Mohammad Rashid, Md. Athar, Afzal Hussain, Norah Almadani, Ashfaq Hussain
The present study was based on an exploration of NCI database for searching specific CDK-7 kinase inhibitor by HTVS, SP, XP, molecular docking, molecular dynamic simulation, and ADMET evaluation. The best CDK-7 kinase inhibitors (NCI613391, NCI169676, NCI281246, NCI339580) were identified via NCI database screening. The stability of binding interaction between receptor protein and protein-ligand complex of potent finding compounds (NCI613391) further confirmed by dynamics simulations and MM-GBSA. The RMSD value of receptor and receptor-ligand complexes was analyzed, and it revealed the stability of binding interactions and remained stable throughout the simulation. The RMSF values and gyration radius of the unbound receptor and backbone atoms of the complex were found to be equal, which indicates that the drug molecule inside the CDK7 receptor is also stable. The study of MM-GBSA data also revealed stronger binding interactions of ligands to CDK7 receptors. With the exception of NCI169676, all compounds were shown to be substrates for CYP450 2D6, CYP450 3A4, inhibitors of CYP450 2C9, and non-inhibitors of p-glycoprotein. All compounds were qualified and found suitable to be as drug-likeness according to the Lipinski rule, Ghose filter, MDDR like rule, and CMC-like rule. The compound (NCI613391) was exhibited human intestinal absorption (76.08%), and display negative AMES and T.E.S.T (US-EPA) toxicity with OSIRIS property and found to be a promising CDK-7 kinase inhibitor and its efficacy may be further explored in clinical trials.
{"title":"A recent tactic for searching CDK-7 kinase inhibitor by NCI database screening","authors":"Mohammad Rashid, Md. Athar, Afzal Hussain, Norah Almadani, Ashfaq Hussain","doi":"10.2298/jsc230624083r","DOIUrl":"https://doi.org/10.2298/jsc230624083r","url":null,"abstract":"The present study was based on an exploration of NCI database for searching specific CDK-7 kinase inhibitor by HTVS, SP, XP, molecular docking, molecular dynamic simulation, and ADMET evaluation. The best CDK-7 kinase inhibitors (NCI613391, NCI169676, NCI281246, NCI339580) were identified via NCI database screening. The stability of binding interaction between receptor protein and protein-ligand complex of potent finding compounds (NCI613391) further confirmed by dynamics simulations and MM-GBSA. The RMSD value of receptor and receptor-ligand complexes was analyzed, and it revealed the stability of binding interactions and remained stable throughout the simulation. The RMSF values and gyration radius of the unbound receptor and backbone atoms of the complex were found to be equal, which indicates that the drug molecule inside the CDK7 receptor is also stable. The study of MM-GBSA data also revealed stronger binding interactions of ligands to CDK7 receptors. With the exception of NCI169676, all compounds were shown to be substrates for CYP450 2D6, CYP450 3A4, inhibitors of CYP450 2C9, and non-inhibitors of p-glycoprotein. All compounds were qualified and found suitable to be as drug-likeness according to the Lipinski rule, Ghose filter, MDDR like rule, and CMC-like rule. The compound (NCI613391) was exhibited human intestinal absorption (76.08%), and display negative AMES and T.E.S.T (US-EPA) toxicity with OSIRIS property and found to be a promising CDK-7 kinase inhibitor and its efficacy may be further explored in clinical trials.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135263181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Thomas Eichhorn, Dusan Dimic, Zoran Markovic, Goran Kaludjerovic
Ruthenium complexes have gained significant attention due to ruthenium similarity to iron, lower toxicity, and higher anticancer effectiveness than other compounds. In this contribution, five new isonicotinate-polyethylene glycol ester ligands were synthesized and characterized by NMR and IR spectroscopies. The corresponding Ru(II) complexes were also obtained, and their structure was elucidated by traditional methods. The optimization of structures was performed at B3LYP/6-31+G(d,p) level of theory for H, C, N, and O atoms and B3LYP/LanL2DZ for Ru. The intramolecular stabilization interactions were assessed through the Natural Bond Orbital approach. The NMR chemical shifts were predicted by the GIAO method and compared to the experimental values. High correlation coefficients and low mean absolute errors between these data sets proved that the predicted structure described well the experimental one. The theoretical and experimental IR spectra were also compared, and differences in the most notable bands were described. One of the ligands (L5) and complexes (5) showed fluorescent properties due to methylisatoic moiety. The electronic spectra of this compound were modeled by the TD-DFT method. The difference of 11 nm between experimental and theoretical wavelength was explained by the interactions between solvent and solute. Further biological and theoretical studies are advised for this series of compounds.
{"title":"Synthesis, spectroscopic characterization, and DFT analysis of dichlorido(η6-p-cymene)ruthenium(II) complexes with isonicotinate-polyethylene glycol ester ligands","authors":"Thomas Eichhorn, Dusan Dimic, Zoran Markovic, Goran Kaludjerovic","doi":"10.2298/jsc230412070e","DOIUrl":"https://doi.org/10.2298/jsc230412070e","url":null,"abstract":"Ruthenium complexes have gained significant attention due to ruthenium similarity to iron, lower toxicity, and higher anticancer effectiveness than other compounds. In this contribution, five new isonicotinate-polyethylene glycol ester ligands were synthesized and characterized by NMR and IR spectroscopies. The corresponding Ru(II) complexes were also obtained, and their structure was elucidated by traditional methods. The optimization of structures was performed at B3LYP/6-31+G(d,p) level of theory for H, C, N, and O atoms and B3LYP/LanL2DZ for Ru. The intramolecular stabilization interactions were assessed through the Natural Bond Orbital approach. The NMR chemical shifts were predicted by the GIAO method and compared to the experimental values. High correlation coefficients and low mean absolute errors between these data sets proved that the predicted structure described well the experimental one. The theoretical and experimental IR spectra were also compared, and differences in the most notable bands were described. One of the ligands (L5) and complexes (5) showed fluorescent properties due to methylisatoic moiety. The electronic spectra of this compound were modeled by the TD-DFT method. The difference of 11 nm between experimental and theoretical wavelength was explained by the interactions between solvent and solute. Further biological and theoretical studies are advised for this series of compounds.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135595464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jovana Stevanovic, D. Robajac, O. Nedić, Zorana Dobrijević
After sample processing for RNA and DNA analysis, the leftover protein pellets are usually discarded due to the limited efficiency of pellet reconstitution/solubilisation. As the pelleted proteins are tightly packed, they are most often solubilised using chaotropic agents (e.g. guanidine hydrochloride or urea), detergents (e.g. SDS), salts (NaCl), or basic buffer (Tris). The aim of this study was to define and optimise the procedure for the efficient extraction of proteins from human peripheral blood mononuclear cells (PBMCs), obtained by a single blood draw and lysed in TRIzol reagent, by varying experimental conditions in terms of protein precipitation solvent (isopropanol or acetone), washing (with or without guanidine hydrochloride) and solubilisation solution (containing SDS, NaCl, urea and/or Tris). We evaluated the efficacy of final, optimised protocol to solubilise both small cytoplasmic and larger transmembrane proteins, and the compatibility with methods employed for the subsequent analysis of protein posttranslational modifications, such as glycosylation. The optimised protocol for the extraction and isolation of post-TRIzol leftover proteins from PBMCs can be defined as follows: protein precipitation from the organic phase with ice-cold acetone, pellet washing with absolute ethanol and solubilisation in 1% SDS employing 20 min heating at 50?C and vortexing.
{"title":"Post-trizol protein extraction from peripheral blood mononuclear cells","authors":"Jovana Stevanovic, D. Robajac, O. Nedić, Zorana Dobrijević","doi":"10.2298/jsc230330037s","DOIUrl":"https://doi.org/10.2298/jsc230330037s","url":null,"abstract":"After sample processing for RNA and DNA analysis, the leftover protein pellets are usually discarded due to the limited efficiency of pellet reconstitution/solubilisation. As the pelleted proteins are tightly packed, they are most often solubilised using chaotropic agents (e.g. guanidine hydrochloride or urea), detergents (e.g. SDS), salts (NaCl), or basic buffer (Tris). The aim of this study was to define and optimise the procedure for the efficient extraction of proteins from human peripheral blood mononuclear cells (PBMCs), obtained by a single blood draw and lysed in TRIzol reagent, by varying experimental conditions in terms of protein precipitation solvent (isopropanol or acetone), washing (with or without guanidine hydrochloride) and solubilisation solution (containing SDS, NaCl, urea and/or Tris). We evaluated the efficacy of final, optimised protocol to solubilise both small cytoplasmic and larger transmembrane proteins, and the compatibility with methods employed for the subsequent analysis of protein posttranslational modifications, such as glycosylation. The optimised protocol for the extraction and isolation of post-TRIzol leftover proteins from PBMCs can be defined as follows: protein precipitation from the organic phase with ice-cold acetone, pellet washing with absolute ethanol and solubilisation in 1% SDS employing 20 min heating at 50?C and vortexing.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68517721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The aim of this research is to study the bactericidal effects of copper-polypyrrole composites deposited onto 316L SS modified with silver nanoparticles. The antimicrobial properties were evaluated against twenty-four strains of Gram-positive and Gram-negative bacteria. Among the twenty-four strains studied, isolates included reference strains (E. coli ATCC 25922, E. coli 0157:H7 EDL 933, S. aureus ATCC 25923 and L. monocytogenes ATCC 7644), as well as strains isolated from food and clinical samples. The antimicrobial activity of the composites demonstrated that all PPy-modified films had antibacterial properties. Notably, Cu-PPyAgNp500 exhibited the strongest inhibitory activity against both Gram-negative and Gram-positive bacteria. Surface modification of 316L SS with these films is a promising and viable alternative for the development of novel antibacterial composites that can inhibit the growth of a significant number of bacteria.
{"title":"Bactericidal effects of copper-polypyrrole composites modified with silver nanoparticles against gram-positive and gram-negative bacteria","authors":"P. Marucci, M. Sica, L. Brugnoni, María González","doi":"10.2298/jsc230213047m","DOIUrl":"https://doi.org/10.2298/jsc230213047m","url":null,"abstract":"The aim of this research is to study the bactericidal effects of copper-polypyrrole composites deposited onto 316L SS modified with silver nanoparticles. The antimicrobial properties were evaluated against twenty-four strains of Gram-positive and Gram-negative bacteria. Among the twenty-four strains studied, isolates included reference strains (E. coli ATCC 25922, E. coli 0157:H7 EDL 933, S. aureus ATCC 25923 and L. monocytogenes ATCC 7644), as well as strains isolated from food and clinical samples. The antimicrobial activity of the composites demonstrated that all PPy-modified films had antibacterial properties. Notably, Cu-PPyAgNp500 exhibited the strongest inhibitory activity against both Gram-negative and Gram-positive bacteria. Surface modification of 316L SS with these films is a promising and viable alternative for the development of novel antibacterial composites that can inhibit the growth of a significant number of bacteria.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"88 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68517315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Katarina Bozic, M. Pavlovic, G. Šekularac, Stefan Panic, Marijana Pantovic-Pavlovic
Electrophoretic deposition (EPD) can occur as a cataphoretic deposition - the coating is deposited on the cathode, and anaphoretic deposition - the coating is deposited on the anode. The primary purpose of EPD is to obtain compact and uniform organic/inorganic coatings of the desired thickness and adhesion on metal surfaces by applying an electric field to the particles of coating precursor. EPD basic principles for coatings deposition concerning fundamental explanations and considerations of practical parameters of the process are presented. Cataphoretic deposition has become popular because it can apply organic coatings to complex structures that are otherwise very difficult to coat. These coatings were found to improve the characteristics of the substrate, such as biocompatibility, appearance and the resistance to the corrosion processes. The key EPD parameters are composition, pH value and viscosity of deposition medium, as well as zeta potential of the particles, electric field strength, etc. A special survey is given to the process of anaphoretic deposition, which is relatively new, and its advantages over cataphoretic deposition are discussed. Through the process of joint anaphoresis/substrate anodization process, the surface of the substrate is simultaneously anodized and modified by incorporation of the foreign particles into the anodic layer. Resulting coatings of mixed composition of better adhesion and corrosion resistance with respect to cataphoretically-deposited coatings are obtained.
{"title":"Application aspects of joint anaphoresis/substrate anodization in production of biocompatible ceramic coatings","authors":"Katarina Bozic, M. Pavlovic, G. Šekularac, Stefan Panic, Marijana Pantovic-Pavlovic","doi":"10.2298/jsc230118034b","DOIUrl":"https://doi.org/10.2298/jsc230118034b","url":null,"abstract":"Electrophoretic deposition (EPD) can occur as a cataphoretic deposition - the coating is deposited on the cathode, and anaphoretic deposition - the coating is deposited on the anode. The primary purpose of EPD is to obtain compact and uniform organic/inorganic coatings of the desired thickness and adhesion on metal surfaces by applying an electric field to the particles of coating precursor. EPD basic principles for coatings deposition concerning fundamental explanations and considerations of practical parameters of the process are presented. Cataphoretic deposition has become popular because it can apply organic coatings to complex structures that are otherwise very difficult to coat. These coatings were found to improve the characteristics of the substrate, such as biocompatibility, appearance and the resistance to the corrosion processes. The key EPD parameters are composition, pH value and viscosity of deposition medium, as well as zeta potential of the particles, electric field strength, etc. A special survey is given to the process of anaphoretic deposition, which is relatively new, and its advantages over cataphoretic deposition are discussed. Through the process of joint anaphoresis/substrate anodization process, the surface of the substrate is simultaneously anodized and modified by incorporation of the foreign particles into the anodic layer. Resulting coatings of mixed composition of better adhesion and corrosion resistance with respect to cataphoretically-deposited coatings are obtained.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68516583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In the present work a computational study of the chemical reactivity of alliin at the X/DGDZVP level of theory (where X=B3LYP, M06, M06L and wB97XD) was performed. The distribution of active sites on alliin was determined by evaluating the Fukui function. For electrophilic attacks, the more reactive sites are on the carbon atoms of the prop-2-ene moiety. The more active sites for nucleophilic attacks are located on the thioether group. In the case of free radical attacks, the more reactive sites are on the carbonyl, thioether and prop-2-ene moieties. Additionally, the molecular docking study revealed that, alliin is able to dock to the Mproteasepro of SARS-CoV-2 through interactions with the catalytic CYS145-HSD164 dyad via Van der Waals interactions, with MET49 with interactions alkyl-type ions and with PHE140 by hydrogen bonds. Also, the molecular dynamic study indicates that alliin remains in the pocket site. Last result suggests that this molecule is a potential candidate for further in vitro evaluation as a drug for the treatment of the major protease-based SARS-CoV-2 virus.
{"title":"Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-COV-2","authors":"Wendolyne López-Orozco, Humberto Mendoza-Huizar, Giaan Álvarez-Romero, Jesús Torres-Valencia, Maricruz Sanchez-Zavala","doi":"10.2298/jsc230817078l","DOIUrl":"https://doi.org/10.2298/jsc230817078l","url":null,"abstract":"In the present work a computational study of the chemical reactivity of alliin at the X/DGDZVP level of theory (where X=B3LYP, M06, M06L and wB97XD) was performed. The distribution of active sites on alliin was determined by evaluating the Fukui function. For electrophilic attacks, the more reactive sites are on the carbon atoms of the prop-2-ene moiety. The more active sites for nucleophilic attacks are located on the thioether group. In the case of free radical attacks, the more reactive sites are on the carbonyl, thioether and prop-2-ene moieties. Additionally, the molecular docking study revealed that, alliin is able to dock to the Mproteasepro of SARS-CoV-2 through interactions with the catalytic CYS145-HSD164 dyad via Van der Waals interactions, with MET49 with interactions alkyl-type ions and with PHE140 by hydrogen bonds. Also, the molecular dynamic study indicates that alliin remains in the pocket site. Last result suggests that this molecule is a potential candidate for further in vitro evaluation as a drug for the treatment of the major protease-based SARS-CoV-2 virus.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135009393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In recent years, there has been a growing focus on the reuse of metallic components from waste electrical and electronic equipment (WEEE) which refers to electrical and electronic equipment that has become obsolete, stopped working, or developed defects during production. In this research, shaking table was selected as a gravity concentration tool for the recovery of copper from the light components. The flowsheet included comminution, gravimetric concentration and physical/chemical characterization of feed material and products. The process parameters were deck angle (degrees), motion frequency (Hz), wash water rate (Lpm), and particle size diameter. The Box Behnken Design (BBD) was used to optimize the performance of the wet shaking table and to identify the ideal combination of its operating parameters. By analysing the experimental design, it was found that the optimal settings for deck angle, motion frequency, wash water rate, and particle size diameter were 2 degrees, 50 Hz, 12 Lpm, and -500+300 mm, respectively. These optimal settings were located near the central points of the experimental design, suggesting that the actual optimal point could be within the design space.
{"title":"Recovery of copper from printed circuit boards (PCBS) using shaking table","authors":"Özge Gök, Şen Akar","doi":"10.2298/jsc230316056g","DOIUrl":"https://doi.org/10.2298/jsc230316056g","url":null,"abstract":"In recent years, there has been a growing focus on the reuse of metallic components from waste electrical and electronic equipment (WEEE) which refers to electrical and electronic equipment that has become obsolete, stopped working, or developed defects during production. In this research, shaking table was selected as a gravity concentration tool for the recovery of copper from the light components. The flowsheet included comminution, gravimetric concentration and physical/chemical characterization of feed material and products. The process parameters were deck angle (degrees), motion frequency (Hz), wash water rate (Lpm), and particle size diameter. The Box Behnken Design (BBD) was used to optimize the performance of the wet shaking table and to identify the ideal combination of its operating parameters. By analysing the experimental design, it was found that the optimal settings for deck angle, motion frequency, wash water rate, and particle size diameter were 2 degrees, 50 Hz, 12 Lpm, and -500+300 mm, respectively. These optimal settings were located near the central points of the experimental design, suggesting that the actual optimal point could be within the design space.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68517146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The interactions of actinomycin D (ActD) anticancer drug with two bile salts having different hydrophobicity (sodium cholate (NaC) and sodium deoxycolate (NaDC)) and the influence of these bile salts aggregates on the (ActD-DNA) complex was investigated in 10 mM phosphate buffer (pH 7.4) by UV-Vis spectroscopy (absorption and thermal denaturation). The binding strength of ActD to NaDC is higher than for NaC, and this difference attests stronger hydrophobic interactions between ActD and NaDC micelles. Also, the partition coefficient is significantly higher for NaDC micelles than NaC micelles, in line with larger aggregates formed by NaDC. The spectral profile of actinomycin D molecules into NaC and NaDC micelles in comparison with different solvents implies that actinomycin D molecule experiences a hydrophobic environment in bile salts aggregates. Regarding the influence of NaC and NaDC aggregates on the (ActD-DNA) complex, it was shown that the presence of both bile salts micelles do not induce the deintercalation of actinomycin D molecules from DNA duplex.
{"title":"Binding interactions of actinomycin D anticancer drug with bile salts micelles","authors":"A. Toader, I. Dascalu, E. Neacsu, M. Enache","doi":"10.2298/jsc221102004t","DOIUrl":"https://doi.org/10.2298/jsc221102004t","url":null,"abstract":"The interactions of actinomycin D (ActD) anticancer drug with two bile salts having different hydrophobicity (sodium cholate (NaC) and sodium deoxycolate (NaDC)) and the influence of these bile salts aggregates on the (ActD-DNA) complex was investigated in 10 mM phosphate buffer (pH 7.4) by UV-Vis spectroscopy (absorption and thermal denaturation). The binding strength of ActD to NaDC is higher than for NaC, and this difference attests stronger hydrophobic interactions between ActD and NaDC micelles. Also, the partition coefficient is significantly higher for NaDC micelles than NaC micelles, in line with larger aggregates formed by NaDC. The spectral profile of actinomycin D molecules into NaC and NaDC micelles in comparison with different solvents implies that actinomycin D molecule experiences a hydrophobic environment in bile salts aggregates. Regarding the influence of NaC and NaDC aggregates on the (ActD-DNA) complex, it was shown that the presence of both bile salts micelles do not induce the deintercalation of actinomycin D molecules from DNA duplex.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68515512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohamed Aissaoui, B. Belhani, Abdelmoumen Boulebnane, A. Bouzina, S. Djilani
The absence of designated coronavirus disease 19 (Covid-19) remedies and lack of treatment protocols drove scientists to propose new small molecules and to attempt to repurpose existing drugs against various targets of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in order to bring forward efficient solutions. The main protease (Mpro) is one of the most promising drug targets due to its crucial role in fighting viral replication. Several antiviral drugs have been used in an attempt to overcome the pandemic, such as Hydroxychloroquine (HCQ). Despite its perceived positive outcomes in the beginning of the disease, HCQ was associated with a few drawbacks such as insolubility, toxicity, and cardiac adverse effects. Therefore, in the present study, we have performed a structure-based virtual screening approach to identify structurally modified ligands of chloroquinoline (CQ) scaffold with good solubility, absorption, and permeation aiming to eventually suggest a more dependable alternative. PDB ID: 7BRP Mpro was chosen as the most reliable receptor after cross-docking calculation using 30 crystal structures. Then, a SiteMap analysis was carried out and a total of 231,456 structurally modified compounds of CQ scaffold were suggested. After Lipinski criteria filtration, 64,312 molecules were docked and their MM-GBSA free binding energy was calculated. Next, ADME descriptors were calculated, and 12 molecules with ADME properties better than that of HCQ were identified. The resultant molecules were subjected to molecular dynamics (MD) simulation for 100 ns. The results of the study indicate that 3 molecules (CQ_22; CQ_2 and CQ_56) show better interactions and stability with the Mpro receptor. Binding interaction analysis indicates that GLU143, THR26, and HIS41 amino acids are potential binding hot-spot residues for the remaining 3 ligands.
{"title":"Diversifying the chloroquinoline scaffold against SARS-COV-2 main protease: Virtual screening approach using cross-docking, sitemap analysis and molecular dynamics simulation","authors":"Mohamed Aissaoui, B. Belhani, Abdelmoumen Boulebnane, A. Bouzina, S. Djilani","doi":"10.2298/jsc221017003a","DOIUrl":"https://doi.org/10.2298/jsc221017003a","url":null,"abstract":"The absence of designated coronavirus disease 19 (Covid-19) remedies and lack of treatment protocols drove scientists to propose new small molecules and to attempt to repurpose existing drugs against various targets of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in order to bring forward efficient solutions. The main protease (Mpro) is one of the most promising drug targets due to its crucial role in fighting viral replication. Several antiviral drugs have been used in an attempt to overcome the pandemic, such as Hydroxychloroquine (HCQ). Despite its perceived positive outcomes in the beginning of the disease, HCQ was associated with a few drawbacks such as insolubility, toxicity, and cardiac adverse effects. Therefore, in the present study, we have performed a structure-based virtual screening approach to identify structurally modified ligands of chloroquinoline (CQ) scaffold with good solubility, absorption, and permeation aiming to eventually suggest a more dependable alternative. PDB ID: 7BRP Mpro was chosen as the most reliable receptor after cross-docking calculation using 30 crystal structures. Then, a SiteMap analysis was carried out and a total of 231,456 structurally modified compounds of CQ scaffold were suggested. After Lipinski criteria filtration, 64,312 molecules were docked and their MM-GBSA free binding energy was calculated. Next, ADME descriptors were calculated, and 12 molecules with ADME properties better than that of HCQ were identified. The resultant molecules were subjected to molecular dynamics (MD) simulation for 100 ns. The results of the study indicate that 3 molecules (CQ_22; CQ_2 and CQ_56) show better interactions and stability with the Mpro receptor. Binding interaction analysis indicates that GLU143, THR26, and HIS41 amino acids are potential binding hot-spot residues for the remaining 3 ligands.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68515720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Todan, D. Culiță, Mirabela Soare, R. Ion, R. Fierăscu, M. Maganu
search of new food-grade pH sensitive formulations, red beet extract rich in betacyanin was included in different inorganic matrices based on silica and aluminosilicate to improve the stability of the dye. By the direct method of encapsulation of the pigments in silica support, stabilizing agents such as inclusion complex forming ?-cyclodextrin and ascorbic acid were added. The post loading system assumes the synthesis of porous silica and aluminosilicate powders and the adsorption of the beet extract by these supports. The unloaded carriers were structurally and texturally characterized (X-ray diffraction, FTIR, N2-physisorption). The presence of betanin, approved as a red food colorant, was evidenced by UV-vis spectroscopy in all the hosts. Color properties were investigated as well as the pH generated color variations of the powders exposed to ammonia in the head-space of a sealed vessel. The obtained results could widen the field of applications of beet extract, the prepared ecological formulations could provide added value to edible products packaging.
{"title":"Immobilization of natural betalain pigments in inorganic hosts","authors":"L. Todan, D. Culiță, Mirabela Soare, R. Ion, R. Fierăscu, M. Maganu","doi":"10.2298/jsc221028010t","DOIUrl":"https://doi.org/10.2298/jsc221028010t","url":null,"abstract":"search of new food-grade pH sensitive formulations, red beet extract rich in betacyanin was included in different inorganic matrices based on silica and aluminosilicate to improve the stability of the dye. By the direct method of encapsulation of the pigments in silica support, stabilizing agents such as inclusion complex forming ?-cyclodextrin and ascorbic acid were added. The post loading system assumes the synthesis of porous silica and aluminosilicate powders and the adsorption of the beet extract by these supports. The unloaded carriers were structurally and texturally characterized (X-ray diffraction, FTIR, N2-physisorption). The presence of betanin, approved as a red food colorant, was evidenced by UV-vis spectroscopy in all the hosts. Color properties were investigated as well as the pH generated color variations of the powders exposed to ammonia in the head-space of a sealed vessel. The obtained results could widen the field of applications of beet extract, the prepared ecological formulations could provide added value to edible products packaging.","PeriodicalId":17489,"journal":{"name":"Journal of The Serbian Chemical Society","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68515916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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