In silico prospective analysis of the medicinal plants activity on the CagA oncoprotein from Helicobacter pylori

BACKGROUND Colonization with Helicobacter pylori(H.pylori)has a strong correlation with gastric cancer,and the virulence factor CagA is implicated in carcinogenesis.Studies have been conducted using medicinal plants with the aim of eliminating the pathogen;however,the possibility of blocking H.pylori-induced cell differentiation to prevent the onset and/or progression of tumors has not been addressed.This type of study is expensive and time-consuming,requiring in vitro and/or in vivo tests,which can be solved using bioinformatics.Therefore,prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the CagA oncoprotein.AIM To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the CagA oncoprotein of H.pylori.METHODS In this in silico study,the structures of the phenolic compounds(ligands)kaempferol,myricetin,quercetin,ponciretin(flavonoids),and chlorogenic acid(phenolic acid)were selected from the PubChem database.These phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate H.pylori infection.The three-dimensional structure model of the CagA oncoprotein of H.pylori(receptor)was obtained through molecular modeling using computational tools from the I-Tasser platform,employing the threading methodology.The primary sequence of CagA was sourced from GenBank(BAK52797.1).A screening was conducted to identify binding sites in the structure of the CagA oncoprotein that could potentially interact with the ligands,utilizing the GRaSP online platform.Both the ligands and receptor were prepared for molecular docking using AutoDock Tools 4(ADT)software,and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 software.Two sets of simulations were performed:One involving the central region of CagA with phenolic compounds,and another involving the carboxy-terminus region of CagA with phenolic compounds.The receptor-ligand complexes were then analyzed using PyMol and BIOVIA Discovery Studio software.RESULTS The structure model obtained for the CagA oncoprotein exhibited high quality(C-score=0.09)and was validated using parameters from the MolProbity platform.The GRaSP online platform identified 24 residues(phenylalanine and leucine)as potential binding sites on the CagA oncoprotein.Molecular docking simulations were conducted with the three-dimensional model of the CagA oncoprotein.No complexes were observed in the simulations between the carboxy-terminus region of CagA and the phenolic compounds;however,all phenolic compounds interacted with the central region of the oncoprotein.Phenolic compounds and CagA exhibited significant affinity energy(-7.9 to-9.1 kcal/mol):CagA/kaempferol formed 28 chemical bonds,CagA/myricetin formed 18 chemical bonds,CagA/quercetin formed 16 chemical bonds,CagA/ponciretin formed 13 chemical bonds,and CagA/chlorogenic acid formed 17 chemical bonds.Although none of the phenolic compounds directly bound to the amino acid residues of the K-Xn-R-X-R membrane binding motif,all of them bound to residues,mostly positively or negatively charged,located near this region.CONCLUSION In silico,the tested phenolic compounds formed stable complexes with CagA.Therefore,they could be tested in vitro and/or in vivo to validate the findings,and to assess interference in CagA/cellular target interactions and in the oncogenic differentiation of gastric cells.

Structural and Functional Annotation of Hypothetical Protein of Fusobacterium nucleatum Strain MJR7757B: An in Silico Approach

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.

New 4-imino-4H-Chromeno[2,3-d]Pyrimidin-3(5H)-Amine: Synthesis, Cytotoxic Effects on Tumoral Cell Lines and in Silico ADMET Properties

The synthesis of new 4-imino-4H-chromeno[2,3-d]pyrimidin-3(5H)-amine in four steps including one step under microwave dielectric heating is reported. The structural identity of the synthesized compounds was established according to their spectroscopic analysis, such as FT-IR, NMR and mass spectroscopy. These new compounds were tested for their antiproliferative activities on seven representative human tumoral cell lines (Huh7 D12, Caco2, MDA-MB231, MDA-MB468, HCT116, PC3 and MCF7) and also on fibroblasts. Among them, only the compounds 6c showed micromolar cytotoxic activity on tumor cell lines (1.8 50 50 > 25 μM). Finally, in silico ADMET studies ware performed to investigate the possibility of using of the identified compound 6c as potential anti-tumor compound.

New Insights in the Biodegradability and the Ecotoxicological Effects of Solar Products Containing Mineral and Chemical UV-Filters on Marine Zoo- and Phytoplanktons: An in silico and in vitro Study

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), 9th 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. .

基于in silico技术探究益母草在化妆品中的应用前景

益母草具有行血养血,活血化瘀的作用,临床应用广泛,常用来主治妇科疾病,近年来益母草的美容应用逐渐受到关注。本研究利用in silico技术平台,通过文献计量学对益母草的研究现状和未来的发展态势进行了预测,同时结合网络药理学对益母草皮肤美容的功效及物质基础进行预测,结果表明益母草的活性成分萜类化合物及益母草碱可通过NADPH、PDPK1、MAOB、VEGF2、SIRT2等靶点有效促进血液流动,改善皮肤微循环,调节激素代谢,降低炎症反应,抵御氧化应激,具有延缓皮肤老化,滋养皮肤的功效。本研究为益母草作为化妆品植物功效原料的物质基础及功效机理提供了理论基础,同时证明了益母草作为化妆品功效原料的独特性,具备良好的发展前景。

In vitro and in silico studies of salicylic acid on systemic induced resistance against bacterial leaf blight disease and enhancement of crop yield

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.

Comparative studies on the binding site of anesthetics to GABA a receptors using in silico docking methods

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.

Three-dimensional models of antigens with serodiagnostic potential for leprosy:An in silico study

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.

In Silico Evaluation of the Potential Interference of Boceprevir, Calpain Inhibitor II, Calpain Inhibitor XII, and GC376 in the Binding of SARS-CoV-2 Spike Protein to Human Nanobody Nb20

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 (Mpro) 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 Mpro: 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.

In Silico Cloning and Sequence Analysis of Phospholipase Dα Gene from Peach Fruit

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.

In silico studies of magnesium-based implants: A review of the current stage and challenges

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.

Electrochemical and in silico approaches for liver metabolic oxidation of antitumor-active triazoloacridinone C-1305

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.

In silico prediction of phytoconstituents from Ehretia laevis targeting TNF-αin arthritis

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.

In vitro - in vivo - in silico approach in the development of inhaled drug products: Nanocrystal-based formulations with budesonide as a model drug

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.

Effectiveness of intermittent preventive treatment in pregnancy with sulfadoxine-pyrimethamine: An in silico pharmacological model

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.

Taxifolin stability: In silico prediction and in vitro degradation with HPLC-UV/UPLCe ESI-MS monitoring

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.

Feasibility Analysis of in silico Cloning of Functional Candidate Genes in Tea (Camellia sinensis)

[ 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.

In Silico Evaluation for the Inhibitory Action of Curcumin Derivatives on the SARS-CoV-2 Proteins

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.

Molecular and genetic markers in hepatocellular carcinoma:In silico analysis to clinical validation(current limitations and future promises)

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.

Diuretic Activity of Ethanol Extract of Piper attenuatum Leaves Might Be Due to the Inhibition of Carbonic Anhydrase Enzyme:An in vivo and in silico Investigation

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.