Background:Epidemiological studies have confirmed that longer exposure to insecticides like cypermethrin(CYP)significantly increases the risk of male reproductive toxicity.Crocus sativus L.has been recognized due to i...Background:Epidemiological studies have confirmed that longer exposure to insecticides like cypermethrin(CYP)significantly increases the risk of male reproductive toxicity.Crocus sativus L.has been recognized due to its therapeutic properties,but its exact role and molecular mechanisms in treatment of reproductive dysfunction remain unclear.Methods:During this study,36 rats were randomly divided into six groups(n=6):control,CYP-induced(60 mg/kg),standard(leuprolide 3 mg/kg)and three treatment groups receiving aqueous,ethanolic,and oil extracts(50 mg/kg or 20 mL/kg)for post-toxicity induction.Results:The finding represented that exposure of CYP significantly increased oxidative stress,disrupted testicular architecture,and markedly reduced testosterone levels(P<0.05).Importantly,Crocus sativus L.treatment alleviated these changes by increasing the expression of Nrf2(nuclear factor erythroid 2-related factor 2),restoring the activity of antioxidant enzymes,and enhancing testicular histomorphology.Surprisingly,molecular docking established a high binding affinity of Crocus sativus L.phytoconstituents such as gallic acid,cinnamic acid and quercetin to the Nrf2-Keap1 complex.It is worth noting that,Crocus sativus L.exhibited a high level of protection against reproductive toxicity caused by CYP in male rats,which was mediated by the activation of Nrf2 pathway,reduction of oxidative damage,and favorable ADMET characteristics.Conclusion:Notably,this research provides a more valid,safe,and effective method of developing new drugs for reproductive disorders,however,further investigation is needed to support the research findings and implement it in clinical practice.展开更多
Negative logarithm of the acid dissociation constant(pK_(a))significantly influences the absorption,dis-tribution,metabolism,excretion,and toxicity(ADMET)properties of molecules and is a crucial indicator in drug rese...Negative logarithm of the acid dissociation constant(pK_(a))significantly influences the absorption,dis-tribution,metabolism,excretion,and toxicity(ADMET)properties of molecules and is a crucial indicator in drug research.Given the rapid and accurate characteristics of computational methods,their role in predicting drug properties is increasingly important.Although many pK_(a) prediction models currently exist,they often focus on enhancing model precision while neglecting interpretability.In this study,we present GraFpKa,a pK_(a) prediction model using graph neural networks(GNNs)and molecular finger-prints.The results show that our acidic and basic models achieved mean absolute errors(MAEs)of 0.621 and 0.402,respectively,on the test set,demonstrating good predictive performance.Notably,to improve interpretability,GraFpKa also incorporates Integrated Gradients(IGs),providing a clearer visual description of the atoms significantly affecting the pK_(a) values.The high reliability and interpretability of GraFpKa ensure accurate pKa predictions while also facilitating a deeper understanding of the relation-ship between molecular structure and pK_(a) values,making it a valuable tool in the field of pK_(a) prediction.展开更多
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
The present study was designed to target fish for potential bioactive components contained in a Huang Lian Jie Du decoction(HLJDD) and identify the underlying mechanisms of action for the treatment of sepsis at the mo...The present study was designed to target fish for potential bioactive components contained in a Huang Lian Jie Du decoction(HLJDD) and identify the underlying mechanisms of action for the treatment of sepsis at the molecular level. he bioactive components database of HLJDD was constructed and the sepsis-associated targets were comprehensively investigated. The 3D structures of the PAFR and TXA2 R proteins were established using the homology modelling(HM) method, and the molecular effects for sepsis treatment were analysed by comparing the bioactive components database and the sepsis targets using computational biology methods. The results of the screening were validated with biological testing against the human oral epidermal carcinoma cell line KB in vitro. We found that multiple bioactive compounds contained in the HLJDD interacted with multiple targets. We also predicted the promising compound leads for sepsis treatment, and the first 28 compounds were characterized. Several compounds, such as berberine, berberrubine and epiberberine, dose-dependently inhibited PGE2 production in human KB cells, and the effects were similar in the presence or absence of TPA. This study demonstrates a novel approach to identifying natural chemical compounds as new leads for the treatment of sepsis.展开更多
MicroRNAs are small non-coding RNAs that play crucial roles in the regulation of gene expression and protein synthesis during brain development. MiR-3099 is highly expressed throughout embryogenesis, especially in the...MicroRNAs are small non-coding RNAs that play crucial roles in the regulation of gene expression and protein synthesis during brain development. MiR-3099 is highly expressed throughout embryogenesis, especially in the developing central nervous system. Moreover, miR-3099 is also expressed at a higher level in differentiating neurons in vitro, suggesting that it is a potential regulator during neuronal cell development. This study aimed to predict the target genes of miR-3099 via in-silico analysis using four independent prediction algorithms（miRDB,miRanda, Target Scan, and DIANA-micro-T-CDS） with emphasis on target genes related to brain development and function. Based on the analysis, a total of 3,174 miR-3099 target genes were predicted. Those predicted by at least three algorithms（324 genes） were subjected to DAVID bioinformatics analysis to understand their overallfunctional themes and representation. The analysis revealed that nearly 70% of the target genes were expressed in the nervous system and a significant proportion were associated with transcriptional regulation and protein ubiquitination mechanisms. Comparison of in situ hybridization（ISH） expression patterns of miR-3099 in both published and in-house-generated ISH sections with the ISH sections of target genes from the Allen Brain Atlas identified 7 target genes（Dnmt3a, Gabpa, Gfap, Itga4,Lxn, Smad7, and Tbx18） having expression patterns complementary to miR-3099 in the developing and adult mouse brain samples. Of these, we validated Gfap as a direct downstream target of miR-3099 using the luciferase reporter gene system. In conclusion, we report the successful prediction and validation of Gfap as an miR-3099 target gene using a combination of bioinformatics resources with enrichment of annotations based on functional ontologies and a spatio-temporal expression dataset.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
Duloxetine(DUL), an antidepressant drug, has been detected in surface water and wastewater effluents, however, there is little information on the formation of its transformation products(TPs). In this work, hydrolysis...Duloxetine(DUL), an antidepressant drug, has been detected in surface water and wastewater effluents, however, there is little information on the formation of its transformation products(TPs). In this work, hydrolysis, photodegradation(UV irradiation) and chlorination experiments were performed on spiked distillated water, under controlled experimental conditions to simulate abiotic processes that can occur in the environment and wastewater treatment plants(WWTPs). Eleven TPs, nine from reaction with UV light and two from chlorine contact, were formed and detected by ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry, and nine of them had their chemical structures elucidated upon analyses of their fragmentation patterns in MS/MS spectra. The formation and degradation of the TPs were observed. The parent compound was completely degraded after30 min in photodegradation and after 24 hr in chlorination. Almost all TPs were completely degraded in the experiments. The ecotoxicity and mutagenicity of the TPs were predicted based on several in silico models and it was found that a few of these products presented more ecotoxicity than DUL itself and six TPs showed positive mutagenicity. Finally, wastewater samples were analyzed and DUL and one TP, possibly formed by chlorination process, were detected in the effluent, which showed that WWTP not only did not remove DUL, but also formed a TP.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
The present manuscript describes solid-state synthesis of some reported steroidal pyrazolines by a novel eco-friendly route. The synthesized pyrazolines were compared with those obtained from conventional methods in t...The present manuscript describes solid-state synthesis of some reported steroidal pyrazolines by a novel eco-friendly route. The synthesized pyrazolines were compared with those obtained from conventional methods in terms of reaction time and overall yield. A substantial enhancement in reaction rate and yield was observed. The antimicrobial activity and the subsequent molecular docking studies of the steroidal pyrazolines have also been carried out.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
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
Hepatocellular carcinoma(HCC)is the second cause of cancer-related mortality.The diagnosis of HCC depends mainly on-fetoprotein,which is limited in its diagnostic and screening capabilities.There is an urgent need for...Hepatocellular carcinoma(HCC)is the second cause of cancer-related mortality.The diagnosis of HCC depends mainly on-fetoprotein,which is limited in its diagnostic and screening capabilities.There is an urgent need for a biomarker that detects early HCC to give the patients a chance for curative treatment.New targets of therapy could enhance survival and create future alternative curative methods.In silico analysis provides both;discovery of biomarkers,and understanding of the molecular pathways,to pave the way for treatment development.This review discusses the role of in silico analysis in the discovery of biomarkers,molecular pathways,and the role the author has contributed to this area of research.It also discusses future aspirations and current limitations.A literature review was conducted on the topic using various databases(PubMed,Science Direct,and Wiley Online Library),searching in various reviews,and editorials on the topic,with overviewing the author’s own published and unpublished work.This review discussed the steps of the validation process from in silico analysis to in vivo validation,to incorporation into clinical practice guidelines.In addition,reviewing the recent lines of research of bioinformatic studies related to HCC.In conclusion,the genetic,molecular and epigenetic markers discoveries are hot areas for HCC research.Bioinformatics will enhance our ability to accomplish this understanding in the near future.We face certain limitations that we need to overcome.展开更多
Salicylic acid(SA)is an effective elicitor to promote plant defenses and growth.This study aimed to investigate rice(Oryza sativa L.)cv.Khao Dawk Mali 105 treated with salicylic acid(SA)-Ricemate as an enhanced plant ...Salicylic acid(SA)is an effective elicitor to promote plant defenses and growth.This study aimed to investigate rice(Oryza sativa L.)cv.Khao Dawk Mali 105 treated with salicylic acid(SA)-Ricemate as an enhanced plant protection mechanism against bacterial leaf blight(BLB)disease caused by Xanthomonas oryzae pv.oryzae(Xoo).Results indicated that the use of SA-Ricemate as a foliar spray at concentrations of more than 100 mg L^(-1)can reduce the severity of BLB disease by 71%.SA-Ricemate treatment also increased the hydrogen peroxide(H_(2)O_(2))content of rice leaf tissues over untreated samples by 39–61%.Malondialdehyde(MDA)in rice leaves treated with SA-Ricemate also showed an increase of 50–65%when comparing to non-treated samples.The differential development of these defense compounds was faster and distinct when the SA-Ricemate-treated rice was infected with Xoo,indicating plant-induced resistance.Besides,SA-Ricemate elicitor at a concentration of 50–250 mg L^(-1)was correlated with a substantial increase in the accumulation of total chlorophyll content at 2.53–2.73 mg g^(-1)of fresh weight which suggests that plant growth is activated by SA-Ricemate.The catalase-and aldehyde dehydrogenase-binding sites were searched for using the CASTp server,and the findings were compared to the template.Chemsketch was used to design and optimize SA,which was then docked to the catalase and aldehyde dehydrogenase-binding domains of the enzymes using the GOLD 3.0.1 Software.SA is shown in several docked conformations with the enzymes catalase and aldehyde dehydrogenase.All three catalase amino acids(GLN7,VAL27,and GLU38)were discovered to be involved in the creation of a strong hydrogen bond with SA when SA was present.In this mechanism,the aldehyde dehydrogenase amino acids LYS5,HIS6,and ASP2 were all implicated,and these amino acids created strong hydrogen bonds with SA.In field conditions,SA-Ricemate significantly reduced disease severity by 78%and the total grain yield was significantly increased which was an increase of plant height,tiller per hill,and panicle in three field trials during Aug–Nov 2017 and 2018.Therefore,SA-Ricemate can be used as an alternative elicitor on replacing harmful pesticides to control BLB disease with a high potential of increasing rice defenses,growth,and yield components.展开更多
This study aims to understand the absorption patterns of three different kinds of inhaled formulations via in silico modeling using budesonide(BUD)as a model drug.The formulations investigated in this study are:(i)com...This study aims to understand the absorption patterns of three different kinds of inhaled formulations via in silico modeling using budesonide(BUD)as a model drug.The formulations investigated in this study are:(i)commercially available micronized BUD mixed with lactose(BUD-PT),(ii)BUD nanocrystal suspension(BUD-NC),(iii)BUD nanocrystals embedded hyaluronic acid microparticles(BUD-NEM).The deposition patterns of the three inhaled formulations in the rats’lungs were determined in vivo and in silico predicted,which were used as inputs in GastroPlus TM software to predict drug absorption following aerosolization of the tested formulations.BUD pharmacokinetics,estimated based on intravenous data in rats,was used to establish a drug-specific in silico absorption model.The BUD-specific in silico model revealed that drug pulmonary solubility and absorption rate constant were the key factors affecting pulmonary absorption of BUD-NC and BUD-NEM,respectively.In the case of BUD-PT,the in silico model revealed significant gastrointestinal absorption of BUD,which could be overlooked by traditional in vivo experimental observation.This study demonstrated that in vitro-in vivo-in silico approach was able to identify the key factors that influence the absorption of different inhaled formulations,which may facilitate the development of orally inhaled formulations with different drug release/absorption rates.展开更多
We designed a disulfide-crosslinked mini-protein with a two-helical topology consisting of L-and Damino acids,which was exceptionally stable in serum.Therefore,we further used it as a scaffold to design mini-proteins ...We designed a disulfide-crosslinked mini-protein with a two-helical topology consisting of L-and Damino acids,which was exceptionally stable in serum.Therefore,we further used it as a scaffold to design mini-proteins targeting p53 positive tumor cells.Based on bifunctional grafting,key residues from the transactivation domain of p53 and a designed unnatural amino acid were grafted into the helix constituted by L-amino acids to confer the mini-protein with MDM2 inhibitory activity.Meanwhile,ten Arg residues were introduced to improve its membrane penetrating capacity.Among the mini-proteins,UPROL-10e showed nano-molar binding affinity on MDM2 and cellular toxicity on p53 expressing HCT116cells.展开更多
Objective:To explore the efficacy of intermittent preventive treatment in pregnancy(IPTp)with sulfadoxine and pyrimethamine(SP)against sensitive parasites.Methods:A pharmacological model was used to investigate the ef...Objective:To explore the efficacy of intermittent preventive treatment in pregnancy(IPTp)with sulfadoxine and pyrimethamine(SP)against sensitive parasites.Methods:A pharmacological model was used to investigate the effectiveness of the previous recommended at least two-dose regimen,currently recommended three-dose regimen and 4,6,8-weekly regimens with specific focus on the impact of various nonadherence patterns in multiple transmission settings.Results:The effectiveness of the recommended three-dose regimen is high in all the transmission intensities,i.e.>99%,98%and 92%in low,moderate and high transmission intensities respectively.The simulated 4 and 6 weekly IPTp-SP regimens were able to prevent new infections with sensitive parasites in almost all women(>99%)regardless of transmission intensity.However,8 weekly interval dose schedules were found to have 71%and 86%protective efficacies in high and moderate transmission areas,respectively.It highlights that patients are particularly vulnerable to acquiring new infections if IPTp-SP doses are missed.Conclusions:The pharmacological model predicts that full adherence to the currently recommended three-dose regimen should provide almost complete protection from malaria infection in moderate and high transmission regions.However,it also highlights that patients are particularly vulnerable to acquiring new infections if IPTp doses are spaced too widely or if doses are missed.Adherence to the recommended IPTp-SP schedules is recommended.展开更多
Taxifolin has a plethora of therapeutic activities and is currently isolated from the stem bark of the tree Larix gmelinni(Dahurian larch). It is a flavonoid of high commercial interest for its use in supplements or i...Taxifolin has a plethora of therapeutic activities and is currently isolated from the stem bark of the tree Larix gmelinni(Dahurian larch). It is a flavonoid of high commercial interest for its use in supplements or in antioxidant-rich functional foods. However, its poor stability and low bioavailability hinder the use of flavonoid in nutritional or pharmaceutical formulations. In this work, taxifolin isolated from the seeds of Mimusops balata, was evaluated by in silico stability prediction studies and in vitro forced degradation studies(acid and alkaline hydrolysis, oxidation, visible/UV radiation, dry/humid heating) monitored by high performance liquid chromatography with ultraviolet detection(HPLC-UV) and ultrahigh performance liquid chromatography-electrospray ionization-mass spectrometry(UPLC-ESI-MS). The in silico stability prediction studies indicated the most susceptible regions in the molecule to nucleophilic and electrophilic attacks, as well as the sites susceptible to oxidation. The in vitro forced degradation tests were in agreement with the in silico stability prediction, indicating that taxifolin is extremely unstable(class 1) under alkaline hydrolysis. In addition, taxifolin thermal degradation was increased by humidity.On the other hand, with respect to photosensitivity, taxifolin can be classified as class 4(stable).Moreover, the alkaline degradation products were characterized by UPLC-ESI-MS/MS as dimers of taxifolin. These results enabled an understanding of the intrinsic lability of taxifolin, contributing to the development of stability-indicating methods, and of appropriate drug release systems, with the aims of preserving its stability and improving its bioavailability.展开更多
Although the GABAA receptor(GABAAR)has been proposed as the main action site for sevoflurane,isoflurane,halothane,enflurane,propofol,and benzodiazepines(BZDs),binding of these anesthetics with high-resolution structur...Although the GABAA receptor(GABAAR)has been proposed as the main action site for sevoflurane,isoflurane,halothane,enflurane,propofol,and benzodiazepines(BZDs),binding of these anesthetics with high-resolution structures of the GABAAR have been rarely examined by comparative docking analyses.Moreover,various combinations of ligands on more GABAARs with various subtypes need to be analyzed to understand the elaborate action mechanism of GABAARs better because some GABAA ligands showed specificity toward the distinct subtypes of the GABAAR.Methods:We performed in silico docking analysis to compare the binding modes of sevoflurane,isoflurane,halothane,enflurane,propofol,and BZDs to the GABAAR based on one of the most recently provided 3D structures.We performed the docking analysis and the affinity-based ranking of the binding sites.Results:Our docking studies revealed that isoflurane,halothane,and enflurane docked in an extracellular domain(ECD)on GABAARs,in contrast to sevoflurane.Conclusion:Our results supported a multi-site mechanism for the allosteric modulation of propofol.Propofol was bound to the pore or favored various subsites in the transmembrane domain(TMD).Our result confirmed that different chemically related BZD ligands interact via distinct binding modes rather than by using a common binding mode,as previously suggested.展开更多
[ Objective ] This study aimed to verify the feasibility of in silico cloning of functional candidate genes in tea. [ Method ] Theobroma cacao caffeine syn- thase gene BCS1 was used as a probe to search the establishe...[ Objective ] This study aimed to verify the feasibility of in silico cloning of functional candidate genes in tea. [ Method ] Theobroma cacao caffeine syn- thase gene BCS1 was used as a probe to search the established tea EST database using BLAST; 26 tea ESTs highly homologous to BCS1 were obtained, which were assembled using CAP （contig assembly program） of BioEdit software; subsequently, two EST configs harboring ORF were obtained, which were named TCSnewl and TCSnew2, respectively. Nucleotide sequences and deduced amino acid sequences of theses two genes were compared with those of cDNA of tea caffeine synthase gene TCS in the GenBank database that was cloned with experimental biological method. A phylogenetic tree was constructed for homalogous analysis of the deduced amino acid sequences of theses three genes. [ Result] in silico cloning of functional candidate genes in tea using a homologous gene of distantly related species as a probe is a feasible technical means. [ Conclusion] This study provided the basis for in silico cloning of other functional genes in tea.展开更多
文摘Background:Epidemiological studies have confirmed that longer exposure to insecticides like cypermethrin(CYP)significantly increases the risk of male reproductive toxicity.Crocus sativus L.has been recognized due to its therapeutic properties,but its exact role and molecular mechanisms in treatment of reproductive dysfunction remain unclear.Methods:During this study,36 rats were randomly divided into six groups(n=6):control,CYP-induced(60 mg/kg),standard(leuprolide 3 mg/kg)and three treatment groups receiving aqueous,ethanolic,and oil extracts(50 mg/kg or 20 mL/kg)for post-toxicity induction.Results:The finding represented that exposure of CYP significantly increased oxidative stress,disrupted testicular architecture,and markedly reduced testosterone levels(P<0.05).Importantly,Crocus sativus L.treatment alleviated these changes by increasing the expression of Nrf2(nuclear factor erythroid 2-related factor 2),restoring the activity of antioxidant enzymes,and enhancing testicular histomorphology.Surprisingly,molecular docking established a high binding affinity of Crocus sativus L.phytoconstituents such as gallic acid,cinnamic acid and quercetin to the Nrf2-Keap1 complex.It is worth noting that,Crocus sativus L.exhibited a high level of protection against reproductive toxicity caused by CYP in male rats,which was mediated by the activation of Nrf2 pathway,reduction of oxidative damage,and favorable ADMET characteristics.Conclusion:Notably,this research provides a more valid,safe,and effective method of developing new drugs for reproductive disorders,however,further investigation is needed to support the research findings and implement it in clinical practice.
基金upported by the National Key Research and Development Program of China(Grant No.:2023YFF1204904)the National Natural Science Foundation of China(Grant Nos.:U23A20530 and 82173746)Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism(Shanghai Municipal Education Commission,China).
文摘Negative logarithm of the acid dissociation constant(pK_(a))significantly influences the absorption,dis-tribution,metabolism,excretion,and toxicity(ADMET)properties of molecules and is a crucial indicator in drug research.Given the rapid and accurate characteristics of computational methods,their role in predicting drug properties is increasingly important.Although many pK_(a) prediction models currently exist,they often focus on enhancing model precision while neglecting interpretability.In this study,we present GraFpKa,a pK_(a) prediction model using graph neural networks(GNNs)and molecular finger-prints.The results show that our acidic and basic models achieved mean absolute errors(MAEs)of 0.621 and 0.402,respectively,on the test set,demonstrating good predictive performance.Notably,to improve interpretability,GraFpKa also incorporates Integrated Gradients(IGs),providing a clearer visual description of the atoms significantly affecting the pK_(a) values.The high reliability and interpretability of GraFpKa ensure accurate pKa predictions while also facilitating a deeper understanding of the relation-ship between molecular structure and pK_(a) values,making it a valuable tool in the field of pK_(a) prediction.
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.
基金supported by the Youth Fund from Anhui Science and Technology University(No.ZRC2013341)the National Science and Technology Major Project'Creation of Major New Drugs'of China(No.2012ZX09303009-002)+2 种基金China College Students Innovation and Entrepreneurship(No.2013108 79009)the National Natural Science Fundation of China(81403268)the Natural Science Foundation of the Education Bureau of Anhui Province(KJ2013z055)
文摘The present study was designed to target fish for potential bioactive components contained in a Huang Lian Jie Du decoction(HLJDD) and identify the underlying mechanisms of action for the treatment of sepsis at the molecular level. he bioactive components database of HLJDD was constructed and the sepsis-associated targets were comprehensively investigated. The 3D structures of the PAFR and TXA2 R proteins were established using the homology modelling(HM) method, and the molecular effects for sepsis treatment were analysed by comparing the bioactive components database and the sepsis targets using computational biology methods. The results of the screening were validated with biological testing against the human oral epidermal carcinoma cell line KB in vitro. We found that multiple bioactive compounds contained in the HLJDD interacted with multiple targets. We also predicted the promising compound leads for sepsis treatment, and the first 28 compounds were characterized. Several compounds, such as berberine, berberrubine and epiberberine, dose-dependently inhibited PGE2 production in human KB cells, and the effects were similar in the presence or absence of TPA. This study demonstrates a novel approach to identifying natural chemical compounds as new leads for the treatment of sepsis.
基金supported by the Science Fund(02-01-04-SF2336)the Fundamental Research Grant Scheme,Ministry of Higher Education,Malaysia(FRGS-04-01-15-1663FR)
文摘MicroRNAs are small non-coding RNAs that play crucial roles in the regulation of gene expression and protein synthesis during brain development. MiR-3099 is highly expressed throughout embryogenesis, especially in the developing central nervous system. Moreover, miR-3099 is also expressed at a higher level in differentiating neurons in vitro, suggesting that it is a potential regulator during neuronal cell development. This study aimed to predict the target genes of miR-3099 via in-silico analysis using four independent prediction algorithms（miRDB,miRanda, Target Scan, and DIANA-micro-T-CDS） with emphasis on target genes related to brain development and function. Based on the analysis, a total of 3,174 miR-3099 target genes were predicted. Those predicted by at least three algorithms（324 genes） were subjected to DAVID bioinformatics analysis to understand their overallfunctional themes and representation. The analysis revealed that nearly 70% of the target genes were expressed in the nervous system and a significant proportion were associated with transcriptional regulation and protein ubiquitination mechanisms. Comparison of in situ hybridization（ISH） expression patterns of miR-3099 in both published and in-house-generated ISH sections with the ISH sections of target genes from the Allen Brain Atlas identified 7 target genes（Dnmt3a, Gabpa, Gfap, Itga4,Lxn, Smad7, and Tbx18） having expression patterns complementary to miR-3099 in the developing and adult mouse brain samples. Of these, we validated Gfap as a direct downstream target of miR-3099 using the luciferase reporter gene system. In conclusion, we report the successful prediction and validation of Gfap as an miR-3099 target gene using a combination of bioinformatics resources with enrichment of annotations based on functional ontologies and a spatio-temporal expression dataset.
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.
基金supported by Brazilian Federal Agency Coordenacao de Aperfeicoamento de Pessoal de Nível Superior(CAPES)for PhD grants(No.99999.000845/2014-00)Fundacao para a Ciência e a Tecnologia(FCT)Portugal(Projects UID/MULTI/00612/2013,PEst-OE/QUI/UI0612/2013 and LISBOA-01-0145-FEDER-022125)
文摘Duloxetine(DUL), an antidepressant drug, has been detected in surface water and wastewater effluents, however, there is little information on the formation of its transformation products(TPs). In this work, hydrolysis, photodegradation(UV irradiation) and chlorination experiments were performed on spiked distillated water, under controlled experimental conditions to simulate abiotic processes that can occur in the environment and wastewater treatment plants(WWTPs). Eleven TPs, nine from reaction with UV light and two from chlorine contact, were formed and detected by ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry, and nine of them had their chemical structures elucidated upon analyses of their fragmentation patterns in MS/MS spectra. The formation and degradation of the TPs were observed. The parent compound was completely degraded after30 min in photodegradation and after 24 hr in chlorination. Almost all TPs were completely degraded in the experiments. The ecotoxicity and mutagenicity of the TPs were predicted based on several in silico models and it was found that a few of these products presented more ecotoxicity than DUL itself and six TPs showed positive mutagenicity. Finally, wastewater samples were analyzed and DUL and one TP, possibly formed by chlorination process, were detected in the effluent, which showed that WWTP not only did not remove DUL, but also formed a TP.
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.
文摘The present manuscript describes solid-state synthesis of some reported steroidal pyrazolines by a novel eco-friendly route. The synthesized pyrazolines were compared with those obtained from conventional methods in terms of reaction time and overall yield. A substantial enhancement in reaction rate and yield was observed. The antimicrobial activity and the subsequent molecular docking studies of the steroidal pyrazolines have also been carried out.
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.
文摘Hepatocellular carcinoma(HCC)is the second cause of cancer-related mortality.The diagnosis of HCC depends mainly on-fetoprotein,which is limited in its diagnostic and screening capabilities.There is an urgent need for a biomarker that detects early HCC to give the patients a chance for curative treatment.New targets of therapy could enhance survival and create future alternative curative methods.In silico analysis provides both;discovery of biomarkers,and understanding of the molecular pathways,to pave the way for treatment development.This review discusses the role of in silico analysis in the discovery of biomarkers,molecular pathways,and the role the author has contributed to this area of research.It also discusses future aspirations and current limitations.A literature review was conducted on the topic using various databases(PubMed,Science Direct,and Wiley Online Library),searching in various reviews,and editorials on the topic,with overviewing the author’s own published and unpublished work.This review discussed the steps of the validation process from in silico analysis to in vivo validation,to incorporation into clinical practice guidelines.In addition,reviewing the recent lines of research of bioinformatic studies related to HCC.In conclusion,the genetic,molecular and epigenetic markers discoveries are hot areas for HCC research.Bioinformatics will enhance our ability to accomplish this understanding in the near future.We face certain limitations that we need to overcome.
基金supported by the Suranaree University of Technology,Thailand,the Thailand Science Research and Innovation(TSRI)the National Science,Research and Innovation Fund,Thailand(NSRF)(90464).
文摘Salicylic acid(SA)is an effective elicitor to promote plant defenses and growth.This study aimed to investigate rice(Oryza sativa L.)cv.Khao Dawk Mali 105 treated with salicylic acid(SA)-Ricemate as an enhanced plant protection mechanism against bacterial leaf blight(BLB)disease caused by Xanthomonas oryzae pv.oryzae(Xoo).Results indicated that the use of SA-Ricemate as a foliar spray at concentrations of more than 100 mg L^(-1)can reduce the severity of BLB disease by 71%.SA-Ricemate treatment also increased the hydrogen peroxide(H_(2)O_(2))content of rice leaf tissues over untreated samples by 39–61%.Malondialdehyde(MDA)in rice leaves treated with SA-Ricemate also showed an increase of 50–65%when comparing to non-treated samples.The differential development of these defense compounds was faster and distinct when the SA-Ricemate-treated rice was infected with Xoo,indicating plant-induced resistance.Besides,SA-Ricemate elicitor at a concentration of 50–250 mg L^(-1)was correlated with a substantial increase in the accumulation of total chlorophyll content at 2.53–2.73 mg g^(-1)of fresh weight which suggests that plant growth is activated by SA-Ricemate.The catalase-and aldehyde dehydrogenase-binding sites were searched for using the CASTp server,and the findings were compared to the template.Chemsketch was used to design and optimize SA,which was then docked to the catalase and aldehyde dehydrogenase-binding domains of the enzymes using the GOLD 3.0.1 Software.SA is shown in several docked conformations with the enzymes catalase and aldehyde dehydrogenase.All three catalase amino acids(GLN7,VAL27,and GLU38)were discovered to be involved in the creation of a strong hydrogen bond with SA when SA was present.In this mechanism,the aldehyde dehydrogenase amino acids LYS5,HIS6,and ASP2 were all implicated,and these amino acids created strong hydrogen bonds with SA.In field conditions,SA-Ricemate significantly reduced disease severity by 78%and the total grain yield was significantly increased which was an increase of plant height,tiller per hill,and panicle in three field trials during Aug–Nov 2017 and 2018.Therefore,SA-Ricemate can be used as an alternative elicitor on replacing harmful pesticides to control BLB disease with a high potential of increasing rice defenses,growth,and yield components.
基金This work was supported by National Natural Science Foundation of China(Nos.81302720 and No.81573380)Liaoning Pan Deng Xue Zhe Scholarship+1 种基金supported by the Ministry of Education,Science and Technological Development,Republic of Serbia(grant number 451-03-68/2020-14/200161)Cun D.is grateful to Liaoning Provincial Education officer’s Excellent Talents Supporting Plan for financial support.
文摘This study aims to understand the absorption patterns of three different kinds of inhaled formulations via in silico modeling using budesonide(BUD)as a model drug.The formulations investigated in this study are:(i)commercially available micronized BUD mixed with lactose(BUD-PT),(ii)BUD nanocrystal suspension(BUD-NC),(iii)BUD nanocrystals embedded hyaluronic acid microparticles(BUD-NEM).The deposition patterns of the three inhaled formulations in the rats’lungs were determined in vivo and in silico predicted,which were used as inputs in GastroPlus TM software to predict drug absorption following aerosolization of the tested formulations.BUD pharmacokinetics,estimated based on intravenous data in rats,was used to establish a drug-specific in silico absorption model.The BUD-specific in silico model revealed that drug pulmonary solubility and absorption rate constant were the key factors affecting pulmonary absorption of BUD-NC and BUD-NEM,respectively.In the case of BUD-PT,the in silico model revealed significant gastrointestinal absorption of BUD,which could be overlooked by traditional in vivo experimental observation.This study demonstrated that in vitro-in vivo-in silico approach was able to identify the key factors that influence the absorption of different inhaled formulations,which may facilitate the development of orally inhaled formulations with different drug release/absorption rates.
基金supported by the National Natural Science Foundation of China(Nos.3217110331 and 8212200560)Major new drug development in Shandong Province(No.2020CXGC010503)。
文摘We designed a disulfide-crosslinked mini-protein with a two-helical topology consisting of L-and Damino acids,which was exceptionally stable in serum.Therefore,we further used it as a scaffold to design mini-proteins targeting p53 positive tumor cells.Based on bifunctional grafting,key residues from the transactivation domain of p53 and a designed unnatural amino acid were grafted into the helix constituted by L-amino acids to confer the mini-protein with MDM2 inhibitory activity.Meanwhile,ten Arg residues were introduced to improve its membrane penetrating capacity.Among the mini-proteins,UPROL-10e showed nano-molar binding affinity on MDM2 and cellular toxicity on p53 expressing HCT116cells.
基金funded by the Bill and Melinda Gates Foundation(grant No.37999.01)the Medical Research Council(grant No.G110052)supported by the Liverpool School of Tropical Medicine
文摘Objective:To explore the efficacy of intermittent preventive treatment in pregnancy(IPTp)with sulfadoxine and pyrimethamine(SP)against sensitive parasites.Methods:A pharmacological model was used to investigate the effectiveness of the previous recommended at least two-dose regimen,currently recommended three-dose regimen and 4,6,8-weekly regimens with specific focus on the impact of various nonadherence patterns in multiple transmission settings.Results:The effectiveness of the recommended three-dose regimen is high in all the transmission intensities,i.e.>99%,98%and 92%in low,moderate and high transmission intensities respectively.The simulated 4 and 6 weekly IPTp-SP regimens were able to prevent new infections with sensitive parasites in almost all women(>99%)regardless of transmission intensity.However,8 weekly interval dose schedules were found to have 71%and 86%protective efficacies in high and moderate transmission areas,respectively.It highlights that patients are particularly vulnerable to acquiring new infections if IPTp-SP doses are missed.Conclusions:The pharmacological model predicts that full adherence to the currently recommended three-dose regimen should provide almost complete protection from malaria infection in moderate and high transmission regions.However,it also highlights that patients are particularly vulnerable to acquiring new infections if IPTp doses are spaced too widely or if doses are missed.Adherence to the recommended IPTp-SP schedules is recommended.
基金supported by CAPES(PVE,Grant No.88887.116106/2016-00)(Coordenaao de Aperfei-oamento de Pessoal de Nível Superior)Brazil,which provided financial support in the form of a doctoral’s degree scholarship to Stenger,F.C.and financial support(Science Program Without Borders-Researcher Special Visitor-PVE)CNPq(Conselho Nacional de Desenvolvimento Científico e Tecnológico),Edital Universal(Grant No.88887.122964/2016-00)。
文摘Taxifolin has a plethora of therapeutic activities and is currently isolated from the stem bark of the tree Larix gmelinni(Dahurian larch). It is a flavonoid of high commercial interest for its use in supplements or in antioxidant-rich functional foods. However, its poor stability and low bioavailability hinder the use of flavonoid in nutritional or pharmaceutical formulations. In this work, taxifolin isolated from the seeds of Mimusops balata, was evaluated by in silico stability prediction studies and in vitro forced degradation studies(acid and alkaline hydrolysis, oxidation, visible/UV radiation, dry/humid heating) monitored by high performance liquid chromatography with ultraviolet detection(HPLC-UV) and ultrahigh performance liquid chromatography-electrospray ionization-mass spectrometry(UPLC-ESI-MS). The in silico stability prediction studies indicated the most susceptible regions in the molecule to nucleophilic and electrophilic attacks, as well as the sites susceptible to oxidation. The in vitro forced degradation tests were in agreement with the in silico stability prediction, indicating that taxifolin is extremely unstable(class 1) under alkaline hydrolysis. In addition, taxifolin thermal degradation was increased by humidity.On the other hand, with respect to photosensitivity, taxifolin can be classified as class 4(stable).Moreover, the alkaline degradation products were characterized by UPLC-ESI-MS/MS as dimers of taxifolin. These results enabled an understanding of the intrinsic lability of taxifolin, contributing to the development of stability-indicating methods, and of appropriate drug release systems, with the aims of preserving its stability and improving its bioavailability.
文摘Although the GABAA receptor(GABAAR)has been proposed as the main action site for sevoflurane,isoflurane,halothane,enflurane,propofol,and benzodiazepines(BZDs),binding of these anesthetics with high-resolution structures of the GABAAR have been rarely examined by comparative docking analyses.Moreover,various combinations of ligands on more GABAARs with various subtypes need to be analyzed to understand the elaborate action mechanism of GABAARs better because some GABAA ligands showed specificity toward the distinct subtypes of the GABAAR.Methods:We performed in silico docking analysis to compare the binding modes of sevoflurane,isoflurane,halothane,enflurane,propofol,and BZDs to the GABAAR based on one of the most recently provided 3D structures.We performed the docking analysis and the affinity-based ranking of the binding sites.Results:Our docking studies revealed that isoflurane,halothane,and enflurane docked in an extracellular domain(ECD)on GABAARs,in contrast to sevoflurane.Conclusion:Our results supported a multi-site mechanism for the allosteric modulation of propofol.Propofol was bound to the pore or favored various subsites in the transmembrane domain(TMD).Our result confirmed that different chemically related BZD ligands interact via distinct binding modes rather than by using a common binding mode,as previously suggested.
基金Supported by National Science and Technology Support Program of China(2011BAD01B01)Youth Talent Innovation Fund of Fujian Academy of Agricultural Sciences(2011QC-2)Special Fund for"Double Hundred Plan"of Fujian Academy of Agricultural Sciences(sbmx1303-1)
文摘[ Objective ] This study aimed to verify the feasibility of in silico cloning of functional candidate genes in tea. [ Method ] Theobroma cacao caffeine syn- thase gene BCS1 was used as a probe to search the established tea EST database using BLAST; 26 tea ESTs highly homologous to BCS1 were obtained, which were assembled using CAP （contig assembly program） of BioEdit software; subsequently, two EST configs harboring ORF were obtained, which were named TCSnewl and TCSnew2, respectively. Nucleotide sequences and deduced amino acid sequences of theses two genes were compared with those of cDNA of tea caffeine synthase gene TCS in the GenBank database that was cloned with experimental biological method. A phylogenetic tree was constructed for homalogous analysis of the deduced amino acid sequences of theses three genes. [ Result] in silico cloning of functional candidate genes in tea using a homologous gene of distantly related species as a probe is a feasible technical means. [ Conclusion] This study provided the basis for in silico cloning of other functional genes in tea.
