Pub Date : 2023-10-24DOI: 10.33435/tcandtc.1327841
A. Mittal, Mudita Nagpal, Varun Chahal, V. K. Vashistha
In the present article, various conformers of licochalcone L, a chalcone derivative extracted from the G. inflata root, have been analyzed in the aqueous solution and gaseous phase using calculation based on density functional theory (DFT). Nonlinear optical parameters such as dipole moment (µ), mean polarizability (α), polarizability anisotropy (Δα) and the first order hyperpolarizability (β) have been estimated to examine the NLO properties of the title molecule. The analysis of natural bond orbitals (NBO) has been carried out to characterize various intramolecular interactions. The nucleus-independent chemical shift (NICS) technique has been used to investigate the aromaticity. Further, the pKa values have been computed for each hydroxyl group. The impact of solvation on the molecular electrostatic potentials and frontier molecular orbitals has been investigated for the neutral as well as monoanionic form of licochalcone L. A variety of global chemical reactivity descriptors have been calculated to highlight the structure-activity relationship.
{"title":"The structural, electronic and nonlinear optical properties of licochalcone L in the gas phase and aqueous solution: A DFT study","authors":"A. Mittal, Mudita Nagpal, Varun Chahal, V. K. Vashistha","doi":"10.33435/tcandtc.1327841","DOIUrl":"https://doi.org/10.33435/tcandtc.1327841","url":null,"abstract":"In the present article, various conformers of licochalcone L, a chalcone derivative extracted from the G. inflata root, have been analyzed in the aqueous solution and gaseous phase using calculation based on density functional theory (DFT). Nonlinear optical parameters such as dipole moment (µ), mean polarizability (α), polarizability anisotropy (Δα) and the first order hyperpolarizability (β) have been estimated to examine the NLO properties of the title molecule. The analysis of natural bond orbitals (NBO) has been carried out to characterize various intramolecular interactions. The nucleus-independent chemical shift (NICS) technique has been used to investigate the aromaticity. Further, the pKa values have been computed for each hydroxyl group. The impact of solvation on the molecular electrostatic potentials and frontier molecular orbitals has been investigated for the neutral as well as monoanionic form of licochalcone L. A variety of global chemical reactivity descriptors have been calculated to highlight the structure-activity relationship.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"197 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139314804","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 : 2023-07-12DOI: 10.33435/tcandtc.1277724
Boulanouar Messaoudi, M. Cheriet, Rayanne Djemil, Khatmi DJAMEL EDDİNE
Several levels of theory such as Møller-Plesset MP2, G3, and CBS-QB3, have been used in order to investigate the complex and multichannel potential energy surface of the reaction of but-3-enal with the triplet oxygen atom. The results show that the O-addition channel is dominant. The different possible pathways of oxygen atom attack are thoroughly studied to better understand and explain the reaction mechanism. Regarding the oxidation of but-3-enal by triplet oxygen O(3P), it is shown that the major thermodynamic product is H3CC(O)CH2C(O)H (P3) being the most stable for the whole reaction. However, the most favored product kinetically is H2CC(OH)CH2C(O)H (P2). For the H-abstraction second possible pathway, the most favored product both kinetically and thermodynamically is found to be P8. The activation energy and calculated rate constants are consistent with the proposed addition mechanism.
{"title":"Theoretical kinetic investigation of the multichannel mechanism of O(3P) atmospheric oxidation reaction of but-3-enal","authors":"Boulanouar Messaoudi, M. Cheriet, Rayanne Djemil, Khatmi DJAMEL EDDİNE","doi":"10.33435/tcandtc.1277724","DOIUrl":"https://doi.org/10.33435/tcandtc.1277724","url":null,"abstract":"Several levels of theory such as Møller-Plesset MP2, G3, and CBS-QB3, have been used in order to investigate the complex and multichannel potential energy surface of the reaction of but-3-enal with the triplet oxygen atom. The results show that the O-addition channel is dominant. The different possible pathways of oxygen atom attack are thoroughly studied to better understand and explain the reaction mechanism. Regarding the oxidation of but-3-enal by triplet oxygen O(3P), it is shown that the major thermodynamic product is H3CC(O)CH2C(O)H (P3) being the most stable for the whole reaction. However, the most favored product kinetically is H2CC(OH)CH2C(O)H (P2). For the H-abstraction second possible pathway, the most favored product both kinetically and thermodynamically is found to be P8. The activation energy and calculated rate constants are consistent with the proposed addition mechanism.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79162970","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 : 2023-07-10DOI: 10.33435/tcandtc.1232636
A. Ghasemi̇, Batoul Maki̇abadi̇, M. Zakari̇anezhad, F. Ashrafi̇, Mohammad Bagher BAGHERİ POOR
In this study, the physicochemical characteristics of the adsorption of the anticancer drug Streptozocin (STZ, Zanosar) on the extern surface of Cr-doped carbon nanotube (CNTCr) have been investigated. Optimization all structures were performed using the DFT method at the mpw1pw91/6-311G level of theory. The energies, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), the density of states (DOS), the distribution of electric charges, and the dipole moments have been calculated to investigate the physical chemistry behaviors of the structures. As well as, the molecular descriptors such as electrophilicity (ω), chemical potential (μ), chemical hardness (h) and chemical softness (S) of compounds were investigated. Examination of the intramolecular and intermolecular bonds indicates that the adsorption of the drug on the nanotube surface has been taking place. Also, the calculated adsorption energy was negative and indicates that the adsorption is thermodynamically possible. All the obtained results of the theoretical calculations have shown that CNTCr is suitable for delivering the anti-cancer drug STZ.
{"title":"Evaluation of absorption behavior of Streptozocin anti-cancer drug on Cr doped Carbon Nanotube (5,5) using DFT theoretical method","authors":"A. Ghasemi̇, Batoul Maki̇abadi̇, M. Zakari̇anezhad, F. Ashrafi̇, Mohammad Bagher BAGHERİ POOR","doi":"10.33435/tcandtc.1232636","DOIUrl":"https://doi.org/10.33435/tcandtc.1232636","url":null,"abstract":"In this study, the physicochemical characteristics of the adsorption of the anticancer drug Streptozocin (STZ, Zanosar) on the extern surface of Cr-doped carbon nanotube (CNTCr) have been investigated. Optimization all structures were performed using the DFT method at the mpw1pw91/6-311G level of theory. The energies, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), the density of states (DOS), the distribution of electric charges, and the dipole moments have been calculated to investigate the physical chemistry behaviors of the structures. As well as, the molecular descriptors such as electrophilicity (ω), chemical potential (μ), chemical hardness (h) and chemical softness (S) of compounds were investigated. Examination of the intramolecular and intermolecular bonds indicates that the adsorption of the drug on the nanotube surface has been taking place. Also, the calculated adsorption energy was negative and indicates that the adsorption is thermodynamically possible. All the obtained results of the theoretical calculations have shown that CNTCr is suitable for delivering the anti-cancer drug STZ.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81622327","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 : 2023-07-06DOI: 10.33435/tcandtc.1151666
H. Saraç, B. Tüzün
In this study, it was aimed to determine the chemical components in the ethanol extract of the turmeric (Curcuma longa L.) plant rhizomes sold as powder in spice-sellers and to determine its antioxidant activity properties. For this purpose, turmeric rhizomes powder was extracted by maceration method using ethanol solvent and its chemical content was determined by Gas chromatography-Mass spectrometry (GC-MS) analysis. After chemical components were determinate for the turmeric ethanol extract, the inhibitory activities of these chemicals against the Crystal structure of Human peroxiredoxin 5 (HP5) (PDB ID: 1HD2) and Bovine Xanthine Oxidase (BXO) (PDB ID: 3NRZ) downloaded from the Protein Data Bank site were compared.
{"title":"Antioxidant Activity Properties of Extract of Turmeric (Curcuma longa L.) Plant","authors":"H. Saraç, B. Tüzün","doi":"10.33435/tcandtc.1151666","DOIUrl":"https://doi.org/10.33435/tcandtc.1151666","url":null,"abstract":"In this study, it was aimed to determine the chemical components in the ethanol extract of the turmeric (Curcuma longa L.) plant rhizomes sold as powder in spice-sellers and to determine its antioxidant activity properties. For this purpose, turmeric rhizomes powder was extracted by maceration method using ethanol solvent and its chemical content was determined by Gas chromatography-Mass spectrometry (GC-MS) analysis. After chemical components were determinate for the turmeric ethanol extract, the inhibitory activities of these chemicals against the Crystal structure of Human peroxiredoxin 5 (HP5) (PDB ID: 1HD2) and Bovine Xanthine Oxidase (BXO) (PDB ID: 3NRZ) downloaded from the Protein Data Bank site were compared.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76750969","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 : 2023-07-04DOI: 10.33435/tcandtc.1224592
Yahya Hasan, A. AL-HAMASHİ
Sirtuins family are a Nicotinamide Adenine Dinucleotide (NAD+) dependent histone deacetylase enzyme. Sirtuins have been implicated in the pathogenesis of various diseases including cancer, neurological disorders and metabolic syndromes, hence sirtuins appointed as a promising therapeutic target for diseases, by regulating of its activity by small molecules modulators. The indole containing selisistat (EX-527) and its derivatives set as the most potent and selective SIRT1 inhibitors. Selisistat showed an effective sirtuin inhibition on various cancer cell line, and has reached the clinical trials for endometriosis and Huntington’s disease. In this study a set of selisistat derivatives were designed and virtually studied by means of molecular docking, ADMET, and molecular dynamics (MD) simulations. Two molecules were showed promising virtual binding affinity on the SIRT1-3 proteins. Compound 1 exhibits stronger in silico SIRT1 and SIRT2 affinities than EX-527, whereas compound 8 prefers SIRT3 binding. The ADMET analysis of the virtually active molecules demonstrated an acceptable drug-like profile and desirable pharmacokinetics properties. The MD simulation analysis revealed that compound 1 had significantly better alignment with SIRT1 and SIRT2 proteins than EX-527 according to Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) data, while compound 8 had a perfect alignment and fitting with SIRT3 protein than EX-527.
{"title":"Identification of Selisistat Derivatives as SIRT1-3 Inhibitors by in Silico Virtual Screening","authors":"Yahya Hasan, A. AL-HAMASHİ","doi":"10.33435/tcandtc.1224592","DOIUrl":"https://doi.org/10.33435/tcandtc.1224592","url":null,"abstract":"Sirtuins family are a Nicotinamide Adenine Dinucleotide (NAD+) dependent histone deacetylase enzyme. Sirtuins have been implicated in the pathogenesis of various diseases including cancer, neurological disorders and metabolic syndromes, hence sirtuins appointed as a promising therapeutic target for diseases, by regulating of its activity by small molecules modulators. The indole containing selisistat (EX-527) and its derivatives set as the most potent and selective SIRT1 inhibitors. Selisistat showed an effective sirtuin inhibition on various cancer cell line, and has reached the clinical trials for endometriosis and Huntington’s disease. In this study a set of selisistat derivatives were designed and virtually studied by means of molecular docking, ADMET, and molecular dynamics (MD) simulations. Two molecules were showed promising virtual binding affinity on the SIRT1-3 proteins. Compound 1 exhibits stronger in silico SIRT1 and SIRT2 affinities than EX-527, whereas compound 8 prefers SIRT3 binding. The ADMET analysis of the virtually active molecules demonstrated an acceptable drug-like profile and desirable pharmacokinetics properties. The MD simulation analysis revealed that compound 1 had significantly better alignment with SIRT1 and SIRT2 proteins than EX-527 according to Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) data, while compound 8 had a perfect alignment and fitting with SIRT3 protein than EX-527.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73519603","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 : 2023-07-04DOI: 10.33435/tcandtc.1246320
H. Al-Madhagi
1.1 Objective Atherosclerosis is a chronic, immune-implicated, disease with high numbers of mortality globally. The aim of the current study is to target these genes by specific siRNA utilizing bioinformatics tools. 1.2 Methods 8 siRNAs were designed via RNAxs from C1QA and ITBG2 gene sequences retrieved from NCBI database. GC% and Tm of siRNAs were calculated through OligoCalc web interface. In addition, hybridization energy of siRNAs with the corresponding target sequences as well as docking to argonaute 2 protein were performed using DuplexFold and HDock. 1.3 Results The designed siRNAs exhibited acceptable GC content and Tm values. Besides, the hybridization energy and docking scores were highly significant to block the expression of the mentioned genes. 1.4 Conclusion The designed siRNAs are superior candidates for silencing immune-mediated atherosclerotic genes which deserve further consideration.
{"title":"Design of siRNAs Against Immune-Implicated Atherosclerosis Genes: Computational Study","authors":"H. Al-Madhagi","doi":"10.33435/tcandtc.1246320","DOIUrl":"https://doi.org/10.33435/tcandtc.1246320","url":null,"abstract":"1.1 Objective \u0000Atherosclerosis is a chronic, immune-implicated, disease with high numbers of mortality globally. The aim of the current study is to target these genes by specific siRNA utilizing bioinformatics tools. \u00001.2 Methods \u00008 siRNAs were designed via RNAxs from C1QA and ITBG2 gene sequences retrieved from NCBI database. GC% and Tm of siRNAs were calculated through OligoCalc web interface. In addition, hybridization energy of siRNAs with the corresponding target sequences as well as docking to argonaute 2 protein were performed using DuplexFold and HDock. \u00001.3 Results \u0000The designed siRNAs exhibited acceptable GC content and Tm values. Besides, the hybridization energy and docking scores were highly significant to block the expression of the mentioned genes. \u00001.4 Conclusion \u0000The designed siRNAs are superior candidates for silencing immune-mediated atherosclerotic genes which deserve further consideration.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"62 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84993624","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 : 2023-05-26DOI: 10.33435/tcandtc.1249159
Ceren Öğütçü, Rumeysa Demir, Ebru Kirmiziay, H. S. Portakal
Cathepsin D (Cat D) is a lysosomal aspartic acid protease encoded by CTSD gene and has significant biological roles such as degradation of extracellular and intracellular proteins, regulation of apoptosis, hormone processing, antigen processing etc. Furthermore, it is overexpressed by breast cancer cells and it acts a role in many processes affecting the cancer prognosis such as metastasis, angiogenesis, invasion, and drug resistance through regulation of the metabolic pathways and digesting the extracellular matrix (ECM) proteins. Due to that there is no drug targeting Cat D in clinical trial phases, a virtual drug screening in order to reveal possible drugs with high Cat D inhibitory activity from a library composed of 12,111 ligands is carried out with this study. Results have demonstrated that ZINC000003922429 (Adozelesin), ZINC000012358610 (Phthalocyanine), ZINC000051951669 (Bemcentinib), ZINC000003786250 (YM022), and ZINC000150338819 (Ledipasvir) have high binding affinity to Cat D. Among these chemical ligands, YM022 from Drugs in Clinical Trials dataset has been evaluated as most promising one that might be repurposed in the treatment of breast cancer due to its high affinity, convenient ADME and Toxicity properties, and highest bioactivity profiles. However, the possible activity of YM022 should be analyzed with further molecular dynamics (MD) simulations, in vitro and in vivo studies.
{"title":"Discovery of Repurposable Drugs in the Combination Therapy of Breast Cancer: A Virtual Drug Screening Study","authors":"Ceren Öğütçü, Rumeysa Demir, Ebru Kirmiziay, H. S. Portakal","doi":"10.33435/tcandtc.1249159","DOIUrl":"https://doi.org/10.33435/tcandtc.1249159","url":null,"abstract":"Cathepsin D (Cat D) is a lysosomal aspartic acid protease encoded by CTSD gene and has significant biological roles such as degradation of extracellular and intracellular proteins, regulation of apoptosis, hormone processing, antigen processing etc. Furthermore, it is overexpressed by breast cancer cells and it acts a role in many processes affecting the cancer prognosis such as metastasis, angiogenesis, invasion, and drug resistance through regulation of the metabolic pathways and digesting the extracellular matrix (ECM) proteins. Due to that there is no drug targeting Cat D in clinical trial phases, a virtual drug screening in order to reveal possible drugs with high Cat D inhibitory activity from a library composed of 12,111 ligands is carried out with this study. Results have demonstrated that ZINC000003922429 (Adozelesin), ZINC000012358610 (Phthalocyanine), ZINC000051951669 (Bemcentinib), ZINC000003786250 (YM022), and ZINC000150338819 (Ledipasvir) have high binding affinity to Cat D. Among these chemical ligands, YM022 from Drugs in Clinical Trials dataset has been evaluated as most promising one that might be repurposed in the treatment of breast cancer due to its high affinity, convenient ADME and Toxicity properties, and highest bioactivity profiles. However, the possible activity of YM022 should be analyzed with further molecular dynamics (MD) simulations, in vitro and in vivo studies.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79327519","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 : 2023-05-26DOI: 10.33435/tcandtc.1196019
E. Edache, A. Uzairu, P. Mamza, G. Shallangwa
The propagation of emerging diseases and the expensive cost and time lost by using the classic methods, especially in the current scenario with the world being plagued by SARS-CoV-2 and Chlamydia trachomatis diseases, make finding another way to invent new medication very important. That's why we used computational approaches to predict protein-ligand interactions of thiazolino 2-pyridone amide derivatives. The high-throughput virtual screening requires extensive combing through existing datasets in the hope of finding possible matches to screen for new molecules able to inhibit SARS-CoV-2 and Chlamydia trachomatis diseases. In this study, 46 thiazolino-2-pyridone amide derivatives were chosen for planning the powerful inhibitors by utilizing various strategies: QSAR analysis, phylogenetic analysis, homology modeling, docking simulation, molecular dynamics (MD) simulation, as well as ADMET Screening. The 2D QSAR investigation uncovers that these compounds show a satisfactory connection with bioactivity. From that point onward, phylogenetic analysis and homology modeling were used to model the selected receptors, which were then evaluated using both the SAVES and PROSA servers, indicating the best correctness of the modeled protein with the experimental results. Additionally, a docking simulation investigation was carried out to comprehend the 46 thiazolino-2-pyridone amide derivatives' interactions with homologous proteins. Additionally, MD simulations coupled with MM/GBSA verified the chosen complex systems' stability over 1000 ps. Two compounds were chosen as possible inhibitors based on these findings. The expected thiazolino-2-pyridone amide's oral bioavailability and toxicity have been discovered under the ADMET. Thus, these discoveries can be leveraged to develop novel molecules with the necessary action.
{"title":"Molecular phylogeny, Sequence-based drug design, Docking built virtual screening, dynamics simulations, and ADMET properties of thiazolino 2-pyridone amide derivatives as an inhibitor of Chlamydia trachomatis and SARS-CoV-2 protein","authors":"E. Edache, A. Uzairu, P. Mamza, G. Shallangwa","doi":"10.33435/tcandtc.1196019","DOIUrl":"https://doi.org/10.33435/tcandtc.1196019","url":null,"abstract":"The propagation of emerging diseases and the expensive cost and time lost by using the classic methods, especially in the current scenario with the world being plagued by SARS-CoV-2 and Chlamydia trachomatis diseases, make finding another way to invent new medication very important. That's why we used computational approaches to predict protein-ligand interactions of thiazolino 2-pyridone amide derivatives. The high-throughput virtual screening requires extensive combing through existing datasets in the hope of finding possible matches to screen for new molecules able to inhibit SARS-CoV-2 and Chlamydia trachomatis diseases. In this study, 46 thiazolino-2-pyridone amide derivatives were chosen for planning the powerful inhibitors by utilizing various strategies: QSAR analysis, phylogenetic analysis, homology modeling, docking simulation, molecular dynamics (MD) simulation, as well as ADMET Screening. The 2D QSAR investigation uncovers that these compounds show a satisfactory connection with bioactivity. From that point onward, phylogenetic analysis and homology modeling were used to model the selected receptors, which were then evaluated using both the SAVES and PROSA servers, indicating the best correctness of the modeled protein with the experimental results. Additionally, a docking simulation investigation was carried out to comprehend the 46 thiazolino-2-pyridone amide derivatives' interactions with homologous proteins. Additionally, MD simulations coupled with MM/GBSA verified the chosen complex systems' stability over 1000 ps. Two compounds were chosen as possible inhibitors based on these findings. The expected thiazolino-2-pyridone amide's oral bioavailability and toxicity have been discovered under the ADMET. Thus, these discoveries can be leveraged to develop novel molecules with the necessary action.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78378425","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 : 2023-05-26DOI: 10.33435/tcandtc.1252038
Boulanouar Messaoudi, Naceur Benhadria, T. Attar
The concept of detection limit was combined with quantum chemical calculations for trace analysis of cadmium and lead in aqueous solution using deprotonated 8-hydroxyquinoline (oxine) as ligand. The DFT study was performed using 6-31G(d), cc-pVTZ and SDD basis sets in combination with different theoretical methods such as; B3LYP, MP2 and M06L implemented in Gaussian 09 program package. The obtained results of the study in the gas and aqueous phases show that the chemical stability of the complex was found in the order Pb-oxine > Cd-oxine. Based on the calculations done, the stability order was relative to the detection limit (LOD) for the two metals Cd and Pb. Thus, a reverse relationship between LOD and binding energy has been found.
{"title":"Theoretical insights on the relationship between detection limit and complex stability of oxine ligand","authors":"Boulanouar Messaoudi, Naceur Benhadria, T. Attar","doi":"10.33435/tcandtc.1252038","DOIUrl":"https://doi.org/10.33435/tcandtc.1252038","url":null,"abstract":"The concept of detection limit was combined with quantum chemical calculations for trace analysis of cadmium and lead in aqueous solution using deprotonated 8-hydroxyquinoline (oxine) as ligand. The DFT study was performed using 6-31G(d), cc-pVTZ and SDD basis sets in combination with different theoretical methods such as; B3LYP, MP2 and M06L implemented in Gaussian 09 program package. The obtained results of the study in the gas and aqueous phases show that the chemical stability of the complex was found in the order Pb-oxine > Cd-oxine. Based on the calculations done, the stability order was relative to the detection limit (LOD) for the two metals Cd and Pb. Thus, a reverse relationship between LOD and binding energy has been found.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81371071","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 : 2023-05-26DOI: 10.33435/tcandtc.1173392
Rajaganapathy Kaliyaperumal, Dr.tharını K
The proof of concept presents the results of molecular docking analysis in common Japanese knotweed leaf compounds compared to the four different proteases 4GQQ, 2B17, 2FW3 and 1ZB6 obtained from the Protein Data Bank. Several of these compounds show binding energy for the various proteases and according to our data compare favorably to a known antibacterial, anti-inflammatory, anti diabetic and antioxidant drugs. The advancement of improved docking techniques has also made it possible to more accurately predict the biological activity of substances. This paper provides compounds of a Japanese knotweed plant leaf to determine the result of gas chromatography-mass spectrometry to calculate binding energy compared to standardized drugs. The lowest amount of binding energy for good biological activity. The compound undecane had a higher negative binding energy than 2-hydroxyethyl cyclohexanecarboxylate. As we can see from the docking results, by comparing the values of the binding energies of the four proteins obtained from the protein data bank (PDB) (4GQQ, 2B17, 2FW3 and 1ZB6) we propose that the undecane molecule better is antibacterial, anti-inflammatory anti diabetic and antioxidant nature then cyclohexane carboxylic acid 2-hydroxyethyl ester compound. The DFT results HOMO-LUMO energy difference value (E=-0.44eV) indicated that the compounds more stability and reactivity. So energy difference minimum value of 2-hydroxyethyl clohexane carboxylate has good chemical stability and reactivity nature compared to other compound.
{"title":"AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS","authors":"Rajaganapathy Kaliyaperumal, Dr.tharını K","doi":"10.33435/tcandtc.1173392","DOIUrl":"https://doi.org/10.33435/tcandtc.1173392","url":null,"abstract":"The proof of concept presents the results of molecular docking analysis in common Japanese knotweed leaf compounds compared to the four different proteases 4GQQ, 2B17, 2FW3 and 1ZB6 obtained from the Protein Data Bank. Several of these compounds show binding energy for the various proteases and according to our data compare favorably to a known antibacterial, anti-inflammatory, anti diabetic and antioxidant drugs. The advancement of improved docking techniques has also made it possible to more accurately predict the biological activity of substances. This paper provides compounds of a Japanese knotweed plant leaf to determine the result of gas chromatography-mass spectrometry to calculate binding energy compared to standardized drugs. The lowest amount of binding energy for good biological activity. The compound undecane had a higher negative binding energy than 2-hydroxyethyl cyclohexanecarboxylate. As we can see from the docking results, by comparing the values of the binding energies of the four proteins obtained from the protein data bank (PDB) (4GQQ, 2B17, 2FW3 and 1ZB6) we propose that the undecane molecule better is antibacterial, anti-inflammatory anti diabetic and antioxidant nature then cyclohexane carboxylic acid 2-hydroxyethyl ester compound. The DFT results HOMO-LUMO energy difference value (E=-0.44eV) indicated that the compounds more stability and reactivity. So energy difference minimum value of 2-hydroxyethyl clohexane carboxylate has good chemical stability and reactivity nature compared to other compound.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90242513","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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