scholarly journals Exploring structure indenture for some Schiff bases as anti-Salmonella typhi drugs: A QSAR Approach

2016 ◽  
Vol 2 (2) ◽  
pp. 48
Author(s):  
Ameji John ◽  
Awe Emmanuel Femi ◽  
Adedirin Oluwaseye ◽  
Olusupo Sabitu
Keyword(s):  
Schiff Bases ◽  
Molecular Size ◽  
Salmonella Typhi ◽  
Qsar Analysis ◽  
Robust Model ◽  
3D Descriptors ◽  
2D And 3D ◽  
Size Descriptor ◽  
Insight Into ◽  
Dominant Influence

There are many drugs available in the market for treating typhoid infection, but the emergence of multi-drug resistant strain of Salmonella typhi (S.typhi) has necessitated the exploration and development of newer structural moiety of Schiff bases as anti-S. typhi agents owing to their enormous inhibitory activity against this bacterium. In this present study, a Genetic function approximation (GFA) QSAR analysis of some selected Schiff bases with anti-S. typhi activity was performed using OD,1D, 2D and 3D descriptors resulting in the generation of three statistically significant models from which an octa-parametric model was selected as the most robust model with R2 = 0.8589, R2adj = 0.8155, Q2 = 0.7437,R2 - Q2 = 0.1152, r2 r02 / r2 =0.00, r2 r02 / r2 = 0.0263, K = 1.0E-7, K = 0.1969. The optimization model hinted the dominant influence of the size descriptor ETA-Eta-B (Branching index EtaB relative to molecular size) on the observed anti-S.typhi activity of Schiff bases. It is envisaged that the QSAR results identified in this study will offer important structural insight into designing novel anti-S.typhi drugs from Schiff bases.

Novel TOPP descriptors in 3D-QSAR analysis of apoptosis inducing 4-aryl-4H-chromenes: Comparison versus other 2D- and 3D-descriptors

2007 ◽  
Vol 15 (19) ◽  
pp. 6450-6462 ◽  
Author(s):  
Simone Sciabola ◽  
Emanuele Carosati ◽  
Lourdes Cucurull-Sanchez ◽  
Massimo Baroni ◽  
Raimund Mannhold
Keyword(s):  
3D Qsar ◽  
Qsar Analysis ◽  
3D Descriptors ◽  
2D And 3D

scholarly journals Structure of Nanobody Nb23

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3567
Author(s):  
Mathias Percipalle ◽  
Yamanappa Hunashal ◽  
Jan Steyaert ◽  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Solution Structure ◽  
Chemical Shifts ◽  
Molecular Size ◽  
Side Chain ◽  
3D Nmr ◽  
Target Antigen ◽  
Internuclear Distances ◽  
2D And 3D

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.

Recent progress in the freeze-etching technique

1971 ◽  
Vol 261 (837) ◽  
pp. 121-131 ◽  
Keyword(s):  
High Vacuum ◽  
Molecular Size ◽  
Etching Technique ◽  
Structural Distortions ◽  
Shadow Casting ◽  
Structural Details ◽  
Freeze Etching ◽  
The One ◽  
Insight Into ◽  
Made In

The freeze-etching technique must be improved if structures at the molecular size level are to be seen. The limitations of the technique are discussed here together with the progress made in alleviating them. The vitrification of living specimens is limited by the fact that very high freezing rates are needed. The critical freezing rate can be lowered on the one hand by the introduction of antifreeze agents, on the other hand by the application of high hydrostatic pressure. The fracture process may cause structural distortions in the fracture face of the frozen specimen. The ‘double-replica’ method allows one to evaluate such artefacts and provides an insight into the way that membranes split. During etching there exists the danger of contaminating the fracture faces with condensable gases. Because of specimen temperatures below —110 °C, special care has to be taken in eliminating water vapour from the high vacuum. An improvement in coating freeze-etched specimens has resulted from the application of electron guns for evaporation of the highest melting-point metals. If heat transfer from gun to specimen is reduced to a minimum, Pt, Ir, Ta, W and C can be used for shadow casting. Best results are obtained with Pt-C and Ta-W . With the help of decoration effects Pt-C shadow castings give the most information about the fine structural details of the specimen.

An insight into synthetic Schiff bases revealing antiproliferative activities in vitro

2013 ◽  
Vol 21 (13) ◽  
pp. 3648-3666 ◽  
Author(s):  
Krzysztof Sztanke ◽  
Agata Maziarka ◽  
Anna Osinka ◽  
Małgorzata Sztanke
Keyword(s):  
Schiff Bases ◽  
Insight Into ◽  
Antiproliferative Activities

Quinoxalinones Based Aldose Reductase Inhibitors: 2D and 3D‐QSAR Analysis

2019 ◽  
Vol 38 (8-9) ◽  
pp. 1800149
Author(s):  
Vijay H. Masand ◽  
Nahed N. Elsayed ◽  
Sumersingh D. Thakur ◽  
Nandkishor Gawhale ◽  
Mithilesh M. Rathore
Keyword(s):  
Aldose Reductase ◽  
3D Qsar ◽  
Qsar Analysis ◽  
Aldose Reductase Inhibitors ◽  
Reductase Inhibitors ◽  
2D And 3D

scholarly journals 2D AND 3D-QSAR ANALYSIS OF AMINO (3-((3, 5-DIFLUORO-4-METHYL-6-PHENOXYPYRIDINE-2-YL) OXY) PHENYL) METHANIMINIUM DERIVATIVES AS FACTOR XA INHIBITOR

2019 ◽  
pp. 104-114
Author(s):  
Smita Suhane ◽  
A. G. Nerkar ◽  
Kumud Modi ◽  
Sanjay D. Sawant
Keyword(s):  
Factor Xa ◽  
3D Qsar ◽  
Qsar Model ◽  
Regression Method ◽  
Field Analysis ◽  
Factor Xa Inhibitors ◽  
Nearest Neighbour ◽  
Qsar Analysis ◽  
Qsar Models ◽  
2D And 3D

Objective: The main objective of the present study was to evolve a novel pharmacophore of methaniminium derivatives as factor Xa inhibitors by developing best 2D and 3D QSAR models. The models were developed for amino (3-((3, 5-difluoro-4-methyl-6-phenoxypyridine-2-yl) oxy) phenyl) methaniminium derivatives as factor Xa inhibitors. Methods: With the help of Marvin application, 2D structures of thirty compounds of methaniminium derivatives were drawn and consequently converted to 3D structures. 2D QSAR using multiple linear regression (MLR) analysis and PLS regression method was performed with the help of molecular design suite VLife MDS 4.3.3. 3D QSAR analysis was carried out using k-Nearest Neighbour Molecular Field Analysis (k-NN-MFA). Results: The most significant 2D models of methaniminium derivatives calculated squared correlation coefficient value 0.8002 using multiple linear regression (MLR) analysis. Partial Least Square (PLS) regression method was also employed. The results of both the methods were compared. In 2D QSAR model, T_C_O_5, T_2_O_2, s log p, T_2_O_1 and T_2_O_6 descriptors were found significant. The best 3D QSAR model with k-Nearest Neighbour Molecular Field Analysis have predicted q2 value 0.8790, q2_se value 0.0794, pred r2 value 0.9340 and pred_r2 se value 0.0540. The stepwise regression method was employed for anticipating the inhibitory activity of this class of compound. The 3D model demonstrated that hydrophobic, electrostatic and steric descriptors exhibit a crucial role in determining the inhibitory activity of this class of compounds. Conclusion: The developed 2D and 3D QSAR models have shown good r2 and q2 values of 0.8002 and 0.8790 respectively. There is high agreement in inhibitory properties of experimental and predicted values, which suggests that derived QSAR models have good predicting properties. The contour plots of 3D QSAR (k-NN-MFA) method furnish additional information on the relationship between the structure of the compound and their inhibitory activities which can be employed to construct newer potent factor Xa inhibitors.

Sign in / Sign up

Export Citation Format

Share Document