Turkish Computational and Theoretical Chemistry最新文献_第3页

Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach 分枝杆菌生物膜相关蛋白的结构和功能表征:一种计算机方法

Turkish Computational and Theoretical Chemistry Pub Date : 2023-05-26 DOI: 10.33435/tcandtc.1191117

Ayşe Hümeyra Taşkın Kafa, Rukiye Aslan, Hanaou Ahamada, B. Atron

{"title":"Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach","authors":"Ayşe Hümeyra Taşkın Kafa, Rukiye Aslan, Hanaou Ahamada, B. Atron","doi":"10.33435/tcandtc.1191117","DOIUrl":"https://doi.org/10.33435/tcandtc.1191117","url":null,"abstract":"Biofilm-associated infections are characterized by the chronicity, recurrence, and the requirement of a prolonged administration of multiple drugs. Several non-pathogenic and pathogenic species of microorganism including Mycobacteria spp form biofilm. Mycobacterial biofilms present a unique composition. Instead of exopolysaccharides in other bacteria, proteins are essential compounds of the biofilm matrix in mycobacteria. To tackle mycobacterial infections, a detailed understanding of the biofilm-forming mechanisms is crucial. In this present study, all available Mycobacterial proteins involved in the biofilm were selected. Their sequences were retrieved and characterized through the determination of their physicochemical properties, secondary structure, 3D structure, subcellular localization, conserved domain, ubiquitination sites, and virulence potentiality. Furthermore, druggability testing was undertaken after excluding proteins with homology to human proteins to identify possible drug targets. The results showed that they possess functionally important domains and families. All of the selected hypothetical proteins were stable. Six of them were classified as soluble and the remaining as transmembrane proteins. A sole protein was found to lack ubiquitination sites. Additionally, three of these were discovered to be virulent. Moreover, host non-homology results indicated eight pathogen-specific proteins that might be potential therapeutic targets. Among them, D-alanyl-D-alanine carboxypeptidase is a druggable target that is inhibited by beta-lactam antibiotics. The remainder of the proteins were categorized as new targets. \u0000In conclusion, this study may increase our knowledge of pathogenesis and host adaptation, drug resistance, and identification of drug and vaccine targets against infections caused by Mycobacteria. It can also guide new research.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"86 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73316775","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}

引用次数: 0

Theoretical Methods for coding a strand of DNA bases and nucleotides with C2Fe+, A DFT study 用C2Fe+编码DNA碱基和核苷酸链的理论方法，DFT研究

Turkish Computational and Theoretical Chemistry Pub Date : 2023-05-15 DOI: 10.33435/tcandtc.1181765

Leila Hojatkashani̇, Amir Ali Omi̇di̇

{"title":"Theoretical Methods for coding a strand of DNA bases and nucleotides with C2Fe+, A DFT study","authors":"Leila Hojatkashani̇, Amir Ali Omi̇di̇","doi":"10.33435/tcandtc.1181765","DOIUrl":"https://doi.org/10.33435/tcandtc.1181765","url":null,"abstract":"DNA strands are essential in a cell for growth, metabolism regulation and carrying genetic information bases to new generations, in every creatures . The function of DNA bases is a 0 and 1 system. In this theoretical research , we try to make two other 0 and 1 systems for DNA bases .In both methods, C2Fe+ is attached to DNA bases and nucleotides like a flag to make derivatives. In the first method NMR susceptibility and Magnetization of pristine DNA bases, nucleotides and their C2Fe varieties are determined theoretically by using Gauss view and Gaussian programs. With effect of a magnetic field (H) and NMR susceptibility of these compounds, their calculate magnetizations , certain signals can be created as a mark of DNA bases and their compounds. These resulted not only can be considered as a method to make a new (0) and (1) system. In the second method, by using Gauss view and Gaussian programs the theoretically UV-Visible spectrum of pristine DNA bases, nucleotides and their C2Fe varieties are determined which the spectrum absorption of the pristine compounds are in different range with the absorption range of C2Fe varieties. With a little change in spectrophotometer construction another 0 and 1 coding system can be created, again.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74270141","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}

引用次数: 1

Quantum investigation of the reaction between triplet oxygen O(3P) atom and butadiene 三态氧O(3P)原子与丁二烯反应的量子研究

Turkish Computational and Theoretical Chemistry Pub Date : 2023-05-15 DOI: 10.33435/tcandtc.1144794

Boulanouar Messaoudi, M. Cheriet, Rayenne Djemil, D. Khatmi̇

引用次数: 0

IN SILICO STUDY OF APTAMER SPECIFICITY FOR DETECTION OF ADENOSINE TRIPHOSPHATE (ATP) AS BIOSENSOR DEVELOPMENT FOR MITOCHONDRIA DIABETES DIAGNOSIS 核酸适配体特异性检测三磷酸腺苷(atp)作为线粒体糖尿病诊断生物传感器的硅片研究

Turkish Computational and Theoretical Chemistry Pub Date : 2023-05-15 DOI: 10.33435/tcandtc.1181299

Rustaman Rustaman, Rizky RAFİ RAHMAWAN, I. Maksum

{"title":"IN SILICO STUDY OF APTAMER SPECIFICITY FOR DETECTION OF ADENOSINE TRIPHOSPHATE (ATP) AS BIOSENSOR DEVELOPMENT FOR MITOCHONDRIA DIABETES DIAGNOSIS","authors":"Rustaman Rustaman, Rizky RAFİ RAHMAWAN, I. Maksum","doi":"10.33435/tcandtc.1181299","DOIUrl":"https://doi.org/10.33435/tcandtc.1181299","url":null,"abstract":"Diabetes Mellitus (DM) is characterized by increased blood glucose levels. It is generally caused by the pancreas' inability to produce insulin due to cell damage or insulin resistance. Due to the inhibition of adenosine triphosphate (ATP) production, which is essential for insulin secretion, one clinical pathology of this complication is insulin secretion dysfunction. Common methods of blood sugar diagnostics cannot distinguish mitochondrial diabetes and can lead to medication errors. Furthermore, an approach was developed through ATP biomarkers using an electrochemical biosensor with the help of an aptamer. However, it remains unknown precisely how and where the molecular interactions between the modified aptamer and ATP occur. Simulations were conducted in this study for 100 ns in silico using the amber18 computer program to determine the stability of the interaction and specificity between aptamer-ATP were compared to ADP and AMP. The results showed that the significant interactions are three hydrogen bonds between ATP and G7, G8, and A24. It was discovered that the aptamer-ATP complex had moderately good interaction and better potential for specificity than ADP and AMP. According to the RMSD, RMSF, and binding energy profiles, the system is still searching for the best conformation, necessitating a longer simulation time and additional studies to optimize the system. As a result, the system can reach a stable state and determine a more accurate energy calculation, hence, it is interpreted according to real applications.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89243208","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}

引用次数: 1

Effects of flavonoids on SARS–CoV–2 main protease (6W63): A molecular docking study 黄酮类化合物对SARS-CoV-2主蛋白酶(6W63)影响的分子对接研究

Turkish Computational and Theoretical Chemistry Pub Date : 2023-05-15 DOI: 10.33435/tcandtc.1151841

T. Ertan-Bolelli, K. Bolelli, C. Altunayar‐Unsalan, Ozan Ünsalan, Bergüzar Yilmaz

{"title":"Effects of flavonoids on SARS–CoV–2 main protease (6W63): A molecular docking study","authors":"T. Ertan-Bolelli, K. Bolelli, C. Altunayar‐Unsalan, Ozan Ünsalan, Bergüzar Yilmaz","doi":"10.33435/tcandtc.1151841","DOIUrl":"https://doi.org/10.33435/tcandtc.1151841","url":null,"abstract":"Public health is still under attack by a worldwide pandemic caused by a coronavirus which is known to cause mainly respiratory and enteric disease in humans. Currently, still limited knowledge exists on the exact action mechanism and biology of SARS‒CoV‒2 although there are several effective vaccines and antiviral treatment. Besides, there is a considerable amount of 3D protein structures for SARS–CoV–2, related to its main protease resolved by X–ray diffraction. Here, we used molecular docking strategy to predict possible inhibitory activities of flavonoids on SARS–CoV–2 Mpro enzyme. For this, 800 flavonoids were retrieved from the ZINC database. Results suggested that avicularin was the lead flavonoid which docked to Mpro with the best binding energy. However, most of flavonoids showed H–bond interactions with Hie–41 and Cys–145 catalytic dyad, which were important residues for the catalytic activity of SARS–CoV–2 Mpro. Strong hydrogen bonding (2.36 Å) with Sγ atom of Cys145 residue was observed. This might suggest an initial formation of covalent bonding. Findings showed that selected flavonoids could be promising inhibitors of this enzyme and have the potential for future therapeutic drugs against COVID–19 after immediate experimental validation and clinical approvals.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"184 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73961098","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}

引用次数: 0

A class of two-dimensional WSeTe monolayers under pressures with novel electronic and optical properties 一类在压力下具有新颖电子和光学性质的二维WSeTe单层材料

Turkish Computational and Theoretical Chemistry Pub Date : 2023-05-15 DOI: 10.33435/tcandtc.1161253

Idrees Orei̇bi̇, Jassim M. AL-ISSAWE

引用次数: 0

Electronic Properties of Poly(N-vinylcarbazole) Using semi-empirical oligomer extrapolation approximations 用半经验低聚物外推近似法研究聚(n -乙烯基咔唑)的电子性质

Turkish Computational and Theoretical Chemistry Pub Date : 2023-04-28 DOI: 10.33435/tcandtc.1206061

Ahmad NAZİB ALİAS, Zubainun MOHAMED ZABİDİ, A. Ali̇

引用次数: 0

Computational analysis using ADMET profiling, DFT calculations and molecular docking of two anti-cancer drugs 利用ADMET分析、DFT计算和两种抗癌药物的分子对接进行计算分析

Turkish Computational and Theoretical Chemistry Pub Date : 2023-01-15 DOI: 10.33435/tcandtc.1102295

Anaridha S., Mohamed IMRAN P K, Khaja MOHİDEEN A, Salım MEERAN I, Shabeer T. K.

{"title":"Computational analysis using ADMET profiling, DFT calculations and molecular docking of two anti-cancer drugs","authors":"Anaridha S., Mohamed IMRAN P K, Khaja MOHİDEEN A, Salım MEERAN I, Shabeer T. K.","doi":"10.33435/tcandtc.1102295","DOIUrl":"https://doi.org/10.33435/tcandtc.1102295","url":null,"abstract":"U.S. FDA approved anti-cancer drugs, namely ribociclib and copanlisib used for treating breast cancer and follicular lymphoma, respectively, were chosen for computational study. Quantum chemical calculations via DFT and MP2 were used for energy optimization of the drugs. Chemical descriptor parameters were compared between DFT and MP2 values for each atom, and the most reactive and stable atoms were reported. To describe the reactivity and stability of the drug molecules, Fukui functions were calculated. Molecular docking of the drugs was performed against epidermal growth factor receptor (EGFR) and cellular inhibitor of apoptosis protein-1 (cIAP1) receptor proteins to study the drug-protein binding interactions. The binding energy values before optimization and after optimization were found to be -11.21 and -14.41 kcal.mol-1 for copanlisib and -13.58 kcal and -29.08 kcal for ribociclib respectively. Atoms O27 and O10 are reported to be the most reactive atom based on high softness value. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of the drugs were evaluated using open-source in-silico tools. ADME profiling of drug molecules indicated good to moderate solubility and low to high absorption in the gastrointestinal tract. Predicted toxicity was class five for both anti-cancer drugs. The structural and bioactive properties of the drugs focused on in this study help evaluate the better reactivity patterns of anticancer medicines.","PeriodicalId":36025,"journal":{"name":"Turkish Computational and Theoretical Chemistry","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80325477","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}

引用次数: 0

An in silico investigation of allosteric inhibition potential of Dihydroergotamine against Sars-CoV-2 Main Protease (MPro) 二氢麦角胺对Sars-CoV-2主蛋白酶(MPro)变构抑制电位的计算机模拟研究

Turkish Computational and Theoretical Chemistry Pub Date : 2023-01-15 DOI: 10.33435/tcandtc.1121985

M. Yaşar, Ekrem Yaşar, Nuri Yorulmaz, Emin Tenekeci̇, İ. Sarpün, E. Eroglu

引用次数: 0

Simple model for the calculation of concentration and temperature dependent refractive index of different solutions 计算不同溶液随浓度和温度变化折射率的简单模型

Turkish Computational and Theoretical Chemistry Pub Date : 2023-01-01 DOI: 10.33435/tcandtc.1227137

Umar Farooque, Sandhir Kumar Si̇ngh, Tarique Rashid, Md. Iftekhar Alam

引用次数: 0