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.     

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.     

Generation and reactivity of 3‐carbethoxy‐5‐phenyl‐5H,7H‐thiazolo[3,4‐c]oxazol‐4‐ium‐1‐olate

3‐Carbethoxy‐5‐phenyl‐5H,7H‐thiazolo[3,4‐c]oxazol‐4‐ium‐1‐olate was generated from (2R,4R)‐N‐ethoxyoxalyl‐2‐phenylthiazolidine‐4‐carboxylic acid and its reactivity studied. This münchnone showed low reactivity as dipole although from the reaction with dimethyl acetylenedicarboxylate the corresponding (3R)‐3‐phenyl‐17H,3H‐pyrrolo[1,2‐c]thiazole‐5,6,7‐tricarboxylate could be isolated. The thermolysis of (2R,4R)‐N‐ethoxyoxalyl‐2‐phenylthiazolidine‐4‐carboxylic acid in refluxing acetic anhydride led to the synthesis of N‐(1‐ethoxycarbonyl‐2‐phenylvinyl)‐2‐phenyl‐4‐thioxo‐1,3‐thiazolidine. The structure of methyl (2R,4R)‐N‐ethoxyoxalyl‐2‐phenylthiazoliddine‐4‐carboxylate was determined by X‐ray crystallography.     

Development and validation of a rapid RP‐HPLC method for analysis of (−)‐copalic acid in copaíba oleoresin

The Copaifera species (Leguminoseae) are popularly known as ‘copaíba’ or ‘copaíva’ and are grown in the states of Amazonas, Pará and Ceará in northern Brazil. The oleoresins obtained from these species have been extensively used owing to their pharmacological potential and their application in cosmetic and pharmaceutical preparations. In the present study, the development and validation of a novel, rapid and efficient RP‐HPLC methodology for the analysis of the diterpene (?)‐copalic acid (CA), pointed out as the only chemical marker of the Copaifera genus, are described. The regression equation (Y = 26,707x ? 29,498) was obtained with good linearity (r² = 0.9993) and the limits of quantification and detection were 9.182 and 3.032 µg/mL, respectively. The precision and the accuracy of the method were adequate (lower than 4%). Finally, the validation parameters evaluated were satisfactorily met, so the developed method represents a suitable tool for application in the quality control of such natural products. Further studies aiming to develop analytical methodologies for each Copaifera species using a more representative number of chemical markers should be performed. Copyright © 2012 John Wiley & Sons, Ltd.     

Layer‐by‐layer deposition of antimicrobial polymers on cellulosic fibers: a new strategy to develop bioactive textiles

In recent years, there has been an increase of infectious diseases caused by different microorganisms and the development of antibiotic resistance. In this way, the search for new and efficient antibacterial materials is imperative. The main polysaccharides currently used in the biomedical and pharmaceutical domains are chitin and its derivative chitosan (CH) and alginates (ALG). In this study, a simple technique of Layer by Layer (LbL) of applying polycation CH and polyanion ALG was used to prepare CH/ALG multilayers on cotton samples via the electrostatic assembly with success. The CH/ALG cotton samples (functionalized) were investigated for their antibacterial properties towards Staphylococcus aureus and Klebsiella pneumonia using the international standard method JIS L 1902:2002. The antibacterial activity of the functionalized samples was tested in terms of bacteriostatic and bactericidal activity, and results showed that the samples exhibited a bacteriostatic effect on the two bacteria tested, as expected. In addition, samples with five layers (CH/ALG/CH/ALG/CH) were more effective in inhibiting bacterial growth. This new coating for cellulosic fibers is a new strategy and may open new avenues for the development of antimicrobial polymers with potential application in health‐care field. Copyright © 2013 John Wiley & Sons, Ltd.     

Synthesis and characterization of organic–inorganic hybrid materials prepared by sol–gel and containing CdS nanoparticles prepared by a colloidal method using poly(N-vinyl-2-pyrrolidone)

This paper describes the synthesis and characterization of CdS nanoparticles (NPs) stabilized with poly(N-vinyl-2-pyrrolidone) and their further immobilization on a hybrid organic–inorganic matrix produced by the sol–gel process. The production of the hybrid matrix doped with CdS NPs was carried out in two steps. In the first step a precursor, designated diureasil precursor, was synthesized from the reaction between the terminal amine groups of α,ω-diamine-poly(oxyethylene-co-oxypropylene) and the isocyanate group of 3-isocyanatopropyltriethoxysilane. The next step involved the hydrolysis and condensation reactions of ethoxy groups attached to silicon, this step resulting in the formation of a crosslinked siliceous network linked through urea bonds to a poly(oxyethylene)/poly(oxypropylene) chain. The NPs were added to the diureasil precursor before the gelation process to allow a homogeneous dispersion of the NPs within the matrix. The developed method allowed the transfer of colloidal NPs to a solid matrix without the need of exchange the capping agents or the solvent. The materials were characterized by absorption, steady-state photoluminescence spectroscopy and by TEM. The results obtained showed the presence of CdS NPs with quantum size effect dispersed within the diureasil matrix. The obtained nanocomposites show a high transparency in the visible range accounting for the good dispersion of the NPs within the matrix. The TEM analysis confirmed that the NPs are uniformly dispersed within the diureasil matrix.     

Hybrid sol–gel silica adsorbent materials synthesized by molecular imprinting for tannin removal

Journal of Sol-Gel Science and Technology - This study reports the development of a functional adsorbent synthesized by the molecular imprinting method in a sol–gel matrix. The adsorption...     

Zn[aminoacid]2 hybrid materials applied as heterogeneous catalysts in the synthesis of β-enaminones

Hybrid materials have seized attention from scientific community mainly as heterogenic catalysts in organic reactions on a large scale succeeding in some organic compounds with high yields. One of the most important classes of hybrid materials used for this purpose involves the complexation of Zn and aminoacids. Herein, we introduced Zn[Pro]₂ and Zn[Gly]₂ in the synthesis of several β-enaminones via solvent free protocol and using an ultrasound device.