Thymus serpyllum L.,often known as wild thyme,has been used since ancient times due to its multifaceted culinary and medicinal attributes.It is usually utilized in folk medicine to manage different health issues.This ...Thymus serpyllum L.,often known as wild thyme,has been used since ancient times due to its multifaceted culinary and medicinal attributes.It is usually utilized in folk medicine to manage different health issues.This work aimed to investigate the chemical composition and biological characteristics of T.serpyllum essential oil(EO),including its antimicrobial,antioxidant,and anti-inflammatory capabilities.Moreover,we have prompted an in-silico simulation to reveal the underlying mode of action of these properties.The chemical characterization of T.serpyllum(EO)by Gas Chromatography-Mass Spectrometry(GC-MS)indicated sabinene(17.33%),terpinen-4-ol(11.73%),phellandral(13.18%),and thymol(10.54%)as main components.The antimicrobial screening utilized the disc-diffusion technique,MIC,and MBC assays.The disc-diffusion test’s results revealed significant anti-Candida activity and notable antibacterial efficacy.The MIC and MBC tests showed that T.serpyllum EO effectively stops bacterial growth,including Gram-positive and Gram-negative strains and Candida strains.The tolerance level ratio demonstrated that this EO exhibits bactericidal and fungicidal effects on all tested bacteria and Candida strains.Also,T.serpyllum EO presented effective inhibitory activity against the 5-lipoxygenase(5-LOX)enzyme(IC50=744.19±0.1µg/mL)(p<0.05).It also effectively affected FRAP,β-carotene,DPPH,and ABTS radicals.In light of these findings,T.serpyllum holds promise for diverse applications across pharmaceuticals,nutraceuticals,and the food industry.However,further research and collaboration between traditional knowledge and modern medicine are crucial to fully realizing its potential benefits in these fields.展开更多
Fusobacterium nucleatum is an anaerobic, commensal, gram-negative oral bacterium that is carcinogenic and causes a wide range of human diseases. The present study focused on the analysis of the hypothetical protein, H...Fusobacterium nucleatum is an anaerobic, commensal, gram-negative oral bacterium that is carcinogenic and causes a wide range of human diseases. The present study focused on the analysis of the hypothetical protein, HMPREF3221_01179, derived from F. nucleatum strain MJR7757B, employing various computational methods to anticipate both its structure and functional characteristics. NCBI conserved domain analysis, NCBI BLASTp and MEGA Phylogenetic tree study characterize the target protein as an outer membrane efflux protein (ToIC family) which facilitate the bacterial transmembrane transport. With a molecular weight of 52120.02 Da, an isoelectric point (pI) of 8.33, and an instability index of 29.47, the protein is anticipated to exhibit good solubility in the extracellular space and crucial stability for pharmaceutical applications. The protein’s structure meets quality standards during the construction and refinement of its 3D model. The efflux inhibitor Arginine beta-naphthylamide exhibits a significant binding affinity (-7.1 kcal/mol) to the binding site of the target protein. The in-silico analysis improves the understanding of the protein and facilitates future investigations into therapeutic medication.展开更多
BACKGROUND Colonization with Helicobacter pylori(H.pylori)has a strong correlation with gastric cancer,and the virulence factor CagA is implicated in carcinogenesis.Studies have been conducted using medicinal plants w...BACKGROUND Colonization with Helicobacter pylori(H.pylori)has a strong correlation with gastric cancer,and the virulence factor CagA is implicated in carcinogenesis.Studies have been conducted using medicinal plants with the aim of eliminating the pathogen;however,the possibility of blocking H.pylori-induced cell differentiation to prevent the onset and/or progression of tumors has not been addressed.This type of study is expensive and time-consuming,requiring in vitro and/or in vivo tests,which can be solved using bioinformatics.Therefore,prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the CagA oncoprotein.AIM To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the CagA oncoprotein of H.pylori.METHODS In this in silico study,the structures of the phenolic compounds(ligands)kaempferol,myricetin,quercetin,ponciretin(flavonoids),and chlorogenic acid(phenolic acid)were selected from the PubChem database.These phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate H.pylori infection.The three-dimensional structure model of the CagA oncoprotein of H.pylori(receptor)was obtained through molecular modeling using computational tools from the I-Tasser platform,employing the threading methodology.The primary sequence of CagA was sourced from GenBank(BAK52797.1).A screening was conducted to identify binding sites in the structure of the CagA oncoprotein that could potentially interact with the ligands,utilizing the GRaSP online platform.Both the ligands and receptor were prepared for molecular docking using AutoDock Tools 4(ADT)software,and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 software.Two sets of simulations were performed:One involving the central region of CagA with phenolic compounds,and another involving the carboxy-terminus region of CagA with phenolic compounds.The receptor-ligand complexes were then analyzed using PyMol and BIOVIA Discovery Studio software.RESULTS The structure model obtained for the CagA oncoprotein exhibited high quality(C-score=0.09)and was validated using parameters from the MolProbity platform.The GRaSP online platform identified 24 residues(phenylalanine and leucine)as potential binding sites on the CagA oncoprotein.Molecular docking simulations were conducted with the three-dimensional model of the CagA oncoprotein.No complexes were observed in the simulations between the carboxy-terminus region of CagA and the phenolic compounds;however,all phenolic compounds interacted with the central region of the oncoprotein.Phenolic compounds and CagA exhibited significant affinity energy(-7.9 to-9.1 kcal/mol):CagA/kaempferol formed 28 chemical bonds,CagA/myricetin formed 18 chemical bonds,CagA/quercetin formed 16 chemical bonds,CagA/ponciretin formed 13 chemical bonds,and CagA/chlorogenic acid formed 17 chemical bonds.Although none of the phenolic compounds directly bound to the amino acid residues of the K-Xn-R-X-R membrane binding motif,all of them bound to residues,mostly positively or negatively charged,located near this region.CONCLUSION In silico,the tested phenolic compounds formed stable complexes with CagA.Therefore,they could be tested in vitro and/or in vivo to validate the findings,and to assess interference in CagA/cellular target interactions and in the oncogenic differentiation of gastric cells.展开更多
The synthesis of new 4-imino-4H-chromeno[2,3-d]pyrimidin-3(5H)-amine in four steps including one step under microwave dielectric heating is reported. The structural identity of the synthesized compounds was establishe...The synthesis of new 4-imino-4H-chromeno[2,3-d]pyrimidin-3(5H)-amine in four steps including one step under microwave dielectric heating is reported. The structural identity of the synthesized compounds was established according to their spectroscopic analysis, such as FT-IR, NMR and mass spectroscopy. These new compounds were tested for their antiproliferative activities on seven representative human tumoral cell lines (Huh7 D12, Caco2, MDA-MB231, MDA-MB468, HCT116, PC3 and MCF7) and also on fibroblasts. Among them, only the compounds 6c showed micromolar cytotoxic activity on tumor cell lines (1.8 50 50 > 25 μM). Finally, in silico ADMET studies ware performed to investigate the possibility of using of the identified compound 6c as potential anti-tumor compound.展开更多
Background: Cosmetic formulations, and particularly solar products which contain mineral and chemical UV-filters, are often suspected of causing harmful effects on marine fauna and flora. After the publication of our ...Background: Cosmetic formulations, and particularly solar products which contain mineral and chemical UV-filters, are often suspected of causing harmful effects on marine fauna and flora. After the publication of our work in 2019 concerning the ecotoxicological effects of such formulations on corals (Seriatopora hystrix), we here provide some new information about the biodegradability and the ecotoxicological effects of these products on marine zoo- and phytoplankton. Therefore, we choose to realize in silico and in vitro studies of the biodegradability of several solar products but also to evaluate the ecotoxicological effects of these products on one phytoplankton, i.e. Phaeodactylum tricornutum, and one zooplankton, i.e. Acartia tonsa, of a great importance for sea species survival (notably as sources of food). Materials and methods: Two different approaches were used to study the biodegradability of the tested products: One in silico method and an in vitro one. 2 solar products were involved in the in silico study which consisted in the determination of the degradation factor (DF) of each ingredient of the tested formulas in order to finally obtain their estimated biodegradability percentage. Already available data concerning each ingredient coupled to a computer model developed with one of our partners were used to achieve this study. The in vitro study involved 8 formulas containing UV-filters and was led by following the OECD 301 F guidelines. Ecotoxicological studies of 7 of the formulas containing UV-filters were for their part realized by following the ISO 10253 guidelines for the experiments led with Phaeodactylum tricornutum, and the ISO 14669 guidelines for the experiments led with Acartia tonsa. In these studies, the effect of each tested product on crustaceans’ mortality and algal growth inhibition was assessed. Results: The in silico study predicted that formulas containing chemical UV-filters display a high biodegradability (superior to the threshold value of 60% given by the OECD 301 F guidelines). In the in vitro part of our work, the 8 tested formulas showed a biodegradability slightly inferior to the one predicted in the in silico experiments. Therefore, in order to evaluate if these calculated biodegradability value could have significant harmful effects on zoo- or phytoplankton, we studied the effect of our products regarding the growth inhibition on Phaeodactylum tricornutum and the mortality on Acartia tonsa. In this last part of the study, all the tested products were classified as “non ecotoxic” following an internal classification based on Part 4 entitled “Environmental Hazards” of Globally Harmonized System of Classification and Labelling of Chemicals (GHS), 9<sup>th</sup> edition (2021). Conclusions: These results are notably in line with those published by our teams in 2019 on the effects of solar cosmetic products on corals and seem to confirm that formulas containing mineral and chemical UV-filters can be daily used without displaying significant noxious effects on marine fauna and flora. .展开更多
根据日本晴cab4基因序列(GenBank:AK104499.1)设计引物,用RT-PCR的方法从籼稻9311中克隆了叶绿素a/b结合蛋白基因的全长cDNA,命名为cab-9311(cab gene from 9311)。insilico分析表明:cab-9311与cab4基因同源性为99%,编码的蛋白含有244...根据日本晴cab4基因序列(GenBank:AK104499.1)设计引物,用RT-PCR的方法从籼稻9311中克隆了叶绿素a/b结合蛋白基因的全长cDNA,命名为cab-9311(cab gene from 9311)。insilico分析表明:cab-9311与cab4基因同源性为99%,编码的蛋白含有244个氨基酸,与cab4基因编码的蛋白同源性为98%。蛋白分子质量为26.9kD,理论等电点为6.52。第54位~第216位氨基酸是一个典型的叶绿素a/b结合蛋白功能域(chlorophyll a/bbinding domain)。跨膜分析和蛋白质三级预测显示,该蛋白在C端有一个典型的跨膜区。亚细胞定位分析表明该蛋白定位于叶绿体,是一个叶绿体内囊体膜上的锚定蛋白。展开更多
There are many studies on enzymatic pathways of anthocyanin biosynthesis, but little is known about the anthocyanins transport in Oryze sativa. In silico analysis, the OsMRP15 (LOC_Os06g06440), an orthologous gene of ...There are many studies on enzymatic pathways of anthocyanin biosynthesis, but little is known about the anthocyanins transport in Oryze sativa. In silico analysis, the OsMRP15 (LOC_Os06g06440), an orthologous gene of mazie anthocyanin transporter ZmMRP3, has been identified in rice. The OsMRP15 contained a 4425bp open reading frame (ORF) encoding a 1475 amino acid protein, belonging to a MRP subfamily of ABC transporters, and has a high sequence identity, very similar protein structure, and the same arrangement of domains to ZmMRP3, but the genomic structure of OsMRP15 was significant difference with ZmMRP3. The prediction promoter of OsMRP15 has many presumed anthocyanin regulatory sites. The phylogenetic analysis of MRPs in rice, mazie and Arabidopsis showed that OsMRP15 and ZmMRP3 belonged to the same subbranch. The expression pattern indicated that OsMRP15 was co-expression with two anthocyanin transcription factors. These analysis results implied that as an ortholog of ZmMRP3, the function of OsMRP15 was possibly as a membrane-bound transporter required for vacuolar uptake of anthocyanins in rice.展开更多
Phospholipase D (PLD, EC 3.1.4.4) plays an important role in adaptive response of postharvest fruit to environment. In this study, a novel cDNA of PLDα was isolated with the strategy of in silico cloning in combina...Phospholipase D (PLD, EC 3.1.4.4) plays an important role in adaptive response of postharvest fruit to environment. In this study, a novel cDNA of PLDα was isolated with the strategy of in silico cloning in combination with RT-PCR from peach (Prunus persica L. cv. Jiubao). The obtained PLDα gene contained a complete open reading frame encoding a 92- kDa protein of 810 amino acid residues, which possessed the characteristic C2 domain and two catalytic HKD motifs. The alignment analysis of the deduced peach PLDa protein with other known PLDα family proteins indicated that peach PLDα was conserved and highly homologous with strawberry PLDα. Semi-quantitative RT-PCR and Northern blot analysis indicated PLDα mRNA in peach fruits could be induced by low temperature. This work provided a scientific basis for further investigating the mechanism of postharvest fruit adaptation to low temperature.展开更多
In recent years, Jatropha curcas L. has gained popularity as a potential biodiesel plant. The varying oil content, reported between accessions belonging to different agroclimatic zones, has necessitated the assessment...In recent years, Jatropha curcas L. has gained popularity as a potential biodiesel plant. The varying oil content, reported between accessions belonging to different agroclimatic zones, has necessitated the assessment of the existing genetic variability to generate reliable molecular markers for selection of high oil yielding variety. EST derived SSR markers are more useful than genomic markers as they represent the transcriptome, thus, directly linked to functional genes. The present report describes the in silico mining of the microsatellites (SSRs) using J. curcas ESTs from various tissues viz. embryo, root, leaf and seed available in the public domain of NCBI. A total of 13,513 ESTs were downloaded. From these ESTs, 7552 unigenes were obtained and 395 SSRs were generated from 377 SSR-ESTs. These EST-SSRs can be used as potential microsatellite markers for diversity analysis, MAS etc. Since the Jatropha genes carrying SSRs have been identified in this study, thus, EST-SSRs directly linked to genes will be useful for developing trait linked markers.展开更多
In silico methods to study biodegradable implants have recently received increasing attention due to their potential in reducing experimental time and cost. An important application case for in silico methods are magn...In silico methods to study biodegradable implants have recently received increasing attention due to their potential in reducing experimental time and cost. An important application case for in silico methods are magnesium(Mg)-based biodegradable implants, as they represent a powerful alternative to traditional materials used for temporary orthopaedic applications. Controlling Mg alloy degradation is critical to designing an implant that supports the bone healing process. To simulate different aspects of this biodegradation process, several mathematical models have been proposed with the ultimate aim of replacing laboratory experiments with computational modeling. In this review, we provide a comprehensive and critical discussion of the published models and their performance with respect to capturing the complexity of the biodegradation process. This complexity is presented initially. Additionally, the present review discusses the different approaches of optimizing and quantifying the different sources of errors and uncertainties within the proposed models.展开更多
5-Dimethylaminopropylamino-8-hydroxytriazoloacridinone(C-1305)is a promising antitumor compound developed in our laboratory.A better understanding of its metabolic transformations is still needed to explain the multid...5-Dimethylaminopropylamino-8-hydroxytriazoloacridinone(C-1305)is a promising antitumor compound developed in our laboratory.A better understanding of its metabolic transformations is still needed to explain the multidirectional mechanism of pharmacological action of triazoloacridinone derivatives at all.Thus,the aim of the current work was to predict oxidative pathways of C-1305 that would reflect its phase I metabolism.The multi-tool analysis of C-1305 metabolism included electrochemical conversion and in silico sites of metabolism predictions in relation to liver microsomal model.In the framework of the first approach,an electrochemical cell was coupled on-line to an electrospray ionization mass spectrometer.The effluent of the electrochemical cell was also injected onto a liquid chromatography column for the separation of different products formed prior to mass spectrometry analysis.In silico studies were performed using MetaSite software.Standard microsomal incubation was employed as a reference procedure.We found that C-1305 underwent electrochemical oxidation primarily on the dialkylaminoalkylamino moiety.An unknown N-dealkylated and hydroxylated C-1305 products have been identified.The electrochemical system was also able to simulate oxygenation reactions.Similar pattern of C-1305 metabolism has been predicted using in silico approach.Both proposed strategies showed high agreement in relation to the generated metabolic products of C-1305.Thus,we conclude that they can be considered as simple alternatives to enzymatic assays,affording time and cost efficiency.展开更多
The formation of calcium phosphate phases is extremely important in a biomedical engineering context. These phosphates are used in many applications, such as grafts, drug-delivery processes and evaluation of the bioac...The formation of calcium phosphate phases is extremely important in a biomedical engineering context. These phosphates are used in many applications, such as grafts, drug-delivery processes and evaluation of the bioactivity of metallic surfaces. Considering this scenario, it is useful to evaluate the thermodynamic conditions for the precipitation of phosphates of biomedical interest, mainly hydroxyapatite. In this work, we investigate the effects of two important factors using a thermodynamic framework: 1) carbon dioxide partial pressure;and 2) buffer type (2-Amino-2-hydroxy- methyl-propane-1,3-diol, known as TRIS and 2-[4-(2-hydroxyethyl)piperazin-1-yl] ethanesulfonic acid, also called HEPES), on the driving force behind the precipitation of calcium phosphates in simulated body fluids. The in silico results show that the pH value is governed by carbon dioxide content, as expected to occur in vivo. Moreover, the buffers can deplete the free calcium available in solution and, consequently, can cause difficulties in the calcium phosphate precipitation.展开更多
Objective Rheumatoid arthritis(RA)is an autoimmune disease involving the synovial lining of the major joints.Current therapies have noteworthy side effects.Our study involved in silico evaluation of Ehretia laevis(E.l...Objective Rheumatoid arthritis(RA)is an autoimmune disease involving the synovial lining of the major joints.Current therapies have noteworthy side effects.Our study involved in silico evaluation of Ehretia laevis(E.laevis)phytoconstituents targeting tumor necrosis factor-α(TNF-α).Methods Molecular docking studies performed to investigate the binding pattern of the plant E.laevis phytoconstituents along with the crystal structure of TNF-α(PDB ID:2 AZ5)using AutoDock Vina followed by a study of interacting amino acid residues and their influence on the inhibitory potentials of the active constituents.Further the pharmacokinetic profile and toxicity screening carried out using Swiss ADME and pk CSM.Results The docked results suggest that lupeol(-9.4 kcal/mol)andα-amyrin(-9.4 kcal/mol)has best affinity towards TNF-αcompared to standard drug thalidomide(-7.4 kcal/mol).The active chemical constituents represents better interaction with the conserved catalytic residues,leading to the inhibition/blockade of the TNF-α-associated signaling pathway in RA.Furthermore,pharmacokinetics and toxicity parameters of these phytochemicals were within acceptable limits according to ADMET studies.Conclusion The binding potential of phytoconstituents targeting TNF-αshowed promising results.Nonetheless,it encourages the traditional use of E.laevis and provides vital information on drug development and clinical treatment.展开更多
文摘Thymus serpyllum L.,often known as wild thyme,has been used since ancient times due to its multifaceted culinary and medicinal attributes.It is usually utilized in folk medicine to manage different health issues.This work aimed to investigate the chemical composition and biological characteristics of T.serpyllum essential oil(EO),including its antimicrobial,antioxidant,and anti-inflammatory capabilities.Moreover,we have prompted an in-silico simulation to reveal the underlying mode of action of these properties.The chemical characterization of T.serpyllum(EO)by Gas Chromatography-Mass Spectrometry(GC-MS)indicated sabinene(17.33%),terpinen-4-ol(11.73%),phellandral(13.18%),and thymol(10.54%)as main components.The antimicrobial screening utilized the disc-diffusion technique,MIC,and MBC assays.The disc-diffusion test’s results revealed significant anti-Candida activity and notable antibacterial efficacy.The MIC and MBC tests showed that T.serpyllum EO effectively stops bacterial growth,including Gram-positive and Gram-negative strains and Candida strains.The tolerance level ratio demonstrated that this EO exhibits bactericidal and fungicidal effects on all tested bacteria and Candida strains.Also,T.serpyllum EO presented effective inhibitory activity against the 5-lipoxygenase(5-LOX)enzyme(IC50=744.19±0.1µg/mL)(p<0.05).It also effectively affected FRAP,β-carotene,DPPH,and ABTS radicals.In light of these findings,T.serpyllum holds promise for diverse applications across pharmaceuticals,nutraceuticals,and the food industry.However,further research and collaboration between traditional knowledge and modern medicine are crucial to fully realizing its potential benefits in these fields.
文摘Fusobacterium nucleatum is an anaerobic, commensal, gram-negative oral bacterium that is carcinogenic and causes a wide range of human diseases. The present study focused on the analysis of the hypothetical protein, HMPREF3221_01179, derived from F. nucleatum strain MJR7757B, employing various computational methods to anticipate both its structure and functional characteristics. NCBI conserved domain analysis, NCBI BLASTp and MEGA Phylogenetic tree study characterize the target protein as an outer membrane efflux protein (ToIC family) which facilitate the bacterial transmembrane transport. With a molecular weight of 52120.02 Da, an isoelectric point (pI) of 8.33, and an instability index of 29.47, the protein is anticipated to exhibit good solubility in the extracellular space and crucial stability for pharmaceutical applications. The protein’s structure meets quality standards during the construction and refinement of its 3D model. The efflux inhibitor Arginine beta-naphthylamide exhibits a significant binding affinity (-7.1 kcal/mol) to the binding site of the target protein. The in-silico analysis improves the understanding of the protein and facilitates future investigations into therapeutic medication.
文摘BACKGROUND Colonization with Helicobacter pylori(H.pylori)has a strong correlation with gastric cancer,and the virulence factor CagA is implicated in carcinogenesis.Studies have been conducted using medicinal plants with the aim of eliminating the pathogen;however,the possibility of blocking H.pylori-induced cell differentiation to prevent the onset and/or progression of tumors has not been addressed.This type of study is expensive and time-consuming,requiring in vitro and/or in vivo tests,which can be solved using bioinformatics.Therefore,prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the CagA oncoprotein.AIM To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the CagA oncoprotein of H.pylori.METHODS In this in silico study,the structures of the phenolic compounds(ligands)kaempferol,myricetin,quercetin,ponciretin(flavonoids),and chlorogenic acid(phenolic acid)were selected from the PubChem database.These phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate H.pylori infection.The three-dimensional structure model of the CagA oncoprotein of H.pylori(receptor)was obtained through molecular modeling using computational tools from the I-Tasser platform,employing the threading methodology.The primary sequence of CagA was sourced from GenBank(BAK52797.1).A screening was conducted to identify binding sites in the structure of the CagA oncoprotein that could potentially interact with the ligands,utilizing the GRaSP online platform.Both the ligands and receptor were prepared for molecular docking using AutoDock Tools 4(ADT)software,and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 software.Two sets of simulations were performed:One involving the central region of CagA with phenolic compounds,and another involving the carboxy-terminus region of CagA with phenolic compounds.The receptor-ligand complexes were then analyzed using PyMol and BIOVIA Discovery Studio software.RESULTS The structure model obtained for the CagA oncoprotein exhibited high quality(C-score=0.09)and was validated using parameters from the MolProbity platform.The GRaSP online platform identified 24 residues(phenylalanine and leucine)as potential binding sites on the CagA oncoprotein.Molecular docking simulations were conducted with the three-dimensional model of the CagA oncoprotein.No complexes were observed in the simulations between the carboxy-terminus region of CagA and the phenolic compounds;however,all phenolic compounds interacted with the central region of the oncoprotein.Phenolic compounds and CagA exhibited significant affinity energy(-7.9 to-9.1 kcal/mol):CagA/kaempferol formed 28 chemical bonds,CagA/myricetin formed 18 chemical bonds,CagA/quercetin formed 16 chemical bonds,CagA/ponciretin formed 13 chemical bonds,and CagA/chlorogenic acid formed 17 chemical bonds.Although none of the phenolic compounds directly bound to the amino acid residues of the K-Xn-R-X-R membrane binding motif,all of them bound to residues,mostly positively or negatively charged,located near this region.CONCLUSION In silico,the tested phenolic compounds formed stable complexes with CagA.Therefore,they could be tested in vitro and/or in vivo to validate the findings,and to assess interference in CagA/cellular target interactions and in the oncogenic differentiation of gastric cells.
文摘The synthesis of new 4-imino-4H-chromeno[2,3-d]pyrimidin-3(5H)-amine in four steps including one step under microwave dielectric heating is reported. The structural identity of the synthesized compounds was established according to their spectroscopic analysis, such as FT-IR, NMR and mass spectroscopy. These new compounds were tested for their antiproliferative activities on seven representative human tumoral cell lines (Huh7 D12, Caco2, MDA-MB231, MDA-MB468, HCT116, PC3 and MCF7) and also on fibroblasts. Among them, only the compounds 6c showed micromolar cytotoxic activity on tumor cell lines (1.8 50 50 > 25 μM). Finally, in silico ADMET studies ware performed to investigate the possibility of using of the identified compound 6c as potential anti-tumor compound.
文摘Background: Cosmetic formulations, and particularly solar products which contain mineral and chemical UV-filters, are often suspected of causing harmful effects on marine fauna and flora. After the publication of our work in 2019 concerning the ecotoxicological effects of such formulations on corals (Seriatopora hystrix), we here provide some new information about the biodegradability and the ecotoxicological effects of these products on marine zoo- and phytoplankton. Therefore, we choose to realize in silico and in vitro studies of the biodegradability of several solar products but also to evaluate the ecotoxicological effects of these products on one phytoplankton, i.e. Phaeodactylum tricornutum, and one zooplankton, i.e. Acartia tonsa, of a great importance for sea species survival (notably as sources of food). Materials and methods: Two different approaches were used to study the biodegradability of the tested products: One in silico method and an in vitro one. 2 solar products were involved in the in silico study which consisted in the determination of the degradation factor (DF) of each ingredient of the tested formulas in order to finally obtain their estimated biodegradability percentage. Already available data concerning each ingredient coupled to a computer model developed with one of our partners were used to achieve this study. The in vitro study involved 8 formulas containing UV-filters and was led by following the OECD 301 F guidelines. Ecotoxicological studies of 7 of the formulas containing UV-filters were for their part realized by following the ISO 10253 guidelines for the experiments led with Phaeodactylum tricornutum, and the ISO 14669 guidelines for the experiments led with Acartia tonsa. In these studies, the effect of each tested product on crustaceans’ mortality and algal growth inhibition was assessed. Results: The in silico study predicted that formulas containing chemical UV-filters display a high biodegradability (superior to the threshold value of 60% given by the OECD 301 F guidelines). In the in vitro part of our work, the 8 tested formulas showed a biodegradability slightly inferior to the one predicted in the in silico experiments. Therefore, in order to evaluate if these calculated biodegradability value could have significant harmful effects on zoo- or phytoplankton, we studied the effect of our products regarding the growth inhibition on Phaeodactylum tricornutum and the mortality on Acartia tonsa. In this last part of the study, all the tested products were classified as “non ecotoxic” following an internal classification based on Part 4 entitled “Environmental Hazards” of Globally Harmonized System of Classification and Labelling of Chemicals (GHS), 9<sup>th</sup> edition (2021). Conclusions: These results are notably in line with those published by our teams in 2019 on the effects of solar cosmetic products on corals and seem to confirm that formulas containing mineral and chemical UV-filters can be daily used without displaying significant noxious effects on marine fauna and flora. .
文摘There are many studies on enzymatic pathways of anthocyanin biosynthesis, but little is known about the anthocyanins transport in Oryze sativa. In silico analysis, the OsMRP15 (LOC_Os06g06440), an orthologous gene of mazie anthocyanin transporter ZmMRP3, has been identified in rice. The OsMRP15 contained a 4425bp open reading frame (ORF) encoding a 1475 amino acid protein, belonging to a MRP subfamily of ABC transporters, and has a high sequence identity, very similar protein structure, and the same arrangement of domains to ZmMRP3, but the genomic structure of OsMRP15 was significant difference with ZmMRP3. The prediction promoter of OsMRP15 has many presumed anthocyanin regulatory sites. The phylogenetic analysis of MRPs in rice, mazie and Arabidopsis showed that OsMRP15 and ZmMRP3 belonged to the same subbranch. The expression pattern indicated that OsMRP15 was co-expression with two anthocyanin transcription factors. These analysis results implied that as an ortholog of ZmMRP3, the function of OsMRP15 was possibly as a membrane-bound transporter required for vacuolar uptake of anthocyanins in rice.
基金supported by China Post doctoral Science Foundation (20070420095)the National Natural Science Foundation of China (30571279,30871699,30901012)+1 种基金Innovative Foundation of Shanghai UniversitySystems Biology Research Foundation of Shanghai University
文摘Phospholipase D (PLD, EC 3.1.4.4) plays an important role in adaptive response of postharvest fruit to environment. In this study, a novel cDNA of PLDα was isolated with the strategy of in silico cloning in combination with RT-PCR from peach (Prunus persica L. cv. Jiubao). The obtained PLDα gene contained a complete open reading frame encoding a 92- kDa protein of 810 amino acid residues, which possessed the characteristic C2 domain and two catalytic HKD motifs. The alignment analysis of the deduced peach PLDa protein with other known PLDα family proteins indicated that peach PLDα was conserved and highly homologous with strawberry PLDα. Semi-quantitative RT-PCR and Northern blot analysis indicated PLDα mRNA in peach fruits could be induced by low temperature. This work provided a scientific basis for further investigating the mechanism of postharvest fruit adaptation to low temperature.
文摘In recent years, Jatropha curcas L. has gained popularity as a potential biodiesel plant. The varying oil content, reported between accessions belonging to different agroclimatic zones, has necessitated the assessment of the existing genetic variability to generate reliable molecular markers for selection of high oil yielding variety. EST derived SSR markers are more useful than genomic markers as they represent the transcriptome, thus, directly linked to functional genes. The present report describes the in silico mining of the microsatellites (SSRs) using J. curcas ESTs from various tissues viz. embryo, root, leaf and seed available in the public domain of NCBI. A total of 13,513 ESTs were downloaded. From these ESTs, 7552 unigenes were obtained and 395 SSRs were generated from 377 SSR-ESTs. These EST-SSRs can be used as potential microsatellite markers for diversity analysis, MAS etc. Since the Jatropha genes carrying SSRs have been identified in this study, thus, EST-SSRs directly linked to genes will be useful for developing trait linked markers.
基金funding from the Helmholtz-Incubator project Uncertainty Quantification。
文摘In silico methods to study biodegradable implants have recently received increasing attention due to their potential in reducing experimental time and cost. An important application case for in silico methods are magnesium(Mg)-based biodegradable implants, as they represent a powerful alternative to traditional materials used for temporary orthopaedic applications. Controlling Mg alloy degradation is critical to designing an implant that supports the bone healing process. To simulate different aspects of this biodegradation process, several mathematical models have been proposed with the ultimate aim of replacing laboratory experiments with computational modeling. In this review, we provide a comprehensive and critical discussion of the published models and their performance with respect to capturing the complexity of the biodegradation process. This complexity is presented initially. Additionally, the present review discusses the different approaches of optimizing and quantifying the different sources of errors and uncertainties within the proposed models.
基金This work was supported by the National Science Center(Poland)(2012/07/D/NZ7/03395).
文摘5-Dimethylaminopropylamino-8-hydroxytriazoloacridinone(C-1305)is a promising antitumor compound developed in our laboratory.A better understanding of its metabolic transformations is still needed to explain the multidirectional mechanism of pharmacological action of triazoloacridinone derivatives at all.Thus,the aim of the current work was to predict oxidative pathways of C-1305 that would reflect its phase I metabolism.The multi-tool analysis of C-1305 metabolism included electrochemical conversion and in silico sites of metabolism predictions in relation to liver microsomal model.In the framework of the first approach,an electrochemical cell was coupled on-line to an electrospray ionization mass spectrometer.The effluent of the electrochemical cell was also injected onto a liquid chromatography column for the separation of different products formed prior to mass spectrometry analysis.In silico studies were performed using MetaSite software.Standard microsomal incubation was employed as a reference procedure.We found that C-1305 underwent electrochemical oxidation primarily on the dialkylaminoalkylamino moiety.An unknown N-dealkylated and hydroxylated C-1305 products have been identified.The electrochemical system was also able to simulate oxygenation reactions.Similar pattern of C-1305 metabolism has been predicted using in silico approach.Both proposed strategies showed high agreement in relation to the generated metabolic products of C-1305.Thus,we conclude that they can be considered as simple alternatives to enzymatic assays,affording time and cost efficiency.
文摘The formation of calcium phosphate phases is extremely important in a biomedical engineering context. These phosphates are used in many applications, such as grafts, drug-delivery processes and evaluation of the bioactivity of metallic surfaces. Considering this scenario, it is useful to evaluate the thermodynamic conditions for the precipitation of phosphates of biomedical interest, mainly hydroxyapatite. In this work, we investigate the effects of two important factors using a thermodynamic framework: 1) carbon dioxide partial pressure;and 2) buffer type (2-Amino-2-hydroxy- methyl-propane-1,3-diol, known as TRIS and 2-[4-(2-hydroxyethyl)piperazin-1-yl] ethanesulfonic acid, also called HEPES), on the driving force behind the precipitation of calcium phosphates in simulated body fluids. The in silico results show that the pH value is governed by carbon dioxide content, as expected to occur in vivo. Moreover, the buffers can deplete the free calcium available in solution and, consequently, can cause difficulties in the calcium phosphate precipitation.
文摘Objective Rheumatoid arthritis(RA)is an autoimmune disease involving the synovial lining of the major joints.Current therapies have noteworthy side effects.Our study involved in silico evaluation of Ehretia laevis(E.laevis)phytoconstituents targeting tumor necrosis factor-α(TNF-α).Methods Molecular docking studies performed to investigate the binding pattern of the plant E.laevis phytoconstituents along with the crystal structure of TNF-α(PDB ID:2 AZ5)using AutoDock Vina followed by a study of interacting amino acid residues and their influence on the inhibitory potentials of the active constituents.Further the pharmacokinetic profile and toxicity screening carried out using Swiss ADME and pk CSM.Results The docked results suggest that lupeol(-9.4 kcal/mol)andα-amyrin(-9.4 kcal/mol)has best affinity towards TNF-αcompared to standard drug thalidomide(-7.4 kcal/mol).The active chemical constituents represents better interaction with the conserved catalytic residues,leading to the inhibition/blockade of the TNF-α-associated signaling pathway in RA.Furthermore,pharmacokinetics and toxicity parameters of these phytochemicals were within acceptable limits according to ADMET studies.Conclusion The binding potential of phytoconstituents targeting TNF-αshowed promising results.Nonetheless,it encourages the traditional use of E.laevis and provides vital information on drug development and clinical treatment.