Three-dimensional Crystallographic Structure Research Articles

Homology Modeling of Alpha-Glucosidase from Candida albicans: Sequence Analysis and Structural Validation Studies in silico

The alpha-glucosidase enzyme of Candida albicans plays a vital role in the pathogenesis of candidiasis, a serious fatal disease in immune-compromised patients. The unavailability of the threedimensional crystallographic structure of this enzyme creates a hindrance in developing novel and potent inhibitors. Here, an attempt has been made to design a stable three-dimensional conformer of alpha-glucosidase through in silico analysis which may be helpful for the designing of effective drugs. For this purpose, the oligo-1-6-glucosidase enzyme is used as a template for homology modeling of the alpha-glucosidase structure by Molecular Operating Environment 2011-12 software. The generated model was validated through ERRAT and Ramachandran tools, whereas its stability was studied through the molecular dynamics simulation technique. The obtained results indicate that model of alpha-glucosidase has stable secondary and tertiary arrangements. This finding may spur new directions for the rational designing and development of new antifungal inhibitors. Nevertheless, additional experimental investigations and validation are needed to confirm the in silico results of this study.

Molecular docking and admet properties of anacardium occidentale methanolic nut extract against inflammatory, oxidative and apoptotic markers of diabetes

Background. The contemporary antidiabetic drugs have side effects and adverse reactions. This demand to search for less toxic and effective treatments for diabetes from medicinal plants using computational methods. The present research investigated the molecular docking of Anacadium occidentale nut methanolic extract compounds with selected proteins related to diabetes and the compounds’ AMDET properties. Material and Methods. The compounds were identified using Gas chromatography-mass spectrometry analysis. The compounds'2-dimensional structure was retrieved from the PubChem compound database. Three-dimensional crystallographic structure of selected proteins; B-cell-lymphoma-2 (Bcl-2), caspase-3, glucocorticoids, interleukin-1β, myeloperoxidase and tumor necrosis factor-alpha (TNF-α) was downloaded from Protein Data Bank. Molecular docking was performed using Autodoc kvina and the active site of binding interactions was detected with the Computed Atlas of Surface Topography of proteins (CAST-P). The compounds' drug-likeness, physicochemical and ADMET were evaluated using molininspiration and admetSAR online tools. Results. Ten compounds were identified from the Anacardium occidentale nut methanolic extract. All the compounds exhibited drug-likeness properties with violation of one Lipinski’s rule. Two compounds, oleic acid and 3-(p-methoxyphenyl)-propionic acid exhibited the best binding energy with the active receptors site of Bcl-2, caspase-3, TNF-α and glucocorticoid. Also, tridecanoic acid exhibited good binding energy with the active site of glucocorticoid receptors. Only 3-(p-methoxyphenyl)-propionic acid exhibited moderate binding energy with the active receptors site of interleukin-1β and myeloperoxidase. All the compounds displayed excellent ADMET properties. Conclusions. Antidiabetic drugs with the least side effects could be explored from these compounds.

Stable organic lead iodides with three-dimensional crystallographic and electronic structures showing high photoresponse

3D lead iodide perovskite analogs display both high stability and quasi-isotropic photoresponse, consistent with both 3D crystallographic and electronic structures.

Confining ultrafine tin monophosphide in Ti3C2Tx interlayers for rapid and stable sodium ion storage

Phase separation in conversion/alloying-based anodes easily causes crystal disintegration and leads to bad cycling performance. Tin monophosphide (SnP) is an excellent anode material for sodium ion battery due to its unique three-dimensional crystallographic layered structure. In this work, we report the in situ growth of ultrafine SnP nanocrystals within Ti3C2Tx MXene interlayers. The MXene framework is used as a conductive matrix to provide high ionic/electrical transfer paths and reduce the Na+ diffusion barrier in the electrode. In situ and ex situ measurements reveal that the synergy between small SnP crystal domains and the confinement provided by the MXene host prevents mechanical disintegration and major phase separation during the sodiation and desodiation cycles. The resultant electrode exhibits fast Na+ storage kinetics and excellent cycling stability for over 1000 cycles. A full cell assembled with this new SnP-based anode and a Na3V2(PO4)3 cathode delivers a high energy density of 265.4 ​Wh kg−1 and a power density of 3252.4 ​W ​kg–1, outperforming most sodium-ion batteries reported to date.

D-Mannoside FimH Inhibitors as Non-Antibiotic Alternatives for Uropathogenic Escherichia coli.

FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, mannosides, and molecules that inhibit their assembly. This work has focused on the ability of a set of monosubstituted and disubstituted phenyl mannosides to inhibit FimH. To determine the 3D structure of FimH for our in silico studies, we obtained fifteen sequences by PCR amplification of the fimH gene from 102 UPEC isolates. The fimH sequences in BLAST had a high homology (97–100%) to our UPEC fimH sequences. A search for the three-dimensional crystallographic structure of FimH proteins in the PDB server showed that proteins 4X5P and 4XO9 were found in 10 of the 15 isolates, presenting a 67% influx among our UPEC isolates. We focused on these two proteins to study the stability, free energy, and the interactions with different mannoside ligands. We found that the interactions with the residues of aspartic acid (ASP 54) and glutamine (GLN 133) were significant to the binding stability. The ligands assessed demonstrated high binding affinity and stability with the lectin domain of FimH proteins during the molecular dynamic simulations, based on MM-PBSA analysis. Therefore, our results suggest the potential utility of phenyl mannoside derivatives as FimH inhibitors to mitigate urinary tract infections produced by UPEC; thus, decreasing colonization, disease burden, and the costs of medical care.

In silico virtual screening of lead compounds for major antigenic sites in respiratory syncytial virus fusion protein

Human respiratory syncytial virus (RSV) is a leading ubiquitous respiratory pathogen in newborn infants, young children, and the elderly, with no vaccine available to date. The viral fusion glycoprotein (RSV F) plays an essential role in the infection process, and it is a primary target of neutralizing antibodies, making it an attractive site for vaccine development. With this in view, there is a persistent need to identify selective antiviral drugs against RSV, targeting the major antigenic sites on the F protein. We aimed to conduct a robust in silico high-throughput drug screening of one million compounds to explore potential inhibitors that bind the major antigenic site Ø and site II on RSV F protein, which are the main target of neutralizing antibodies (NAb). We utilized the three-dimensional crystallographic structure of both antigenic site Ø on pre-F and antigenic II on post-F to screen for potential anti-RSV inhibitors. A library of one million small compounds was docked to explore lead binders in the major antigenic sites by using virtual lab bench CLC Drug Discovery. We also performed Quantitative Structure-Activity and Relationship (QSAR) for the lead best binders known for their antiviral activity. Among one million tested ligands, seven ligands (PubChem ID: 3714418, 24787350, 49828911, 24802036, 79824892, 49726463, and 3139884) were identified as the best binders to neutralizing epitopes site Ø and four ligands (PubChem ID: 865999, 17505357, 24802036, and 24285058) to neutralizing epitopes site II, respectively. These binders exhibited significant interactions with neutralizing epitopes on RSV F, with an average of six H bonds, docking energy of − 15.43 Kcal·mol−1, and minimum interaction energy of − 7.45 Kcal·mol−1. Using in silico virtual screening, we identified potential RSV inhibitors that bind two major antigenic sites on the RSV F protein. Using structure-based design and combination-based drug therapy, identified molecules could be modified to generate the next generation anti-RSV drugs.

Structure and functional properties of the cold-adapted catalase from Acinetobacter sp. Ver3 native to the Atacama plateau in northern Argentina.

Heme catalases remove hydrogen peroxide by catalyzing its dismutation into water and molecular oxygen, thereby protecting the cell from oxidative damage. The Atacama plateau in northern Argentina, located 4000 m above sea level, is a desert area characterized by extreme UV radiation, high salinity and a large temperature variation between day and night. Here, the heme catalase KatE1 from an Atacama Acinetobacter sp. isolate was cloned, expressed and purified, with the aim of investigating its extremophilic properties. Kinetic and stability assays indicate that KatE1 is maximally active at 50°C in alkaline media, with a nearly unchanged specific activity between 0°C and 40°C in the pH range 5.5-11.0. In addition, its three-dimensional crystallographic structure was solved, revealing minimal structural differences compared with its mesophilic and thermophilic analogues, except for a conserved methionine residue on the distal heme side, which is proposed to comprise a molecular adaptation to oxidative damage.

Bacterial Toxins and Their Modes of Action: A Review Article

Bacterial toxins; the soluble antigens, emitted by various pathogenic microorganisms has a standing notoriety of being a toxin discharged over the span of pathogenesis. Toxins can balance the cell capacities by specifically focusing on various flagging pathways inside the host cell so as to tilt the equalization in microorganisms support. With the upgraded comprehension of the poison refinements strategies, quality cloning, protein arrangements, and three-dimensional crystallographic structures today, we can appreciate the interesting conduct of toxins, for example, restricting capacity to the explicit target cell and a few chemicals capacities. Bacterial pathogens have been causing different infections in people for quite a long time and even today these pathogenic microscopic organisms are coinciding and developing with us, regardless of having diverse means for their control in clinical practices (specifically antimicrobials, immunizations, and phage treatment). Toxins can be grouped into two general classes: exotoxin and endotoxin, and can be delivered by both Gram-positive and Gram-negative microbes. Exotoxins delivered by various microorganisms like botulinum, Clostridium, diphtheria poisons displaying protein exercises like ADP-ribosylation, phospholipase, adenylate cyclase, metalloprotease, deamidase, protease, and deoxyribonuclease action. The vast majority of these microscopic organisms apply their impeding impacts in the contaminated host through toxins. The elucidation of the cellular mechanism of action of the bacterial exotoxins remains a complex problem, but they appear to share a common mechanism of action such as binding to specific receptors on the plasma membranes of the sensitive cells, pore-formation, internalization or translocation across the membrane barrier and direct secretion. Keywords: Bacterial toxins; toxin; bacteria DOI : 10.7176/JMPB/55-03 Publication date :May 31 st 2019

IN SILICO DOCKING ANALYSIS OF YOHIMBINE ALKALOIDS FROM CATHARANTHUS ROSEUS AGAINST DENGUE FEVER

Objective: In this docking study was performed by the active site of NS2B-NS3 protease with selected plant alkaloids derived from Catharanthus roseus. On the basis of docking results, out of the nine alkaloids yohimbine might be considered as the best inhibitors of NS2B-NS3 protease protein.
 Methods: Lipinski rule was employed to check the ligand likeliness of the compound. The three-dimensional crystallographic structure of NS2B-NS3 protease (ID.2FOM) fetched from the protein data bank. The in silico docking studies were performed by “AutoDock version 4.2” software tool.
 Results: Yohimbine is having the best binding score (−7.18 Kcal/mol) than the other eight compounds.
 Conclusion: Hence, it has been concluded yohimbine as a novel inhibitor for NS2B-NS3 protease in dengue fever.

Computational screening of known broad-spectrum antiviral small organic molecules for potential influenza HA stem inhibitors

BackgroundWith the emergence of new influenza virus strains that are resistant to current inhibitors such as oseltamivir (anti-neuraminidase (NA)) and amantadine (anti-M2 proton channel), influenza A viruses continue to be a serious threat to the public health worldwide. With this in view, there is a persistent need for the development of broader and more effective vaccines and therapeutics. Identification of broadly neutralizing antibodies (bNAbs) that recognize relatively invariant structures ‎on influenza haemagglutinin (HA) stem has invigorated efforts to develop universal influenza vaccines.AimThe current computational study is designed to identify potential flavonoid inhibitors that bind to the contact epitopes of HA stem that are targeted by broadly neutralizing antibodies (bNAb).MethodIn this study, we utilized the three-dimensional crystallographic structure of different HA subtypes (H1, H2, H5, H3, and H7) in complex with bNAb to screen for potential broadly reactive influenza inhibitors. We performed Quantitative Structure-Activity and Relationship (QSAR) for 100 natural compounds known for their antiviral activity and performed molecular docking using AutoDock 4.2 suite. Furthermore, we conducted virtual screening of 1413 bioassay hit compounds by using virtual lab bench CLC Drug Discovery.ResultsThe results showed 18 lead flavonoids with strong binding abilities to bNAb epitopes of various HA subtypes. These 18 broadly reactive compounds exhibited significant interactions with an average of seven Hbonds, docking energy of -22.43 kcal·mol−1, and minimum interaction ‎ energy of -4.65 kcal·mol−1, with functional contact residues. Procyanidin depicted strong interactions with group 1 HAs, whereas both sorbitol and procyanidin exhibited significant interactions with group 2 HAs.ConclusionUsing in silico docking analysis, we identified 18 bioactive flavonoids with potential strong binding cababilities to influenza HA-stems of various subtypes, which are the target for bNAb. The virtual screened bioassay hit compounds depicted a high number of Hbonds but low interaction and docking values compared to antiviral flavonoids. Using structure-based design and nanotechnology-based approaches, identified molecules could be modified to generate next generation anti-influenza drugs.

Molecular definition of the transplantation antigens.

In the first half of the 20th century, the major histocompatibility complex (MHC) of the laboratory mouse, the H-2 complex, was defined by a combination of serology and genetics. In the second half of the 20th century, its human counterpart, the human leukocyte antigen (HLA) complex was similarly defined and shown to mediate rejection of allogeneic kidney grafts. The clinical relevance of the transplantation antigens created the field of transplant immunology, which aimed to reduce graft rejection by HLA matching of transplant donors and recipients, and to use immunosuppressive drugs to prevent and treat rejection. Because tissue transplantation is not a natural phenomenon, the relevance of the MHC for immunology and immune defense against microbial pathogens was frequently questioned. In the 1970s, the general observation that cytotoxic T-cell responses to viral infection required recognition of both a viral antigen and a transplantation antigen argued for the immunological importance of the MHC. Proving this point was not achieved until close to the end of the 20th century. This required detailed biochemical and structural analysis of the transplantation antigens, the viral antigens, and the T-cell receptors that recognized them. This century of research culminated in 1996 with the three-dimensional crystallographic structure of the complex of these three components. In this complex is MAC, the very first HLA antigen to be detected and now more formally known as HLA-A*02:01.

Can Ligands of Different Functional Types Induce Distinct Dynamics in G Protein-Coupled Receptors?

G Protein-Coupled Receptors (GPCRs) are the most common therapeutic targets for drug discovery by the pharmaceutical industries. Since 2007, several three-dimensional X-ray crystallographic structures of ligand-activated GPCRs have been determined in their agonist-bound or inverse agonist-bound states, providing a wealth of fundamental resources for the investigation of the atomic-level mechanism of receptor activation and deactivation. A number of computational methods, such as conventional and enhanced sampling Molecular Dynamic (MD) simulations have been applied to investigate the receptor dynamics bound with ligands of different functional types (i.e., agonist and inverse agonist). In this article, we reviewed recent efforts in characterizing the dynamical activation and deactivation mechanisms of GPCRs induced by different functional types of ligands.

Complex network analysis of thermostable mutants of Bacillus subtilis Lipase A

Three-dimensional structures of proteins that regulate their functions can be modelled using complex network based approaches for understanding the structure-function relationship. The six mutants of the protein Lipase A from Bacillus subtilis, harbouring 2 to 12 mutations, retain their function at higher temperatures with negligible variation in their overall three-dimensional crystallographic structures. This enhanced thermostability of the mutants questions the structure-function paradigm. In this paper, a coarse-grained complex network approach is used to elucidate the structural basis of enhanced thermostability in the mutant proteins, by uncovering small but significant local changes distributed throughout the structure, rendering stability to the mutants at higher temperatures. Community structure analysis of the six mutant protein networks uncovers the specific reorganisations among the nodes/residues that occur, in absence of overall structural variations, which induce enhanced rigidity underlying the increased thermostability. This study offers a novel and significant application of complex network analysis that proposes to be useful in the understanding and designing of thermostable proteins.

Revisiting phase diagrams of two-mode phase-field crystal models

In this work, phase diagrams of a modified two-mode phase-field crystal (PFC) that show two-dimensional (2D) and three-dimensional (3D) crystallographic structures were determined by utilizing a free energy minimization method. In this study the modified two-mode PFC model (presented by Asadi and Asle Zaeem, 2015) was used, in which the free energy can be exactly minimized in each stable crystal structure allowing calculation of accurate phase diagrams for two-mode PFC models. Different crystal structures, such as square, triangle, body-centered cubic (bcc), face-centered cubic (fcc), and stripe lattice structures as well as their coexistence regions were considered in the calculations. The model parameters were discussed to calculate phase diagrams that can be used as a guideline by other researchers for studying solidification and solid state phase transformation using two-mode PFC model.

Concomitant charge-density-wave and unit-cell-doubling structural transitions inDy5Ir4Si10

The tetragonal rare-earth transition-metal silicide system with three-dimensional crystallographic structure ${R}_{5}{T}_{4}{\mathrm{Si}}_{10}$, where $R$ is Dy, Ho, Er, Tm, and Lu, and $T\phantom{\rule{0.16em}{0ex}}=\phantom{\rule{0.16em}{0ex}}\mathrm{Ir}$ and Rh, has been shown to exhibit fascinating charge-density-wave (CDW) phase transitions, a phenomenon largely found in otherwise low-dimensional systems. In this study, we report the investigations of CDW in Dy${}_{5}$Ir${}_{4}$Si${}_{10}$ at different temperatures using transmission electron microscopy techniques including electron diffraction and dark-field imaging. Incommensurate superlattice spots along the $c$ axis were observed in the electron-diffraction patterns when the sample was cooled below the CDW transition temperature at $\ensuremath{\sim}$208 K. CDW becomes commensurate with further cooling and configurations of CDW dislocations convincingly show that the CDW phase transition is accompanied by a concomitant cell-doubling crystallographic structural phase transition. Intriguingly, the cell-doubling transition is featured by a broken inversion symmetry along the $c$ axis and a disparity in the CDW-modulation vectors with opposite signs, which gives rise to two sets of CDW domains with reversed contrasts. The profound physics underlining this notable domain-contrast behavior is discussed.

Partially gapped Fermi surfaces in La3Co4Sn13revealed by nuclear magnetic resonance

We report a study of a single-crystal La${}_{3}$Co${}_{4}$Sn${}_{13}$ by means of the specific heat and ${}^{59}$Co nuclear magnetic resonance (NMR) spectroscopy. A first-order phase transition with a marked peak at ${T}^{*}\ensuremath{\simeq}152$ K has been discerned by the specific heat measurement. The observed transition has been connected to a structural change from a simple cubic to a body-centered-cubic superstructure with crystallographic cell doubling, accompanied by the Fermi surface reconstruction. Indeed, NMR observations clearly indicate a significant change in the local electronic characteristics across this phase transition. The spin-lattice-relaxation rate measurement further provides an estimate of Co 3$d$ Fermi-level density of states ${N}_{d}$(${E}_{F}$), revealing a visible reduction in ${N}_{d}$(${E}_{F}$) in the low-temperature phase. This finding essentially associated with the partially gapped Fermi surfaces would be appropriate for the isostructural analog of Sr${}_{3}$Ir${}_{4}$ Sn${}_{13}$, which has been claimed to possess charge-density-wave (CDW) behavior with a three-dimensional crystallographic structure.

Isolation, kinetic analysis, and structural characterization of an antibody targeting the Bacillus anthracis major spore surface protein BclA

One method of laboratory- or field-based testing for anthrax is detection of Bacillus anthracis spores by high-affinity, high specificity binding reagents. From a pool of monoclonal antibodies, we selected one such candidate (A4D11) with high affinity for tBclA, a truncated version of the B. anthracis exosporium protein BclA. Kinetic analysis utilising both standard and kinetic titration on a Biacore biosensor indicated antibody affinities in the 300 pM range for recombinant tBclA, and the A4D11 antibody was also re-formatted into scFv configuration with no loss of affinity. However, assays against B. anthracis and related Bacilli species showed limited binding of intact spores as well as significant cross-reactivity between species. These results were rationalized by determination of the three-dimensional crystallographic structure of the scFv-tBclA complex. A4D11 binds the side of the tBclA trimer, contacting a face of the antigen normally packed against adjacent trimers within the exosporium structure; this inter-spore interface is highly conserved between Bacilli species. Our results indicate the difficulty of generating a high-affinity antibody to differentiate between the highly conserved spore structures of closely related species, but suggest the possibility of future structure-based antibody design for this difficult target.

Interconversion of the Specificities of Human Lysosomal Enzymes Associated with Fabry and Schindler Diseases

The human lysosomal enzymes alpha-galactosidase (alpha-GAL, EC 3.2.1.22) and alpha-N-acetylgalactosaminidase (alpha-NAGAL, EC 3.2.1.49) share 46% amino acid sequence identity and have similar folds. The active sites of the two enzymes share 11 of 13 amino acids, differing only where they interact with the 2-position of the substrates. Using a rational protein engineering approach, we interconverted the enzymatic specificity of alpha- GAL and alpha-NAGAL. The engineered alpha-GAL (which we call alpha-GAL(SA)) retains the antigenicity of alpha-GAL but has acquired the enzymatic specificity of alpha-NAGAL. Conversely, the engineered alpha-NAGAL (which we call alpha-NAGAL(EL)) retains the antigenicity of alpha-NAGAL but has acquired the enzymatic specificity of the alpha-GAL enzyme. Comparison of the crystal structures of the designed enzyme alpha-GAL(SA) to the wild-type enzymes shows that active sites of alpha-GAL(SA) and alpha-NAGAL superimpose well, indicating success of the rational design. The designed enzymes might be useful as non-immunogenic alternatives in enzyme replacement therapy for treatment of lysosomal storage disorders such as Fabry disease.

Characterization of the crystallographic microstructure of the stress-induced void in Cu interconnects

Stepwise cross-sectional crystallographic measurement was performed on the stress-induced void (SIV) of copper interconnect and it was possible to investigate the three-dimensional crystallographic structures near the submicron scale void. The void mainly happened at a triple junction of grain boundaries and there were at least two grains with high biaxial elastic modulus near the triple junction. The preferred site for the SIV could well be understood by considering the elastic anisotropy of each grain and the grain boundary type.

Optical properties of thin films of [Ru(bpy)3][NaCr(ox)3] polymeric networks

The optical properties of a thin film of the [Ru(bpy)3][NaCr(ox)3] network structure obtained by pulsed laser deposition are described. The luminescence shows the characteristic doublet of R lines at 14400cm−1 of the spin-forbidden ligand field transition E2(t2g3)→A24(t2g3) of the [Cr(ox)3]3− chromophore. The resonant energy migration within the R1 line shows that the three-dimensional crystallographic structure is preserved during the coating process. The observation of the R lines of [Cr(bpy)3]3+ at 13710cm−1 indicates that a small fraction of Cr3+ ions migrate from the oxalate network to the tris-bipyridine cation site in the cavities of the network.