electrostatic ligand

Ligand-based virtual screening (LBVS) can be pivotal for identifying potential drug leads, especially when the target protein's structure is unknown. However, current LBVS methods are limited in their ability to consider the ligand conformational flexibility. This study presents AutoDock-SS (Similarity Searching), which adapts protein-ligand docking for use in LBVS. AutoDock-SS integrates novel ligand-based grid maps and AutoDock-GPU into a novel three-dimensional LBVS workflow. Unlike other approaches based on pregenerated conformer libraries, AutoDock-SS's built-in conformational search optimizes conformations dynamically based on the reference ligand, thus providing a more accurate representation of relevant ligand conformations...

Reducing the size of titania (TiO2 ) to the nanoscale promotes the photoactive anatase phase for use in a range of applications from industrial catalysis to environment remediation. The nanoscale dimensions of these systems affect the magnitude of the electronic energy gap by quantum confinement. Upon interaction with aqueous environments or water vapour, the surfaces of these systems will also be hydroxylated to some degree. In turn, this affects the electronic energy levels due to the cumulative electrostatic effect of the dipolar hydroxyl (-OH) ligands ( i...

There has been an increasing demand for simultaneous detection of multiple analytes in one sample. Microbead-based platforms have been developed for multiplexed assays. However, most of the microbeads are made of non-biodegradable synthetic polymers, leading to environmental and human health concerns. In this study, we developed an environmentally friendly dextran microbeads as a new type of multi-analyte assay platform. Biodegradable dextran was utilized as the primary material. Highly uniform magnetic dextran microspheres were successfully synthesized using the Shirasu porous glass (SPG) membrane emulsification technique...

Biologically important macromolecule 1, 1', 3, 3' Bis - [2,3,5,6-Tetramethyl-p-phenylenebis(methylene)] dibenzotriazlinium dibromide hydrate (BTD) was synthesized and characterized using FT-IR, NMR and single-crystal XRD (SCXRD). SCXRD revealed that the compound was crystallized as a monoclinic system and associated through weak intermolecular interactions like H-bonding and π- π stacking interactions. These weak intermolecular interactions in BTD were studied using Crystal Explorer and Gaussian...

INTRODUCTION: We investigated the potential role of HLA molecular mismatches (MM) in achieving stable chimerism, allowing for donor-specific tolerance in patients undergoing combined living donor kidney and hematopoietic stem cell transplantation (HSCT). METHODS: All patients with available DNA samples (N=32) who participated in a phase 2 clinical trial (NCT00498160) where they received an HLA mismatched co-transplantation of living donor kidney and facilitating cell-enriched HSCT were included in this study...

The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem which could enable many practical applications of protein biosensors. In this work, we analyzed two engineer ed biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands...

Sodium alginate (SA) biopolymer has been recognized as an efficient adsorbent material owing to their unique characteristics, including biodegradability, non-toxic nature, and presence of abundant hydrophilic functional groups. Accordingly, in the current research work, UiO-66-OH and UiO-66-(OH)2 metal organic framework (MOF) nanoparticles (NPs) have been integrated into SA biopolymer-based three-dimensional (3-D) membrane capsules (MCs) via a simple and facile approach to remove toxic metal cations (Cu2+ and Cd2+ ) from water and real sewage...

Histidine residues 44 and 48 in yeast alcohol dehydrogenase (ADH) bind to the coenzymes NAD(H) and contribute to catalysis. The individual H44R and H48Q substitutions alter the kinetics and pH dependencies, and now the roles of other ionizable groups in the enzyme were studied in the doubly substituted H44R/H48Q ADH. The substitutions make the enzyme more resistant to inactivation by diethyl pyrocarbonate, modestly improve affinity for coenzymes, and substantially decrease catalytic efficiencies for ethanol oxidation and acetaldehyde reduction...

Seeking noble-metal-free catalysts for efficient synthesis of aryl nitriles under mild conditions poses a significant challenge due to the use of hypertoxic cyanides or high-pressure/temperature NH3 /O2 in conventional synthesis processes. Herein, we developed a novel framework 1 assembled by [Ni72 ] nanocages with excellent solvents/pH stability. To investigate the structure-activity relationship of catalytic performance, several isostructural MOFs with different molar ratios of Ni/Cu by doping Cu2+ into framework 1 (Ni0...

CONTEXT: In this study, we have investigated the structure, reactivity, bonding, and electronic transitions of DPA and PDTC along with their Ni-Zn complexes using DFT/TD-DFT methods. The energy gap between the frontier orbitals was computed to understand the reactivity pattern of the ligands and metal complexes. From the energies of FMO's, the global reactivity descriptors such as electron affinity, ionization potential, hardness (η), softness (S), chemical potential (μ), electronegativity (χ), and electrophilicity index (ω) have been calculated...

Efficient pure-red emission light-emitting diodes (LEDs) are essential for high-definition displays, yet achieving pure-red emission is hindered by challenges like phase segregation and spectral instability when using halide mixing. Additionally, strongly confined quantum dots (QDs) produced through traditional hot-injection methods face byproduct contamination due to poor solubility of metal halide salts in the solvent octadecene (ODE) at low temperatures. Herein, we introduced a novel method using a benzene-series strongly electrostatic potential solvent instead of ODE to prevent PbI2 intermediates and promote their dissolution into [PbI3 ]- ...

In this study, in silico analysis and peptidomics were performed to examine the generation mechanism of the umami taste of fermented broad bean paste (FBBP). Based on the information from peptidomics, a total of 470 free peptides were identified from FBBP, most of which were increased after fermentation. Additionally, the increase of the content of umami peptides, organic acids, and amino acids during fermentation contributed to the perception of umami taste in FBBP. Molecule docking results inferred that these umami molecules were easy to connect with Ser, Glu, His, and Gln in the T1R3 subunit through hydrogen bonds and electrostatic interaction force...

Adsorption, which is a quick and effective method for phosphate management, can effectively address the crisis of phosphorus mineral resources and control eutrophication. Phosphate management systems typically use iron-containing nanominerals (ICNs) with large surface areas and high activity, as well as modified ICNs (mICNs). This paper comprehensively reviews phosphate management by ICNs and mICNs in different water environments. mICNs have a higher affinity for phosphates than ICNs. Phosphate adsorption on ICNs and mICNs occurs through mechanisms such as surface complexation, surface precipitation, electrostatic ligand exchange, and electrostatic attraction...

Glomalin-related soil protein (GRSP) is a significant component in the sequestration of heavy metal in soils, but its mechanisms for metal adsorption are poorly known. This study combined spectroscopic data with molecular docking simulations to reveal metal adsorption onto GRSP's surface functional groups at the molecular level. The EXAFS combined with FTIR and XPS analyses indicated that the adsorption of Cd(II), Sr(II), and Ni(II) by GRSP occurred mainly through the coordination of -OH and -COOH groups with the metal...

Unfolding the solution coordination chemistry of high-valent transuranium elements with the "CHON"-type ligands is important to understand the fundamental chemistry of actinides and to design more efficient extractants for partitioning of transuranium elements in advanced nuclear fuel cycles. Here, the complexation of a hexavalent neptunyl ion (NpO2 2+ or Np(VI)) with oxydiacetic acid (ODA) has been systematically investigated in comparison with its amide analogues N , N -dimethyl-3-oxa-glutaramic acid (DMOGA) and N , N , N' , N '-tetramethyl-3-oxa-glutaramide (TMOGA) both experimentally and computationally...

The efficient removal of phosphate from water environments was extremely significant to control eutrophication of water bodies and prevent further deterioration of water quality. In this study, oxygen vacancy-rich magnesium oxide (OV-MgO) microspheres were synthesized by a simple solvothermal method coupling high-temperature calcination. The effects of adsorbent dosage, contact time, initial pH and coexisting components on phosphate adsorption performance were examined. The physicochemical properties of OV-MgO microspheres and the phosphate removal mechanisms were analyzed by various characterization techniques...

Controllably regulating the electrostatic bilayer of nanogold colloids is a significant premise for synthesizing spherical nucleic acid (SNA) and building ordered plasmonic architectures. We develop a facile acoustic levitation reactor to universally synthesize SNAs with an ultra-high density of DNA strands. Results reveal a new mechanism of DNA grafting via acoustic wave that can reconfigure the ligands on colloidal surfaces. The acoustic levitation reactor enables substrate-free three-dimentional (3D) spatial assembly of SNAs with controllable interparticle nanogaps through regulating DNA lengths...

Graphene-based material is widely used to remove arsenic from water due to its layered structure with high surface area. Here, we have successfully synthesized Fe-La bimetallic modified graphite sheet materials to more efficiently remove As(III) from aqueous solution. The results showed that Fe-La-graphite sheets (FL-graphite sheets) have a larger specific surface area (194.28 m2 ·g-1 ) than graphite sheets (2.80 m2 ·g-1 ). The adsorption capacity of FL-graphite sheets for As(III) was 51.69 mg·g-1 , which was higher than that of graphite sheets (21...

Lupus Nephritis (LN) is an autoimmune disease affecting the kidneys, and conventional drug studies have limitations due to its imprecise and complex pathogenesis. Therefore, the aim of this study was to design a novel Lupus Nephritis-targeted drug with good clinical due potential, high potency and selectivity by computer-assisted approach.NIK belongs to the serine/threonine protein kinase, which is gaining attention as a drug target for Lupus Nephritis. we used bioinformatics, homology modelling and sequence comparison analysis, small molecule ab initio design, ADMET analysis, molecular docking, molecular dynamics simulation, and MM/PBSA analysis to design and explore the selectivity and efficiency of a novel Lupus Nephritis-targeting drug, ClImYnib, and a classical NIK inhibitor, NIK SMI1...

Bacteria can tolerate antibiotics despite lacking the genetic components for resistance. The prevailing notion is that tolerance results from depleted cellular energy or cell dormancy. In contrast to this view, many cells in the tolerant population of Escherichia coli can exhibit motility - a phenomenon that requires cellular energy, specifically, the proton-motive force (PMF). As these motile-tolerant cells are challenging to isolate from the heterogeneous tolerant population, their survival mechanism is unknown...