Longitudinal Comparison of Neutralizing Antibody Responses to COVID-19 mRNA Vaccines after Second and Third Doses.

COVID-19 mRNA vaccines protect against severe disease and hospitalization. Neutralizing antibodies (NAbs) are a first-line defense mechanism, but protective NAb responses are variable. Currently, NAb testing is not widely available.

Third COVID-19 vaccine dose boosts neutralizing antibodies in poor responders.

Background: While evaluating COVID-19 vaccine responses using a rapid neutralizing antibody (NAb) test, we observed that 25% of mRNA vaccine recipients did not neutralize >50%. We termed this group "vaccine poor responders" (VPRs). The objective of this study was to determine if individuals who neutralized <50% would remain VPRs, or if a third dose would elicit high levels of NAbs.

Proof-of-Concept Rapid Diagnostic Test for Onchocerciasis: Exploring Peptide Biomarkers and the Use of Gold Nanoshells as Reporter Nanoparticles.

Three O. volvulus immunogenic peptide sequences recently discovered by peptide microarray were adapted to a lateral flow assay (LFA). The LFA employs gold nanoshells as novel high-contrast reporter nanoparticles and detects a serological response against the 3 peptides, found in OvOC9384, OvOC198, and OvOC5528, respectively.

A novel rapid test for detecting antibody responses to Loa loa infections.

Ivermectin-based mass drug administration (MDA) programs have achieved remarkable success towards the elimination of onchocerciasis and lymphatic filariasis. However, their full implementation has been hindered in Central Africa by the occurrence of ivermectin-related severe adverse events (SAEs) in a subset of individuals with high circulating levels of Loa loa microfilariae. Extending MDA to areas with coincident L.

High-throughput platform for rapid deployment of antimicrobial agents.

A new approach to conducting bacterial binding assays by using an addressable high density random sequence peptide microarray is described. When bacterial binding is carried out in the presence of a competing excess of corresponding bacterial lipopolysaccharide (LPS), most of the observed bacterial binding is inhibited, suggesting that LPS is the major target of the bacterial binding peptides. Importantly, the amino acid composition of the selected peptides closely resembles the composition of natural antimicrobial peptides.

Thermodynamic additivity of sequence variations: an algorithm for creating high affinity peptides without large libraries or structural information.

Background: There is a significant need for affinity reagents with high target affinity/specificity that can be developed rapidly and inexpensively. Existing affinity reagent development approaches, including protein mutagenesis, directed evolution, and fragment-based design utilize large libraries and/or require structural information thereby adding time and expense. Until now, no systematic approach to affinity reagent development existed that could produce nanomolar affinity from small chemically synthesized peptide libraries without the aid of structural information.

Self-assembled micronanoplexes for improved biolistic delivery of nucleic acids.

A new method for biolistic delivery of nucleic acids using a combination of cationic micro- and nanoparticles is reported. The new method is simpler to perform than the conventional calcium/spermidine-based formulations and shows 11-fold improved nucleic acid binding capacity and dose-dependent performance both for in vitro and in vivo applications relative to either the conventional preparation or our recently reported direct cationic microparticle method. These features may enable higher throughput gene delivery and genetic immunization programs and open new venues for the biolistic delivery method.

North- and south-bicyclo[3.1.0]hexene nucleosides: the effect of ring planarity on anti-HIV activity.

The syntheses of new conformationally locked North- and South-bicyclo[3.1.0]hexene nucleosides is reported.

Peptide microarrays for carbohydrate recognition.

An application of high density random sequence peptide microarrays for rapid and reliable identification of artificial carbohydrate receptors is reported.

Bacterial glycoprofiling by using random sequence peptide microarrays.

Current analytical methods have been slow in addressing the growing need for glyco-analysis. A new generation of more empirical high-throughput (HTP) tools is needed to aid the advance of this important field. To this end, we have developed a new HTP screening platform for identification of surface-immobilized peptides that specifically bind O-antigenic glycans of bacterial lipopolysaccharides (LPS).

New QSAR combined strategy for the design of A1 adenosine receptor agonists.

Combined discriminant and regression analysis was carried out on a series of 167 A1 adenosine receptor agonists to identify the best linear and nonlinear models for the design of new compounds with a better biological profile. On the basis of the best linear discriminant analysis and both linear and nonlinear Multi Layer Perceptron neural networks regression, we have designed and synthesized 14 carbonucleoside analogues of adenosine. Their biological activities were predicted and experimentally measured to demonstrate the capability of our model to avoid the prediction of false positives.

Chemical graph theory and n-center electron delocalization indices: a study on polycyclic aromatic hydrocarbons.

Relations between aromaticity indices derived from chemical graph theory and those based on 6-center electron delocalization are investigated for a series of polybenzenoid hydrocarbons. Aromatic stabilization obtained by means of the effective scaled electron delocalization is highly correlated to the resonance energy, RE, obtained both from SCF MO calculations and conjugated ring circuits model. Local aromaticity of benzene rings is discussed using two different criteria, in one of them aromaticity is just given by the cyclic pi-electron conjugation of the ring, whereas terms involving more than one ring are also considered in the other one.

Characterization of pericyclic reactions using multicenter electron delocalization analysis.

This work investigates the applicability of multicenter delocalization analysis to the characterization of pericyclic reactions. The results indicate that multicenter delocalization indices are a powerful tool for studying concerted processes, allowing the characterization of aromatic transition states with a significant increase in the electron delocalization. Moreover, an advantage over magnetic-based indices is that multicenter delocalization indices are not influenced by local electron currents but by the electron delocalization along the multiple (n) centers, and provide, in a quantitative sense, more reliable results.

A computational study on the stacking interaction in quinhydrone.

The stability and electron density topology of quinhydrone complex was studied using multiple computational levels, including MPW1B95 Truhlar's density functional. The QTAIM analysis demonstrates that an electron population transfer from hydroquinone to quinone monomer accompanies the complex formation. The variations undergone by atomic populations indicate that the electron transfer through HOMO LUMO overlap is combined with a reorganization of the electron density within each monomer.

QTAIM N-center delocalization indices as descriptors of aromaticity in mono and poly heterocycles.

The implementation of the n-center electron delocalization indices, n-DIs, and n-order electron localization indices, n-LIs, within the framework of the quantum theory of atoms in molecules, QTAIM, is performed. n-DIs are shown to be very useful to study the local aromaticity in monocyclic and polycyclic compounds. Total and pi n-DIs from n=4 to 7 were computed for a series of typical 4, 5, 6, and 7-center aromatic and antiaromatic rings.

Synthesis and anti-HIV activity of novel cyclopentenyl nucleoside analogues of 8-azapurine.

Novel nucleoside analogues of structure 3-5 were synthesized starting from (+/-)-cis-2-amino-3-cyclopentenylmethanol (1). The chlorine derivative 3 inhibited both HIV-1 and HIV-2 replication in MT-4 cells with IC(50) values of 10.67 microM and of 13.

Do the neighboring residues in a polypeptide affect the electron distribution of an amino acid significantly? A quantitative study using the quantum theory of atoms in molecules (QTAIM).

Geometries, as well as bond and atomic properties obtained with the atoms-in-molecules theory applied on B3LYP/6-31++G//B3LYP/6-31G charge densities, of the N-formyl amides of the nine tripeptides obtained by combining glycine, alanine, and serine around a central glycine residue were analyzed to check how the properties of the central residue are modified by other amino acids bonded to it. All of the molecules were optimized from an alpha-helix conformation that was also displayed by the optimized structure. Significant variations of the geometry (especially remarkable for dihedral angles) and atomic properties of the central glycine residue are observed when it is attached to a serine residue whose side chain is involved in a hydrogen bond.

On the applicability of resonance forms in pyrimidinic bases. II. QTAIM interpretation of the sequence of protonation affinities.

The atomic properties of neutral and protonated forms of uracil and some model compounds, computed from B3LYP/6-31++G//B3LYP/6-31G charge densities with the QTAIM theory, indicate that sigma electron reorganization plays a significant role in the protonation processes. This reorganization is substantially different for O=C-C=C and O=C-C-X (X = N, O) units, involving transfers of electron population between all atoms in the first case but not across the C-X bond in the second unit. O-Protonation is basically favored over the N-protonation because of the lower electron population transferred to the proton.

On the electron donor and the electrophilic substitution activating abilities of substituents in uracil.

QTAIM properties for uracil and 18 derivatives containing the substituents -NH(2), -OH, -OCH(3), -SH, -F, -Cl, -CH(3) -NO(2), and -Li in position 5 or 6 were computed on MP2/6-31++G//MP2/6-31G charge densities. The results indicate that -OH, -OCH(3), and -NH(2) groups are really retrieving charge from the ring. Also, the activating ability of the substituent groups, usually considered as the variation of electron population at the carbon where the electrophilic attack takes place, C, was studied.

Human P2Y(6) receptor: molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference.

Combining molecular dynamics (MD) in a hydrated phospholipid (DOPC) bilayer, a Monte Carlo search, and synthesis of locked nucleotide analogues, we discovered that the Southern conformation of the ribose is preferred for ligand recognition by the P2Y(6) receptor. 2'-Deoxy-(S)-methanocarbaUDP was found to be a full agonist of the receptor and displayed a 10-fold higher potency than that for the corresponding flexible 2'-deoxyUDP. MD results also suggested a conformational change of the second extracellular loop consequent to agonist binding.

BCUT descriptors to predicting affinity toward A3 adenosine receptors.

The BCUT descriptors have been applied to the study of the A(3) adenosine receptor agonist effect of 32 adenosine analogues. A model, able to describe more than 80% of the variance in the experimental activity was developed with the use of the above-mentioned approach. Four different approaches (topological, Galvez topological charges indexes, Randić molecular profiles, and geometrical descriptors) failed to give satisfactory models for this property with the same number of variables in the equation.