan Sundar ◽

Joseph Christina Rosy ◽

Saminathan Balamurali ◽

John Asnet Mary ◽

Rajaiah Shenbagara

Keyword(s):

Drug Design ◽

Qsar Model ◽

Cancer Drug ◽

2D Qsar

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Structure Activity Design, Synthesis and Biological Activity of Newer Imidazole-Triazine Clubbed Derivative as Antimicrobial and Antitubercular Agents

Letters in Organic Chemistry ◽

10.2174/1570178618666210521150011 ◽

2021 ◽

Vol 18 ◽

Author(s):

Jaydeep A. Patel ◽

Navin B. Patel ◽

Pratik K. Maisuriya ◽

Monika R. Tiwari ◽

Amit C. Purohit

Keyword(s):

Thermodynamic Properties ◽

Pharmacological Activity ◽

Predictive Ability ◽

Antitubercular Activity ◽

Qsar Model ◽

Total Surface Area ◽

Lead Target ◽

Antitubercular Agents ◽

Qsar Study ◽

2D Qsar

Background: Imidazole and triazine derivatives act as antimicrobial and antitubercular agents. 2D-QSAR determination estimates the pharmacological activity on the basis of thermodynamic properties of the structure. Objective: The structural arrangements and thermodynamic properties of the imidazole derivatives are necessary for the enhancement of pharmacological activity. So imidazole-triazine clubbed derivatives were designed on the bases of molecular modeling 2D-QSAR study of antitubercular activity. Methods: PLSR method was applied for 2D-QSAR determination of the (Z)-5-ethylidene-3-(4-methoxy-6-methyl-1,3,5-triazin-2-yl)-2-phenyl-3,5-dihydro-4H-imidazol-4-one (B1-B10). The designed compounds were synthesized and spectrally evicted by IR, 1H NMR, 13C NMR, Mass spectra data as well as biologically screened opposite different antitubercular and antimicrobial species. Result: Compounds B4, B6, B7 were founds potent against different antimicrobial species. Compound B3 was more effective against M. tuberculosis H37Rv. Statistically significant QSAR model generated by PLSR methods shows external r2=0.9775 and internal q2=0.2798 predictive ability. Whereas, the model incorporates with three parameters PolarSurfaceAreaExcluding P and S, MomInertiaY and SsCH3count with their corresponding values for each molecule. Conclusion: 2D-QSAR study advised antitubercular activity directly proportional to total surface area of the polar atoms having molecules and moment of inertia on Y-axis. Whereas, inversely proportional to methyl group joined with single bond. The present study afforded favorable results which were further used to generate lead target molecules.

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Sulfonamide Based β-Carbonic Anhydrase Inhibitors: 2D QSAR Study

ISRN Medicinal Chemistry ◽

10.1155/2013/107840 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Meenakshi N. Deodhar ◽

Priyanka L. Khopade ◽

Mahesh G. Varat

Keyword(s):

Carbon Dioxide ◽

Inhibitory Activity ◽

Molecular Design ◽

Qsar Model ◽

Quantitative Structure Activity Relationship ◽

Carbonic Anhydrases ◽

Human Pathogens ◽

Qsar Study ◽

Physiological Concentration ◽

2D Qsar

The carbonic anhydrases (CAs) (or carbonate dehydratases) form a family of metalloenzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate and protons (or vice versa), a reversible reaction that occurs rather slowly in the absence of a catalyst. The β-CAs have been characterized in a high number of human pathogens, such as the fungi/yeasts Candida albicans, Candida glabrata, Cryptococcus neoformans, and Saccharomyces cerevisiae and the bacteria Helicobacter pylori, Mycobacterium tuberculosis, Haemophilus influenzae, Brucella suis, and Streptococcus pneumonia. The β-CAs in microorganisms provide physiological concentration of carbon dioxide and bicarbonate (CO2/HCO3-) for their growth. Inhibition of β-CAs from the pathogenic microorganism is recently being explored as a novel pharmacological target to treat infections caused by the these organisms. The present study aimed to establish a relationship between the β-CAs inhibitory activity for structurally related sulphonamide derivatives and the physicochemical descriptors in quantitative terms. The statistically validated two-dimensional quantitative structure activity relationship (2D QSAR) model was obtained through multiple linear regression (MLR) analysis method using Vlife molecular design suits (MDS). Five descriptors showing positive and negative correlation with the β-CAs inhibitory activity have been included in the model. This validated 2D QSAR model may be used to design sulfonamide derivatives with better inhibitory properties.

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Grass–legume intercropping in integrated crop-livestock systems: a strategy to improve soil quality and soybean yield in the Brazilian Cerrado

10.21203/rs.3.rs-831197/v1 ◽

2021 ◽

Author(s):

Juliana M. A. S. Moraes ◽

Luiz Gustavo de O. Denardin ◽

Gabriela C. Pires ◽

Evelyn C. Gonçalves ◽

Laércio S. Silva ◽

...

Keyword(s):

Microbial Biomass ◽

Enzymatic Activity ◽

Soil Quality ◽

Pigeon Pea ◽

Brazilian Cerrado ◽

Organic C ◽

Soybean Yield ◽

Soil Microbial ◽

C And N ◽

Livestock Systems

Abstract Aims The integrated crop-livestock systems (ICLS) under no-tillage improves soil fertility of the Brazilian Cerrado. We aimed to evaluate the effect of different grass-legume intercropping compared to single grass cultivation in the off-season of an ICLS on (i) soil organic carbon (C) and nitrogen (N) pools, (ii) soil microbial biomass and activity, (iii) soil enzymatic activity, and (iv) soybean grain yield in succession. Methods The field study was conducted in an on-farm experiment in 2016/17 and 2017/18 cropping seasons. The soybean was cultivated in the summer season, with the subsequent treatments in the off-season, using two grasses (Urochloa ruziziensis and U. brizantha), single or intercropped with Cowpea (Vigna unguiculata) or Pigeon pea (Cajanus cajan). We evaluated soil organic C and N pools, microbial biomass and activity, enzyme activity, and soybean yield. Results Cowpea intercropping yielded 24% more soybeans than grasses single cropped. There was a higher microbial biomass and activity, and enzymatic activity in the soil under grass-legume intercropping. In addition to the lower basal respiration and microbial metabolic quotient (qCO2), the greater microbial quotient (qMIC) and microbial biomass C indicate a higher soil microbial C utilization efficiency under grass-legume intercropping. The soil total organic C and N stocks increased under Pigeon pea intercropping by 16% and 27%, respectively, compared to single grasses. Conclusions Grass-legume intercropping in the pasture phase of ICLS is an additional tool to maximize soybean yields in the short term. The intercropping effects on soybean yield were directly related to soil quality improvements through soil biological and biochemical properties.

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Identifying the Structural Features of Diphenyl Ether Analogues for InhA Inhibition: A 2D and 3D QSAR Based Study

Letters in Drug Design & Discovery ◽

10.2174/1570180816666190611153933 ◽

2019 ◽

Vol 17 (1) ◽

pp. 31-47 ◽

Cited By ~ 2

Author(s):

Ashutosh Prasad Tiwari ◽

Varadaraj Bhat Giliyar ◽

Gurypur Gautham Shenoy ◽

Vandana Kalwaja Eshwara

Keyword(s):

Inhibitory Activity ◽

Diphenyl Ether ◽

3D Qsar ◽

Qsar Model ◽

Structural Features ◽

Mycolic Acids ◽

2D Qsar ◽

Qsar Models ◽

Mycobacterial Cell Wall ◽

2D And 3D

Background: Enoyl acyl carrier protein reductase (InhA) is a validated target for Mycobacterium. It is an enzyme which is associated with the biosynthesis of mycolic acids in type II fatty acid synthase system. Mycobacterial cell wall majorly comprises mycolic acids, which are responsible for virulence of the microorganism. Several diphenyl ether derivatives have been known to be direct inhibitors of InhA. Objective: In the present work, a Quantitative Structure Activity Relationship (QSAR) study was performed to identify the structural features of diphenyl ether analogues which contribute to InhA inhibitory activity in a favourable way. Method: Both 2D and 3D QSAR models were built and compared. Several fingerprint based 2D QSAR models were generated and their relationship with the structural features was studied. Models which corroborated the inhibitory activity of the molecules with their structural features were selected and studied in detail. Results: A 2D-QSAR model, with dendritic fingerprints having regression coefficient, for test set molecules Q2 =0.8132 and for the training set molecules, R2 =0.9607 was obtained. Additionally, an atom-based 3D-QSAR model with Q2 =0.7697 and R2 =0.9159 was also constructed. Conclusion: The data reported by various models provides guidance for the designing of structurally new diphenyl ether inhibitors with potential activity against InhA of M. tuberculosis.

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