The first natural infection of Plasmodium knowlesi in humans was recorded in 1965 in peninsular Malaysia. Extensive research was then conducted and it was postulated that it was a rare incident and that simian malaria will not be easily transmitted to humans. However, at the turn of the 21st century, knowlesi malaria was prevalent throughout Southeast Asia and is life threatening. Thus, a longitudinal study was initiated to determine the vectors, their seasonal variation and preference to humans and macaques.
ProBiS is a new method to identify the binding site of protein through local structural alignment against the nonredundant Protein Data Bank (PDB), which may result in unique findings compared to the energy-based, geometry-based, and sequence-based predictors. In this work, binding sites of Hemagglutinin (HA), which is an important target for drugs and vaccines in influenza treatment, have been revisited by ProBiS. For the first time, the identification of conserved binding sites by local structural alignment across all subtypes and strains of HA available in PDB is presented. ProBiS finds three distinctive conserved sites on HA's structure (named Site 1, Site 2, and Site 3). Compared to other predictors, ProBiS is the only one that accurately defines the receptor binding site (Site 1). Apart from that, Site 2, which is located slightly above the TBHQ binding site, is proposed as a potential novel conserved target for membrane fusion inhibitor. Lastly, Site 3, located around Helix A at the stem domain and recently targeted by cross-reactive antibodies, is predicted to be conserved in the latest H7N9 China 2013 strain as well. The further exploration of these three sites provides valuable insight in optimizing the influenza drug and vaccine development.
Fevicordin-A (FevA) isolated from Phaleria macrocarpa (Scheff) Boerl. seeds was evaluated for its potential anticancer activity by in vitro and in silico approaches. Cytotoxicity studies indicated that FevA was selective against cell lines of human breast adenocarcinoma (MCF-7) with an IC50 value of 6.4 µM. At 11.2 µM, FevA resulted in 76.8% cell death of T-47D human breast cancer cell lines. Critical pharmacophore features amongst human Estrogen Receptor-α (hERα) antagonists were conserved in FevA with regard to a hypothesis that they could make notable contributions to its pharmacological activity. The binding stability as well as the dynamic behavior of FevA towards the hERα receptor in agonist and antagonist binding sites were probed using molecular dynamics (MD) simulation approach. Analysis of MD simulation suggested that the tail of FevA was accountable for the repulsion of the C-terminal of Helix-11 (H11) in both agonist and antagonist receptor forms. The flexibility of loop-534 indicated the ability to disrupt the hydrogen bond zipper network between H3 and H11 in hERα. In addition, MM/GBSA calculation from the molecular dynamic simulations also revealed a stronger binding affinity of FevA in antagonistic action as compared to that of agonistic action. Collectively, both the experimental and computational results indicated that FevA has potential as a candidate for an anticancer agent, which is worth promoting for further preclinical evaluation.
Ankle rehabilitation robots are developed to enhance ankle strength, flexibility and proprioception after injury and to promote motor learning and ankle plasticity in patients with drop foot. This article reviews the design elements that have been incorporated into the existing robots, for example, backdrivability, safety measures and type of actuation. It also discusses numerous challenges faced by engineers in designing this robot, including robot stability and its dynamic characteristics, universal evaluation criteria to assess end-user comfort, safety and training performance and the scientific basis on the optimal rehabilitation strategies to improve ankle condition. This article can serve as a reference to design robot with better stability and dynamic characteristics and good safety measures against internal and external events. It can also serve as a guideline for the engineers to report their designs and findings.
Thirty derivatives of flavone hydrazone (5-34) had been synthesized through a five-step reaction and screened for their α-glucosidase inhibition activity. Chalcone 1 was synthesized through aldol condensation then subjected through oxidative cyclization, esterification, and condensation reaction to afford the final products. The result for baker's yeast α-glucosidase (EC 3.2.1.20) inhibition assay showed that all compounds are active with reference to the IC50 value of the acarbose (standard drug) except for compound 3. Increase in activity observed for compounds 2 to 34 clearly highlights the importance of flavone, hydrazide and hydrazone linkage in suppressing the activity of α-glucosidase. Additional functional group on N-benzylidene moiety further enhances the activity significantly. Compound 5 (15.4 ± 0.22 μM), a 2,4,6-trihydroxy substituted compound, is the most active compound in the series. Other compounds which were found to be active are those having chlorine, fluorine, and nitro substituents. Compounds with methoxy, pyridine, and methyl substituents are weakly active. Further studies showed that they are not active in inhibiting histone deacetylase activity and do not possess any cytotoxic properties. QSAR model was being developed to further identify the structural requirements contributing to the activity. Using Discovery Studio (DS) 2.5, various 2D descriptors were being used to develop the model. The QSAR model is able to predict the pIC50 and could be used as a prediction tool for compounds having the same skeletal framework. Molecular docking was done for all compounds using homology model of α-glucosidase to identify important binding modes responsible for inhibition activity.
Increased reports of oseltamivir (OTV)-resistant strains of the influenza virus, such as the H274Y mutation on its neuraminidase (NA), have created some cause for concern. Many studies have been conducted in the attempt to uncover the mechanism of OTV resistance in H274Y NA. However, most of the reported studies on H274Y focused only on the drug-bound system, so the direct effects of the mutation on NA itself prior to drug binding still remain unclear. Therefore, molecular dynamics simulations of NA in apo form, followed by principal component analysis and interaction energy calculations, were performed to investigate the structural changes of the NA binding site as a result of the H274Y mutation. It was observed that the disruption of the NA binding site due to the H274Y mutation was initiated by the repulsive effect of Y274 on the 250-loop, which in turn altered the hydrogen-bonding network around residue 274. The rotated W295 side chain caused the upward movement of the 340-loop. Consequently, sliding box docking results suggested that the binding pathway of OTV was compromised because of the disruption of this binding site. This study also highlighted the importance of the functional group at C6 of the sialic acid mimicry. It is hoped that these results will improve the understanding of OTV resistance and shed some light on the design of a novel anti-influenza drug.
Environmental applications of graphene (GN) are limited by the occurrence of aggregation. Herein, graphene oxide (GO) was synthesized, reduced to GN by ascorbic acid, and intercalated with cetyltrimethylammonium bromide (CTAB). GN-CTAB was characterized by Boehm's titration, N2 adsorption/desorption, Fourier transform infrared spectroscopy, Raman spectroscopy, Fluorescence spectrophotometry, X-ray diffraction and Scanning electron microscopy. Then, GN-CTAB was used for the adsorptive removal of acid red 265 (AR265) and acid orange 7 (AO7) dyes from water both under batch and column operation. Under batch operation, the effect of pH, adsorbent dosage, initial dye concentration, contact time and temperature on dyes adsorption were assessed. Adsorption isotherms, kinetics, and thermodynamics were analyzed systematically. Regarding the fixed bed operation, the effect of both the bed height and flow rate were studied and experimental results fitted to the Thomas and BDST models. Then, the bed loss capacity along five adsorption-regeneration cycles was determined in order to further approach the practical application of GN-CTAB for wastewater treatment, namely for the removal of dyes.
Processing of soybeans to other products and consumption of soy products is increasing worldwide mainly due to acclaimed health benefits. Processing can alter soybean sensory appeal, nutritive value and potentially affect consumer health. Rhizopus oligosporus was used to ferment soybean for 3 days. The tempeh flour (TF) was produced form tempeh while defatted tempeh flour (DTF) was then produced from TF by immersing in hexane solvent while soy protein isolate (SPI) was prepared from DTF by using alkali and acid followed by neutralization treatment. In this study, nutritional properties and amino acid content of tempeh, TF, DTF and SPI were determined. Therefore, the objective of this study is was to evaluate the effect of each treatment on the chemical composition and amino acid content for all the samples. The results showed that the nutritional properties (total ash, moisture, crude fat, total carbohydrate and crude fibre) were reduced significantly (p < 0.05) except for protein content. Protein content was significantly (p < 0.05) increased by 50.5% in SPI. For amino acid content, the results obtained showed that SPI contain highest amount of essential and non-essential amino acid followed by DTF, Tempeh and TF. Glutamic acid was found to be the highest amino acid component in all samples. The evaluation from the results showed that SPI can be considered as potential functional food ingredients.
A large number of rice agronomic traits are complex, multi factorial and polygenic. As the mechanisms and genes determining grain size and yield are largely unknown, the identification of regulatory genes related to grain development remains a preeminent approach in rice genetic studies and breeding programs. Genes regulating cell proliferation and expansion in spikelet hulls and participating in endosperm development are the main controllers of rice kernel elongation and grain size. We review here and discuss recent findings on genes controlling rice grain size and the mechanisms, epialleles, epigenomic variation, and assessment of controlling genes using genome-editing tools relating to kernel elongation.
MPT64 is a specific protein that is secreted by Mycobacterium tuberculosis complex (MTBC). The objective of this study was to obtain optimum culture conditions for MPT64 synthetic gene expression in Escherichia coli BL21 (DE3) by response surface methodology (RSM). The RSM was undertaken to optimize the culture conditions under different cultivation conditions (medium concentration, induction time and inducer concentration), designed by the factorial Box-Bhenken using Minitab 17 statistical software. From the randomized combination, 15 treatments and three center point repetitions were obtained. Furthermore, expression methods were carried out in the flask scale fermentation in accordance with the predetermined design. Then, the MPT64 protein in the cytoplasm of E. coli cell was isolated and characterized using sodium dodecyl sulfate polyacrilamide electrophoresis (SDS-PAGE) then quantified using the ImageJ program. The optimum conditions were two-fold medium concentration (tryptone 20 mg/mL, yeast extract 10 mg/mL, and sodium chloride 20 mg/mL), 5 h of induction time and 4 mM rhamnose. The average concentration of recombinant MPT64 at optimum conditions was 0.0392 mg/mL, higher than the predicted concentration of 0.0311 mg/mL. In conclusion, the relationship between the selected optimization parameters strongly influenced the level of MPT64 gene expression in E. coli BL21 (DE3).
The removal of impurities from water or wastewater by the membrane filtration process has become more reliable due to good hydraulic performance and high permeate quality. The filterability of the membrane can be improved by having a material with a specific pore structure and good hydrophilic properties. This work aims at preparing a polyvinylidene fluoride (PVDF) membrane incorporated with phospholipid in the form of a 2-methacryloyloxyethyl phosphorylcholine, polymeric additive in the form of polyvinylpyrrolidone, and its combination with inorganic nanosilica from a renewable source derived from bagasse. The resulting membrane morphologies were analyzed by using scanning electron microscopy. Furthermore, atomic force microscopy was performed to analyze the membrane surface roughness. The chemical compositions of the resulting membranes were identified using Fourier transform infrared. A lab-scale cross-flow filtration system module was used to evaluate the membrane's hydraulic and separation performance by the filtration of humic acid (HA) solution as the model contaminant. Results showed that the additives improved the membrane surface hydrophilicity. All modified membranes also showed up to five times higher water permeability than the pristine PVDF, thanks to the improved structure. Additionally, all membrane samples showed HA rejections of 75-90%.
Previous studies have reported that compounds bearing an arylamide linked to a heterocyclic planar ring have successfully inhibited the hemopexin-like domain (PEX9) of matrix metalloproteinase 9 (MMP9). PEX9 has been suggested to be more selectively targeted than MMP9's catalytic domain in a degrading extracellular matrix under some pathologic conditions, especially in cancer. In this study, we aim to synthesize and evaluate 10 arylamide compounds as MMP9 inhibitors through an enzymatic assay as well as a cellular assay. The mechanism of inhibition for the most active compounds was investigated via molecular dynamics simulation (MD). Molecular docking was performed using AutoDock4.0 with PEX9 as the protein model to predict the binding of the designed compounds. The synthesis was carried out by reacting aniline derivatives with 3-bromopropanoyl chloride using pyridine as the catalyst at room temperature. The MMP9 assay was conducted using the FRET-based MMP9 kits protocol and gelatin zymography assay. The cytotoxicity assay was done using the MTT method, and the MD simulation was performed using AMBER16. Assay on MMP9 demonstrated activities of three compounds (2, 7, and 9) with more than 50% inhibition. Further inhibition on MMP9 expressed by 4T1 showed that two compounds (7 and 9) inhibited its gelatinolytic activity more than 50%. The cytotoxicity assay against 4T1 cells results in the inhibition of the cell growth with an EC50 of 125 μM and 132 μM for 7 and 9, respectively. The MD simulation explained a stable interaction of 7 and 9 in PEX9 at 100 ns with a free energy of binding of -8.03 kcal/mol and -6.41 kcal/mol, respectively. Arylamides have potential effects as selective MMP9 inhibitors in inhibiting breast cancer cell progression.
Estrogen receptor alpha (ERα) acts as the transcription factor and the main therapeutic target against breast cancer. One of the compounds that has been shown to act as an ERα is α-mangostin. However, it still has weaknesses due to its low solubility and low potent activity. In this study, α-mangostin was modified by substituting -OH group at C6 using benzoyl derivatives through a step by step in silico study, namely pharmacokinetic prediction (https://preadmet.bmdrc.kr/adme/), pharmacophore modeling (LigandScout 4.1), molecular docking simulation (AutoDock 4.2), molecular dynamics simulation (AMBER 16) and a binding free energy analysis using MM-PBSA method. From the computational studies, three compounds which are derived from α-mangostin (AMB-1 (-9.84 kcal/mol), AMB-2 (-6.80 kcal/mol) and AMB-10 (-12.42 kcal/mol)) have lower binding free energy than α-mangostin (-1.77 kcal/mol), as evidenced by the binding free energy calculation using the MM-PBSA method. They can then be predicted to have potent activities as ERα antagonists.Communicated by Ramaswamy H. Sarma.
This present study reports some natural products and one hydroxamic acid synthetic compound which were previously reported as matrix metalloproteinase-9 (MMP-9) inhibitors to be evaluated for their inhibition toward severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) 3-chymotrypsin-like protease (3CLpro). This enzyme is one of the proteins responsible for this coronaviral replication. Two herbal methanolic extracts i.e., Averrhoa carambola leaves and Ageratum conyzoides aerial part demonstrate >50% inhibition at 1000 µg/mL. Interestingly, apigenin, one of flavonoids, demonstrates 92% inhibition at 250 µg/mL (925 µM) as well as hydroxamic acid compound, N-isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid (NNGH), which shows 69% inhibition at 100 µM. The in vitro results are supported by the docking studies revealing that the binding mode of both compounds is mainly by interacting with GLU166 residue in the hydrophobic pocket of the 3CLpro. Pharmacophore mapping further supported the results by confirming that the in vitro activities of both compounds are due to their pharmacophore features employing hydrogen bond acceptor (HBA), hydrogen bond donor (HBD) and hydrophobic. Gas Chromatography-Mass Spectrometry (GC-MS) analysis reported chromene compounds in Ageratum conyzoides aerial part methanolic extract are potential to be this enzyme inhibitor candidate. These all results reflect their potencies to be SARS-CoV-2 inhibitors through 3CLpro inhibition mechanism.
FKBP22 of a psychrophilic bacterium, Shewanella sp. SIB1 (SIB1 FKBP22), is a member of peptidyl-prolyl cis-trans isomerase (PPIase) and consists of N- and C-domains responsible for chaperone-like and PPIase catalytic activities, respectively. The chaperone-like activity of SIB1 FKBP22 was previously evidenced by its ability to prevent dithiothreitol (DTT)-induced insulin aggregation. Nevertheless, the mechanism by which this protein inhibits the aggregation remains unclear. To address this, the binding affinity of SIB1 FKBP22 to the native or reduced states of insulin was examined using surface plasmon resonance (SPR). The native and reduced states refer to insulin in the absence or DTT presence, respectively. The SPR sensorgram showed that SIB1 FKBP22 binds specifically to the reduced state of insulin, with a KD value of 37.31 ± 3.20 μM. This binding was facilitated by the N-domain, as indicated by the comparable KD values of the N-domain and SIB1 FKBP22. Meanwhile, the reduced state of insulin was found to have no affinity towards the C-domain. The KD value of SIB1 FKBP22 was slightly decreased by NaCl but was not severely affected by FK506, a specific FKBP inhibitor. Similarly, the prevention of DTT-induced aggregation by SIB1 FKBP22 was also modulated by the N-domain and was not affected by FK506. Further, the reduced and native states of insulin had no effect on the catalytic efficiency (kcat/KM) of SIB1 FKBP22 towards a peptide substrate. Nevertheless, the reduced state of insulin slightly reduced the catalytic efficiency towards refolding RNase T1, at up to 1.5-fold lower than in the absence of insulin. These results suggested that the binding event was mainly facilitated by hydrophobic interaction and was independent from its PPIase activity. Altogether, a possible mechanism by which SIB1 FKBP22 prevents DTT-induced insulin aggregation was proposed.
The tenacious thirst for fuel-saving and desirable physical and mechanical properties of the materials have compelled researchers to focus on a new generation of aluminum hybrid composites for automotive and aircraft applications. This work investigates the microhardness behavior and microstructural characterization of aluminum alloy (Al 7075)-titanium carbide (TiC)-graphite (Gr) hybrid composites. The hybrid composites were prepared via the powder metallurgy technique with the amounts of TiC (0, 3, 5, and 7 wt.%), reinforced to Al 7075 + 1 wt.% Gr. The microstructural characteristics were investigated by optical microscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD) and energy dispersive X-ray spectroscopy (EDS) elemental mapping. A Box Behnken design (BBD) response surface methodology (RSM) approach was utilized for modeling and optimization of density and microhardness independent parameters and to develop an empirical model of density and microhardness in terms of process variables. Effects of independent parameters on the responses have been evaluated by analysis of variance (ANOVA). The density and microhardness of the Al 7075-TiC-Gr hybrid composites are found to be increased by increasing the weight percentage of TiC particles. The optimal conditions for obtaining the highest density and microhardness are estimated to be 6.79 wt.% TiC at temperature 626.13 °C and compaction pressure of 300 Mpa.
The combined effect of design control factors on the response variables gives valuable information for geometric design optimization of the compound parabolic concentrator. This study presents the data related to the statistical modeling and analysis of variance for aperture width and height of a low concentration symmetric compound parabolic concentrator designed for photovoltaic applications. The design matrix was generated using the response surface modeling approach. The geometric design equations of the proposed concentrator were developed and solved analytically using MATLAB. The empirical models were developed to establish relationships between the control factors and response variables of the proposed system. The analysis of variance was conducted for two significant response variables. The developed statistical models can be used to predict the selected response variables within the permissible range. The presented data can be used for statistical modeling and design optimization of the two-dimensional symmetric compound parabolic concentrator.
2-Phenoxyacetamide group has been identified as one of markers in the discovery and development of SARS-CoV-2 antiviral agent through its main protease (Mpro) inhibition pathway. This study aims to study a series of 2-phenoxyacetamide derivatives using in silico method toward SARS-CoV-2 Mpro as the protein target. The study was initiated by employing structure-based pharmacophore to virtually screen and to select the ligands, which have the best fit score (hits) along with the common pharmacophore features being matched. The result shows that from the 11 ligands designed, four ligands are selected as the hits by demonstrating fit score in the range of 56.20 to 65.53 to the pharmacophore model, employing hydrogen bond acceptor (HBA) and hydrophobic (H) as the common features. The hits were then docked into the binding site of the Mpro to see the binding mode of the corresponding hits as well as its affinity. The docking results free energy of binding (ΔGbind) of the hits are in agreement with the pharmacophore fit score, in the range of -6.83 to -7.20 kcal/ mol. To gain the information of the hits as a potential drug to be developed, the in silico study was further proceed by predicting the mutagenic potency, toxicity and pharmacokinetic profiles. Based on the efficiency percentage, all hits meet the criteria as drug candidates by showing 84-88% leading to a conclusion that 2-phenoxyacetamide derivatives are beneficial to be marked as the lead compound for SARS-CoV-2 Mpro inhibitor.
Strict environmental concerns, depleting natural recourses, and rising demand for building construction materials have promoted scientific research toward alternative building materials. This research supports the idea of sustainability and a circular economy via the utilization of waste to produce value-added products. The research explored the potential of waste plastics and silica sand for developing thermoplastic composite as floor tiles. The samples were characterized by water absorption, compressive strength, flexural strength, and sliding wear. The morphological analysis of the sand-plastic interfaces was covered under the umbrella of this study. The maximum compressive and flexural strength were found to be 46.20 N/mm2 and 6.24 N/mm2, respectively, with the minimum water absorption and sliding wear rate of 0.039% and 0.143 × 10-8 kg/m, respectively. The study suggests the workability of the developed floor tiles in non-traffic areas of public places. Thus, the study provides a green building material through recycling waste plastics for sustainable development.