Photoelectrochemical biosensing platform for the SARS-CoV-2 spike and nucleocapsid proteins

The COVID-19 pandemic is still a continuing worldwide challenge for public health systems. Early and ultrasensitive identification of the infection is essential for preventing the spread of COVID-19 by pre-symptomatic or asymptomatic individuals, particularly in the community and in-home settings. This work presents a versatile photoelectrochemical (PEC) immunosensor for SARS-CoV-2 detection based on a composite material formed by bismuth vanadate (BiVO₄) and strontium titanate (SrTiO₃). The PEC platform was denoted as BiVO₄/SrTiO₃/FTO, and it can be tuned for the detection of either Spike (S) or Nucleocapsid (N) protein by simply altering the antibody immobilized on the platform's surface. Chemical, morphological, and electrochemical characterizations were performed by X-Ray Diffraction, Scanning Electron microscopy, Energy-dispersive X-ray spectroscopy, Electrochemical Impedance Spectroscopy, and Amperometry. With a simple sensing architecture of the PEC platform, it was possible to achieve a linear response range of 0.1 pg mL⁻¹ to 1000 ng mL⁻¹ for S protein and 0.01 pg mL⁻¹ to 1000 ng mL⁻¹ for N protein. The PEC immunosensors presented recovery values for the two SARS-CoV-2 proteins in artificial saliva samples between 97 % and 107.20 % suggesting a good accuracy for the proposed immunosensors.     

Crystallographic and biophysical analysis of the fusion core from SARS-CoV-2 spike protein

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a newly emerging infectious pathogen causing coronavirus disease 2019 (COVID-19). The virus primarily infects cells via its spike glycoprotein, which is cleaved into S1 and S2 subunits to aid in cell attachment and membrane fusion, respectively. Heptad repeat 1 (HR1) and heptad repeat 2 (HR2) of the S2 subunit are essential for membrane fusion, culminating in an expected six-helix bundle termed fusion core. To better understand the structural and biophysical features of the SARS-CoV-2 fusion core, we designed, constructed, and bacterially produced a recombinant single-chain HR1-L6-HR2 protein and conducted a series of biochemical and biophysical experiments. Our findings demonstrate that the HR1-L6-HR2 protein spontaneously assembles into a highly stable trimeric complex, further confirmed by x-ray crystallographic analysis. The crystal structure of the fusion core reveals a trimeric coiled-coil structure of HR1 antiparallelly surrounded by three HR2 to form a six-helical bundle. Additionally, four residues of HR1 that contribute to binding with HR2 through the formation of hydrogen bonds and salt bridges were observed. These results indicate that the SARS-CoV-2 fusion core exhibits similar characteristics to other class I viral glycoproteins, suggesting potential for drug repurposing as an alternative strategy to combat COVID-19.     

Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses

Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blocking antibody. However, the molecular recognition mechanism—critical information for drug and antibody design—has not been fully clarified at the amino acid residue level. Elucidating such a microscopic mechanism in detail requires a more accurate molecular interpretation that includes quantum mechanics to quantitatively evaluate hydrogen bonds, XH/π interactions (X = N, O, and C), and salt bridges. In this study, we applied the fragment molecular orbital (FMO) method to characterize the SARS-CoV-2 S-protein binding interactions with not only ACE2 but also the B38 Fab antibody involved in ACE2-inhibitory binding. By analyzing FMO-based interaction energies along a wide range of binding interfaces carefully, we identified amino acid residues critical for molecular recognition between S-protein and ACE2 or B38 Fab antibody. Importantly, hydrophobic residues that are involved in weak interactions such as CH–O hydrogen bond and XH/π interactions, as well as polar residues that construct conspicuous hydrogen bonds, play important roles in molecular recognition and binding ability. Moreover, through these FMO-based analyses, we also clarified novel hot spots and epitopes that had been overlooked in previous studies by structural and molecular mechanical approaches. Altogether, these hot spots/epitopes identified between S-protein and ACE2/B38 Fab antibody may provide useful information for future antibody design, evaluation of the binding property of the SARS-CoV-2 variants including its N501Y, and small or medium drug design against the SARS-CoV-2.

Quantum chemical calculations investigated molecular recognition of SARS-CoV-2 spike glycoproteins including its N501Y variant for ACE2 and antibody. Hot spot and epitope analyses revealed key residues to design drugs and antibodies against COVID-19.     

Structural colors in nature: the role of regularity and irregularity in the structure.

Coloring in nature mostly comes from the inherent colors of materials, but it sometimes has a purely physical origin, such as diffraction or interference of light. The latter, called structural color or iridescence, has long been a problem of scientific interest. Recently, structural colors have attracted great interest because their applications have been rapidly progressing in many fields related to vision, such as the paint, automobile, cosmetics, and textile industries. As the research progresses, however, it has become clear that these colors are due to the presence of surprisingly minute microstructures, which are hardly attainable even by ultramodern nanotechnology. Fundamentally, most of the structural colors originate from basic optical processes represented by thin-film interference, multilayer interference, a diffraction grating effect, photonic crystals, light scattering, and so on. However, to enhance the perception of the eyes, natural creatures have produced various designs, in the course of evolution, to fulfill simultaneously high reflectivity in a specific wavelength range and the generation of diffusive light in a wide angular range. At a glance, these two characteristics seem to contradict each other in the usual optical sense, but these seemingly conflicting requirements are realized by combining appropriate amounts of regularity and irregularity of the structure. In this Review, we first explain the fundamental optical properties underlying the structural colors, and then survey these mysteries of nature from the viewpoint of regularity and irregularity of the structure. Finally, we propose a general principle of structural colors based on structural hierarchy and show their up-to-date applications.     

Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19, a highly infectious disease that is severely affecting our society and welfare systems. In order to develop therapeutic interventions against this condition, one promising strategy is to target spike, the trimeric transmembrane glycoprotein that the virus uses to recognise and bind its host cells. Here we use a metainference cryo-electron microscopy approach to determine the opening pathway that brings spike from its inactive (closed) conformation to its active (open) one. The knowledge of the structures of the intermediate states of spike along this opening pathway enables us to identify a cryptic pocket that is not exposed in the open and closed states. These results underline the opportunities offered by the determination of the structures of the transient intermediate states populated during the dynamics of proteins to allow the therapeutic targeting of otherwise invisible cryptic binding sites.

A structural ensemble derived from cryo-electron microscopy reveals a cryptic pocket site in intermediate states along the opening pathway of the SARS-CoV-2 spike protein.     

On the role of the counter-ion in defining water structure and dynamics: order, structure and dynamics in hydrophilic and hydrophobic gadolinium salt complexes

The crystal structures of the hydrated salts of [Gd.DOTAM]3+ and its more hydrophobic derivative [Gd.]3+, bearing 4 alpha-phenylethyl groups, (both Gd and Yb salts) are reported and compared. The nature of the anion determines the degree of ordering in the lattice and the extent of hydration. These effects are correlated with the results of 17O and 1H NMR measurements of water exchange dynamics in solution. With [Gd.DOTAM]3+, structural ordering or the extent of hydration in the hydrated lattice follows the sequence Cl->Br->I- and this order also defines the water exchange rate in solution: 7.3, 19.5, 33.3x10(4) s-1 (298 K), respectively. For [Gd.]3+ salts, the measured relaxivity is determined purely by the outer sphere term and the water exchange rate at 298 K is very similar (typically 1x10(4) s-1) for chloride, bromide, iodide, acetate, triflate and nitrate salts, notwithstanding the different nature and extent of hydration found in the crystalline lattice.     

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking,ADMET properties and molecular dynamics simulation study

Phytochemicals present in medicinal plants have a variety of biological activities that help to combat against diseases. As part of efforts to study the binding performance of different phytochemicals derived from different plants like Zingiber officinale, Citrus limon, Syzygiumaromaticum, Ocimum tenuiflorum and Curcumin. We have screened 424 molecules. The binding affinity as well as physicochemical properties of the thebaine, acacetin, indomethacin, crinamineacetate, (S)-1-Piperideine-6-carboxylate, levamisole, melatonin, nicotinicacid, curcumin, methotrimeprazine, omeprazole, and methaqualone phytocompounds were analyzed through computational study. From the molecular docking study we found that, LEU50, ASN72, PRO96, TYR154, GLY170, ALA193, ARG222, and MET274 residues of main protease play a crucial role in binding with ligands. The present study revealed a noticeable interaction of GLY446, SER477, GLY482, THR500 and LEU518 residues with mutant of spike receptor binding domain SARS-CoV-2 protein were observed. Finally, 100 ns molecular dynamics simulation were used to study their dynamic properties as well as conformational flexibility. Free energy landscape analysis was performed of the 6LU7- acacetin and 6Y2E-acacetin systems and spike RBD-acacetin system. From molecular docking study and molecular dynamics study revealed that, the compound acacetin shows promising inhibitor towards both main protease as well as mutant spike RBD of SARS-CoV-2 protein.     

Electrochemical immunosensor nanoarchitectonics with the Ag-rGO nanocomposites for the detection of receptor-binding domain of SARS-CoV-2 spike protein

As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a grave threat to human life and health, it is essential to develop an efficient and sensitive detection method to identify infected individuals. This study described an electrode platform immunosensor to detect SARS-CoV-2-specific spike receptor-binding domain (RBD) protein based on a bare gold electrode modified with Ag-rGO nanocomposites and the biotin-streptavidin interaction system. The Ag-rGO nanocomposites was obtained by chemical synthesis and characterized by electrochemistry and scanning electron microscope (SEM). Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to record the electrochemical signals in the electrode modification. The differential pulse voltammetry (DPV) results showed that the limit of detection (LOD) of the immunosensor was 7.2 fg mL⁻¹ and the linear dynamic detection range was 0.015 ~ 158.5 pg mL⁻¹. Furthermore, this sensitive immunosensor accurately detected RBD in artificial saliva with favorable stability, specificity, and reproducibility, indicating that it has the potential to be used as a practical method for the detection of SARS-CoV-2.

     

Influence of particle size on the SARS-CoV-2 spike protein detection using IgG-capped gold nanoparticles and dynamic light scattering

Due to the unprecedented and ongoing nature of the coronavirus outbreak, the development of rapid immunoassays to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its highly contagious variants is an important and challenging task. Here, we report the development of polyclonal antibody-functionalized spherical gold nanoparticle biosensors as well as the influence of the nanoparticle sizes on the immunoassay response to detect the SARS-CoV-2 spike protein by dynamic light scattering. By monitoring the increment in the hydrodynamic diameter (ΔD_H) by dynamic light scattering measurements in the antigen–antibody interaction, SARS-CoV-2 S-protein can be detected in only 5 min. The larger the nanoparticles, the larger ΔD_H in the presence of spike protein. From adsorption isotherm, the calculated binding constant (K_D) was 83 nM and the estimated limit of detection was 13 ng/mL (30 pM). The biosensor was stable up to 90 days at 4 °C. Therefore, the biosensor developed in this work could be potentially applied as a fast and sensible immunoassay to detect SARS-CoV-2 infection in patient samples.     

Structure rationalization and topology prediction of two-distinct-component organic crystals: the role of volume fraction and interface topology

We consider here small-length-scale crystal structures with two clearly different molecular components (e.g., hydrophobic and hydrophilic). Using a perspective developed by studies on large-length-scale block copolymers and liquid crystals, we focus on the crystalline interface between the two components. We examine four types of two-component crystals: aromatic ammonium carboxylates, aromatic oligo(ethylene oxides), cyclohexylammonium carboxylates, and ether-thioether compounds. Of the 111 crystal structures found in the Cambridge Structure Database (CSD), 108 adopt one of the five generic topologies found in diblock copolymers: spheres, columns, perforated layers, layers, and bicontinuous structures. As in diblock copolymers, a key factor controlling the interfacial topology is shown to be the volume ratio of the two components. When the volume fraction of one component is less than 30% of the whole, more than five-sixths of the examined crystal structures are of columnar or spherical type. For volume fractions between 40 and 50% more than three-quarters are of lamellar or bicontinuous type. We use this model to predict the topologies of small-length-scale two-component crystals. We predict the crystal topolgies of six new crystal structures: three are predicted to be columnar, and the other three, lamellar or bicontinuous. The crystal structures of these systems were then determined by single-crystal X-ray methods. Five of the structures form in topologies consistent with the predictions: three in columns and two in layers. The remaining one forms as a perforated layer instead of the predicted columnar structure. Such predictive accuracy is consistent with the statistics of the CSD investigation.     

S2 fluorescence and ultrafast relaxation dynamics of the S2 and S1 states of a ketocyanine dye

Dynamics of the excited singlet (both the S2 and S1) states of a ketocyanine dye, namely, 2,5-bis[(2,3-dihydroindolyl)-propylene]-cyclopentanone (KCD), have been investigated in different kinds of media using steady-state absorption and emission as well as femtosecond transient absorption spectroscopic techniques. Steady-state fluorescence measurements, following photoexcitation of KCD to its second excited singlet state, reveal dual fluorescence (emission from both the S2 and S1 states) behavior. Although the intensity of the S2 --> S0 fluorescence is weaker than that of the S1 --> S0 fluorescence in solutions at room temperature (298 K), the former becomes as much as or more intense than the latter in rigid matrixes at 77 K. The lifetime of the S2 state is short and varies between 0.2 and 0.6 ps in different solvents. After its creation, the S2 state undergoes two simultaneous processes, namely, S2 --> S0 fluorescence and S2 --> S1 internal conversion. Time-resolved measurements reveal the presence of an ultrafast component in the decay dynamics of the S1 state. A good correlation between the lifetime of this component and the longitudinal relaxation times (tauL) of the solvents suggests that this component arises due to solvation in polar solvents. More significant evolution of the spectroscopic properties of the S1 state in alcoholic solvents in the ultrafast time domain has been explained by the occurrence of the repositioning of the hydrogen bonds around the carbonyl group in the excited state of KCD. In 2,2,2-trifluoroethanol, a strongly hydrogen bond donating solvent, it has even been possible to establish the existence of two distinct forms of the S1 state, namely, the non-hydrogen-bonded (or free) molecule and the hydrogen-bonded complex.     

Polymer dynamics and topology: Extension of stars and dendrimers in external fields

We study the influence of topology on the extension of branched polymers subjected to external forces. Such forces can be applied mechanically (by micromanipulation techniques such as laser tweezers) or electrically (in the case of charged polymers). We focus on the unfold dynamics of star and dendrimer type structures. Some of the dynamical quantities of interest are: (i) the structural average of the mean monomer displacement, (ii) the elastic and the loss moduli and (iii) the mean displacement of a specified monomer. In a Gaussian‐type approach, (i) and (ii) depend only on the eigenvalues of the adjacency matrix whereas (iii) also requires the knowledge of the eigenvectors. Thus one can sometimes dispense with a full diagonalisation and use efficient recursion procedures. We highlight how the dynamic properties depend on topology: the number of branches and their length for stars and the number of generations for dendrimers. The intermediate time (crossover) behavior turns out to be most revealing of the underlying structure. We compare our results to those for fractal structures in external fields.     

Potassium S2N-heteroscorpionates: structure and iridaboratrane formation

The potassium salts of the new S(2)N-heteroscorpionate ligand hydrobis(methimazolyl)(3,5-dimethylpyrazolyl)borate [HB(mt)(2)(pz(3,5-Me))](-) and its known analogue hydrobis(methimazolyl)(pyrazolyl)borate [HB(mt)(2)(pz)](-) (prepared from KTp' or KTp and methimazole, Hmt), and the adduct KTp·Hmt have polymeric structures in the solid state (the first a ladder and the other two chains). The iridaboratranes [IrHLL'{B(mt)(2)X}] (X = pz(3,5-Me) or pz), prepared from the heteroscorpionate anion and [{Ir(cod)(μ-Cl)}(2)] (LL' = cod), subsequent carbonylation [LL' = (CO)(2)] and then reaction with phosphine [LL' = (CO)(PR(3)), R = Ph or Cy], have a pendant pyrazolyl ring and a bicyclo-[3.3.0] cage formed by an S(2)-bound B(mt)(2) fragment. The binuclear species [(cod)HIr{μ-B(mt)(3)}IrCl(cod)], the only isolated product of the reaction of KTm with [{Ir(cod)(μ-Cl)}(2)], also has an S(2)-bound iridaboratrane unit but with the third mt ring linked to square planar iridium(I).     

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI-SCS-MP2/MM molecular dynamics simulation

The spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd²⁺ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd²⁺. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd²⁺ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd²⁺ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.     

Molecular dynamics simulations of liquid water: Voronoi polyhedra and network topology

We have carried out various runs at different temperatures simulating liquid water via the TIP4P model, a well tested and widely used 4-site intermolecular potential. Voronoi polyhedra have been constructed and the distributions of various quantities analyzed. The higher the temperature, the more the distributions are similar to those of a normal liquid: as a reference for a corresponding liquid without hydrogen bonds, we have examined hydrogen sulphide. The typical shape of the Voronoi polyhedra is not too far from the polyhedra of a perfect ice I_h crystal, although the numbers of vertices and faces are almost doubled. Indeed the actual number of vertices increases rapidly toward the liquid value as the crystal is perturbed by thermal motions. It is remarkable that the total surface and volume are always found closely correlated. It denotes a quasi-constant shape, i.e. the various shapes are not dependent on the volume. Indeed a direct analysis shows that there is no correlation between volume and shape. A quantitative characterization of the Voronoi polyhedra shape is proposed, through an “asphericity” parameter, whose distribution is found to be greatly affected by temperature: a net shift of the centre of the curve toward the value for the ice is found as the temperature is lowered. Finally it is found that there is a positive correlation between the potential energy of a molecule and the local volume, thus indicating that the hypothesis that the four-bonded molecules have a local density lower than average is incorrect.     

S0 and S1 state structure, methyl torsional barrier heights, and fast intersystem crossing dynamics of 5-methyl-2-hydroxypyrimidine

We report the analysis of the S1<--S0 rotational band contours of jet-cooled 5-methyl-2-hydroxypyrimidine (5M2HP), the enol form of deoxythymine. Unlike thymine, which exhibits a structureless spectrum, the vibronic spectrum of 5M2HP is well structured, allowing us to determine the rotational constants and the methyl group torsional barriers in the S0 and S1 states. The 0(0)(0), 6a(0)(1), 6b(0)(1), and 14(0)(1) band contours were measured at 900 MHz (0.03 cm(-1)) resolution using mass-specific two-color resonant two-photon ionization (2C-R2PI) spectroscopy. All four bands are polarized perpendicular to the pyrimidine plane (>90% c type), identifying the S1<--S0 excitation of 5M2HP as a 1nπ* transition. All contours exhibit two methyl rotor subbands that arise from the lowest 5-methyl torsional states 0A" and 1E". The S0 and S1 state torsional barriers were extracted from fits to the torsional subbands. The 3-fold barriers are V3" = 13 cm(-1) and V3' = 51 cm(-1); the 6-fold barrier contributions V6" and V6' are in the range of 2-3 cm(-1) and are positive in both states. The changes of A, B, and C rotational constants upon S1 <--S0 excitation were extracted from the contours and reflect an “anti-quinoidal” distortion. The 0(0)(0) contour can only be simulated if a 3 GHz Lorentzian line shape is included, which implies that the S1(1nπ*) lifetime is ~55 ps. For the 6a(0)(1) and 6b(0)(1) bands, the Lorentzian component increases to 5.5 GHz, reflecting a lifetime decrease to ~30 ps. The short lifetimes are consistent with the absence of fluorescence from the 1nπ* state. Combining these measurements with the previous observation of efficient intersystem crossing (ISC) from the S1 state to a long-lived T1 (3nπ*) state that lies ~2200 cm(-1) below [S. Lobsiger, S. et al. Phys. Chem. Chem. Phys. 2010, 12, 5032] implies that the broadening arises from fast intersystem crossing with k(ISC) ≈ 2 × 10(10) s(-1). In comparison to 5-methylpyrimidine, the ISC rate is enhanced by at least 10 000 by the additional hydroxy group in position 2.     

Identification of natural compounds targeting SARS-CoV-2 Mpro by virtual screening and molecular dynamics simulations

The SARS-CoV-2 main protease (Mpro) has been chosen as a conserved molecular target to develop broad-spectrum antiviral drugs. Using molecular docking and molecular dynamics (MD) simulations, a total of 5600 natural compounds available for virtual screening were tested to identify potential inhibitors of SARS-CoV-2 Mpro. As a result, three natural compounds (pentagalloylglucose, malonylawobanin and gnetin E dihydride) were found to be potential inhibitors of SARS-CoV-2, which confirms the theoretical and practical significance of this approach for the design of SARS-CoV-2 inhibitors.