Antibody-recruiting protein-catalyzed capture agents to combat antibiotic-resistant bacteria

Antibiotic resistant infections are projected to cause over 10 million deaths by 2050, yet the development of new antibiotics has slowed. This points to an urgent need for methodologies for the rapid development of antibiotics against emerging drug resistant pathogens. We report on a generalizable combined computational and synthetic approach, called antibody-recruiting protein-catalyzed capture agents (AR-PCCs), to address this challenge. We applied the combinatorial protein catalyzed capture agent (PCC) technology to identify macrocyclic peptide ligands against highly conserved surface protein epitopes of carbapenem-resistant Klebsiella pneumoniae, an opportunistic Gram-negative pathogen with drug resistant strains. Multi-omic data combined with bioinformatic analyses identified epitopes of the highly expressed MrkA surface protein of K. pneumoniae for targeting in PCC screens. The top-performing ligand exhibited high-affinity (EC₅₀ ∼50 nM) to full-length MrkA, and selectively bound to MrkA-expressing K. pneumoniae, but not to other pathogenic bacterial species. AR-PCCs that bear a hapten moiety promoted antibody recruitment to K. pneumoniae, leading to enhanced phagocytosis and phagocytic killing by macrophages. The rapid development of this highly targeted antibiotic implies that the integrated computational and synthetic toolkit described here can be used for the accelerated production of antibiotics against drug resistant bacteria.

Antibody-recruiting protein-catalyzed capture agent (AR-PCCs) are a new class of all-synthetic and highly targeted antibiotics that recruit endogenous immune responses to eliminate drug-resistant microbes.     

Reaction of ketenes with N,N-disubstituted α-aminomethyleneketones. XVIII. Synthesis of N,N-disubstituted 4-amino-3-phenyl-2H-naphtho[1,2-b]pyran-2-ones

1,4-Cycloaddition of phenylchloroketene to N,N-disubstituted 2-aminomethylene-3,4-dihydro-1(2H)naphthalenones gave the corresponding adducts, namely N,N-disubstituted 4-amino-3-chloro-3,4,5,6-tetrahydro-3-phenyl-2H-naphtho[1,2-b]pyran-2-ones II, in the case of aliphatic N,N-disubstitution or aromatic N-monosubstitution. Apart from IIf (NR₂ = NMePh), adducts II were unstable and were dehydrochlorinated in situ with DBN to give N,N-disubstituted 4-amino-5,6-dihydro-3-phenyl-2H-naphtho[1,2-b]pyran-2-ones III in fair overall yields. Compounds III were dehydrogenated with Pd/C in boiling p-cymene to afford the title compounds generally in high yields.     

On the hypothetical protein F154 of the TTV1 virus/Thermoproteus Tenax. Part II: Synthesis of the trieicosapeptide,corresponding to the protein sequence 79–101

Summary For the identification of a protein predicted by DNA sequence analysis of the TTV1 virus from the archaebacteriumThermoproteus tenax, the trieicosapeptide H-Thr-Pro-Thr-Pro-Thr-Pro-Thr-Tyr-Asp-Ile-Thr-Tyr-Val-Val-Phe-Asp-Val-Thr-Pro-Ser-Pro-Thr-Pro-OH, corresponding to the protein fragment 79–101, was prepared by conventional methods of peptide synthesis. This sequence portion may possibly represent a suitable protein specific immunepitope.

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Zur Hypothese eines TTV1 Virus/Thermoproteus tenax F154-Proteins. Teil II: Synthese des Protein-fragments 79–101

Zusammenfassung Für den Nachweis der Expression des Proteins F154 — nach einer Sequenzanalyse des Genoms des TTV1 Virus im ArchaebakteriumThermoproteus tenax postuliert — wurde das Peptid H-Thr-Pro-Thr-Pro-Thr-Pro-Thr-Tyr-Asp-Ile-Thr-Tyr-Val-Val-Phe-Asp-Val-Thr-Pro-Ser-Pro-Thr-Pro-OH (Proteinfragment 79–101) mit Hilfe konventioneller Peptidsynthese hergestellt. Diese Peptidsequenz sollte ein geeignetes proteinspezifisches Immunepitop darstellen.

     

Quelques considérations sur la structure électronique du naphtalène

Theπ electronic structure of naphtalene is studied, using a semi-empirical approximation for coulombic and resonance integrals; forH andS (H, hamiltonian;S, overlap) the complete matrices are adopted, together withKohlrausch's nuclear effective charges. A non uniform charge distribution is obtained, with charge accumulation at the tertiary carbons. Bond orders between non neighboring atoms indicate contributions to the fundamental state from other structures besides the classical ones. A comparative study of the obtained interatomic distances is carried. It is shown that [H, S]=0 is not a sufficient condition for the identity of the bond orders for the fundamental state calculated with and without overlap.     

Beyond generative models: superfast traversal,optimization, novelty,exploration and discovery (STONED) algorithm for molecules using SELFIES

Inverse design allows the generation of molecules with desirable physical quantities using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED – a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. First, we achieve non-trivial performance on typical benchmarks for generative models without any training. Additionally, we demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. Overall, we anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wider adoption.

Interpolation and exploration within the chemical space for inverse design.     

Capillary gas chromatographic separation of C10–C12 secondary phenylalkanes on modified cyclodextrin stationary phases

The separation of isomers and enantiomers of branched C₁₀-C₁₂ phenylalkanes by gas chromatography on fused silica capillary columns coated with some modified β- and γ-cyclodextrins was studied. It was shown that the separation of positional isomers of C₁₀-C₁₂ phynylalkanes on modified cyclodextrin capillary columns is not better than that on a column coated with modified polyethylene glycol. Differences were found in the enantioselectivity of modified β- and γ-cyclodextrins for the separation of C₁₀-C₁₂ secondary phenylalkane enantiomers. While alkylderivatives of β-CDs resolve enantiomers of 3-phenylalkanes, alkyl derivatives of γ-CD resolve enantiomers of 2-phenylalkanes. Since shape selectivity factors of modified cyclodextrins have indicated no inclusion of the considered solutes in cyclodextrin cavities, enantioselective interactions most probably occur on the outer sphere of cyclodextrins.     

Time evolution of infinite classical systems with singular,long range,two body interactions

Existence of dynamics for infinitely many hard-spheres inv dimensions is proven in a set of full equilibrium measure.Singular unbounded perturbations are considered with pair potentials diverging as (x – a)^–, >2 anda is the hard-core diameter. Long range forces are allowed with potentials decreasing at infinity asx , <v. The result corrects and generalizes a proof given in a previous paper by the same authors.Research partially supported by a CNR fellowship Posit. 204530.Research partially supported by a CNR fellowship.     

Noether's Theorem on Surfaces

In this article we prove a version of Noether's Theorem (of Calculus of Variations) which is valid for a general regular (compact) surface. As a special feature, the Lie group of transformations is allowed to act on the Cartesian product of the surface and the functional space. Additionally, we apply the Theorem to a problem in Classical Differential Geometry of surfaces. The given application is actually an example showing how Noether's Theorem can be used to construct invariant properties of the solutions to variational problems defined on surfaces, or equivalently, of the solutions to the associated Euler-Lagrange equations resulting from them.     

Homodiselenacalix[4]arenes: Molecules with Unique Channelled Crystal Structures

A synthetic route towards homodiselenacalix[4]arene macrocycles is presented, based on the dynamic covalent chemistry of diselenides. The calixarene inner rim is decorated with either alkoxy or tert‐butyl ester groups. Single‐crystal X‐ray analysis of two THF solvates with methoxy and ethoxy substituents reveals the high similarity of their molecular structures and alterations on the supramolecular level. In both crystal structures, solvent channels are present and differ in both shape and capacity. Furthermore, the methoxy‐substituted macrocycle undergoes a single‐crystal‐to‐single‐crystal transformation during which the molecular structure changes its conformation from 1,3‐alternate (loaded with THF/water) to 1,2‐alternate (apohost form). Molecular modelling techniques were applied to explore the conformational and energetic behaviour of the macrocycles.