Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/.
Glycolipids form materials of considerable potential for a wide range of surfactant and thin film applications. Understanding the effect of glycolipid covalent structure on the properties of their thermotropic and lyotropic assemblies is a key step toward rational design of new glycolipid-based materials. Here, we perform molecular dynamics simulations of anhydrous bilayers of dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside, and a C(12)C(10) branched β-maltoside. Specifically, we examine the consequences of chain branching and headgroup identity on the structure and dynamics of the lamellar assemblies. Chain branching of the glycolipid leads to measurable differences in the dimensions and interactions of the lamellar assembly, as well as a more fluid-like hydrophobic chain region. Substitution of the maltosyl headgroup of βMal-C(12) by an isomaltosyl moiety leads to a significant decrease in bilayer spacing as well as a markedly altered pattern of inter-headgroup hydrogen bonding. The distinctive simulated structures of the two regioisomers provide insight into the difference of ~90 °C in their observed clearing temperatures. For all four simulated glycolipid systems, with the exception of the sn-2 chain of the branched maltoside, the alkyl chains are ordered and exhibit a distinct tilt, consistent with recent crystallographic analysis of a branched chain Guerbet glycoside. These insights into structure-property relationships from simulation provide an important molecular basis for future design of synthetic glycolipid materials.
New coumarin derivatives, namely 7-[(5-amino-1,3,4-thiadiazol-2-yl)methoxy]-2H-chromen-2-one, 5-[(2-oxo-2H-chromen-7-yloxy)methyl]-1,3,4-thiadiazol-2(3H)-one, 2-[2-(2-oxo-2H-chromen-7-yloxy)acetyl]-N-phenylhydrazinecarbothioamide, 7-[(5-(phenylamino)-1,3,4-thiadiazol-2-yl)methoxy]-2H-chromen-2-one and 7-[(5-mercapto-4-phenyl-4H-1,2,4-triazol-3-yl)methoxy]-2H-chromen-2-one were prepared starting from the natural compound umbelliferone. The newly synthesized compounds were characterized by elemental analysis and spectral studies (IR, ¹H-NMR and ¹³C-NMR).
Some novel Schiff bases derived from 1-(2-ketoiminoethyl)piperazines were synthesized and characterized by mass spectroscopy, FTIR, UV-Visible, 1H and 13C-NMR. The compounds were tested for inhibitory activities on human acetylcholinesterase (hAChE), antioxidant activities, acute oral toxicity and further studied by molecular modeling techniques. The study identified the compound (DHP) to have the highest activity among the series in hAChE inhibition and DPPH assay while the compound LP revealed the highest activity in the FRAP assay. The hAChE inhibitory activity of DHP is comparable with that of propidium, a known AChE inhibitor. This high activity of DHP was checked by molecular modeling which showed that DHP could not be considered as a bivalent ligand due to its incapability to occupy the esteratic site (ES) region of the 3D crystal structure of hAChE. The antioxidant study unveiled varying results in 1,1-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP) assays. This indicates mechanistic variations of the compounds in the two assays. The potential therapeutic applications and safety of these compounds were suggested for use as human acetylcholinesterase inhibitors and antioxidants.
Anomers and epimers α- and β-gluco and -galactosides are expected to behave differently. However, recent results on a series of Guerbet glycosides have indicated similar liquid crystal clearing temperatures for pure β-glucosides and the corresponding α-galactosides. This observation has led to speculation on similarities in the self-assembly interactions between the two systems, attributed to the trans-configuration of the 4-OH group and the hydrophobic aglycon. Previous simulations on related bilayers systems support this hypothesis, by relating this clearing transition temperature to intralayer (sugar-sugar) hydrogen bonding. In order to confirm the hypothesis, the comparison was expanded to include the cis-configurated pair, that is, α-gluco/β-galactoside. A set of α-configurated Guerbet glucosides as well as octyl α-galactoside were prepared and their thermotropic phase behavior studied. The data obtained enabled a complete comparison of the isomers of interest. While the results in general are in line with a pairing of the stereo-isomers according to the indicated cis/trans-configuration, differences within the pairs can be explained based on the direction of hydrogen bonds from a simple modeling study.
Addition of 1-alkyl-3-methylimidazolium (C(n)-mim) cations 3-5 to a mixture of bis-phosphonium cation 2 and sodium p-sulfonatocalix[4]arene (1) in the presence of lanthanide ions results in the selective binding of an imidazolium cation into the cavity of the calixarene. The result is a multi-layered solid material with an inherently flexible interplay of the components. Incorporating ethyl-, n-butyl- or n-hexyl-mim cations into the multi-layers results in significant perturbation of the structure, the most striking effect is the tilting of the plane of the bowl-shaped calixarene relative to the plane of the multi-layer, with tilt angles of 7.2, 28.9 and 65.5 degrees , respectively. The lanthanide ions facilitate complexation, but are not incorporated into the structures and, in all cases, the calixarene takes on a 5- charge, with one of the lower-rim phenolic groups deprotonated. ROESY NMR experiments and other (1)H NMR spectroscopy studies establish the formation of 1:1 supermolecules of C(n)-mim and calixarene, regardless of the ratio of the two components, and indicate that the supermolecules undergo rapid exchange on the NMR spectroscopy timescale.
A series of hitherto unreported anthracene-embedded dispirooxindoles has been synthesized via a one-pot three-component 1,3-dipolar cycloaddition reaction of an azomethine ylide, generated in situ from the reaction of isatin and sarcosine to 10-benzylideneanthracen-9(10H)-one as a dipolarophile in 1-butyl-3-methylimidazolium bromide([bmim]Br), an ionic liquid. This reaction proceeded regio- and diastereoselectively, in good to excellent yields.
Breast cancer is one of the major issues in the field of oncology, reported with a higher prevalence rate in women worldwide. In attempt to reveal the potential biomarkers for breast cancer, the findings of differentially glycosylated haptoglobin and osteonectin in previous study have drawn our attention towards glycoproteins of secretome from the MCF-7 cancer cell line. In the present study, further analyses were performed on the medium of MCF-7 cells by subjecting it to two-dimensional analyses followed by image analysis in contrast to the medium of human mammary epithelial cells (HMEpC) as a negative control. Carboxypeptidase A4 (CPA4), alpha-1-antitrypsin (AAT), haptoglobin (HP), and HSC70 were detected in the medium of MCF-7, while only CPA4 and osteonectin (ON) were detected in HMEpC medium. In addition, CPA4 was detected as upregulated in the MCF-7 medium. Further analysis by lectin showed that CPA4, AAT, HP, and HSC70 were secreted as N-glycan in the medium of MCF-7, with HP also showing differentially N-glycosylated isoforms. For the HMEpC, only CPA4 was detected as N-glycan. No O-glycan was detected in the medium of HMEpC but MCF-7 expressed O-glycosylated CPA4 and HSC70. All these revealed that glycoproteins could be used as glycan-based biomarkers for the prognosis of breast cancer.
Globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. A putative globin-coupled sensor from Methylacidiphilum infernorum, HGbRL, contains an N-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture. Helices E and F fuse into an elongated helix, resulting in a novel site-swapped globin fold made up of helices A-E, hence the distal site, from one subunit and helices F-H, the proximal site, from another. The open structure possesses a large cavity binding an imidazole molecule, while the closed structure forms a unique Lys-His hexacoordinated species, with the first turn of helix E unravelling to allow Lys52(E10) to bind to the haem. Ligand binding induces reorganization of loop CE, which is stabilized in the closed form, and helix E, triggering a large conformational movement in the open form. These provide a mechanical insight into how a signal may be relayed between the globin domain and the C-terminal domain of HGbRL, a Roadblock/LC7 domain. Comparison with HGbI, a closely related globin, further underlines the high degree of structural versatility that the globin fold is capable of, enabling it to perform a diversity of functions.
With ever-growing aging population and demand for denture treatments, pressure-induced mucosa lesion and residual ridge resorption remain main sources of clinical complications. Conventional denture design and fabrication are challenged for its labor and experience intensity, urgently necessitating an automatic procedure. This study aims to develop a fully automatic procedure enabling shape optimization and additive manufacturing of removable partial dentures (RPD), to maximize the uniformity of contact pressure distribution on the mucosa, thereby reducing associated clinical complications. A 3D heterogeneous finite element (FE) model was constructed from CT scan, and the critical tissue of mucosa was modeled as a hyperelastic material from in vivo clinical data. A contact shape optimization algorithm was developed based on the bi-directional evolutionary structural optimization (BESO) technique. Both initial and optimized dentures were prototyped by 3D printing technology and evaluated with in vitro tests. Through the optimization, the peak contact pressure was reduced by 70%, and the uniformity was improved by 63%. In vitro tests verified the effectiveness of this procedure, and the hydrostatic pressure induced in the mucosa is well below clinical pressure-pain thresholds (PPT), potentially lessening risk of residual ridge resorption. This proposed computational optimization and additive fabrication procedure provides a novel method for fast denture design and adjustment at low cost, with quantitative guidelines and computer aided design and manufacturing (CAD/CAM) for a specific patient. The integration of digitalized modeling, computational optimization, and free-form fabrication enables more efficient clinical adaptation. The customized optimal denture design is expected to minimize pain/discomfort and potentially reduce long-term residual ridge resorption.
In this study 36 new compounds were synthesized by condensing barbituric acid or thiobarbituric acid and respective anilines (bearing different substituents) in the presence of triethyl orthoformate in good yields. In vitro urease inhibition studies against jack bean urease revealed that barbituric acid derived compounds (1-9 and 19-27) were found to exhibit low to moderate activity however thiobarbituric acid derived compounds (10-18 and 28-36) showed significant inhibition activity at low micro-molar concentrations. Among the synthesized compounds, compounds (15), (12), (10), (36), (16) and (35) showed excellent urease inhibition with IC50 values 8.53 ± 0.027, 8.93 ± 0.027, 12.96 ± 0.13, 15 ± 0.098, 18.9 ± 0.027 and 19.7 ± 0.63 μM, respectively, even better than the reference compound thiourea (IC50 = 21 ± 0.011). The compound (11) exhibited comparable activity to the standard with IC50 value 21.83 ± 0.19 μM. In silico molecular docking studies for most active compounds (10), (12), (15), (16), (35) and (36) and two inactive compounds (3) and (6) were performed to predict the binding patterns.
Candida rugosa lipase was modified via reductive alkylation to increase its hydrophobicity to work better in organic solvents. The free amino group of lysines was alkylated using propionaldehyde with different degrees of modification obtained (49 and 86%). Far-ultraviolet circular dichroism (CD) spectroscopy of the lipase in aqueous solvent showed that such chemical modifications at the enzyme surface caused a loss in secondary and tertiary structure that is attributed to the enzyme unfolding. Using molecular modeling, we propose that in an aqueous environment the loss in protein structure of the modified lipase is owing to disruption of stabilizing salt bridges, particularly of surface lysines. Indeed, molecular modeling and simulation of a salt bridge formed by Lys-75 to Asp-79, in a nonpolar environment, suggests the adoption of a more flexible alkylated lysine that may explain higher lipase activity in organic solvents on alkylation.
One of the most challenging issues when facing a Quantitative structure-activity relationship (QSAR) classification model is to deal with the descriptor selection. Penalized methods have been adapted and have gained popularity as a key for simultaneously performing descriptor selection and QSAR classification model estimation. However, penalized methods have drawbacks such as having biases and inconsistencies that make they lack the oracle properties. This paper proposes an adaptive penalized logistic regression (APLR) to overcome these drawbacks. This is done by employing a ratio (BWR) of the descriptors between-groups sum of squares (BSS) to the within-groups sum of squares (WSS) for each descriptor as a weight inside the L1-norm. The proposed method was applied to one dataset that consists of a diverse series of antimicrobial agents with their respective bioactivities against Candida albicans. By experimental study, it has been shown that the proposed method (APLR) was more efficient in the selection of descriptors and classification accuracy than the other competitive methods that could be used in developing QSAR classification models. Another dataset was also successfully experienced. Therefore, it can be concluded that the APLR method had significant impact on QSAR analysis and studies.
De novo approach was applied to design single chain fragment variable (scFv) for BmR1, a recombinant antigen from Bm17DIII gene which is the primary antigen used for the detection of anti-BmR1 IgG4 antibodies in the diagnostic of lymphatic filariasis. Three epitopes of the BmR1 was previously predicted form an ab initio derived three-dimensional structure. A collection of energetically favourable conformations was generated via hot-spot-centric approach. This resulted in a set of three different scFv scaffolds used to compute the high shape complementary conformations via dock-and-design approach with the predicted epitopes of BmR1. A total of 4227 scFv designs were generated where 200 scFv designs produced binding energies of less than -20 R.E.U with shape complementarity higher than 0.5. We further selected the design with at least one hydrogen bond and one salt bridge with the epitope, thus resulted in a total of 10, 1 and 19 sFv designs for epitope 1, 2 and 3, respectively. The results thus showed that de novo design can be an alternative approach to yield high affinity in silico scFv designs as a starting point for antibody or specific binder discovery processes.
Carbon nanotubes (CNTs) have received enormous attention due to their fascinating properties to be used in various applications including electronics, sensing, energy storage and conversion. The first principles calculations within density functional theory (DFT) have been carried out in order to investigate the structural, electronic and optical properties of un-doped and doped CNT nanostructures. O2, CO2, and CH3OH have been chosen as gas molecules to study the adsorption properties based on zigzag (8,0) SWCNTs. The results demonstrate that the adsorption of O2, CO2, and CH3OH gas molecules on pristine, Si-doped and B-doped SWCNTs are either physisorption or chemisorption. Moreover, the electronic properties indicating SWCNT shows significant improvement toward gas adsorption which provides the impact of selecting the best gas sensor materials towards detecting gas molecule. Therefore, these pristine, Si-, and B-doped SWCNTs can be considered to be very good potential candidates for sensing application.
Naturally occurring proteins are emerging as novel therapeutics in the protein-based biopharmaceutical industry for the treatment of diabetes and obesity. However, proteins are not suitable for oral delivery due to short half-life, reduced physical and chemical stability and low permeability across the membrane. Chemical modification has been identified as a formulation strategy to enhance the stability and bioavailability of protein drugs. The present study aims to study the effect of charge-specific modification of basic amino acids (Lys, Arg) and guanidination on the interaction of insulin with its receptor using molecular modelling. Our investigation revealed that the guanidination of insulin (Lys-NHC = NHNH2) enhanced and exerted stronger binding of the protein to its receptor through electrostatic interaction than native insulin (Lys-NH3+). Point mutations of Lys and Arg (R22, K29; R22K, K29; R22, K29R; R22K, K29R) were attempted and the effects on the interaction and stability between insulin/modified insulins and insulin receptor were also analyzed in this study. The findings from the study are expected to provide a better understanding of the possible mechanism of action of the modified protein at a molecular level before advancing to real experiments.
Interaction of pendimethalin (PM) herbicide with the major transporter in human circulation, human serum albumin (HSA), was studied using fluorescence, circular dichroism (CD), and molecular modeling methods. The attenuation of the fluorescence intensity of HSA in the presence of PM revealed formation of the PM-HSA complex. Analysis of the fluorescence quenching data showed moderately strong binding affinity between PM and HSA. Both hydrophobic interactions and hydrogen bonding were suggested to stabilize the PM-HSA complex, based on thermodynamic data. Binding of PM to HSA induced perturbation in the microenvironment around the aromatic fluorophores as well as secondary and tertiary structural changes in the protein. Complexation of PM with HSA led to an increase in its thermal stability. Both site marker displacement and molecular modeling results suggested site I, located in subdomain IIA as the preferred binding site of PM on HSA.
Polyhydroxyalkanoate (PHA) is a promising candidate for use as an alternative bioplastic to replace petroleum-based plastics. Our understanding of PHA synthase PhaC is poor due to the paucity of available three-dimensional structural information. Here we present a high-resolution crystal structure of the catalytic domain of PhaC from Chromobacterium sp. USM2, PhaC Cs -CAT. The structure shows that PhaC Cs -CAT forms an α/β hydrolase fold comprising α/β core and CAP subdomains. The active site containing Cys291, Asp447 and His477 is located at the bottom of the cavity, which is filled with water molecules and is covered by the partly disordered CAP subdomain. We designated our structure as the closed form, which is distinct from the recently reported catalytic domain from Cupriavidus necator (PhaC Cn -CAT). Structural comparison showed PhaC Cn -CAT adopting a partially open form maintaining a narrow substrate access channel to the active site, but no product egress. PhaC Cs -CAT forms a face-to-face dimer mediated by the CAP subdomains. This arrangement of the dimer is also distinct from that of the PhaC Cn -CAT dimer. These findings suggest that the CAP subdomain should undergo a conformational change during catalytic activity that involves rearrangement of the dimer to facilitate substrate entry and product formation and egress from the active site.
To characterize the binding of a widely used herbicide, 2,4-dichlorophenoxyacetic acid (2,4-D) to the major transporter in human circulation, human serum albumin (HSA), multi-spectroscopic approaches such as fluorescence, absorption and circular dichroism along with computational methods were employed. Analysis of the fluorescence and absorption spectroscopic data confirmed the 2,4-D-HSA complex formation. A static quenching mechanism was evident from the inverse temperature dependence of the KSV values. The complex was stabilized by a weak binding affinity (Ka = 5.08 × 103 M-1 at 298 K). Quantitative analysis of thermodynamic data revealed participation of hydrophobic and van der Waals interactions as well as hydrogen bonds in the binding process. Circular dichroism and three-dimensional fluorescence spectral results showed structural (secondary and tertiary) changes in HSA as well as microenvironmental perturbation around protein fluorophores (Trp and Tyr residues) upon 2,4-D binding. Addition of 2,4-D to HSA was found to improve protein's thermal stability. Competitive displacement results as well as computational analyses suggested preferred location of the 2,4-D binding site as Sudlow's site I (subdomain IIA) in HSA.