Molecular basis of N-glycan recognition by pradimicin a and its potential as a SARS-CoV-2 entry inhibitor.

Virus entry inhibitors are emerging as an attractive class of therapeutics for the suppression of viral transmission. Naturally occurring pradimicin A (PRM-A) has received particular attention as the first-in-class entry inhibitor that targets N-glycans present on viral surface. Despite the uniqueness of its glycan-targeted antiviral activity, there is still limited knowledge regarding how PRM-A binds to viral N-glycans. Therefore, in this study, we performed binding analysis of PRM-A with synthetic oligosaccharides that reflect the structural motifs characteristic of viral N-glycans. Binding assays and molecular modeling collectively suggest that PRM-A preferentially binds to branched oligomannose motifs of N-glycans via simultaneous recognition of two mannose residues at the non-reducing ends. We also demonstrated, for the first time, that PRM-A can effectively inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in vitro. Significantly, the anti-SARS-CoV-2 effect of PRM-A is attenuated in the presence of the synthetic branched oligomannose, suggesting that the inhibition of SARS-CoV-2 infection is due to the interaction of PRM-A with the branched oligomannose-containing N-glycans. These data provide essential information needed to understand the antiviral mechanism of PRM-A and suggest that PRM-A could serve as a candidate SARS-CoV-2 entry inhibitor targeting N-glycans.

siRNA Seed Region Is Divided into Two Functionally Different Domains in RNA Interference in Response to 2'-OMe Modifications.

In RNA interference (RNAi), small interfering RNA (siRNA) functions to suppress the expression of its target mRNA with perfect sequence complementarity. In a mechanism different from above, siRNA also suppresses unintended mRNAs with partial sequence complementarities, mainly to the siRNA seed region (nucleotides 2-8). This mechanism is largely utilized by microRNAs (miRNAs) and results in siRNA-mediated off-target effects. Thus, the siRNA seed region is considered to be involved in both RNAi and off-target effects. In this study, we revealed that the impact of 2'-O-methyl (2'-OMe) modification is different according to the nucleotide positions. The 2'-OMe modifications of nucleotides 2-5 inhibited off-target effects without affecting on-target RNAi activities. In contrast, 2'-OMe modifications of nucleotides 6-8 increased both RNAi and off-target activities. The computational simulation revealed that the structural change induced by 2'-OMe modifications interrupts base pairing between siRNA and target/off-target mRNAs at nucleotides 2-5 but enhances at nucleotides 6-8. Thus, our results suggest that siRNA seed region consists of two functionally different domains in response to 2'-OMe modifications: nucleotides 2-5 are essential for avoiding off-target effects, and nucleotides 6-8 are involved in the enhancement of both RNAi and off-target activities.

Selection of Chemical Modifications in the siRNA Seed Region That Repress Off-Target Effect.

RNA interference mediated by small interfering RNA (siRNA) has been widely used as a procedure to knock down the expression of an intended target gene with perfect sequence complementarity. However, siRNA often exhibits off-target effects on genes with partial sequence complementarities. Such off-target effect is an undesirable adverse effect for knocking down a target gene specifically. Here we describe the powerful strategy to avoid off-target effects without affecting the RNAi activity by the introduction of DNA or 2'-O-methyl modifications in the siRNA seed region. These two types of chemical modifications repress off-target effects through different molecular mechanisms.

d-Mannose binding, aggregation property, and antifungal activity of amide derivatives of pradimicin A.

Pradimicin A (PRM-A) and its derivatives comprise a unique family of antibiotics that show antifungal, antiviral, and antiparasitic activities through binding to d-mannose (Man)-containing glycans of pathogenic species. Despite their great potential as drug leads with an exceptional antipathogenic action, therapeutic application of PRMs has been severely limited by their tendency to form water-insoluble aggregates. Recently, we found that attachment of 2-aminoethanol to the carboxy group of PRM-A via amide linkage significantly suppressed the aggregation. Here, we prepared additional amide derivatives (2-8) of PRM-A to examine the possibility that the amide formation of PRM-A could suppress its aggregation propensity. Sedimentation assay and isothermal titration calorimetry experiment confirmed that all amide derivatives can bind Man without significant aggregation. Among them, hydroxamic acid derivative (4) showed the most potent Man-binding activity, which was suggested to be derived from the anion formation of the hydroxamic acid moiety by molecular modeling. Derivative 4 also exhibited significant antifungal activity comparable to that of PRM-A. These results collectively indicate that amide formation of PRM-A is the promising strategy to develop less aggregative derivatives, and 4 could serve as a lead compound for exploring the therapeutic application of PRM-A.

Effect of Molecular Weight on Cloud Point of Aqueous Solution of Poly (ethylene oxide)-Poly (propylene oxide) Alternating Multiblock Copolymer.

A poly(ethylene oxide) (PEO)-poly(propylene oxide) (PPO) alternating multiblock (AMB) copolymer with various molecular weights was prepared via precipitation fractionation from an acetone/n-hexane mixture. The cloud point (Tc) of the aqueous solution of PEO-PPO AMB copolymer decreased as the number-average molecular weight of the sample increased. This phenomenon is generally observed for certain homopolymer systems having a lower critical solution temperature, such as PEO/water and poly(N,N-diethylacrylamide)/water systems. The relationship between the Tc of the solutions and the number of monomer units of the AMB copolymer suggests that the Shultz-Flory theory is applicable to this system.

Photo-Induced Ring-Opening Reaction of Flav-3-en-2-ol Monitored by Time-Resolved Infrared Spectroscopy.

Photo-induced ring-opening reaction from flav-3-en-2-ol to 2-hydroxychalcone has been studied by time-resolved infrared (TR-IR) spectroscopy and quantum chemical calculations. A vibrational band due to the C═O stretching modes for intermediate species, enol forms of 2-hydroxychalcone in the electronic ground state, was observed at 1632 cm-1 in the TR-IR spectra after photoexcitation of flav-3-en-2-ol. We also found that the C═O stretching modes of the keto forms of 2-hydroxychalcone at 1664 cm-1 appeared immediately after photoexcitation and increased in intensity in synchronization with the depletion of the 1632 cm-1 band. Because the decay of the 1632 cm-1 band and the rise of the 1664 cm-1 band were fitted with bi-exponential model functions with common rate constants 0.5 and 11 µs-1, we propose that two kinds of enol form, single bond cis- (s-cis-) and trans- (s-trans-) enols, transformed into keto forms, cis-2-hydroxychalcone (Cc) and trans-2-hydroxychalcone (Ct), respectively. Quantum chemically calculated IR spectra of related species are consistent with the proposal. The observed temporal behavior of the TR-IR spectra indicates that there were reaction paths to the photogeneration of Cc and Ct within the time resolution of the TR-IR spectrometer (∼0.1 µs) in addition to the reaction paths via the enol forms of 2-hydroxychalcone.

Molecular Basis of Mannose Recognition by Pradimicins and their Application to Microbial Cell Surface Imaging.

Naturally occurring pradimicins (PRMs) show specific recognition of d-mannose (d-Man) in aqueous media, which has never been achieved by artificial small molecules. Although the Ca2+-mediated dimerization of PRMs is essential for their d-Man binding, the dimeric structure has yet to be elucidated, leaving the question open as to how PRMs recognize d-Man. Thus, we herein report the structural elucidation of the dimer by a combination of X-ray crystallography and solid-state NMR spectroscopy. Coupled with our previous knowledge regarding the d-Man binding geometry of PRMs, elucidation of the dimer allowed reliable estimation of the mode of d-Man binding. Based on the binding model, we further developed an azide-functionalized PRM derivative (PRM-Azide) with d-Man binding specificity. Notably, PRM-Azide stained Candida rugosa cells having mannans on their cell surface through conjugation with the tetramethylrhodamine fluorophore. The present study provides the practical demonstration that PRMs can serve as lectin mimics for use in glycobiological studies.

Structural Effects of Fusicoccin upon Upregulation of 14-3-3-Phospholigand Interaction and Cytotoxic Activity.

Fusicoccins (FCs) exhibit various cellular activities in mammalian cells, but details of the mechanism of action are not fully understood. In this study, we synthesized two pairs of model derivatives of FCs differing only in the presence and absence of a 12-hydroxyl group and evaluated their binding to a 14-3-3 protein together with various mode 1 and mode 3 phosphopeptide ligands. Our results demonstrate that the 12-hydroxyl group hampers binding to 14-3-3 with mode 1 phospholigands, presumably due to steric repulsion with the i+2 residue. Furthermore, cell-based evaluations showed that only non-substituted FCs exhibit significant cytotoxicity and all 12-hydroxyl derivatives were inactive, demonstrating a clear correlation with their ability to form ternary complexes with 14-3-3 and a mode 1 ligand. These results suggest that binding to 14-3-3 and a partner protein(s) possessing a mode 1 sequence plays a role in the mechanism of action of 12-non-substituted FCs.

Association Behavior of Poly(ethylene oxide)-Poly(propylene oxide) Alternating Multiblock Copolymers in Water toward Thermally Induced Phase Separation.

Thermal changes in the association behavior of poly(ethylene oxide)-poly(propylene oxide) alternating multiblock (PEO-PPO AMB) copolymers in water are investigated by the use of transmittance and light scattering measurements. Two PEO-PPO AMB copolymers with a different weight fraction of PEO, (EO220PO33)8 and (EO68PO33)9, are prepared. The weight-average molecular weights of (EO220PO33)8 and (EO68PO33)9 estimated by static light scattering measurements are 1.3 × 105 and 4.1 × 104 g mol-1, respectively. The number of PEO-PPO repeating pairs is over 8. It is found that the aqueous solution of (EO220PO33)8 undergoes phase separation with a lower critical solution temperature (LCST) of around 58 °C at 0.3 wt %. For the aqueous (EO68PO33)9 solution, the LCST is estimated to be ca. 42 °C. The critical solution concentration for (EO68PO33)9 is not clear because of a small concentration dependence of Tc at a higher concentration range. Dynamic light scattering measurements indicate that a micellelike aggregate is formed below the LCST. From the Debye plot, it is elucidated that the second virial coefficient, A2, starts going down at around 32 °C for (EO220PO33)8 and below 15 °C for (EO68PO33)9. The A2 value of (EO220PO33)8 approaches 0 near 50 °C, whereas that of (EO68PO33)9 approaches 0 at around 35 °C. At a high temperature, the attractive interaction among the copolymers becomes dominant, thereby inducing the formation of micellelike aggregates.

Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets.

Chemical modifications of 2'-O-methyl (2'-OMe) and locked nucleic acid (LNA) of the nucleotides in the seed region (positions 2-8) of the small interfering RNA (siRNA) guide strand significantly reduced seed-matched (SM) off-target effects. The siRNA with 2'-OMe modifications inhibited the expression of a completely-matched (CM) target gene, whereas that with LNA modifications did not inhibit the expression of the CM target. By computational predictions of conformational changes of siRNA by these modifications, we revealed that both modifications in the siRNA seed region reduce SM off-target effects by steric hindrance to base-pairing with target transcripts but LNA modifications also disturb the association of the siRNA guide strand with the Argonaute (AGO) protein by altering RNA conformation. Thus, chemical modifications of the siRNA guide strand, which alter steric conformation to disturb base-pairing with target transcripts but do not disturb the association with the AGO protein, may successfully suppress off-target effects without substantial loss of RNA silencing activity.

Correction to "Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets".

[This corrects the article DOI: 10.1021/acsomega.7b00291.].

Hydration structure of trimethylamine N-oxide in aqueous solutions revealed by soft X-ray emission spectroscopy and chemometric analysis.

The hydration structure of trimethylamine N-oxide (TMAO) in aqueous solutions has been investigated by means of soft X-ray spectroscopy and chemometric analysis. Soft X-ray absorption spectra in the O 1s region have a concentration-dependent shoulder at 533 eV, which is assigned to the 6a1 resonance of TMAO. Soft X-ray emission spectra acquired at this resonance comprise both TMAO and water components, with a prominent peak at 525.6 eV which is assigned to the emission caused by the 5e to O 1s transition. An apparent inverse concentration dependence of around 523 eV suggests that the electronic structure of water is modified by the strong interaction with TMAO. Such an effect has been included in the quantitative spectral analysis, called the classical least squares regression method, to obtain information on the hydration structure of the system. The analysis indicates that nine or more water molecules interact with a TMAO molecule. The present method offers a useful technique for probing the solvation structure around the solute which interacts strongly with the solvent.

Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24.

The influence of the nearest neighbor and next-nearest neighbor water molecules on the strength of the hydrogen (H) bonds was examined for the polyhedral clusters of cubic (H2O)8, dodecahedral (H2O)20 and tetrakaidecahedral (H2O)24 cages. The relative stability and the characteristics of the H bond networks are also studied. The charge-transfer (CT) and dispersion interaction terms of every pair of H bonds are evaluated using perturbation theory based on the locally-projected molecular orbitals (LPMO PT). Every water molecule and every H-bonded pair in these polyhedral clusters are classified by the types of the neighbor molecules and H bonds. The relative binding energies among the polyhedral clusters are grouped by these classifications. The optimized OO distances, which are strongly correlated with the calculated pairwise CT terms, are dependent on the 49 sub-groups of the H bonds determined by the type of the neighbor molecules. The electronic origin of this dependence is analyzed using Mulliken's charge-transfer theory, and employing a few assumptions, the analytical formulas for the contribution of the CT terms to the H bond energy are derived.

Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts.

DNA interstrand crosslinks (ICLs) are the primary mechanism for the cytotoxic activity of many clinical anticancer drugs, and numerous strategies for forming ICLs have been developed. One such method is using crosslink-forming oligonucleotides (CFOs). In this study, we designed a 4-amino-6-oxo-2-vinylpyrimidine (AOVP) derivative with an acyclic spacer to react selectively with guanine. The AOVP CFO exhibited selective crosslinking reactivity with guanine and thymine in DNA, and with guanine in RNA. These crosslinking reactions with guanine were accelerated in the presence of CoCl2, NiCl2, ZnCl2 and MnCl2. In addition, we demonstrated that the AOVP CFO was reactive toward 8-oxoguanine opposite AOVP in the duplex DNA. The structural analysis of each guanine and 8-oxoguanine adduct in the duplex DNA was investigated by high-resolution NMR. The results suggested that AOVP reacts at the N2 amine in guanine and at the N1 or N2 amines in 8-oxoguanine in the duplex DNA. This study demonstrated the first direct determination of the adduct structure in duplex DNA without enzyme digestion.

Synthesis and biological activities of the amide derivative of aplog-1, a simplified analog of aplysiatoxin with anti-proliferative and cytotoxic activities.

Aplog-1 is a simplified analog of the tumor-promoting aplysiatoxin with anti-proliferative and cytotoxic activities against several cancer cell lines. Our recent findings have suggested that protein kinase Cδ (PKCδ) could be one of the target proteins of aplog-1. In this study, we synthesized amide-aplog-1 (3), in which the C-1 ester group was replaced with an amide group, to improve chemical stability in vivo. Unfortunately, 3 exhibited seventy-fold weaker binding affinity to the C1B domain of PKCδ than that of aplog-1, and negligible anti-proliferative and cytotoxic activities even at 10(-4) M. A conformational analysis and density functional theory calculations indicated that the stable conformation of 3 differed from that of aplog-1. Since 27-methyl and 27-methoxy derivatives (1, 2) without the ability to bind to PKC isozymes exhibited marked anti-proliferative and cytotoxic activities at 10(-4) M, 3 may be an inactive control to identify the target proteins of aplogs.

Fundamental frequency from classical molecular dynamics.

We give a theoretical validation for calculating fundamental frequencies of a molecule from classical molecular dynamics (MD) when its anharmonicity is small enough to be treated by perturbation theory. We specifically give concrete answers to the following questions: (1) What is the appropriate initial condition of classical MD to calculate the fundamental frequency? (2) From that condition, how accurately can we extract fundamental frequencies of a molecule? (3) What is the benefit of using ab initio MD for frequency calculations? Our analytical approaches to those questions are classical and quantum normal form theories. As numerical examples we perform two types of MD to calculate fundamental frequencies of H2O with MP2/aug-cc-pVTZ: one is based on the quartic force field and the other one is direct ab initio MD, where the potential energies and the gradients are calculated on the fly. From those calculations, we show comparisons of the frequencies from MD with the post vibrational self-consistent field calculations, second- and fourth-order perturbation theories, and experiments. We also apply direct ab initio MD to frequency calculations of C-H vibrational modes of tetracene and naphthalene. We conclude that MD can give the same accuracy in fundamental frequency calculation as second-order perturbation theory but the computational cost is lower for large molecules.

Distribution of topologically distinct isomers of water clusters and dipole moments of constituent water molecules at finite atmospheric temperatures.

Hydrogen-bonding (HB) patterns correspond to topologically distinct isomers of a water cluster and can be expressed by digraphs. We make use of the HB pattern to divide the configuration space of a water cluster ((H2O)n, n = 3-8) at a finite temperature. Each configuration of a water cluster generated in Monte Carlo (MC) simulation is classified into an HB pattern. The number of observed HB patterns increases exponentially with the cluster size, whereas the population of the most abundant HB pattern decreases. The populations of the HB patterns are transformed into the relative Helmholtz energies. At a finite temperature, it can be observed that isomers other than local minimum structures on the potential energy surface are highly populated. The dipole moment of a constituent molecule in a water cluster is enhanced, depending on the molecular circumstance. The change is rationalized by the difference in the local HB type of the water molecule in the HB network.

Structures of molecules in ground and excited vibrational states from quasiclassical direct ab initio molecular dynamics.

We demonstrate that the mean structures of molecules derived from quasiclassical direct ab initio molecular dynamics (MD) simulation, the classical simulation that takes into account quantum vibrational levels, agree well with those determined from quantum-mechanical (QM) expectation values and/or experimentally observed values. First, for a one-dimensional model potential that includes anharmonicity as the third-order potential energy term, we show that the time-averaged structure over the classical trajectory with taking account of a quantum vibrational energy level correlates with a QM structure averaged using a vibrational wave function based on the first-order perturbation theory. Next, quasiclassical direct ab initio MD and Fourier grid Hamiltonian method are applied to OH and OD radicals; the mean structures at several vibrational levels of both classical and QM methods coincide, and they are in good agreement with the structures determined experimentally. Quasiclassical direct ab initio MD is then applied to H(2)O, C(2)H(2), and C(6)H(6). For H(2)O and C(2)H(2), the classical mechanically calculated mean structural parameters agree well with the experimental values and the QM values obtained from vibrational self-consistent field. For C(2)H(2), we find that r(g)(C-H) is longer than r(e)(C-H), whereas r(mean)((0))(C-H), which is equal to r(z)(C-H), is slightly shorter than r(e)(C-H).

Self-assembled monolayers of double-chain disulfides of adenine on Au: an IR-UV sum-frequency generation spectroscopic study.

We have synthesized double-chain disulfides of adenine with different chain lengths (n = 2, 4, 5, 9, and 10) and studied their self-assembled monolayers (SAM) on gold surface by IR-UV doubly resonant sum frequency generation spectroscopy with the help of DFT calculation. A versatile way to investigate the orientation angle of functional groups of SAMs and their surface coverage has been demonstrated. It was revealed that the IR dipoles of the band at around 1630 cm(-1), which were almost parallel to the long molecular axis of the adenine ring, were less tilted with respect to the substrate surface in the SAMs with longer chains (n = 9 and 10) in comparison to those with shorter chains (n = 2, 4, and 5).

Chiral sum frequency spectroscopy of thin films of porphyrin J-aggregates.

Thin films of chiral porphyrin J-aggregates have been studied by vibrationally and electronically doubly resonant sum frequency generation (SFG) spectroscopy. It was revealed that the chiral supramolecular structures of porphyrin aggregates in solutions were retained in the thin film samples, and their chirality was determined by using chiral vibrational SFG spectroscopy. Electronic resonance profiles of some vibrational bands in achiral and chiral SFG were different from each other, and both were distinct from electronic absorption spectra. To account for these peculiar profiles, we have proposed interference effects of Raman tensor components in achiral and chiral SFG susceptibilities, which is analogous to that of resonance Raman scattering.