Stereoisomers of oseltamivir – synthesis, in silico prediction and biological evaluation

2017 ◽  
Vol 15 (8) ◽  
pp. 1828-1841 ◽  
Author(s):  
Viktória Hajzer ◽  
Roman Fišera ◽  
Attila Latika ◽  
Július Durmis ◽  
Jakub Kollár ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
In Silico ◽  
Quantum Chemical ◽  
Biological Evaluation ◽  
In Silico Prediction ◽  
Antiviral Activities

Three diastereoisomers of oseltamivir were synthesized, their properties predicted by quantum-chemical calculations and their antiviral activities evaluated.

scholarly journals Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2

2021 ◽  
pp. 66-67
Author(s):  
P.V. Artyushenko ◽  
◽  
V.A. Mironov ◽  
D.I. Morozov ◽  
I.A. Shchugoreva ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Molecular Dynamic ◽  
Quantum Chemical Calculations ◽  
In Silico ◽  
Quantum Chemical ◽  
Computational Approach ◽  
Receptor Binding Domain ◽  
Dynamic Simulations ◽  
X Ray ◽  
X Ray Scattering

The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifi cations in order to increase the binding with the RBD. Th us, a new aptamer Apt25 was designed. Th e procedure of 1) aptamer structure modeling/modifi cation, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed several times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. Th e proposed computational approach to selection and refi nement of aptamers is universal and can be used for wide range of molecular ligands and targets

In silico study on the mechanism of formation of hydrazine and nitrogen in the reactions of excess hydroxylamine with 2,4-dinitrophenyl diethyl phosphate

2015 ◽  
Vol 39 (5) ◽  
pp. 3558-3563 ◽  
Author(s):  
Nellore Bhanu Chandar ◽  
Bishwajit Ganguly
Keyword(s):  
Quantum Chemical Calculations ◽  
In Silico ◽  
Quantum Chemical ◽  
Mechanism Of Formation ◽  
Nitrogen Gas ◽  
In Silico Study ◽  
Diethyl Phosphate

Decomposition study of 2,4-dinitrophenyl diethyl phosphate to hydrazine and nitrogen gas with excess of hydroxylamine using quantum chemical calculations.

scholarly journals Quantum chemical study on the in silico prediction of protein functions.

2003 ◽  
Vol 43 (supplement) ◽  
pp. S26
Author(s):  
K. Fukushima ◽  
Mituhito M. ◽  
Y. Inoue ◽  
M. Sakurai
Keyword(s):  
In Silico ◽  
Quantum Chemical ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
In Silico Prediction ◽  
Protein Functions

Discovery of a Difluoroglycine Synthesis Method through Quantum Chemical Calculations

2020 ◽  
Author(s):  
Tsuyoshi Mita ◽  
Yu Harabuchi ◽  
Satoshi Maeda
Keyword(s):  
Quantum Chemical Calculations ◽  
Experimental Verification ◽  
Quantum Chemical ◽  
Synthesis Method ◽  
Target Product ◽  
Systematic Exploration ◽  
Hands On ◽  
Retrosynthetic Analysis ◽  
Synthetic Routes ◽  
Verification Process

The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced ‘quantum chemistry aided retrosynthetic analysis’ (QCaRA), which uses quantum chemical calculations to search systematically for decomposition paths of the target product and propose a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the seemingly most promising path led to the discovery of a synthesis method for the difluoroglycine derivative. The extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.

Discovery of a Difluoroglycine Synthesis Method through Quantum Chemical Calculations

2020 ◽  
Author(s):  
Tsuyoshi Mita ◽  
Yu Harabuchi ◽  
Satoshi Maeda
Keyword(s):  
Quantum Chemical Calculations ◽  
Experimental Verification ◽  
Quantum Chemical ◽  
Synthesis Method ◽  
Target Product ◽  
Systematic Exploration ◽  
Hands On ◽  
Retrosynthetic Analysis ◽  
Synthetic Routes ◽  
Verification Process

The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced ‘quantum chemistry aided retrosynthetic analysis’ (QCaRA), which uses quantum chemical calculations to search systematically for decomposition paths of the target product and propose a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the seemingly most promising path led to the discovery of a synthesis method for the difluoroglycine derivative. The extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.

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