Pub Date : 2023-01-01DOI: 10.33435/tcandtc.1270359
Elif Güney, K. Sayın
Cancer is one of the most important diseases threatening human health today, and gastric cancer is among the top five in terms of mortality rate. Synthesized eight isoxazole derivatives were investigated in this study as computationally. Structural properties of them were examined in detail and chemical/electronic properties of these compounds are investigated using contour plot of HOMO/LUMO and molecular electrostatic potential (MEP) map. Anticancer properties of these compounds are investigated using molecular docking calculations against H. Pylori and VEGFR2. Additionally, the pharmacokinetics and pharmacology properties are investigated using ADME and p450 analyses Finally, it was found that compound 5a is the best inhibitor candidate.
{"title":"Structural, Spectral, Antibacterial and Anticancer Investigations of Synthesized Isoxazole Derivatives","authors":"Elif Güney, K. Sayın","doi":"10.33435/tcandtc.1270359","DOIUrl":"https://doi.org/10.33435/tcandtc.1270359","url":null,"abstract":"Cancer is one of the most important diseases threatening human health today, and gastric cancer is among the top five in terms of mortality rate. Synthesized eight isoxazole derivatives were investigated in this study as computationally. Structural properties of them were examined in detail and chemical/electronic properties of these compounds are investigated using contour plot of HOMO/LUMO and molecular electrostatic potential (MEP) map. Anticancer properties of these compounds are investigated using molecular docking calculations against H. Pylori and VEGFR2. Additionally, the pharmacokinetics and pharmacology properties are investigated using ADME and p450 analyses Finally, it was found that compound 5a is the best inhibitor candidate.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88684253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.33435/tcandtc.1168638
I. Vakulin, E. Latypova, Rifkat Faatovi̇ch, Gumer Yusupovich Ishmuratov, G. R. Talipova
In this work we was study correlation between electronic structure of (R)-4-menthen-3-one and restricted transitions between its conformers. By NBO analysis, carried out in ab inition methods, we found special orbital interactions and sterical effects in conformers of (R)-4-menthen-3-one, which explained difficults of inversion and rotation.
本文研究了(R)-4- menn -3- 1的电子结构与其构象之间的限制跃迁之间的关系。通过初始化方法进行的NBO分析，我们发现(R)-4- menn -3- 1构象中存在特殊的轨道相互作用和立体效应，这解释了反转和旋转的困难。
{"title":"Influence of electronic structure of (R)-4-menten-3-one on its restricted rotation and inversion","authors":"I. Vakulin, E. Latypova, Rifkat Faatovi̇ch, Gumer Yusupovich Ishmuratov, G. R. Talipova","doi":"10.33435/tcandtc.1168638","DOIUrl":"https://doi.org/10.33435/tcandtc.1168638","url":null,"abstract":"In this work we was study correlation between electronic structure of (R)-4-menthen-3-one and restricted transitions between its conformers. By NBO analysis, carried out in ab inition methods, we found special orbital interactions and sterical effects in conformers of (R)-4-menthen-3-one, which explained difficults of inversion and rotation.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83283633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.33435/tcandtc.1196259
Akshay Ti̇wari̇
QSAR study has been carried out on the set of 35 Beta-blocker drugs for the modelling of toxicity (Ld50), using topological indices. The stepwise multilinear regression analysis method is used for modelling and the obtained models are critically discussed and examined by various types of cross validation parameters
{"title":"Mimic toxicity of Beta-blocker drugs by structural base descriptors","authors":"Akshay Ti̇wari̇","doi":"10.33435/tcandtc.1196259","DOIUrl":"https://doi.org/10.33435/tcandtc.1196259","url":null,"abstract":"QSAR study has been carried out on the set of 35 Beta-blocker drugs for the modelling of toxicity (Ld50), using topological indices. The stepwise multilinear regression analysis method is used for modelling and the obtained models are critically discussed and examined by various types of cross validation parameters","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76313625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.33435/tcandtc.1196422
E. Lanez, T. Lanez, N. Zegheb
Afzelin has been designed and tested for its in silico antibacterial activity against DNA gyrase complex of Staphyloccocus aureus. The results of the toxicity study indicate that afzelin displayed moderate antibacterial potential against staphylococcus aureus with LD50 = 5000 mg/Kg, which is almost four times and a half weaker than that obtained for the commercial antibiotic chloramphenicol. The afzelin and the commercial antibiotic chloramphenicol were subjected to docking studies to understand their interaction with DNA gyrase complex of Staphyloccocus aureus. Results indicated a good affinity of afzelin to the chosen target with the formation of four hydrogen bonds and binding energy of 29.82 KJ/mol. ADME study shows that afzelin is not inhibitors of CYP450 IA2, 2C19, 2C9, 2D6, 3A4 isoenzymes which suggests a decrease in their plasma concentrations and a rapid elimination route. Molecular dynamics simulations were performed for 10 ns for afzelin using the gromacs package to assess the conformational stability of protein-ligand complexes during the simulation.
{"title":"In silico ADMET, toxicological analysis, molecular docking studies and Molecular dynamics simulation of Afzelin with potential antibacterial effects against Staphylococcus aureus","authors":"E. Lanez, T. Lanez, N. Zegheb","doi":"10.33435/tcandtc.1196422","DOIUrl":"https://doi.org/10.33435/tcandtc.1196422","url":null,"abstract":"Afzelin has been designed and tested for its in silico antibacterial activity against DNA gyrase complex of Staphyloccocus aureus. The results of the toxicity study indicate that afzelin displayed moderate antibacterial potential against staphylococcus aureus with LD50 = 5000 mg/Kg, which is almost four times and a half weaker than that obtained for the commercial antibiotic chloramphenicol. The afzelin and the commercial antibiotic chloramphenicol were subjected to docking studies to understand their interaction with DNA gyrase complex of Staphyloccocus aureus. Results indicated a good affinity of afzelin to the chosen target with the formation of four hydrogen bonds and binding energy of 29.82 KJ/mol. ADME study shows that afzelin is not inhibitors of CYP450 IA2, 2C19, 2C9, 2D6, 3A4 isoenzymes which suggests a decrease in their plasma concentrations and a rapid elimination route. Molecular dynamics simulations were performed for 10 ns for afzelin using the gromacs package to assess the conformational stability of protein-ligand complexes during the simulation.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89656845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oleuropein is a natural product revealing a large variety of biological activity. The natural products are functionalized to increase the activity in the pharmaceutical industry. Theoretical calculations were carried out for oleuropein derivatives to display the target compound exhibiting the most biological effects. Hence, synthetic chemists are able to get inspired to synthesize the most active oleuropein derivatives. The chemical properties of oleuropein derivatives have been investigated theoretically. Gaussian method was used for quantum calculations of these compounds. The properties of compounds were presented and the utilization of these compounds in pharmaceutical industries was investigated. The quantum calculations revealed that 2H-oleuropein (3) and 4-aminobutyl-2-oleuropein (2) were unstable and were prone to react to the radical compounds.
{"title":"A theoretical study of oleuropein derivatives as drugs","authors":"Faik Gökalp, R. Erenler","doi":"10.33435/tcandtc.977727","DOIUrl":"https://doi.org/10.33435/tcandtc.977727","url":null,"abstract":"Oleuropein is a natural product revealing a large variety of biological activity. The natural products are functionalized to increase the activity in the pharmaceutical industry. Theoretical calculations were carried out for oleuropein derivatives to display the target compound exhibiting the most biological effects. Hence, synthetic chemists are able to get inspired to synthesize the most active oleuropein derivatives. The chemical properties of oleuropein derivatives have been investigated theoretically. Gaussian method was used for quantum calculations of these compounds. The properties of compounds were presented and the utilization of these compounds in pharmaceutical industries was investigated. The quantum calculations revealed that 2H-oleuropein (3) and 4-aminobutyl-2-oleuropein (2) were unstable and were prone to react to the radical compounds.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85689613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-12-15DOI: 10.33435/tcandtc.1080492
A. Köse, N. Yüksel, M. F. Fellah
It has been performed hydrogen adsorption on four metallo-porphyrin complexes by Density Functional Theory (DFT) calculations at room temperature. The WB97XD hybrid formalism method was used for hydrogen adsorption on metallo-porphyrin complexes formed with alkaline metal and alkaline earth metal (Na, K, Mg and Ca) atoms. It was determined that the adsorption energies for all complexes were negative, so that each of them could be a potential adsorbent for hydrogen storage. The adsorption enthalpy (ΔH) was calculated as -21.9 kJ/mol for the Na-Porphyrin (Na-P) complex structure. Moreover, the gravimetric hydrogen storage capacity for the Na-P complex was calculated to be ≈5.5 wt%. Thus, the DOE's target for 2025 has been achieved. In addition, van der Waals weak interactions were found to be effective in hydrogen adsorption and storage studies. Based on the electronic properties the metallo-porphyrin complexes could not be used as electronic sensors against the hydrogen molecule.
{"title":"Metal-Porphyrin Complexes: A DFT Study of Hydrogen Adsorption and Storage","authors":"A. Köse, N. Yüksel, M. F. Fellah","doi":"10.33435/tcandtc.1080492","DOIUrl":"https://doi.org/10.33435/tcandtc.1080492","url":null,"abstract":"It has been performed hydrogen adsorption on four metallo-porphyrin complexes by Density Functional Theory (DFT) calculations at room temperature. The WB97XD hybrid formalism method was used for hydrogen adsorption on metallo-porphyrin complexes formed with alkaline metal and alkaline earth metal (Na, K, Mg and Ca) atoms. It was determined that the adsorption energies for all complexes were negative, so that each of them could be a potential adsorbent for hydrogen storage. The adsorption enthalpy (ΔH) was calculated as -21.9 kJ/mol for the Na-Porphyrin (Na-P) complex structure. Moreover, the gravimetric hydrogen storage capacity for the Na-P complex was calculated to be ≈5.5 wt%. Thus, the DOE's target for 2025 has been achieved. In addition, van der Waals weak interactions were found to be effective in hydrogen adsorption and storage studies. Based on the electronic properties the metallo-porphyrin complexes could not be used as electronic sensors against the hydrogen molecule.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73663675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-12-15DOI: 10.33435/tcandtc.1089782
Y. Is
In this work, the interaction energies of some commercial molecules that are still used clinically with aminoacids in the active region of the tyrosine kinase were calculated by semi-empirical methods such as AM1 and PM3. There are already some results calculated with DFT methods and published in an article previously. By comparing the results there with those found here, it has been discussed whether semi-empirical methods with much shorter computation times can be used to estimate the most critical aminoacids for the tyrosine kinase enzyme instead of DFT methods which take much more time. According to the results obtained here, in order for semi-empirical methods to be used instead of DFT methods for this purpose, the examined ligands must have an electrical charge in the physiological environment. In other words, the hypothesis put forward remains valid only if the ligand under consideration has a charge. The use of semi-empirical methods such as AM1 and PM3 instead of DFT methods to estimate the residues with which a molecule that does not have any electrical charge interacts most strongly did not yield overlapping results.
{"title":"Investigation of the interactions of anticancer drugs with tyrosine kinase enzyme using semi-empirical methods and comparisons with DFT Calculations","authors":"Y. Is","doi":"10.33435/tcandtc.1089782","DOIUrl":"https://doi.org/10.33435/tcandtc.1089782","url":null,"abstract":"In this work, the interaction energies of some commercial molecules that are still used clinically with aminoacids in the active region of the tyrosine kinase were calculated by semi-empirical methods such as AM1 and PM3. There are already some results calculated with DFT methods and published in an article previously. By comparing the results there with those found here, it has been discussed whether semi-empirical methods with much shorter computation times can be used to estimate the most critical aminoacids for the tyrosine kinase enzyme instead of DFT methods which take much more time. According to the results obtained here, in order for semi-empirical methods to be used instead of DFT methods for this purpose, the examined ligands must have an electrical charge in the physiological environment. In other words, the hypothesis put forward remains valid only if the ligand under consideration has a charge. The use of semi-empirical methods such as AM1 and PM3 instead of DFT methods to estimate the residues with which a molecule that does not have any electrical charge interacts most strongly did not yield overlapping results.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87128794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-09-09DOI: 10.33435/tcandtc.1140158
Yeni Yeni, Nining Nining
Pancreatic ductal adenocarcinoma (PDAC) is among the world's deadliest cancers. Multiple studies demonstrated that PDAC is frequently characterized by the presence of Kirsten Rat Sarcoma (KRAS) G12D, G12V, and G12R protein mutants. The mutants are potential immunotherapy targets due to their potential as cancer-specific neoantigens. KRAS G12D, G12V and G12R contain vaccine-immunogenic epitopes. KRAS G12D, G12V and G12R epitopes were presented at major histocompatibility complexes (MHC) class I. The rational design of peptide vaccines to enhance the efficacy of cancer immunotherapy is facilitated by developing a peptide structural data library and knowledge of the MHC and antigen presentation processes. Before predicting peptide activity against MHC, homology modeling must transform the peptide into a three-dimensional structure. In this study, I-TASSER was used to perform homology modeling with the assistance of other applications. In silico methods for predicting epitopes to produce rationally designed peptide vaccines can increase the efficacy of these vaccines. This study yielded four epitope models that are potential PDAC vaccination candidates, KSFEDIHHYR, GIPFIETSAK, VVVGARGVGK and VVVGADGVGK.
{"title":"Homology Modeling Epitopes of Kirsten Rat Sarcoma (KRAS) G12D, G12V and G12R as Pancreatic Ductal Adenocarcinoma Vaccine Candidates","authors":"Yeni Yeni, Nining Nining","doi":"10.33435/tcandtc.1140158","DOIUrl":"https://doi.org/10.33435/tcandtc.1140158","url":null,"abstract":"Pancreatic ductal adenocarcinoma (PDAC) is among the world's deadliest cancers. Multiple studies demonstrated that PDAC is frequently characterized by the presence of Kirsten Rat Sarcoma (KRAS) G12D, G12V, and G12R protein mutants. The mutants are potential immunotherapy targets due to their potential as cancer-specific neoantigens. KRAS G12D, G12V and G12R contain vaccine-immunogenic epitopes. KRAS G12D, G12V and G12R epitopes were presented at major histocompatibility complexes (MHC) class I. The rational design of peptide vaccines to enhance the efficacy of cancer immunotherapy is facilitated by developing a peptide structural data library and knowledge of the MHC and antigen presentation processes. Before predicting peptide activity against MHC, homology modeling must transform the peptide into a three-dimensional structure. In this study, I-TASSER was used to perform homology modeling with the assistance of other applications. In silico methods for predicting epitopes to produce rationally designed peptide vaccines can increase the efficacy of these vaccines. This study yielded four epitope models that are potential PDAC vaccination candidates, KSFEDIHHYR, GIPFIETSAK, VVVGARGVGK and VVVGADGVGK.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91130585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-03-03DOI: 10.33435/tcandtc.1055649
A. Ataş, H. Ataseven, K. Sayın
{"title":"Investigation of Antiparasitic Properties of Benzimidazole Derivatives Against Amebiasis","authors":"A. Ataş, H. Ataseven, K. Sayın","doi":"10.33435/tcandtc.1055649","DOIUrl":"https://doi.org/10.33435/tcandtc.1055649","url":null,"abstract":"","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81305231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-10DOI: 10.33435/tcandtc.1023777
Jayalakshmi Palaniappan, Jothi Balakri̇shnan, Selvaraju Karuppannan, A. DAVİD STEPHEN
{"title":"Density functional analysis of conducting molecules: A Theoretical Investigation via QTAIM approach","authors":"Jayalakshmi Palaniappan, Jothi Balakri̇shnan, Selvaraju Karuppannan, A. DAVİD STEPHEN","doi":"10.33435/tcandtc.1023777","DOIUrl":"https://doi.org/10.33435/tcandtc.1023777","url":null,"abstract":"","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87315293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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