journal of biological chemistry

The β-hemolytic factor streptolysin S (SLS) is an important linear azol(in)e-containing peptide (LAP) that contributes significantly to the virulence of Streptococcus pyogenes. Despite its discovery 85 years ago, SLS has evaded structural characterizing owing to its notoriously problematic physicochemical properties. Here, we report the discovery and characterization of a structurally analogous hemolytic peptide from Enterococcus caccae, termed enterolysin S (ELS). Through heterologous expression, site-directed mutagenesis, chemoselective modification, and high-resolution mass spectrometry, we found that ELS contains an intriguing contiguous octathiazole moiety...

It is now known that RNAs play more active roles in cellular pathways beyond simply serving as transcription templates. These biological mechanisms might be mediated by higher RNA stereo conformations, triggering the need to understand RNA secondary structures first. However, experimental protocols for solving RNA structures are unavailable for large-scale investigation due to their high costs and time-consuming nature. Various computational tools were thus developed to predict the RNA secondary structures from sequences...

Tauopathy, neuronal atrophy, and psychological impairments are hallmarks of neurodegenerative diseases, such as Alzheimer's disease, that currently lack efficacious clinical treatments capable of rectifying these issues. To address these unmet needs, we used rational drug design to combine the pharmacophores of DYRK1A inhibitors and isoDMTs to develop psychoplastogenic DYRK1A inhibitors. Using this approach, we discovered a nonhallucinogenic compound capable of promoting cortical neuron growth and suppressing tau hyperphosphorylation while also having the potential to mitigate the biological and psychological symptoms of dementia...

We present a novel three-layer approach based on multilevel density functional theory (MLDFT) and polarizable molecular mechanics to simulate the electronic excitations of chemical systems embedded in an external environment within the time-dependent DFT formalism. In our method, the electronic structure of a target system, the chromophore, is determined in the field of an embedded inactive layer, which is treated as frozen. Long-range interactions are described by employing the polarizable fluctuating charge (FQ) force field...

In recent years, generative machine learning algorithms have been successful in designing innovative drug-like molecules. SMILES is a sequence-like language used in most effective drug design models. Due to data's sequential structure, models such as recurrent neural networks and transformers can design pharmacological compounds with optimized efficacy. Large language models have advanced recently, but their implications on drug design have not yet been explored. Although one study successfully pre-trained a large chemistry model (LCM), its application to specific tasks in drug discovery is unknown...

The production of herbivore-induced plant volatiles (HIPVs) is a type of indirect defense used by plants to attract natural enemies and reduce herbivory by insect pests. In many crops little is known about genotypic variation in HIPV production or how this may affect natural enemy attraction. In this study, we identified and quantified HIPVs produced by 10 sorghum (Sorghum bicolor) cultivars infested with a prominent aphid pest, the sorghum aphid (Melanaphis sorghi Theobald). Volatiles were collected using dynamic headspace sampling techniques and identified and quantified using GC-MS...

Protein-ligand binding prediction typically relies on docking methodologies and associated scoring functions to propose the binding mode of a ligand in a biological target. Significant challenges are associated with this approach, including the flexibility of the protein-ligand system, solvent-mediated interactions, and associated entropy changes. In addition, scoring functions are only weakly accurate due to the short time required for calculating enthalpic and entropic binding interactions. The workflow described here attempts to address these limitations by combining supervised molecular dynamics with dynamical averaging quantum mechanics fragment molecular orbital...

During the process of wound healing, the stimulation of inflammatory factors often leads to abnormal proliferation of blood vessels and collagen, ultimately resulting in scar formation. To address this challenge, we fabricate a novel dermal extracellular matrix (DECM) hydrogel scaffold loaded with ginsenoside Rg3 (Rg3) using 3D printing technology. Mesoporous silica nanoparticles (MSNs) are introduced into the system to encase the Rg3 to control its release rate and enhance its bioavailability. We systematically evaluate the biological, physicochemical, and wound healing properties of this scaffold...

The formation of transient structures plays important roles in biological processes, capturing temporary states of matter through influx of energy or biological reaction networks catalyzed by enzymes. These natural transient structures inspire efforts to mimic this elegant mechanism of structural control in synthetic analogues. Specifically, though traditional supramolecular materials are designed on the basis of equilibrium formation, recent efforts have explored out-of-equilibrium control of these materials using both direct and indirect mechanisms; the preponderance of such works has been in the area of low molecular weight gelators...

Direct coupling of benzotriazole to unsaturated substrates such as allenes represents an atom-efficient method for the construction of biologically and pharmaceutically interesting functional structures. In this work, the mechanism of the N 2 -selective Rh complex-catalyzed coupling of benzotriazoles to allenes was investigated in depth using a combination of experimental and theoretical techniques. Substrate coordination, inhibition, and catalyst deactivation was probed in reactions of the neutral and cationic catalyst precursors [Rh(μ-Cl)(DPEPhos)]2 and [Rh(DPEPhos)(MeOH)2 ]+ with benzotriazole and allene, giving coordination, or coupling of the substrates...

An efficient algorithm for compressing a given many-body potential energy surface (PES) of molecular systems into a grid-based matrix product operator (MPO) is proposed. The PES is once represented by a full-dimensional or truncated many-body expansion form, which is obtained by ab initio calculations at each grid mesh point, and then all terms in the expansion are compressed and merged into a single MPO while maintaining the bond dimension of the MPO as small as possible. It was shown that the ab initio PES of the H2 CO was compressed by more than 2 orders of magnitude in the size of the site operators without loss of accuracy...

One of the key challenges in diagnosing thyroid cancer lies in the substantial percentage of indeterminate diagnoses of thyroid nodules that have undergone ultrasound-guided fine-needle aspiration (FNA) biopsy for cytological evaluation. This delays the definitive diagnosis and treatment plans. We recently demonstrated that hydroxyapatite microcalcifications (MCs) aspirated from thyroid nodules may aid nodule diagnosis based on their composition. In particular, Zn-enriched MCs have emerged as potential cancer biomarkers...

Ultrasmall iron oxide nanoparticles (USIO NPs) are expected to become the next generation T 1 contrast agents; however, their diagnostic and therapeutic potential for primary brain tumors (such as glioblastoma multiforme, GBM) is yet to be explored. At present, the main challenge is the effective hindering of biological barriers, including the blood-brain barrier (BBB) and the blood-brain tumor barrier (BBTB). Herein, we aimed to investigate whether the USIO NPs, in combination with MR-guided focused ultrasound (MRgFUS), could intensify MR imaging of GBM...

Development of metal-free nanozymes has raised concern for their extensive applications in photocatalysis and sensing fields. As novel metal-free nanomaterials, covalent organic frameworks (COFs) have engendered intense interest in the construction of nanozymes due to their structural controllability and molecular functionality. The formation of the molecular arrangement by embedding orderly donor-acceptors (D-A) linked in the framework topology to modulate material properties for highly efficient enzyme mimicking activity is of importance but challenging...

Neurodegenerative diseases (amyloid diseases such as Alzheimer's and Parkinson's), stemming from protein misfolding and aggregation, encompass a spectrum of disorders with severe systemic implications. Timely detection is pivotal in managing these diseases owing to their significant impact on organ function and high mortality rates. The diverse array of amyloid disorders, spanning localized and systemic manifestations, underscores the complexity of these conditions and highlights the need for advanced detection methods...

Developing soft wearable sensors with high sensitivity, low cost, and a wide monitoring range is crucial for monitoring human health. Despite advances in strain sensor technology, achieving high sensitivity and a wide operating range in a single device remains a major challenge in its design and preparation. Herein, a liquid metal (LM) is innovatively ultrasonically anchored to the gaps and surfaces of thermoplastic polyurethane (TPU) electrospun fibers, and then a conductive pathway is constructed through polypyrrole (PPy) self-polymerization to prepare a composite film...

The four new ligands, dialkyl esters of ( S , S )-propylenediamine- N , N '-di-(2,2'-di-(4-hydroxy-benzil))acetic acid (R2 - S , S -pddtyr·2HCl) (R = ethyl (L1), propyl (L2), butyl (L3), and pentyl (L4)) and corresponding palladium(II) complexes have been synthesized and characterized by microanalysis, infrared, 1 H NMR and 13 C NMR spectroscopy. In vitro cytotoxicity was evaluated using the MTT assay on four tumor cell lines, including mouse mammary (4T1) and colon (CT26), and human mammary (MDA-MD-468) and colon (HCT116), as well as non-tumor mouse mesenchymal stem cells...

Orthopedic device-related infection (ODRI) poses a significant threat to patients with titanium-based implants. The challenge lies in developing antibacterial surfaces that preserve the bulk mechanical properties of titanium implants while exhibiting characteristics similar to bone tissue. In response, we present a two-step approach: silver nanoparticle (AgNP) coating followed by selective laser-assisted surface alloying on commonly used titanium alumina vanadium (TiAl6V4) implant surfaces. This process imparts antibacterial properties without compromising the bulk mechanical characteristics of the titanium alloy...

A terminal [NiII-OH] complex 1, supported by triflamide-functionalized NHC ligands, showed divergent reactivity for the reaction of sulfone with alcohol, contingent on base concentration, temperature, and time. Julia-type olefination of alcohols with sulfones was achieved using one equiv. of base, whereas lowering base loading to 0.5 equiv. afforded α-alkylated sulfones. Besides excellent substrate scope and selectivity, biologically active stilbene derivatives DMU-212, pinosylvin, resveratrol, and piceatannol were synthesized in high yield under Julia-type olefination conditions...

We report an idea for the synthesis of oligopeptides using a solvent-free ball milling approach. Our concept is inspired by block play, in which it is possible to construct different objects using segments (blocks) of different sizes and lengths. We prove that by having a library of short peptides and employing the ball mill mechanosynthesis (BMMS) method, peptides can be easily coupled to form different oligopeptides with the desired functional and biological properties. Optimizing the BMMS process we found that the best yields we obtained when TBTU and cesium carbonate were used as reagents...