Integrating computational and experimental approaches in discovery and validation of MmpL3 pore domain inhibitors for specific labelling of Mycobacterium tuberculosis.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), continues to pose a significant global health threat. Identifying new druggable targets is crucial for the advancement of drug development. Equally critical is the development of precise methods for monitoring Mtb to effectively combat this disease.

Design and Discovery of New Collagen V-Derived FGF2-Blocking Natural Peptides Inhibiting Lung Squamous Cell Carcinoma and .

Aberrant FGF2/FGFR signaling is implicated in lung squamous cell carcinoma (LSCC), posing treatment challenges due to the lack of targeted therapeutic options. Designing drugs that block FGF2 signaling presents a promising strategy different from traditional kinase inhibitors. We previously reported a ColVα1-derived fragment, HEPV (127AA), that inhibits FGF2-induced angiogenesis.

Create artilysins from a recombinant library to serve as bactericidal and antibiofilm agents targeting Pseudomonas aeruginosa.

Pseudomonas aeruginosa is a critical pathogen and novel treatments are urgently needed. The out membrane of P. aeruginosa facilitates biofilm formation and antibiotic resistance, and hinders the exogenous application against Gram-negative bacteria of endolysins.

Peptide Drug Design Using Alchemical Free Energy Calculation: An Application and Validation on Agonists of Ghrelin Receptor.

With recent large-scale applications and validations, the relative binding free energy (RBFE) calculated using alchemical free energy methods has been proven to be an accurate measure to probe the binding of small-molecule drug candidates. On the other hand, given the flexibility of peptides, it is of great interest to find out whether sufficient sampling could be achieved within the typical time scale of such calculation, and a similar level of accuracy could be reached for peptide drugs. However, the systematic evaluation of such calculations on protein-peptide systems has been less reported.

Transport Parameters for Combustion Species Based on cAMOEBA Polarizable Force Field.

In this study, we report a simplified yet accurate general AMOEBA polarizable force field for combustion-interested molecular species, denoted as Combustion-AMOEBA or cAMOEBA. By eliminating the permanent atomic dipoles and quadrupoles, retaining the explicit polarization and defining the general atom types of each molecule species, including alkanes, alkenes, alkynes, alcohols, peroxides, and aldehydes, a simplified and general cAMOEBA force field was constructed and validated using the benchmark results obtained at the QCISD(T)/CBS level of theory. In this way, the tedious parametrization step for permanent atomic multipoles of each new molecule in the original AMOEBA (PoltypeMP2) force field could be avoided, hence providing the capability of accurate high-throughput calculation for a large number of molecules at lower computational cost.

Reliable Prediction of the Protein-Ligand Binding Affinity Using a Charge Penetration Corrected AMOEBA Force Field: A Case Study of Drug Resistance Mutations in Abl Kinase.

Protein mutations that directly impair drug binding are related to therapeutic resistance, and accurate prediction of their impact on drug binding would benefit drug design and clinical practice. Here, we have developed a scoring strategy that predicts the effect of the mutations on the protein-ligand binding affinity. In view of the critical importance of electrostatics in protein-ligand interactions, the charge penetration corrected AMOEBA force field (AMOEBA_CP model) was employed to improve the accuracy of the calculated electrostatic energy.

Importance of Three-Body Problems and Protein-Protein Interactions in Proteolysis-Targeting Chimera Modeling: Insights from Molecular Dynamics Simulations.

Proteolysis-targeting chimeras (PROTACs) are a class of bifunctional molecules that can induce the ubiquitin degradation of its target protein by hijacking the E3 ligase to form a target protein-PROTAC-E3 ligase ternary complex. Its underlying principle has inspired the development of a wide range of protein degraders that are similar to or beyond PROTACs in recent years. The formation of the ternary complexes is the key to the success of PROTAC-induced protein degradation.

Synthesis, antiepileptic effects, and structure-activity relationships of α-asarone derivatives: In vitro and in vivo neuroprotective effect of selected derivatives.

In the present study, we compared the antiepileptic effects of α-asarone derivatives to explore their structure-activity relationships using the PTZ-induced seizure model. Our research revealed that electron-donating methoxy groups in the 3,4,5-position on phenyl ring increased antiepileptic potency but the placement of other groups at different positions decreased activity. Besides, in allyl moiety, the optimal activity was reached with either an allyl or a 1-butenyl group in conjugation with the benzene ring.

3-Silaazetidine: An Unexplored yet Versatile Organosilane Species for Ring Expansion toward Silaazacycles.

Small-ring silacycles are important organosilane species in main-group chemistry and have found numerous applications in organic synthesis. 3-Silaazetidine, a unique small silacycle bearing silicon and nitrogen atoms, has not been adequately explored due to the lack of a general synthetic scheme and its sensitivity to air. Here, we describe that 3-silaazetidine can be easily prepared from diverse air-stable precursors (RSONHCHSiRCHCl).

Calculation of Transport Parameters Using and AMOEBA Polarizable Force Field Methods.

The transport properties of chemical species such as coefficients of diffusion, thermal conductivity, and viscosity have been widely used in combustion modeling. Lennard-Jones parameters fitted from the accurate intermolecular potential energy surfaces are crucial to obtain such information. Hence, a fast and accurate energy function is always desired for this purpose.

The development of an Amber-compatible organosilane force field for drug-like small molecules.

As members of the group IVA elements, silicon and carbon have long been thought of as isosteres of each other in drug design. However, the lack of silicon parameters in current main stream force fields hinders the computational study of this important element in drug discovery. Thus, in this study, we attempted to supplement the parameters of organosilanes in the General Amber Force Field (GAFF2).

Filling the Gap in Understanding the Mechanism of GABAR and Propofol Using Computational Approaches.

γ-Aminobutyric acid type-A receptors (GABARs) play a critical role in neural transmission by mediating the inhibitory neural firing and are the target of many psychiatric drugs. Among them, propofol is one of the most widely used and important general anesthetics in clinics. Recent advances in structural biology revealed the structure of a human GABAR in both open and closed states.

Alpha-asarone Improves Cognitive Function of APP/PS1 Mice and Reducing Aβ P-tau and Neuroinflammation, and Promoting Neuron Survival in the Hippocampus.

Alzheimer's disease (AD) is a progressive neurodegenerative disease most often characterized by memory impairment and cognitive decline. Alpha-asarone has been reported to have the potential to treat AD. Our previous studies have found that alpha-asarone improves aged rats' cognitive function by alleviating neuronal excitotoxicity via type A gamma-aminobutyric acid (GABA) receptors.

The application of the MM/GBSA method in the binding pose prediction of FGFR inhibitors.

The success of a structure-based drug is highly dependent on a known binding pose of the protein-ligand system. However, this is not always available. In this study, we set out to explore the applicability of the popular and easy-to-use MD-based MM/GBSA method to determine the binding poses of known FGFR inhibitors.

Practical Synthesis of Benzimidazo[1,2-]quinolines via Rh(III)-Catalyzed C-H Activation Cascade Reaction from Imidamides and Anthranils.

We report a novel and practical one-pot Rh(III)-catalyzed strategy to construct benzimidazo[1,2-]quinolines from readily available imidamides and anthranils. The cascade reaction proceeds via a C-H amination-cyclization-cyclization process in ionic liquid without any additives and possesses simple operation, moderate-to-high yield, and broad substrate scope features, which will provide the reference for the construction of biologically active fused benzimidazoles.

Alpha-asarone improves cognitive function of aged rats by alleviating neuronal excitotoxicity via GABA receptors.

Alzheimer's disease (AD), the most common form of dementia, still lacks effective treatment at present. Alpha-asarone (ASA) is the major compound isolated from the Chinese medicinal herb Acorus gramineus. It has been reported to enhance cognitive function in rodent models, yet its mechanism was not fully understood.

Iridium-Catalyzed B-H Bond Insertion Reactions Using Sulfoxonium Ylides as Carbene Precursors toward α-Boryl Carbonyls.

An iridium-catalyzed B-H bond insertion reaction between borane adducts and sulfoxonium ylides to afford α-boryl carbonyls has been developed. The starting materials are safe and readily available. In addition, analogues of sulfoxonium ylides, such as sulfonium salts and sulfonium ylides could also be amenable to the reaction.

Water-mediated C-H activation of arenes with secure carbene precursors: the reaction and its application.

A water-mediated C-H activation using sulfoxonium ylides is reported, providing a general, green and step-economic approach to construct a C-C bond and varieties of useful N-heterocycle scaffolds. Notably, the "water-mediated" activation, in contrast to that in organic solvents, shows great potential in pharmaceutical, biochemistry and chemical industries.

Correction: Synthesis of indoles and quinazolines via additive-controlled selective C-H activation/annulation of N-arylamidines and sulfoxonium ylides.

Correction for 'Synthesis of indoles and quinazolines via additive-controlled selective C-H activation/annulation of N-arylamidines and sulfoxonium ylides' by Ruizhi Lai et al., Chem. Commun.

Synthesis of indoles and quinazolines via additive-controlled selective C-H activation/annulation of N-arylamidines and sulfoxonium ylides.

Selective synthesis of indole and quinazoline products was achieved through a precise control of the C-H activation/annulation by changing the additives from NaOAc to CuF2/CsOAc. This strategy constructs indole and quinazoline scaffolds efficiently, and hence is of great interest in pharmaceutical, agricultural and chemical industries.

A stabilized retro-inverso peptide ligand of transferrin receptor for enhanced liposome-based hepatocellular carcinoma-targeted drug delivery.

The application of tumor targeting ligands to the treatment of cancer holds promise for improving efficacy and reducing toxicity. T7 ((HAIYPRH)) peptide, a phage display-selected peptide, exhibited high binding affinity to transferrin receptor (TfR) overexpressed on tumor cells. However, its in vivo tumor targeting efficiency was impaired due to enzymatic degradation in blood circulation.

[Cp*Rh ]/Ionic Liquid as a Highly Efficient and Recyclable Catalytic Medium for C-H Amidation.

A [Cp*Rh ]-catalyzed direct C-H amidation is carried out in ionic liquid. Both C(sp )-H bonds of (hetero)arenes and alkenes and unactivated C(sp )-H bonds can be easily amidated with high functional-group tolerance and excellent yields under these conditions. Notably, using [Cp*Rh ]/[BMIM]BF (BMIM=1-butyl-3-methylimidazolium) as the green and recyclable medium is environmentally benign, in light of characteristics such as the reusability of the expensive rhodium catalyst, avoidance of highly toxic organic solvents, and mild reaction conditions, as well as a short reaction time.

State variable technique islanding detection using time-frequency energy analysis for DFIG wind turbine in microgrid system.

This paper introduces a new combined technique for wind turbine islanding detection using the trajectory of state variables and wavelet transform in microgrid system. The proposed relay is utilized of energy variation state of time-frequency transform coefficients of local signals in two-dimensional space. In order to improve of the proposed relay performance, a signal selection method based on the correlation concept between islanding and non-islanding signals.