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: 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
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
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
BACKGROUND Leprosy is a disease caused by Mycobacterium leprae(M.leprae),an intracellular pathogen that has tropism and affects skin and nervous system cells.The disease has two forms of presentation:Paucibacillary an...BACKGROUND Leprosy is a disease caused by Mycobacterium leprae(M.leprae),an intracellular pathogen that has tropism and affects skin and nervous system cells.The disease has two forms of presentation:Paucibacillary and multibacillary,with different clinical and immunological manifestations.Unlike what occurs in the multibacillary form,the diagnostic tests for the paucibacillary form are nonspecific and not very sensitive,allowing the existence of infected individuals without treatment,which contributes to the spread of the pathogen in the population.To mitigate this contamination,more sensitive diagnostic tests capable of detecting paucibacillary patients are needed.AIM To predict the three-dimensional structure models of M.leprae antigens with serodiagnostic potential for leprosy.METHODS In this in silico study,satisfactory templates were selected in the Protein Data Bank(PDB)using Basic Local Alignment Search Tool to predict the structural templates of ML2038,ML0286,ML0050,and 85B antigens by comparative modeling.The templates were selected according to general criteria such as sequence identity,coverage,X-ray resolution,Global Model Quality Estimate value and phylogenetic relationship;Clustal X 2.1 software was used in this analysis.Molecular modeling was completed using the software Modeller 9v13.Visualization of the models was made using ViewerLite 4.2 and PyMol software,and analysis of the quality of the predicted models was performed using the QMEAN score and Z-score.Finally,the three-dimensional moels were validated using the MolProbity and Verify 3D platforms.RESULTS The three-dimensional structure models of ML2038,ML0286,ML0050,and 85B antigens of M.leprae were predicted using the templates PDB:3UOI(90.51%identity),PDB:3EKL(87.46%identity),PDB:3FAV(40.00%identity),and PDB:1F0N(85.21%identity),respectively.The QMEAN and Z-score values indicated the good quality of the structure models.These data refer to the monomeric units of antigens,since some of these antigens have quaternary structure.The validation of the models was performed with the final three-dimensional structure-monomer(ML0050 and 85B antigens)and quaternary structures(ML2038 and ML0286).The majority of amino acid residues were observed in favorable and allowed regions in the Ramachandran plot,indicating correct positioning of the side chain and absence of steric impediment.The MolProbity score value and Verify 3D results of all models indicated a satisfactory prediction.CONCLUSION The polarized immune response against M.leprae creates a problem in leprosy detection.The selection of immunodominant epitopes is essential for the development of more sensitive serodiagnostic tests,for this it is important to know the three-dimensional structure of the antigens,which can be predicted with bioinformatics tools.展开更多
Virtual screening can be a helpful approach to propose treatments for COVID-19 by developing inhibitors for blocking the attachment of the virus to human cells. This study uses molecular docking, recovery time and dyn...Virtual screening can be a helpful approach to propose treatments for COVID-19 by developing inhibitors for blocking the attachment of the virus to human cells. This study uses molecular docking, recovery time and dynamics to analyze if potential inhibitors of main protease (M<sup>pro</sup>) of SARS-CoV-2 can interfere in the attachment of nanobodies, specifically Nb20, in the receptor binding domain (RBD) of SARS-CoV-2. The potential inhibitors are four compounds previously identified in a fluorescence resonance energy transfer (FRET)-based enzymatic assay for the SARS-CoV-2 M<sup>pro</sup>: Boceprevir, Calpain Inhibitor II, Calpain Inhibitor XII, and GC376. The findings reveal that Boceprevir has the higher affinity with the RBD/Nb20 complex, followed by Calpain Inhibitor XII, GC376 and Calpain Inhibitor II. The recovery time indicates that the RBD/Nb20 complex needs a relatively short time to return to what it was before the presence of the ligands. For the RMSD the Boceprevir and Calpain Inhibitor II have the shortest interaction times, while Calpain Inhibitor XII shows slightly more interaction, but with significant pose fluctuations. On the other hand, GC376 remains stably bound for a longer duration compared to the other compounds, suggesting that they can potentially interfere with the neutralization process of Nb20.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
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
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
Purpose of the Study: COVID-19 is caused by the SARS-CoV-2 virus that had a global pandemic spread in the last two years. Symptoms of the disease include respiratory distress and, in severe cases may consequently lead...Purpose of the Study: COVID-19 is caused by the SARS-CoV-2 virus that had a global pandemic spread in the last two years. Symptoms of the disease include respiratory distress and, in severe cases may consequently lead to death. Blocking the viral proteins can aid in treating this disease and alleviating its symptoms. Two target proteins of the coronavirus that are hot spots in drug discovery are the papain-like protease PL-pro and the main protease M-pro. PL-pro is an enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread. M-pro is the major protease of SARS-CoV-2, which is a keystone in viral replication and transcription. Methods: In this study, we shed the light on the route of targeting viral proteins for disease alleviation, by targeting the two aforementioned enzymes, PL-pro and M-pro using in silico studies. Docking experiments, using AutoDock algorithms, were performed to predict the inhibitory effect of recently produced synthetic derivatives of curcumin on the viral proteins. Results: Most of the curcumin derivatives have shown variable levels of inhibition, e.g., S1 - S6, mainly on the papain-like protease, and to a lesser extent on the main protease. Conclusion: The results indicated that curcumin derivatives can be potent anti-viral drug of SARS-CoV-2, namely targeting the papain-like protease.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
Background:Ayurvedic system of medicine is well established for prevention and treatment of renal problems.There are vast number of medicinal plants mentioned in Ayurvedic system of medicine,including Piper attenuatum...Background:Ayurvedic system of medicine is well established for prevention and treatment of renal problems.There are vast number of medicinal plants mentioned in Ayurvedic system of medicine,including Piper attenuatum Buch.-Ham.ex Miq.,which has been known to exhibit diuretic properties.Objective:To investigate possible mechanism and diuretic activity of ethanol extract of P.attenuatum leaves.Methods:Present study reports an in vivo diuretic activity of ethanol extracts of P.attenuatum leaves.Twenty-four Sprague-Dawley male rats were deprived from food and water for 20 h,followed by being divided into four groups to receive normal saline,Furosemide,and two doses of the ethanol extract,respectively.Further,the ethanol extract were subjected for prelimnary phytochemical screening test,and analytical investigation was performed via high-performance thin-layer chromatography(HPTLC),followed by effectiveness exploration of putative bioactive compounds from P.attenuatum against human carbonic anhydrase(hCA)enzyme using molecular docking tool.Results:During phytochemicals screening,several groups of compounds such as amides,terpenoids,proteins,flavonoids,and glycosides have been identified.Further,HPTLC reveals presence of carbohydrates,proteins,amino acids,steroids,alkaloids,flavonoids,tannins,glycosides,and terpenoids.Significant diuretic action was revealed for both 200 mg/kg bw and 400 mg/kg bw of ethanol extract of P.attenuatum leaves.Interestingly,molecular docking analysis demonstrated greater binding affinity of compounds such as Cepharadione A,Nor-cepharadione B,Galbelgin,Crotepoxide,and Pipoxide chlorohydrin out of total 23 studied compounds against hCA isoforms(a key biomarker for diuretic)and score is comparable with standard drug Acetazolamide.Conclusion:It was concluded from the present studies that ethanol extract of P.attenuatum leaves exhibits signifi-cant diuretic activity.The activity may be correlated due to the presence of Cepharadione A,Norcepharadione B,Galbelgin,Crotepoxide,and Pipoxide chlorohydrin as key component responsible for inhibition of hCA isoforms.展开更多
Coalescence of traditional medicine Ayurveda and in silico technology is a rigor for supplementary development of future-ready effective traditional medicine. Ayurveda is a popular traditional medicine in South Asia, ...Coalescence of traditional medicine Ayurveda and in silico technology is a rigor for supplementary development of future-ready effective traditional medicine. Ayurveda is a popular traditional medicine in South Asia, emanating worldwide for the treatment of metabolic disorders and chronic illness. Techniques of in silico biology are not much explored for the investigation of a variety of bioactive phytochemicals of Ayurvedic herbs. Drug repurposing, reverse pharmacology, and polypharmacology in Ayurveda are areas in silico explorations that are needed to understand the rich repertoire of herbs, minerals, herbo-minerals, and assorted Ayurvedic formulations. This review emphasizes exploring the concept of Ayurveda with in silico approaches and the need for Ayurinformatics studies. It also provides an overview of in silico studies done on phytoconstituents of some important Ayurvedic plants, the utility of in silico studies in Ayurvedic phytoconstituents/formulations, limitations/challenges, and prospects of in silico studies in Ayurveda. This article discusses the convergence of in silico work, especially in the least explored field of Ayurveda. The focused coalesce of these two domains could present a predictive combinatorial platform to enhance translational research magnitude. In nutshell, it could provide new insight into an Ayurvedic drug discovery involving an in silico approach that could not only alleviate the process of traditional medicine research but also enhance its effectiveness in addressing health care.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
Mechanobiological study of chondrogenic cells and multipotent stem cells for articular cartilage tissue engineering(CTE)has been widely explored.The mechanical stimulation in terms of wall shear stress,hydrostatic pre...Mechanobiological study of chondrogenic cells and multipotent stem cells for articular cartilage tissue engineering(CTE)has been widely explored.The mechanical stimulation in terms of wall shear stress,hydrostatic pressure and mechanical strain has been applied in CTE in vitro.It has been found that the mechanical stimulation at a certain range can accelerate the chondrogenesis and articular cartilage tissue regeneration.This review explicitly focuses on the study of the influence of the mechanical environment on proliferation and extracellular matrix production of chondrocytes in vitro for CTE.The multidisciplinary approaches used in previous studies and the need for in silico methods to be used in parallel with in vitro methods are also discussed.The information from this review is expected to direct facial CTE research,in which mechanobiology has not been widely explored yet.展开更多
Background: Retinoblastoma, the most common intraocular pediatric cancer, presents complexities in its genetic landscape that necessitate a deeper understanding for improved therapeutic interventions. This study lever...Background: Retinoblastoma, the most common intraocular pediatric cancer, presents complexities in its genetic landscape that necessitate a deeper understanding for improved therapeutic interventions. This study leverages computational tools to dissect the differential gene expression profiles in retinoblastoma. Methods: Employing an in silico approach, we analyzed gene expression data from public repositories by applying rigorous statistical models, including limma and de seq 2, for identifying differentially expressed genes DEGs. Our findings were validated through cross-referencing with independent datasets and existing literature. We further employed functional annotation and pathway analysis to elucidate the biological significance of these DEGs. Results: Our computational analysis confirmed the dysregulation of key retinoblastoma-associated genes. In comparison to normal retinal tissue, RB1 exhibited a 2.5-fold increase in expression (adjusted p Conclusions: Our analysis reinforces the critical genetic alterations known in retinoblastoma and unveils new avenues for research into the disease’s molecular basis. The discovery of chemoresistance markers and immune-related genes opens potential pathways for personalized treatment strategies. The study’s outcomes emphasize the power of in silico analyses in unraveling complex cancer genomics.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
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: 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. .
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.
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.
文摘BACKGROUND Leprosy is a disease caused by Mycobacterium leprae(M.leprae),an intracellular pathogen that has tropism and affects skin and nervous system cells.The disease has two forms of presentation:Paucibacillary and multibacillary,with different clinical and immunological manifestations.Unlike what occurs in the multibacillary form,the diagnostic tests for the paucibacillary form are nonspecific and not very sensitive,allowing the existence of infected individuals without treatment,which contributes to the spread of the pathogen in the population.To mitigate this contamination,more sensitive diagnostic tests capable of detecting paucibacillary patients are needed.AIM To predict the three-dimensional structure models of M.leprae antigens with serodiagnostic potential for leprosy.METHODS In this in silico study,satisfactory templates were selected in the Protein Data Bank(PDB)using Basic Local Alignment Search Tool to predict the structural templates of ML2038,ML0286,ML0050,and 85B antigens by comparative modeling.The templates were selected according to general criteria such as sequence identity,coverage,X-ray resolution,Global Model Quality Estimate value and phylogenetic relationship;Clustal X 2.1 software was used in this analysis.Molecular modeling was completed using the software Modeller 9v13.Visualization of the models was made using ViewerLite 4.2 and PyMol software,and analysis of the quality of the predicted models was performed using the QMEAN score and Z-score.Finally,the three-dimensional moels were validated using the MolProbity and Verify 3D platforms.RESULTS The three-dimensional structure models of ML2038,ML0286,ML0050,and 85B antigens of M.leprae were predicted using the templates PDB:3UOI(90.51%identity),PDB:3EKL(87.46%identity),PDB:3FAV(40.00%identity),and PDB:1F0N(85.21%identity),respectively.The QMEAN and Z-score values indicated the good quality of the structure models.These data refer to the monomeric units of antigens,since some of these antigens have quaternary structure.The validation of the models was performed with the final three-dimensional structure-monomer(ML0050 and 85B antigens)and quaternary structures(ML2038 and ML0286).The majority of amino acid residues were observed in favorable and allowed regions in the Ramachandran plot,indicating correct positioning of the side chain and absence of steric impediment.The MolProbity score value and Verify 3D results of all models indicated a satisfactory prediction.CONCLUSION The polarized immune response against M.leprae creates a problem in leprosy detection.The selection of immunodominant epitopes is essential for the development of more sensitive serodiagnostic tests,for this it is important to know the three-dimensional structure of the antigens,which can be predicted with bioinformatics tools.
文摘Virtual screening can be a helpful approach to propose treatments for COVID-19 by developing inhibitors for blocking the attachment of the virus to human cells. This study uses molecular docking, recovery time and dynamics to analyze if potential inhibitors of main protease (M<sup>pro</sup>) of SARS-CoV-2 can interfere in the attachment of nanobodies, specifically Nb20, in the receptor binding domain (RBD) of SARS-CoV-2. The potential inhibitors are four compounds previously identified in a fluorescence resonance energy transfer (FRET)-based enzymatic assay for the SARS-CoV-2 M<sup>pro</sup>: Boceprevir, Calpain Inhibitor II, Calpain Inhibitor XII, and GC376. The findings reveal that Boceprevir has the higher affinity with the RBD/Nb20 complex, followed by Calpain Inhibitor XII, GC376 and Calpain Inhibitor II. The recovery time indicates that the RBD/Nb20 complex needs a relatively short time to return to what it was before the presence of the ligands. For the RMSD the Boceprevir and Calpain Inhibitor II have the shortest interaction times, while Calpain Inhibitor XII shows slightly more interaction, but with significant pose fluctuations. On the other hand, GC376 remains stably bound for a longer duration compared to the other compounds, suggesting that they can potentially interfere with the neutralization process of Nb20.
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.
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Purpose of the Study: COVID-19 is caused by the SARS-CoV-2 virus that had a global pandemic spread in the last two years. Symptoms of the disease include respiratory distress and, in severe cases may consequently lead to death. Blocking the viral proteins can aid in treating this disease and alleviating its symptoms. Two target proteins of the coronavirus that are hot spots in drug discovery are the papain-like protease PL-pro and the main protease M-pro. PL-pro is an enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread. M-pro is the major protease of SARS-CoV-2, which is a keystone in viral replication and transcription. Methods: In this study, we shed the light on the route of targeting viral proteins for disease alleviation, by targeting the two aforementioned enzymes, PL-pro and M-pro using in silico studies. Docking experiments, using AutoDock algorithms, were performed to predict the inhibitory effect of recently produced synthetic derivatives of curcumin on the viral proteins. Results: Most of the curcumin derivatives have shown variable levels of inhibition, e.g., S1 - S6, mainly on the papain-like protease, and to a lesser extent on the main protease. Conclusion: The results indicated that curcumin derivatives can be potent anti-viral drug of SARS-CoV-2, namely targeting the papain-like protease.
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.
文摘Background:Ayurvedic system of medicine is well established for prevention and treatment of renal problems.There are vast number of medicinal plants mentioned in Ayurvedic system of medicine,including Piper attenuatum Buch.-Ham.ex Miq.,which has been known to exhibit diuretic properties.Objective:To investigate possible mechanism and diuretic activity of ethanol extract of P.attenuatum leaves.Methods:Present study reports an in vivo diuretic activity of ethanol extracts of P.attenuatum leaves.Twenty-four Sprague-Dawley male rats were deprived from food and water for 20 h,followed by being divided into four groups to receive normal saline,Furosemide,and two doses of the ethanol extract,respectively.Further,the ethanol extract were subjected for prelimnary phytochemical screening test,and analytical investigation was performed via high-performance thin-layer chromatography(HPTLC),followed by effectiveness exploration of putative bioactive compounds from P.attenuatum against human carbonic anhydrase(hCA)enzyme using molecular docking tool.Results:During phytochemicals screening,several groups of compounds such as amides,terpenoids,proteins,flavonoids,and glycosides have been identified.Further,HPTLC reveals presence of carbohydrates,proteins,amino acids,steroids,alkaloids,flavonoids,tannins,glycosides,and terpenoids.Significant diuretic action was revealed for both 200 mg/kg bw and 400 mg/kg bw of ethanol extract of P.attenuatum leaves.Interestingly,molecular docking analysis demonstrated greater binding affinity of compounds such as Cepharadione A,Nor-cepharadione B,Galbelgin,Crotepoxide,and Pipoxide chlorohydrin out of total 23 studied compounds against hCA isoforms(a key biomarker for diuretic)and score is comparable with standard drug Acetazolamide.Conclusion:It was concluded from the present studies that ethanol extract of P.attenuatum leaves exhibits signifi-cant diuretic activity.The activity may be correlated due to the presence of Cepharadione A,Norcepharadione B,Galbelgin,Crotepoxide,and Pipoxide chlorohydrin as key component responsible for inhibition of hCA isoforms.
基金Indian National Science Academy for granting visiting scientist fellowship in 2019 for learning in silico studies in AyurvedaAIIA, New Delhi for laboratory support。
文摘Coalescence of traditional medicine Ayurveda and in silico technology is a rigor for supplementary development of future-ready effective traditional medicine. Ayurveda is a popular traditional medicine in South Asia, emanating worldwide for the treatment of metabolic disorders and chronic illness. Techniques of in silico biology are not much explored for the investigation of a variety of bioactive phytochemicals of Ayurvedic herbs. Drug repurposing, reverse pharmacology, and polypharmacology in Ayurveda are areas in silico explorations that are needed to understand the rich repertoire of herbs, minerals, herbo-minerals, and assorted Ayurvedic formulations. This review emphasizes exploring the concept of Ayurveda with in silico approaches and the need for Ayurinformatics studies. It also provides an overview of in silico studies done on phytoconstituents of some important Ayurvedic plants, the utility of in silico studies in Ayurvedic phytoconstituents/formulations, limitations/challenges, and prospects of in silico studies in Ayurveda. This article discusses the convergence of in silico work, especially in the least explored field of Ayurveda. The focused coalesce of these two domains could present a predictive combinatorial platform to enhance translational research magnitude. In nutshell, it could provide new insight into an Ayurvedic drug discovery involving an in silico approach that could not only alleviate the process of traditional medicine research but also enhance its effectiveness in addressing health care.
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EPSRC-IAA Research Impact Fund,(No.RIF202/RIR1035-109)Royal Society Research Grant(No.RGS\R2\212280).
文摘Mechanobiological study of chondrogenic cells and multipotent stem cells for articular cartilage tissue engineering(CTE)has been widely explored.The mechanical stimulation in terms of wall shear stress,hydrostatic pressure and mechanical strain has been applied in CTE in vitro.It has been found that the mechanical stimulation at a certain range can accelerate the chondrogenesis and articular cartilage tissue regeneration.This review explicitly focuses on the study of the influence of the mechanical environment on proliferation and extracellular matrix production of chondrocytes in vitro for CTE.The multidisciplinary approaches used in previous studies and the need for in silico methods to be used in parallel with in vitro methods are also discussed.The information from this review is expected to direct facial CTE research,in which mechanobiology has not been widely explored yet.
文摘Background: Retinoblastoma, the most common intraocular pediatric cancer, presents complexities in its genetic landscape that necessitate a deeper understanding for improved therapeutic interventions. This study leverages computational tools to dissect the differential gene expression profiles in retinoblastoma. Methods: Employing an in silico approach, we analyzed gene expression data from public repositories by applying rigorous statistical models, including limma and de seq 2, for identifying differentially expressed genes DEGs. Our findings were validated through cross-referencing with independent datasets and existing literature. We further employed functional annotation and pathway analysis to elucidate the biological significance of these DEGs. Results: Our computational analysis confirmed the dysregulation of key retinoblastoma-associated genes. In comparison to normal retinal tissue, RB1 exhibited a 2.5-fold increase in expression (adjusted p Conclusions: Our analysis reinforces the critical genetic alterations known in retinoblastoma and unveils new avenues for research into the disease’s molecular basis. The discovery of chemoresistance markers and immune-related genes opens potential pathways for personalized treatment strategies. The study’s outcomes emphasize the power of in silico analyses in unraveling complex cancer genomics.
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.
