Unraveling Bacterial Single-Stranded Sequence Specificities: Insights from Molecular Dynamics and MMPBSA Analysis of Oligonucleotide Probes.

We utilized molecular dynamics (MD) simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) free energy calculations to investigate the specificity of two oligonucleotide probes, namely probe B and probe D, in detecting single-stranded DNA (ssDNA) within three bacteria families: Enterobacteriaceae, Pasteurellaceae, and Vibrionaceae. Due to the limited understanding of molecular mechanisms in the previous research, we have extended the discussion to focus specifically on investigating the binding process of bacteria-probe DNA duplexes, with an emphasis on analyzing the binding free energy. The role of electrostatic contributions in the specificity between the oligonucleotide probes and the bacterial ssDNAs was investigated and found to be crucial. Our calculations yielded results that were highly consistent with the experimental data. Through our study, we have successfully exhibited the benefits of utilizing in-silico approaches as a powerful virtual-screening tool, particularly in research areas that demand a thorough comprehension of molecular interactions.

Correction: Turn-on fluorogenic sensors based on an anthraquinone signaling unit for the detection of Zn(II) and Cd(II) ions.

Correction for 'Turn-on fluorogenic sensors based on an anthraquinone signaling unit for the detection of Zn(II) and Cd(II) ions' by Chawanakorn Kongsak et al., Org. Biomol. Chem., 2023, 21, 7367-7381, https://doi.org/10.1039/D3OB01223A.

Effect of surface topography and wettability on shear bond strength of Y-TZP ceramic.

Zirconia ceramics have been widely used as dental restorations due to their esthetic appearance and high flexural strength. The bonding of zirconia with resin cement should rely on both mechanical and chemical bonds. This study was performed to investigate the effect of zirconia surface topography and its wettability after surface pretreatments on the microshear bond strength (µSBS) of a resin cement. Zirconia slabs were prepared and randomly divided into 5 groups based on the surface treatment as follows: no treatment (control), air abrasion (AB), etching with hydrofluoric acid (F), the mixture of hydrofluoric acid and nitric acid (FN), or the mixture of hydrochloric acid and nitric acid (CN) for 10 min. The specimens were subjected to investigation of surface roughness characteristics [average roughness (Ra), peak-to-valley average distance (Rpv), skewness (Rsk), and kurtosis (Rku)] using atomic force microscopy (AFM) and measurements of surface contact angle (θc) and µSBS of a resin cement. In addition, the area % of the nanoscale surface irregularity (nSI%) was calculated from the AFM images. The effects of nSI%, Ra and θc on the µSBS were analyzed by multiple linear regression analysis (p < 0.05). Multiple regression analysis revealed that the nSI% was the most predominant factor for the µSBS (p < 0.001). A surface with larger nSI%, higher Ra and relatively lower θc was essential for establishing a reliable resin-zirconia bond.

Turn-on fluorogenic sensors based on an anthraquinone signaling unit for the detection of Zn(II) and Cd(II) ions.

Turn-on fluorescent chemosensors based on an anthraquinone moiety, N,N'-(9,10-dioxo-9,10-dihydroanthracene-1,8-diyl)bis(2-(bis(pyridin-2-ylmethyl)amino)acetamide) (1) and N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,6-diyl)bis(2-(bis(pyridin-2-ylmethyl)amino)acetamide) (2), have been successfully synthesized with the overall yields of 61% and 90%, respectively. The structures of both chemosensors 1 and 2 were elucidated using several spectroscopic techniques such as 1H NMR, 13C NMR, 2D-NMR, FTIR and HRMS. The target chemosensor 1 is a promising tool for the detection of trace levels of d10 metal ions, such as Zn(II) and Cd(II) ions, by exhibiting a significant fluorescence enhancement via a turn-on photoinduced electron transfer (PET) mechanism with a rapid and highly reproducible signal, and low detection limit values of 0.408 µM and 0.246 µM, for Zn(II) and Cd(II), respectively.

Theoretical Analysis of the Role of Water in Ligand Binding to Cucurbit[n]uril of Different Sizes.

The role of water in host-ligand binding was investigated using a combination of molecular dynamics simulation and three-dimensional reference interaction site model theory. Three different hosts were selected (CB6, CB7, and CB8). Six organic molecules were used as representative ligands: dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF), acetone, 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO), cyclopentanone (CPN), and pyrrole. From the binding free energy and its components, we divided the ligands into two groups: those with relatively small molecular size (DMSO, DMF, acetone, and pyrrole) and those with relatively large molecular size (DBO and CPN). We established that the solvent water in the CB6 cavity can be completely displaced by small ligands, resulting in a greater binding affinity compared with larger CBs, except in the case of the small pyrrole ligand, due to outstanding intrinsic properties such as the relatively high hydrophobicity and low dipole moment. In the case of the large ligands, the solvent water can be displaced by DBO and CPN in both CB6 and CB7; there were similar tendencies in their binding affinities, with the greatest affinity in the CB7 complexes. However, the tendencies of the binding affinity components are completely different due to the difference between the complex structure and the solvation structure when a ligand binds with a CB structure. The binding affinities suggest that the size fit between the ligand and CB cannot guarantee the greatest binding affinity gain because the binding structure and intrinsic properties of CB and ligand equally play a crucial role.

Evaluation of the acute oral toxicity and antipsychotic activity of a dual inhibitor of PDE1B and PDE10A in rat model of schizophrenia.

Phosphodiesterase 1B (PDE1B) and PDE10A are dual-specificity PDEs that hydrolyse both cyclic adenosine monophosphate and cyclic guanosine monophosphate, and are highly expressed in the striatum. Several reports have suggested that PDE10A inhibitors may present a promising approach for the treatment of positive symptoms of schizophrenia, whereas PDE1B inhibitors may present a novel mechanism to modulate cognitive deficits. Previously, we have reported a novel dual inhibitor of PDE1B and PDE10A, compound 2 [(3-fluorophenyl)(2-methyl-2,3-dihydro-4H-benzo[b][1,4]oxazin-4-yl)methanone] which has shown inhibitory activity for human recombinant PDE1B and PDE10A in vitro. In the present study, the safety profile of compound 2 has been evaluated in rats in the acute oral toxicity study, as well as; the antipsychotic-like effects in the rat model of schizophrenia. Compound 2 was tolerated up to 1 g/kg when administered at a single oral dose. Additionally, compound 2 has strongly suppressed ketamine-induced hyperlocomotion, which presented a model for the positive symptoms of schizophrenia. It has also shown an ability to attenuate social isolation induced by chronic administration of ketamine and enhanced recognition memory of rats ​in the novel object recognition test. Altogether, our results suggest that compound 2 represents a promising therapy for the treatment of the three symptomatic domains of schizophrenia.

Mercury removal efficiency of disulfide- and thiol-functionalized lanthanide coordination polymers.

To compare efficiency of disulfide and thiol groups in removing mercury from aqueous medium without noteworthy influence from structural differences, a series of new [LnIII(dtba)1.5(H2O)2] (LnIII = EuIII (I), GdIII (II) and TbIII (III), H2dtba = 4,4'-dithiobenzoic acid) were synthesized and characterized. The single crystal structure of I was elucidated and is described. Reaction of II with hydrazine gave IISH containing disulfide and thiol groups. Experimental data confirmed the preserved framework structure and the co-existing of disulfide and thiol groups in IISH. Robustness of II and IISH over a wide range of pH (2-10) was confirmed and their mercury removal performances at different pH were evaluated in terms of removal efficiencies (%R), equilibrium uptake capacities (qe) and distribution constant (Kd). The dependence of these parameters on pH is reported. The best values of %R, qe and Kd could be achieved at pH 10 at which surfaces of the adsorbents were negatively charged; 86%R, 429 mg g-1, and 6.04 × 103 mL g-1 (II), and 98%R, 490 mg g-1 and 5.08 × 104 mL g-1 (IISH). At pH 7, influences of the initial concentration of mercury on performances of the adsorbents as well as the adsorption isotherms and kinetics were examined from which the better performance of IISH has been concluded. The characterization of the adsorptions by the Langmuir model and the pseudo-second-order kinetic as well as their excellent consistency with the experimental data are included. At neutral pH, selectivity to the adsorption of mercury and tolerance to common anions were illustrated. The better affinity between mercury and thiol group and therefore its contribution to the better performance of IISH was then ascertained by a computational study.

Immunoreactivity of humanized single-chain variable fragment against its functional epitope on domain 1 of CD147.

Domain 1 of CD147 participates in matrix metalloproteinase (MMP) production and is a candidate for targeted therapy to prevent cancer invasion and metastasis. A functional mouse anti-CD147 monoclonal antibody, M6-1B9, was found to recognize domain 1 of CD147, and its respective mouse single-chain variable fragment (ScFvM61B9) was subsequently generated. The EDLGS epitope candidate for M6-1B9 was identified using the phage display peptide technique in this study. For future clinical applications, humanized ScFv specific to domain 1 of CD147 (HuScFvM61B9) was partially adopted from the hypervariable sequences of parental mouse ScFvM61B9 and grafted onto suitable human immunoglobulin frameworks. Molecular modelling and simulation were performed in silico to generate the conformational structure of HuScFvM61B9. These results elucidated the amino acid residues that contributed to the interactions between CDRs and the epitope motif. The expressed HuScFvM61B9 specifically interacted with CD147 at the same epitope as the original mAb, M6-1B9, and retained immunoreactivity against CD147 in SupT1 cells. The reactivity of HuScFvM61B9 was confirmed using CD147 knockout Jurkat cells. In addition, the inhibitory effect of HuScFvM61B9 on OKT3-induced T-cell proliferation as M6-1B9 mAb was preserved. As domain 1 is responsible for cancer invasion and metastasis, HuScFvM61B9 would be a candidate for cancer targeted therapy in the future.

Structure-based discovery and bio-evaluation of a cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one as a phosphodiesterase 10A inhibitor.

Phosphodiesterase10A (PDE10A) is a potential therapeutic target for the treatment of several neurodegenerative disorders. Thus, extensive efforts of medicinal chemists have been directed toward developing potent PDE10A inhibitors with minimal side effects. However, PDE10A inhibitors are not approved as a treatment for neurodegenerative disorders, possibly due to the lack of research in this area. Therefore, the discovery of novel and diverse scaffolds targeting PDE10A is required. In this study, we described the identification of a new PDE10A inhibitor by structure-based virtual screening combining pharmacophore modelling, molecular docking, molecular dynamics simulations, and biological evaluation. Zinc42657360 with a cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one scaffold from the zinc database exhibited a significant inhibitory activity of 1.60 µM against PDE10A. The modelling studies demonstrated that Zinc42657360 is involved in three hydrogen bonds with ASN226, THR187 and ASP228, and two aromatic interactions with TYR78 and PHE283, besides the common interactions with the P-clamp residues PHE283 and ILE246. The novel scaffold of Zinc42657360 can be used for the rational design of PDE10A inhibitors with improved affinity.

Combination gemcitabine and PD-L1xCD3 bispecific T cell engager (BiTE) enhances T lymphocyte cytotoxicity against cholangiocarcinoma cells.

Cholangiocarcinoma (CCA) is a lethal cancer with rapid progression and poor survival. Novel and more effective therapies than those currently available are, therefore, urgently needed. Our research group previously reported the combination of gemcitabine and cytotoxic T lymphocytes to be more effective than single-agent treatment for the elimination of CCA cells. However, gemcitabine treatment of CCA cells upregulates the expression of an immune checkpoint protein (programmed death-ligand 1 [PD-L1]) that consequently inhibits the cytotoxicity of T lymphocytes. To overcome this challenge and take advantage of PD-L1 upregulation upon gemcitabine treatment, we generated recombinant PD-L1xCD3 bispecific T cell engagers (BiTEs) to simultaneously block PD-1/PD-L1 signaling and recruit T lymphocytes to eliminate CCA cells. Two recombinant PD-L1xCD3 BiTEs (mBiTE and sBiTE contain anti-PD-L1 scFv region from atezolizumab and from a published sequence, respectively) were able to specifically bind to both CD3 on T lymphocytes, and to PD-L1 overexpressed after gemcitabine treatment on CCA (KKU213A, KKU055, and KKU100) cells. mBiTE and sBiTE significantly enhanced T lymphocyte cytotoxicity against CCA cells, especially after gemcitabine treatment, and their magnitudes of cytotoxicity were positively associated with the levels of PD-L1 expression. Our findings suggest combination gemcitabine and PD-L1xCD3 BiTE as a potential alternative therapy for CCA.

Correction: Synthesis and application of methyl itaconate-anthracene adducts in configuration assignment of chiral secondary alcohols by 1H NMR.

Correction for 'Synthesis and application of methyl itaconate-anthracene adducts in configuration assignment of chiral secondary alcohols by 1H NMR' by Puracheth Rithchumpon et al., Org. Biomol. Chem., 2021, DOI: 10.1039/D1OB01387D.

Synthesis and application of methyl itaconate-anthracene adducts in configuration assignment of chiral secondary alcohols by 1H NMR.

Novel chiral derivatising agents (CDAs) such as methyl itaconate-anthracene adducts (MIAs) were reported for the absolute configuration determination of chiral secondary alcohols by the 1H NMR technique. These adducts were facilely prepared through well-known reactions, and furthermore, commercially available starting materials. According to these synthetic routes, the desired MIAs were afforded in 6 steps with 49% overall yield from dimethyl itaconate. Moreover, the represented MIAs provided significantly large differences of chemical shift values (ΔδSR). No racemisation from the tertiary characteristics of the adjacent alpha carbon was observed.

Protein-Protein Interactions: Insight from Molecular Dynamics Simulations and Nanoparticle Tracking Analysis.

Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process and predicting the binding affinity. Our case study of designed ankyrin repeats proteins (DARPins)-AnkGAG1D4 and the single point mutated AnkGAG1D4-Y56A for HIV-1 capsid protein (CA) were investigated. As reported, AnkGAG1D4 bound with CA for inhibitory activity; however, it lost its inhibitory strength when tyrosine at residue 56 AnkGAG1D4, the most key residue was replaced by alanine (AnkGAG1D4-Y56A). Through NTA, the binding of DARPins and CA was measured by monitoring the increment of the hydrodynamic radius of the AnkGAG1D4-gold conjugated nanoparticles (AnkGAG1D4-GNP) and AnkGAG1D4-Y56A-GNP upon interaction with CA in buffer solution. The size of the AnkGAG1D4-GNP increased when it interacted with CA but not AnkGAG1D4-Y56A-GNP. In addition, a much higher binding free energy (∆GB) of AnkGAG1D4-Y56A (-31 kcal/mol) obtained from MD further suggested affinity for CA completely reduced compared to AnkGAG1D4 (-60 kcal/mol). The possible mechanism of the protein-protein binding was explored in detail by decomposing the binding free energy for crucial residues identification and hydrogen bond analysis.

Molecular Dynamics Simulations in Designing DARPins as Phosphorylation-Specific Protein Binders of ERK2.

Extracellular signal-regulated kinases 1 and 2 (ERK1/2) play key roles in promoting cell survival and proliferation through the phosphorylation of various substrates. Remarkable antitumour activity is found in many inhibitors that act upstream of the ERK pathway. However, drug-resistant tumour cells invariably emerge after their use due to the reactivation of ERK1/2 signalling. ERK1/2 inhibitors have shown clinical efficacy as a therapeutic strategy for the treatment of tumours with mitogen-activated protein kinase (MAPK) upstream target mutations. These inhibitors may be used as a possible strategy to overcome acquired resistance to MAPK inhibitors. Here, we report a class of repeat proteins-designed ankyrin repeat protein (DARPin) macromolecules targeting ERK2 as inhibitors. The structural basis of ERK2-DARPin interactions based on molecular dynamics (MD) simulations was studied. The information was then used to predict stabilizing mutations employing a web-based algorithm, MAESTRO. To evaluate whether these design strategies were successfully deployed, we performed all-atom, explicit-solvent molecular dynamics (MD) simulations. Two mutations, Ala → Asp and Ser → Leu, were found to perform better than the original sequence (DARPin E40) based on the associated energy and key residues involved in protein-protein interaction. MD simulations and analysis of the data obtained on these mutations supported our predictions.

Characteristic Structural Knowledge for Morphological Identification and Classification in Meso-Scale Simulations Using Principal Component Analysis.

Meso-scale simulations have been widely used to probe aggregation caused by structural formation in macromolecular systems. However, the limitations of the long-length scale, resulting from its simulation box, cause difficulties in terms of morphological identification and insufficient classification. In this study, structural knowledge derived from meso-scale simulations based on parameters from atomistic simulations were analyzed in dissipative particle dynamic (DPD) simulations of PS-b-PI diblock copolymers. The radial distribution function and its Fourier-space counterpart or structure factor were proposed using principal component analysis (PCA) as key characteristics for morphological identification and classification. Disorder, discrete clusters, hexagonally packed cylinders, connected clusters, defected lamellae, lamellae and connected cylinders were effectively grouped.

Cordycepin Inhibits Virus Replication in Dengue Virus-Infected Vero Cells.

Dengue virus (DENV) infection causes mild to severe illness in humans that can lead to fatality in severe cases. Currently, no specific drug is available for the treatment of DENV infection. Thus, the development of an anti-DENV drug is urgently required. Cordycepin (3'-deoxyadenosine), which is a major bioactive compound in Cordyceps (ascomycete) fungus that has been used for centuries in Chinese traditional medicine, was reported to exhibit antiviral activity. However, the anti-DENV activity of cordycepin is unknown. We hypothesized that cordycepin exerts anti-DENV activity and that, as an adenosine derivative, it inhibits DENV replication. To test this hypothesis, we investigated the anti-DENV activity of cordycepin in DENV-infected Vero cells. Cordycepin treatment significantly decreased DENV protein at a half-maximal effective concentration (EC50) of 26.94 µM. Moreover, DENV RNA was dramatically decreased in cordycepin-treated Vero cells, indicating its effectiveness in inhibiting viral RNA replication. Via in silico molecular docking, the binding of cordycepin to DENV non-structural protein 5 (NS5), which is an important enzyme for RNA synthesis, at both the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, was predicted. The results of this study demonstrate that cordycepin is able to inhibit DENV replication, which portends its potential as an anti-dengue therapy.

Temperature-responsive morphology formation of a PS-b-PI copolymer: a dissipative particle dynamics simulation study.

Self-assembly responsiveness to stimuli of polystyrene-block-polyisoprene (PS-b-PI) diblock copolymer materials is explored by means of classical molecular dynamics (MD) and dissipative particle dynamics (DPD) simulations. A concerted relationship between the parameters achieved from atomistic and DPD simulations is obtained for this molecular recognition as clearly pronounced in a phase transition. Effects of temperature, model size and composition on the morphological formation were systematically investigated for the diblock copolymeric system. Structural changes resulting in the evolution of rheology as well as an equilibrium ordered structure were analyzed in terms of order parameters and radial distribution functions. From our models, various morphologies were observed including discrete clusters (sphere-liked morphology), connected clusters (gyroid-liked morphology), hexagonally packed cylinders (HEX), connected cylinders, irregular cylinders, perfect lamellae, perforated lamellae and defected lamellae. Based on this finding, a bottom-up multi-scale simulation of the PS-b-PI diblock copolymer provides a link between equilibrium copolymeric morphologies and the crucial parameters.

A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution.

Conformational search for the most stable geometry connection of 16 sets of polydopamine (PDA) tetramer subunits has been systematically investigated using density functional theory (DFT) calculations. Our results indicated that the more planar subunits are, the more stable they are. This finding is in good agreement with recent experimental observations, which have suggested that PDA are composed of the nearly planar subunits that appear to be stacked together via the π-π interactions to form graphite-like layered aggregates associated with the balance of the intramolecular hydrogen bonds and steric effects from the indole and catechol moieties. Molecular dynamics (MD) simulations of 16 spherical clusters of the tetramer subunits of PDA in the gas and aqueous phase were performed at 298 K and confirmed the stability of supramolecular tetramer aggregates. The complex formation and binding energy of all 16 clusters are very strong although the shapes of the clusters in aqueous solution are not spherical and are very much different from those in the gas phase. The aggregations of all 16 clusters in aqueous solution were also confirmed from the profiles of the Kratky plot and the radius of gyration of all clusters. Our MD results in both gas phase and aqueous solution pointed out that there are high possibilities of aggregations of the 16 kinds of tetramer subunits although the conformations of each tetramer subunit are not flat. In summary, this work brings an insight into the controversial structure of PDA tetramer units and explains some of the important structural features found in the aqueous phase in comparison to the gas phase.

Tentative Peptide‒Lipid Bilayer Models Elucidating Molecular Behaviors and Interactions Driving Passive Cellular Uptake of Collagen-Derived Small Peptides.

Collagen contains hydroxyproline (Hyp), which is a unique amino acid. Three collagen-derived small peptides (Gly-Pro-Hyp, Pro-Hyp, and Gly-Hyp) interacting across a lipid bilayer (POPC model membrane) for cellular uptakes of these collagen-derived small peptides were studied using accelerated molecular dynamics simulation. The ligands were investigated for their binding modes, hydrogen bonds in each coordinate frame, and mean square displacement (MSD) in the Z direction. The lipid bilayers were evaluated for mass and electron density profiles of the lipid molecules, surface area of the head groups, and root mean square deviation (RMSD). The simulation results show that hydrogen bonding between the small collagen peptides and plasma membrane plays a significant role in their internalization. The translocation of the small collagen peptides across the cell membranes was shown. Pro-Hyp laterally condensed the membrane, resulting in an increase in the bilayer thickness and rigidity. Perception regarding molecular behaviors of collagen-derived peptides within the cell membrane, including their interactions, provides the novel design of specific bioactive collagen peptides for their applications.

Coarse-Grained Modelling and Temperature Effect on the Morphology of PS-b-PI Copolymer.

Spontaneous spatial organization behavior and the aggregate morphology of polystyrene-block-polyisoprene (PS-b-PI) copolymer were investigated. Molecular dynamic (MD) and mesoscopic simulations using the dynamic of mean field density functional theory (DDF) were adopted to investigate the morphology changes exhibited by this block copolymer (BCP). In the mesoscopic simulations, several atoms in repeating units were grouped together into a bead representing styrene or isoprene segments as a coarse-grained model. Inter-bead interactions and essential parameters for mesoscopic models were optimized from MD simulations. Study indicated that morphology alternations can be induced in this system at annealing temperature of 393, 493, and 533 K. From our simulations, lamellar, bicontinuous, and hexagonally packed cylindrical equilibrium morphologies were achieved. Our simulated morphologies agree well with the reported experimental evidence at the selected temperature. The process of aggregate formation and morphology evolution were concretely clarified.