Towards new bioactive fluorine-containing 1,3,4-oxadiazole-amide derivatives: synthesis, antibacterial activity, molecular docking and molecular dynamics simulation study

Through the approach of molecular hybridization, this study rationally designed and synthesized new trifluoromethyl-1,3,4-oxadiazole amide derivatives, denoted as 1a-1n. The findings reveal that these novel molecules exhibit potent inhibitory effects against various bacterial strains. Thereinto, compounds 1c, 1d, 1i, 1j and 1n, demonstrate relatively superior antimicrobial performance against B. cereus FM314, with a minimum inhibitory concentration (MIC) of 0.03907 μg/mL. Molecular docking analysis suggests the potential importance of the Ser57 and Thr125 amino acid residues (PDB ID: 4EI9) in contributing to the inhibitory activity against B. cereus. The consistency of these results was further corroborated through subsequent molecular dynamics simulations and MMPBSA validations. The insights gained from this study serve to facilitate the rational design and efficient development of novel eco-friendly antimicrobial inhibitors based on the trifluoromethyl-1,3,4-oxadiazole amide scaffold.

In Silico Docking of Medicinal Herbs Against P. gingivalis for Chronic Periodontitis Intervention

OBJECTIVE

This study aimed to explore the therapeutic potential of medicinal herbs for chronic periodontitis by examining the molecular interactions between specific herbal compounds and the heme-binding protein of Porphyromonas gingivalis, a key pathogen involved in the disease.

METHODS

The crystal structure of heme-binding protein was obtained from the Protein Data Bank. Herbal compounds were identified through an extensive literature review. Molecular docking simulations were performed to predict binding affinities, followed by Absorption, Distribution, Metabolism, and Excretion (ADME) parameter prediction. Drug-likeness was assessed based on Lipinski's Rule of Five, and pharmacophore modeling was conducted to identify key molecular interactions.

RESULTS

The molecular docking simulations revealed that chelidonine, rotenone, and myricetin exhibited significant binding affinities to the heme-binding protein, with docking scores of -6.5 kcal/mol, -6.4 kcal/mol, and -6.1 kcal/mol, respectively. These compounds formed stable interactions with key amino acid residues within the binding pocket. ADME analysis indicated that all 3 compounds had favourable pharmacokinetic properties, with no violations of Lipinski's rules and minimal predicted toxicity. Pharmacophore modeling further elucidated the interaction profiles, highlighting specific hydrogen bonds and hydrophobic interactions critical for binding efficacy.

CONCLUSIONS

Chelidonine, rotenone, and myricetin emerged as promising therapeutic candidates for chronic periodontitis due to their strong binding affinities, favorable ADME profiles, and lack of significant toxicity. The detailed pharmacophore modeling provided insights into the molecular mechanisms underpinning their inhibitory effects on the heme-binding protein of P. gingivalis. These findings suggest that these compounds have the potential for further development as effective treatments for chronic periodontitis. Future research should focus on in vitro and in vivo validation of these findings to confirm the efficacy and safety of these compounds in biological systems.

Extracellular Matrix-Inspired Antibacterial Fibrous Hydrogels Containing Polyhexamethylene Biguanide and Gd3

Traditional bulk hydrogels containing antibiotics or metal ions often fall short in effectively treating wound infections due to mechanical limitations, bacterial resistance, and potential cytotoxicity. To address these challenges, an extracellular matrix (ECM)-inspired antibacterial fibrous hydrogel featuring an anisotropic topological structure is developed that closely mimics the natural ECM environment. A novel antibacterial agent, PHMB-VAN-Gd (PVG), is synthesized by reacting polyhexamethylene biguanide (PHMB) with O-Vanillin (VAN) to form the Schiff base ligand PHMB-VAN (PV), followed by coordination with gadolinium ions (Gd3⁺). Employing silk fibroin (SF) as the matrix, the PVG complex is incorporated into fibrous hydrogels through electrospinning, generating structures that replicate the fibrous architecture of the ECM. The resulting SF-PVG fibrous hydrogels exhibited robust antibacterial activity, effectively inhibiting bacterial growth and biofilm formation. Furthermore, the aligned fiber orientation and substantial mechanical strength of these hydrogels facilitated cellular functions, promoting cell attachment and proliferation. This study underscores the significant potential of SF-PVG hydrogels for wound infection treatment.

σ-Bond insertion reactions of two strained diradicaloids

The development of new synthetic methodologies is instrumental for enabling the discovery of new medicines. The methods that provide efficient access to structural alternatives for aromatic compounds (that is, saturated arene bioisosteres) have become highly coveted1-4. The incorporation of these bioisosteres typically leads to favourable drug-like properties and represents an emerging field of research. Here we report a new synthetic method that furnishes a coveted motif, the bicyclo[2.1.1]hexane scaffold5,6, using mild reaction conditions and an operationally simple protocol. The methodology proceeds through the uncommon coupling of two strained fragments: transiently generated cyclic allenes and bicyclo[1.1.0]butanes, which possess considerable strain energies of about 30 kcal mol-1 (ref. 7) and about 60 kcal mol-1 (ref. 6), respectively. The reaction is thought to proceed by a σ-bond insertion through a diradical pathway. However, rather than requiring an external stimulus to generate radical species, reactivity is thought to arise as a result of innate diradical character present in each reactant. This diradicaloid character8, an underused parameter in reaction design, arises from the severe geometric distortions of each reactant. Our studies provide a means to access functionalized bicyclo[2.1.1]hexanes of value for drug discovery, underscore how geometric distortion of reactants can be used to enable uncommon modes of reactivity and should encourage the further exploration and strategic use of diradicaloids in chemical synthesis.

De novo evolution of antibiotic resistance to Oct-TriA1

The rise of antimicrobial resistance as a global health concern has led to a strong interest in compounds able to inhibit the growth of bacteria without detectable levels of resistance evolution. A number of these compounds have been reported in recent years, including the tridecaptins, a small family of lipopeptides typified by the synthetic analogue octyl-tridecaptin A1. Hypothesizing that prior reports of negligible resistance evolution have been due in part to limitations in the laboratory evolution systems used, we have attempted to select for resistant mutants using a soft agar gradient evolution (SAGE) system developed by our lab. Following optimization of the media conditions by incorporation of the anti-synaeresis agent xanthan gum into the agar matrix, we successfully evolved high-level resistance to both octyl-tridecaptin A1 as well as the challenging lipopeptide antibiotic polymyxin B. Decreased tridecaptin susceptibility was linked to mutations in outer membrane proteins ompC, lptD and mlaA, with the effect of these genes confirmed through a mix of allelic replacement and knockout studies. Overall, this work demonstrates the robust evolutionary potential of bacteria, even in the face of challenging antimicrobial agents.

7-(4-Chlorophenyl)-1-hydroxy-5-methylpyrido[3,4-d]pyridazin-4(3H)-one: synthesis, solvatomorphism, in vitro anti-inflammatory and cytotoxic activity studies and in silico analysis

The newly obtained compound 7-(4-chlorophenyl)-1-hydroxy-5-methylpyrido[3,4-d]pyridazin-4(3H)-one (CPM) was crystallized as two new variable solvates, namely, the dimethyl sulfoxide monosolvate, C14H10ClN3O2·C2H6SO (I), and the sesquisolvate, C14H10ClN3O2·1.5C2H6SO (II), and their structures were confirmed by single-crystal X-ray diffraction analysis. In previous work, 1-hydroxy-5-methyl-7-phenylpyrido[3,4-d]pyridazin-4(3H)-one (PM) was found to display anticancer activity. In the next step of our studies, we synthesized a new derivative of PM, introducing a Cl atom into the PM structure, obtaining CPM, which showed not only anticancer but also anti-inflammatory activity. CPM and the new semi-products of each step of the synthesis were examined by 1H NMR, 13C NMR and FT-IR spectroscopic analyses, and mass spectrometry. CPM forms (I) and (II) crystallize in the triclinic P1 and monoclinic C2/c space groups, respectively, and differ in the stoichiometry of the CPM and DMSO molecules in the crystal lattice, being 1:1 and 1:1.5 for (I) and (II), respectively. A powder X-ray diffraction analysis was performed only for solvate (I) due to the lack of stability of solvate (II). The potential cytotoxicity of CPM was evaluated against the normal cell lines L929 and RPTEC, as well as the cancer cell lines A172, AGS, CACO-2 and HepG2. The anti-inflammatory activity of CPM was also evaluated using colorimetric assay for the inhibition of COX-1 and COX-2. The same biological tests were carried out for PM to compare the activities of both compounds. The biological studies revealed that CPM does not exhibit more activity than PM. Moreover, in silico analysis of the bioavailability and molecular docking were performed.

A review of conjugation technologies for antibody drug conjugates

Antibody-drug conjugates (ADCs) have gained significant attention in biotherapeutics after several years of steady development. Among the multiple factors influencing ADC design, the conjugation method is one of the most critical parameters. This review classifies conjugation strategies into three categories: non-specific, site-specific but non-selective, and fully site-specific and selective methods. The characteristics; advantages and disadvantages; chemistry, manufacturing, and controls (CMC) potential; and clinical status of each conjugation strategy are discussed in detail. The site-specific and selective methods will yield more homogeneous ADC, which may influence the stability and pharmacokinetics (PK) profile of the ADC and then influence the final therapeutic outcome. Additionally, the review also explores challenges and future directions for developing novel conjugation strategies. This review presents the most prevalent conjugation techniques, providing a valuable resource for researchers in selecting conjugation technologies and advancing ADC development.

Nano-Encapsulated Coumarin Derivative, CS-QM2 Inhibits Neoplasm Growth: Experimented in Zebrafish Model

Cancer remains a significant global health challenge with limited therapeutic success, prompting the need for innovative treatment strategies. This study investigates the anticancer potential of nano-encapsulated metal derivatives (CS-QM2) using a zebrafish model with chemically induced cellular neoplasia. Characterization of CS-QM2 nanoparticles revealed successful synthesis with a high entrapment efficiency and enhanced drug release under acidic conditions. Zebrafish embryos exposed to 7,12-Dimethylbenz[a]anthracene (DMBA) exhibited significant malformations, macrophage accumulation, and abnormal tissue growth, which were markedly reduced by CS-QM2 treatment. CS-QM2 significantly increases intracellular ROS, resulting in higher LPO and induces apoptosis in neoplasm tissues. Furthermore, CS-QM2 treatment alters the tumor microenvironment, reducing macrophage accumulation by decreasing neutral lipid droplets, disrupting TAM metabolic support and limiting their protumorigenic activities. Biochemical assays demonstrated restored activities of antioxidant enzymes SOD, CAT, and GSH. Gene expression analysis showed upregulation of apoptosis and tumor suppressor genes (cas3, p53) and downregulation of inflammatory genes (cox-2, nf-kb). Histological assessment and SEM analysis confirmed reduced neoplasm occurrence and tissue abnormalities. These findings suggest that CS-QM2 nanoparticles effectively inhibit neoplasm growth and modulate the tumor microenvironment through oxidative stress induction and gene expression regulation.

The Peptide PROTAC Modality: A New Strategy for Drug Discovery

In recent years, proteolysis targeting chimera (PROTAC) technology has made significant progress in the field of drug development. Traditional drugs mainly focus on inhibiting or activating specific proteins, while PROTAC technology provides new ideas for treating various diseases by inducing the degradation of target proteins. Especially for peptide PROTACs, due to their unique structural and functional characteristics, they have become a hot research topic. This review provides a detailed description of the key components, mechanisms, and design principles of peptide PROTACs, elaborates on their applications in skin-related diseases, oncology, and other potential therapeutic fields, analyzes their advantages and challenges, and looks forward to their future development prospects. The development of peptide PROTAC technology not only opens up new paths for drug research and development, but also provides new ideas for solving the resistance and safety issues faced by traditional small-molecule drugs. Compared with small-molecule PROTACs, peptide PROTACs have advantages such as multitargeting, biodegradability, low toxicity, and flexibility in structural design. With the deepening of research and the continuous maturity of technology, peptide PROTACs are expected to become one of the important strategies for future drug discovery, providing new hope for the treatment of more intractable diseases. Peptide PROTACs are ushering in a new era of precision medicine.

Advances in the Development of Ferroptosis-Inducing Agents for Cancer Treatment

Cancer is the main leading cause of death worldwide and poses a great threat to human life and health. Although pharmacological treatment with chemotherapy and immunotherapy is the main therapeutic strategy for cancer patients, there are still many shortcomings during the treatment such as incomplete killing of cancer cells and development of drug resistance. Emerging evidence indicates the promise of inducing ferroptosis for cancer treatment, particularly for eliminating aggressive malignancies that are resistant to conventional therapies. This review covers recent advances in important regulatory targets in the ferroptosis metabolic pathway and ferroptosis inducers (focusing mainly on the last 3 years) to delineate their design, mechanisms of action, and anticancer applications. To date, many compounds, including inhibitors, degraders, and active molecules from traditional Chinese medicine, have been demonstrated to have ferroptosis-inducing activity by targeting the different biomolecules in the ferroptosis pathway. However, strictly defined ferroptosis inducers have not yet been approved for clinical use; therefore, the discovery of new highly active, less toxic, and selective compounds remains the goal of further research in the coming years.

Peptide-functionalized nanoparticles for brain-targeted therapeutics

Despite the rapid development of nanoparticle (NP)-based drug delivery systems, intravenous delivery of drugs to the brain remains a major challenge due to various biological barriers. To achieve therapeutic effects, NP-encapsulated drugs must avoid accumulation in off-target organs and selectively deliver to the brain, successfully cross the blood-brain barrier (BBB), and reach the target cells in the brain. Conjugating receptor-specific ligands to the surface of NPs is a promising technique for engineering NPs to overcome these barriers. Specifically, peptides as brain-targeting ligands have been of increasing interest given their ease of synthesis, low cytotoxicity, and strong affinity to target proteins. The success of peptides as targeting ligands is largely due to the diverse strategies of designing and modifying peptides with favorable properties, including membrane permeability and multi-receptor targeting. Here, we review the design and implementation of peptide-functionalized NP systems for neurological disease applications. We also explore advances in rational peptide design strategies for brain targeting, including using generative deep-learning models to computationally design new peptides.

Mycobacterium abscessus Virulence Factors: An Overview of Un-Explored Therapeutic Options

Mycobacterium abscessus (Mab) is an opportunistic pathogen gaining increased importance due to its capacity to colonize the respiratory tract of patients with chronic lung diseases such as individuals with Cystic Fibrosis. The actual therapeutic regimen to treat Mab infections is based on repurposed drugs from therapies against Mycobacterium tuberculosis and avium. In addition to the need for new specific drugs against this bacterium, a possible strategy for shortening the therapeutic time and improving the success rate could be targeting Mab virulence factors. These drugs could become an important integration to the actual therapeutic regimen, helping the immune system to fight the infection. Moreover, this strategy applies a low selective pressure on the bacteria, since these elements are not essential for Mab survival but crucial for establishing the infection. This review aims to provide an overview of the Mab's virulence factors that are poorly studied and mostly unknown, suggesting some interesting alternatives to classical drug development.

Diagnostic value of GeneXpert MTB/RIF in bronchoalveolar lavage fluid for pulmonary non-tuberculosis mycobacterial in acid-fast stain smear-positive and GeneXpert MTB/RIF-negative cases

Background

The identification of non-tuberculosis (TB) mycobacterial (NTM) infection remains a significant challenge. This study aims to investigate the diagnostic value of multicolour nested real-time fluorescence quantitative nucleic acid amplification detection technology [Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF)] in bronchoalveolar lavage fluid (BALF) acid-fast smear-positive cases.

Methods

Between 1 January 2017 and 30 June 2022, 365 patients who underwent fibreoptic bronchoscopy and had positive acid-fast smears of BALF were examined using Xpert MTB/RIF. The mycobacteria growth indicator tube (MGIT) 960 was used for rapid sputum culture and traditional drug sensitivity testing. Combined with mycobacterial culture and drug sensitivity results, Xpert results of alveolar lavage fluid were analysed to guide diagnosis and treatment.

Results

The sensitivity (Se), specificity (Sp), positive predictive value (PPV) and negative predictive value (NPV) of Xpert detection for diagnosing NTM lung disease in acid-fast smear-positive cases were 100% (45/45), 99.68% (310/311), 97.83% (45/46) and 100% (310/310), respectively.

Conclusions

Xpert MTB/RIF in alveolar lavage fluid can not only detect RIF resistance but also distinguish pulmonary TB from NTM pulmonary disease in patients with positive acid-fast smears.

Quinoline-linked 1,2,3-Triazole Hybrids: Design, Synthesis, Anticancer Activity and Computational Investigations

Synthesized a library of new quinoline-based 1,2,3-triazole scaffolds involving Suzuki-Miyaura cross-coupling and metal-free multicomponent reactions. Evaluated their in vitro anticancer activities against human breast (MCF-7), lung (A-549) and liver (HepG2) cancer cell lines with reference to Doxorubicin as standard. Four compounds 5a, 5d, 5e and 5f displayed outstanding activity against all three cell lines. Compound 5a, showcasing -Cl in the R2 position of the phenyl ring demonstrated potent activity with IC50 values of 9.25 ± 0.22, 9.56 ± 0.19 and 10.56 ± 0.19 µM against MCF-7, A-549 and HepG2 cell lines respectively. The compound 5f, containing m-Cl and m-OMe groups in R1 and R2 positions demonstrated potent activity with IC50 values of 10.49 ± 0.31 (MCF-7), 10.27 ± 0.27 (A-549) and 11.27 ± 0.30 µM (HepG2). Compound 5f with -Cl and -I group presented potent activity with an IC50 value of 11.40 ± 0.29 (MCF-7), 10.42 ± 0.21 (A-549) and 12.32 ± 0.33 µM (HepG2). Compound 5d gave out a potent activity with IC50 values of 10.42 ± 0.25 (MCF-7), 12.97 ± 0.22 (A-549) and 13.05 ± 0.45 µM (HepG2). Toxicity results against Hek-293 proved that these compounds were not harmful. The computational screening of these compounds revealed favourable drug-likeness properties and important binding interactions against Fibroblast Growth Factor Receptor 1.

Utilizing ADMET Analysis and Molecular Docking to Elucidate the Neuroprotective Mechanisms of a Cannabis-Containing Herbal Remedy (Suk-Saiyasna) in Inhibiting Acetylcholinesterase

Alzheimer's disease is characterized by the degeneration of cholinergic neurons, which is primarily driven by the acetylcholinesterase (AChE) enzyme and oxidative stress. This study investigated the therapeutic potential of the cannabis-containing herbal remedy Suk-Saiyasna in alleviating amyloid β42 (Aβ42)-induced cytotoxicity in SH-SY5Y cells. The DPPH radical-scavenging activity and inhibitory effects on AChE were evaluated in vitro. The AChE inhibitory potential of 167 ligands, including cannabinoids, flavonoids, terpenoids, and alkaloids derived from Suk-Saiyasna, was assessed using ADMET analysis and molecular docking techniques. The results demonstrated that the Suk-Saiyasna extract exhibited a DPPH radical scavenging effect with an IC50 value of 27.40 ± 1.15 µg/mL and notable AChE inhibitory activity with an IC50 of 1.25 ± 0.35 mg/mL. Importantly, at a concentration of 1 µg/mL, the extract significantly protected cells from Aβ42-induced stress compared to controls. Docking studies revealed that delta-9-tetrahydrocannabinol (Δ9-THC), mesuaferrone B, piperine, β-sitosterol, and chlorogenic acid exhibited substantial binding affinities to AChE, surpassing reference drugs like galantamine and rivastigmine. Furthermore, in silico ADMET predictions indicated that Δ9-THC and piperine possessed favorable pharmacokinetic profiles, including solubility, absorption, and blood-brain barrier permeability, with no neurotoxicity or carcinogenicity associated with Δ9-THC.

Modular Synthesis of 3,3-Disubstituted Azetidines via Azetidinylation Reagents

Azetidines represent an attractive and emerging design option in medicinal chemistry owing to their small size and polar nature, as well as their potential to significantly impact the physicochemical properties of drug molecules. However, traditional methods for the synthesis of 3,3-disubstituted azetidines usually require higher step counts or exhibit poor functional group compatibility. Herein, we report a modular synthesis strategy for 3,3-disubstituted azetidines based on azetidinylation reagents. The practicality of this method is further exemplified by the use of readily available starting materials, mild reaction conditions, and a very broad substrate scope.

Bridged Bicyclic γ-Sultams by Intramolecular Flow Photochemical [2 + 2] Cycloaddition

An elegant synthetic approach to the construction of a novel saturated heterocycle─2-thia-3-azabicyclo[2.1.1]hexane 2,2-dioxide─was designed. The key step included intramolecular flow photochemical [2 + 2] cycloaddition of appropriately substituted dienes, which were in turn obtained from readily available starting materials on a multigram scale. Further synthetic transformations of the resulting bicyclic compounds enabled the preparation of numerous functionalized derivatives useful for early drug discovery programs as promising isosteres of pyrrolidine, pyrrolidone, and γ-sultams. These studies also demonstrated the tolerance of the title bicyclic system to typical organic chemistry reaction conditions.

Synergy-Promoted Specific Alkyltriphenylphosphonium Binding to CB[8]

Biological substrate specificity ensures that organisms interact accurately with biomolecular receptors, crucial for key functions such as signaling and immunity. Nevertheless, this phenomenon is still poorly understood, with host-guest chemistry offering a suitable platform for studying simplified models. Herein, we report an in-depth study of the host-guest chemistry of alkyltriphenylphosphonium cations with cucurbit[8]uril (CB[8]), initiated by the serendipitous discovery of salt forming a tightly bound pseudoheteroternary 1:1 complex with CB[8]. A first generation of model substrates was designed to explore an unusual binding mode characterized by the simultaneous introduction of two distinct guest fragments within the host cavity. Structural features of the complexes were elucidated using ESI-MS and NMR 1D/2D techniques; thermodynamic properties were assessed by isothermal titration calorimetry, and kinetic parameters were derived from selective inversion-recovery NMR. Experimental results aligned well with electronic structure calculations, revealing a reproducible binding motif with submicromolar affinities. This peculiar complexation mode involves a synergistic effect caused by steric crowding around the P+ atom, facilitating the insertion of two aromatic units into CB[8] while hindering association with CB[7]. Based on these findings, a second generation of minimalistic substrates was developed, preserving the synergistic interaction mode and exhibiting specific binding to CB[8].

Hybrid Bis-(Imidazole/Benzimidazole)-Pyridine Derivatives with Antifungal Activity of Potential Interest in Medicine and Agriculture via Improved Efficiency Methods

Background/Objectives: Nowadays fungal infections are rising serious threats for the human health system and agriculture, mostly because of antifungal resistance, emergence of new fungal pathogens and adverse effects, pressing the scientific world for exploration of new antifungal compounds. Therefore, the aim of this work was to synthesize and to study antifungal activity against human and plant fungi of a new class of hybrid bis-(imidazole/benzimidazole)-pyridine salt derivatives. Methods: The synthesis of the hybrid derivatives was performed using both conventional thermal heating and ultrasound irradiation methods. Results: The use of ultrasound irradiation has the advantages of a dramatic decrease in reaction time and, consequently, a notable acceleration in reaction rate, a remarkable decrease in consumed energy and higher yields. The antifungal activity against five human fungal strains and for plant fungal strains was determined by the disk diffusion method and minimum inhibitory concentration. Conclusions: The tested hybrid derivatives manifest good antifungal activity against the tested strains. Some of the hybrid compounds have very good quasi-nonselective activity against the tested human and plant pathogenic fungi, in some cases close to the control drug fluconazole, respectively, to many antifungal agents commercially used for plant protection.

Copper-Catalyzed Dynamic Kinetic Asymmetric Arylation of Secondary Phosphine-Boranes for the Synthesis of P(III)-Stereogenic Centers

Transition-metal-catalyzed asymmetric C-P(III) bond formation is a direct method for the construction of P(III)-stereogenic centers; however, achieving high enantioselectivity remains a challenge. Herein, an unprecedented Cu-catalyzed dynamic kinetic resolution of secondary phosphine-boranes was successfully developed. This asymmetric C-P(BH3) coupling reaction provided the direct and highly enantioselective synthesis of P(III)-stereogenic centers, enabling the formation of chiral medium-sized benzophosphine-boranes (7-10-membered cycles). A mechanism of dynamic kinetic resolution involving the unusual rapid racemization of secondary phosphine-boranes has been proposed.

Identification of acrylamide-based covalent inhibitors of SARS-CoV-2 (SCoV-2) Nsp15 using high-throughput screening and machine learning

Non-structural protein 15 (Nsp15) is a SARS-CoV-2 (SCoV-2) endoribonuclease and is a promising target for drug development because of its essential role in evading the host immune system. However, developing inhibitors against Nsp15 has been challenging due to its structural complexity and large RNA binding surface. In this report, we screened a 2640 acrylamide-based compound library against Nsp15 and identified 10 fragments that reacted with cysteine residues on Nsp15 and inhibited its endoribonuclease activity with IC50s less than 5 μM. These compounds had several attractive properties, such as low molecular weight (180-300 g mol-1), log P <3, zero violations to Lipinski's rules, and no apparent pan-assay interference (PAINs) properties. In addition, based on this data as a training set, we developed an artificial intelligence (AI) model that accelerated the hit to lead process and had a 73% accuracy for predicting new acrylamide-based Nsp15 inhibitors. Collectively, these results demonstrate that acrylamide fragments have great potential for developing Nsp15 inhibitors.

Designing Macrocyclic Kinase Inhibitors Using Macrocycle Scaffold Hopping with Reinforced Learning (Macro-Hop)

Macrocycles have gained significant attention in drug discovery, with over 70 macrocyclic compounds currently in clinical use. Despite this progress, the effective methods for designing macrocycles remain elusive. In this study, we present Macro-Hop, a reinforced learning framework designed to rapidly and comprehensively explore the macrocycle chemical space. Macro-Hop efficiently generates novel macrocyclic scaffolds that not only align with predefined physicochemical properties but also exhibit 3D structural similarities to a specified reference compound. As a proof of concept, we applied Macro-Hop to design a new series of macrocycle inhibitors targeting PDGFRαD842 V kinase. The representative compound L7 exhibited high potency against PDGFRαD842 V in both biochemical and cellular assays with IC50 values of 23.8 and 2.1 nM, respectively. L7 effectively inhibited clinically relevant secondary mutants PDGFRαD842 V/G680R (IC50 = 64.1 nM) and PDGFRαD842 V/T674I (IC50 = 27.6 nM), highlighting the rapid effectiveness of wet-leb validation with Macro-Hop.

From DNA-Encoded Library Screening to : An MTA-Cooperative PRMT5 Inhibitor with Potent Oral In Vivo Efficacy

Inhibition of the methyltransferase enzyme PRMT5 by MTA accumulation is a vulnerability of MTAP-deleted cancers. Herein, we report the discovery and optimization of a quinolin-2-amine DEL hit that cooperatively binds PRMT5:MEP50 and MTA to generate a catalytically inhibited ternary complex. X-ray crystallography confirms quinolin-2-amine binding of PRMT5 glutamate-444, while simultaneously exhibiting a hydrophobic interaction with MTA. Lead optimization produced AM-9747, which selectively inhibits PRMT5-directed symmetric dimethylation of arginine residues of proteins, leading to a potent reduction of cell viability in MTAP-del cells compared to MTAP-WT cells. Once-daily oral dosing of AM-9747 in mouse xenografts is well tolerated, displaying a robust and dose-dependent inhibition of symmetric dimethylation of arginine in MTAP-del tumor-xenografts and significant concomitant tumor growth inhibition without any significant effect on MTAP-WT tumor xenografts.

In vitro enzymatic and cell culture assays for SARS-CoV-2 main protease interaction with ambenonium

The 2019 pandemic of coronavirus disease (COVID-19) caused by SARS-CoV-2 led to millions of deaths worldwide since its emergence. The viral genomic material can code structural and non-structural proteins including the main protease or 3CLpro, a cysteine protease that cleavages the viral polyprotein generating 11 proteins that participate in viral pre-replication. Thus, 3CLpro is a promising therapeutic target for SARS-CoV-2 inhibition by new drugs or drug repositioning because 3CLpro is dissimilar to human proteases. We conducted in vitro assays demonstrating the modulation activity of ambenonium, a drug already used in Myasthenia gravis that acts by inhibiting the action of acetylcholinesterase, and had its potential inhibitory activity against viral replication pointed out in a previous in silico study. In concentrations of 100 µM, 50 µM, 25 µM, 10 µM, and 1 µM there was no inhibition in the formation of lysis plates, with a slight increase in the genome copy number at the higher concentrations evaluated. However, in the concentrations of 0,1 µM and 0,01 µM, there was a reduction in the number of lysis plates. This behavior suggests that the ambenonium acts as a modulator of viral activity in vitro. To investigate potential conformational changes in the protein between dimeric and monomeric forms in the presence of the compound, a local docking analysis was performed. Results indicated this conformational shift is possible, though further studies are needed to confirm these findings.

Discovery of a Potent SARM1 Base-Exchange Inhibitor with In Vivo Efficacy

Sterile alpha and TIR Motif Containing 1 (SARM1) is a nicotinamide adenine dinucleotide (NAD+) hydrolase that plays a central role in programmed axonal degeneration. Axonal degeneration has been linked to neurodegenerative and neurological disorders such as multiple sclerosis, amyotrophic lateral sclerosis, Parkinson's disease, and peripheral neuropathies. Therefore, developing potent and selective SARM1 inhibitors could be an effective strategy to treat these disorders. We present herein the structure-guided discovery of two novel SARM1 inhibitors, 7 and 35. Compounds 7 and 35 are potent inhibitors across assays and possess favorable ADMET properties. When tested in vivo, compound 7 showed efficacy after oral dosing in a mouse model of peripheral nerve injury by decreasing plasma neurofilament light (NfL) levels at 50 mg/kg compared with vehicle-treated control mice, holding promise for the treatment of neurodegenerative and neurological disorders.

Monoselective Histone Deacetylase 6 PROTAC Degrader Shows In Vivo Tractability

Herein, we report a potent HDAC6 PROTAC, TO-1187, which selectively degrades HDAC6 in cellulo and demonstrates in vivo efficacy. The design of TO-1187 was achieved by linking our previously reported HDAC6 inhibitor, TO-317, to the cereblon (CRBN) E3 ligase ligand, pomalidomide. TO-1187 achieved monoselective HDAC6 degradation in human multiple myeloma cells, MM.1S, with a Dmax of 94% and a DC50 of 5.81 nM after 6 h. Importantly, at concentrations up to 25 μM, TO-1187 exhibited no cellular degradation of other HDACs. Proteomic evaluation confirmed a highly selective proteome-wide degradation profile, with HDAC6 the only protein observed to be depleted. Notably, TO-1187 did not impact the abundance of well-known CRBN neosubstrates, like IKZF1, IKZF3, CK1α, SALL4, and GSPT1. In vivo evaluation confirmed that TO-1187 efficiently degraded HDAC6 in mouse tissues, measured 6 h after intravenous injection. In summary, TO-1187 represents a viable candidate for advanced preclinical evaluation of HDAC6 biology.

MoA Studies of the TEAD P-Site Binding Ligand MSC-4106 and Its Optimization to TEAD1-Selective Amide M3686

Taking the structural information into account, we were able to tune the TEAD selectivity for a specific chemotype. However, different TEAD selectivity profiles did not affect the compound potency or efficacy in the NCI-H226 viability assay. Amides based on MSC-4106 or analogues showed improved viability efficacy compared with the corresponding acids. The amide M3686 exhibited AUC-driven efficacy in NCI-H226 xenograft models and had an improved 25-fold lower human dose prediction than MSC-4106. MSC-4106 was also used in HDX-MS studies to aid in the understanding of the MoA of P-site binding TEAD inhibitors. Artificial P-site binders rigidify certain areas in the periphery of the transcription factor that seem to be crucial for cofactor interaction, whereas a native fatty acid increased the protein dynamics of cofactor-binding interfaces.

Discovery of Elironrasib (RMC-6291), a Potent and Orally Bioavailable, RAS(ON) G12C-Selective, Covalent Tricomplex Inhibitor for the Treatment of Patients with RAS G12C-Addicted Cancers

The discovery of elironrasib (RMC-6291) represents a significant breakthrough in targeting the previously deemed undruggable GTP-bound, active KRASG12C. To target the active state of RAS (RAS(ON)) directly, we have employed an innovative tri-complex inhibitor (TCI) modality involving formation of a complex with an inhibitor, the intracellular chaperone protein CypA, and the target protein KRASG12C in its GTP-bound form. The resulting tri-complex inhibits oncogenic signaling, inducing tumor regressions across various preclinical models of KRASG12C mutant human cancers. Here we report structure-guided medicinal chemistry efforts that led to the discovery of elironrasib, a potent, orally bioavailable, RAS(ON) G12C-selective, covalent, tri-complex inhibitor. The investigational agent elironrasib is currently undergoing phase 1 clinical trials (NCT05462717, NCT06128551, NCT06162221), with preliminary data indicating clinical activity in patients who had progressed on first-generation inactive state-selective KRASG12C inhibitors.

Virtual Screening and Bioassay of Novel Protoporphyrinogen Oxidase and p-Hydroxyphenylpyruvate Dioxygenase Dual-Target Inhibitors

Novel herbicide development is a challenge for weed control. Protoporphyrinogen oxidase (PPO) and p-hydroxyphenylpyruvate dioxygenase (HPPD) are two key enzymes involved in plant photosynthesis. The multi virtual screening protocol was adopted to design a common skeleton based on the two target enzymes, and fragment growth of the skeleton was performed. The constructed compounds were searched for structural similarity, and the accuracy of the selected compounds was further verified using the Bayesian model. Finally, eight compounds were obtained, and the binding mode with the target was studied deeply. The obtained compounds interact with the key residues of HPPD and PPO proteins similarly to commercial herbicides, and the stability of binding with proteins is also good. The activity of the screening results was determined by an enzyme activity test in vitro. The herbicidal effect of the compound was studied by phenotypic experiment. The final results showed that Z-4 and Z-7 have the potential to become new dual-target herbicides.

The Heterogeneous Kinetic Origins of the Binding Properties of Orthosteric Ligands at Heteromeric Nicotinic Acetylcholine Receptors

A plethora of agonists and competitive antagonists have been developed to explore the therapeutic potential in neuronal nicotinic acetylcholine receptors (nAChRs). Based on equilibrium and kinetic [3H]epibatidine binding studies, we report that the kinetic fingerprints of [3H]epibatidine at five heteromeric αβ nAChRs and of seven classical agonists at α4β2 and α3β4 nAChRs differ substantially. While this diversity depends on both the agonist and receptor subtype, the overall pattern of kinetic determinants emerging from this profiling is complex. The dramatically different binding kinetics displayed by two alkaloids and competitive antagonists, (+)-DHβE and (+)-cocculine, at the α4β2 nAChR further exemplify how dissimilar kinetics can underlie very comparable pharmacological properties exhibited by close structural analogs. Thus, our findings elucidate the heterogeneous kinetic basis for orthosteric ligand binding to αβ nAChRs and emphasize how the binding affinities, selectivity profiles, and structure-activity relationships of these ligands are rooted in their kinetic traits at the receptors.

Choreoisosteres: Pseudoatom Variation in Macrocyclic Hinges Conserves Structure and Dynamics

Differing in pseudoatom, three macrocycles with isosteric substitutions (geminal dimethyl, cyclopropyl, cyclobutyl) can be described as choreoisosteres. Under ambient conditions, they share a dynamic hinge-like motion that can be described as fully revolute in solution. The barriers to hinging, ΔG ‡, are identical within experimental error: ΔG ‡ = 14.2-15.2 kcal/mol as judged by variable-temperature 13C NMR spectroscopy. Consistent with conserved dynamic behavior and isosterism, other physical properties including hydrophobicity and solution/membrane diffusion constants are amenable to prediction.

Computational tools for the prediction of site- and regioselectivity of organic reactions

The regio- and site-selectivity of organic reactions is one of the most important aspects when it comes to synthesis planning. Due to that, massive research efforts were invested into computational models for regio- and site-selectivity prediction, and the introduction of machine learning to the chemical sciences within the past decade has added a whole new dimension to these endeavors. This review article walks through the currently available predictive tools for regio- and site-selectivity with a particular focus on machine learning models while being organized along the individual reaction classes of organic chemistry. Respective featurization techniques and model architectures are described and compared to each other; applications of the tools to critical real-world examples are highlighted. This paper aims to serve as an overview of the field's status quo for both the intended users of the tools, that is synthetic chemists, as well as for developers to find potential new research avenues.

Enantioselective Biosynthesis of (+)- and (-)-Auranthines

In nature, organisms produce various bioactive natural products (NPs). Most NPs target naturally occurring macromolecules, such as proteins and nucleotides. Thus, NPs are produced in a stereocontrolled manner except for the cases where nonenzymatic reactions are involved in the biosynthesis. This is why stereoisomers, especially enantiomers, are rarely found among metabolites from natural sources. During the biosynthetic study of auranthine, a fungal NP containing a nitrile group, we discovered that the (-)-isomer of auranthine (1) is produced by Aspergillus lentulus strains isolated in Japan, while a previously unreported (+)-enantiomer 2 is produced by those isolated elsewhere. The biosynthetic genes for both isomers were determined by transcriptomic, gene deletion, and heterologous expression experiments, revealing that two different nonribosomal peptide synthetases (NRPSs) NitA and NitC were involved in the biosynthesis of 1 and 2, respectively. Both NitA and NitC are bimodular NRPSs, as is the case for the asperlicin-synthesizing enzyme AspA. All incorporate two molecules of anthranilic acid and one molecule of amino acid to form the peptide core. However, only NitC contains an epimerization domain, suggesting that is how the enantiomeric pair is biosynthesized by NitA and NitC. Furthermore, biosynthesis of the nitrile-bearing l-γ-cyanohomoalanine that is incorporated into 1 and 2 was found to be catalyzed by an argininosuccinate synthetase-like NitB using l-glutamine as a substrate. This study reports not only the unique mechanism of nitrile-containing amino acid biosynthesis but also the intriguing production of an enantiomeric pair of secondary metabolites by different strains of the same fungal species (250/250).

Stereoselective synthesis of a KRASG12C inhibitor with a quinoline-piperazine scaffold

We developed a novel synthetic route for the KRASG12C inhibitor, focusing on the efficient construction of its central quinoline scaffold. The method offers several advantages: eliminates the formation of regioselective by-products and avoids the use of high temperatures and nitric acid. The last step of the overall route enables gentle hydrolysis of phenyl esters with methanol and potassium carbonate, which greatly reduces the occurrence of side reactions. In addition, the stereoisomers were successfully separated by silica gel column chromatography.

An updated patent review of antitumor macrocyclic kinase inhibitors (2019 present)

INTRODUCTION

Small molecule kinase inhibitors are crucial in the treatment of tumors, and the development of novel inhibitors is a primary approach to combat the continuous emergence of drug resistance. Macrocyclization has emerged as a cutting-edge strategy to enhance the potency, selectivity, and pharmacokinetic properties of these inhibitors by altering their biological and physicochemical characteristics compared to their acyclic counterparts.

AREAS COVERED

The present article provides a comprehensive overview of the recent advancements in macrocyclic small molecule inhibitors and their inhibitory activities against various cancer cells, which have been patented since 2019.

EXPERT OPINION

To date, small-molecule kinase inhibitors have demonstrated remarkable therapeutic efficacy in clinical settings. Recent patents have primarily focused on addressing challenges associated with resistance mutations. Despite the significant success achieved in developing selective kinase agents, the identification of new targets and emergence of novel mutations necessitate the development of novel small-molecule inhibitors. Macrocyclic compounds possess distinctive conformational constraints, enhanced inhibitor potency and selectivity, as well as favorable pharmacokinetic properties, rendering them safe, efficient, selective, low-toxicity agents with unique structural characteristic.

A Novel LC-APCI-MS/MS Approach for the Trace Analysis of 3,4-Difluoronitrobenzene in Linezolid

Background/Objectives: Oxazolidinones are novel antimicrobial agents used to combat bacterial infections, particularly multidrug-resistant strains. However, the synthesis of oxazolidinone derivatives, such as linezolid, often involves the use of 3,4-difluoronitrobenzene (DFNB) as an initiator. Despite its effectiveness, residual DFNB in drug products raises significant health concerns due to its structural similarity to toxic and carcinogenic nitrobenzenes. This contamination is particularly concerning in pharmaceutical formulations, where it poses potential patient safety hazards. Therefore, strict concentration limits for this impurity are necessary. Methods: To ensure tight control of DFNB concentrations, this study established an 8.3 µg/g target limit. An advanced high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed to overcome current limitations in detecting trace DFNB. Under negative atmospheric pressure chemical ionization (APCI) conditions, DFNB exhibited characteristic ion formations, including [M]•- through electron capture and [M - F + O]- via substitution reactions. The quantitative method utilizes MS/MS ion transitions of the substitution product while optimizing chromatographic and spectrometric parameters to enhance both sensitivity and specificity. Conclusions: Validation tests confirm the efficiency, precision, and accuracy of this method, with a low limit of quantification (LOQ) of 5 ng/mL (0.83 µg/g). This technique enables accurate detection and quantification of DFNB in linezolid active pharmaceutical ingredient (API) and various formulations, providing a reliable tool for quality control. This method ensures the safe use of linezolid by effectively monitoring and minimizing the risks associated with DFNB contamination.

A fragment-based electrophile-first approach to target histidine with aryl-fluorosulfates: application to hMcl-1

Aryl-fluorosulfates are mild electrophiles that are very stable in biological media and in vivo and can efficiently react with the side chains of Lys, Tyr, or His residues, when properly juxtaposed by a high-affinity ligand. A more powerful approach to derive novel ligands would consist in starting from the covalent adduct and building the ligand off those initial interactions. While this strategy has been proven for Cys with molecular fragments containing Cys targeting electrophiles such as acrylamides, a corresponding strategy with fluorosulfates targeting His/Lys/Tyr residues has yet to be reported. We report here that a fragment library of aryl-fluorosulfates, when deployed with proper biophysical screening strategies, can identify initial covalent fragments. We report on novel strategies to enhance the success rate of such electrophile-based fragment screening for His/Lys/Tyr residues and to characterize the resulting hits. As an application we report on novel covalent fragment hits targeting hMcl-1 His 224.

Non-coding RNAs as key regulators of epithelial-mesenchymal transition in breast cancer

This study examines the critical role of non-coding RNAs (ncRNAs) in regulating epithelial-mesenchymal transition (EMT) in breast cancer, a prevalent malignancy with significant metastatic potential. EMT, wherein cancer cells acquire mesenchymal traits, is fundamental to metastasis. ncRNAs-such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs)-modulate EMT by influencing gene expression and signaling pathways, affecting cancer cell migration and invasion. This review consolidates recent findings on ncRNA-mediated EMT regulation and explores their diagnostic and therapeutic potential. Specifically, miRNAs inhibit EMT-related transcription factors, while lncRNAs and circRNAs regulate gene expression through interactions with miRNAs, impacting EMT progression. Given the influence of ncRNAs on metastasis and therapeutic resistance, advancing ncRNA-based biomarkers and treatments holds promise for improving breast cancer outcomes.

5,7-Dihydroxy-4-Methylcoumarin as a Functional Compound for Skin Pigmentation and Human Skin Safety

Background/Objectives: This study aims to investigate the effects of 5,7-dihydroxy-4-methylcoumarin (5,7D-4MC) on melanogenesis in B16F10 murine melanoma cells and to evaluate its safety as a potential ingredient for functional cosmetics and therapeutic agents targeting pigmentation-related disorders. Method: The cytotoxicity of 5,7D-4MC was assessed using an MTT assay, and melanin content and tyrosinase activity were measured at different concentrations (25, 50, 100 µM). Western blot analyses were conducted to evaluate the expression of key melanogenesis-related proteins (TYR, TRP-1, TRP-2, and MITF) and to investigate the regulation of major signaling pathways, including PKA/cAMP, GSK3β, and PI3K/AKT. Additionally, a human primary skin irritation test was performed on 32 participants to assess the dermatological safety of 5,7D-4MC. Results: 5,7D-4MC did not affect cell viability at concentrations below 100 µM and significantly promoted melanin production in a dose-dependent manner. Tyrosinase activity and the expression levels of melanogenic proteins increased significantly following 5,7D-4MC treatment. PKA and GSK3β pathways were activated, while the PI3K/AKT pathway was downregulated. The skin irritation test showed that 5,7D-4MC exhibited low irritation potential at concentrations of 50 µM and 100 µM. Conclusions: 5,7D-4MC enhances melanogenesis and demonstrates low skin irritation, making it a promising candidate for therapeutic applications in treating hypopigmentation disorders, such as vitiligo, as well as a functional cosmetic ingredient. However, further studies involving human melanocytes and clinical trials are required to validate their efficacy.

Exploring bioactive molecules released during inter- and intraspecific competition: A paradigm for novel antiparasitic drug discovery and design for human use

Many antiparasitic drugs have become obsolete and ineffective in treating parasitic diseases. This ineffectiveness arises from parasite drug resistance, high toxicity, and low drug efficacy. Thus, the discovery of novel agents is urgently needed to control parasitic diseases. Various strategies are employed in drug discovery, design, and development. This review highlights the paradigm of searching for bioactive molecules produced during inter- and intraspecific competition among organisms, particularly between microbes and parasites, as a strategy for de novo antiparasitic drug discovery. Competitive interactions occur when individuals of the same or different species coexist in overlapping niches and compete for space and resources. These interactions are well recognized. Therefore, bioactive molecules released during these interactions are promising targets for novel drug discovery. Compelling data indicate that microbes remain a potential source for the discovery of novel antiparasitic drugs because of their diversity. Many antimicrobial producers in nature have yet to be isolated and investigated. This body of evidence underscores the success of numerous therapeutic drugs, including penicillin, β-lactams, and tetracyclines, which have been successfully discovered and developed for treating infectious diseases. This review comprehensively covers these concepts, with a particular focus on inter- and intraspecific competition in the discovery of novel antiparasitic agents. This approach will pave the way for identifying alternative strategies to control and eradicate parasitic diseases that continue to threaten human health. Additionally, this review discusses current antiparasitic drugs and their mechanisms of action, limitations, and existing gaps. This discussion emphasizes the ongoing need to explore novel antiparasitic drugs.

Screening of Covalent Kinase Inhibitors Yields Hits for Cysteine Protease USP7 / HAUSP

Purpose

The ubiquitin-specific protease 7 (USP7), also known as herpes-associated ubiquitin-specific protease (HAUSP) is an interesting target due to its role in the tumor suppressor p53 pathway. In recent years targeted covalent inhibitors have gained significant importance in pharmaceutical research. Thus, we have investigated a small library of 129 ligands bearing different types of covalent reactive groups ("warheads") from various kinase drug discovery projects for their reactivity towards the catalytic cysteine of USP7, as well as their influence on its melting temperature. These compounds mainly encompassed α,β-unsaturated amides specifically acrylamides, SNAr reacting compounds, aryl fluorosulfates and sulfonyl fluorides.

Methods

We analyzed an array of 129 electrophilic compounds which had been designed as covalent kinase inhibitors in a DSF-based (differential scanning fluorimetry) screen against USP7. The hits were evaluated for their ability to cause similar thermal shifts for a CYS-deficient USP7 control mutant (USP7asoc), where only the catalytic Cys223 was retained. Additionally, covalent binding was evaluated by intact protein mass spectrometry (MS).

Results

The DSF screen revealed that, predominantly 18 of the 129 tested compounds decreased the melting temperature of USP7 and its mutant USP7asoc. For 8 of these, the hypothesized covalent binding mode was corroborated with native and mutant USP7 by intact protein MS. Nearly all identified hits have a covalent warhead that reacts via nucleophilic aromatic substitution (SNAr).

Conclusion

The screening and evaluation of the kinase library revealed several initial hits of interest. Seven SNAr warheads and one acrylamide warhead compound covalently modified the target protein (USP7) and showed clear shifts in the melting temperatures ranging from -6.0 °C to +1.7 °C.

Visible-Light Photoredox Catalytic Direct N-(Het)Arylation of Lactams

Lactam rings are essential structural motifs in organic chemistry, widely present in natural products and clinically important drugs, such as antibiotics and antiepileptics. Existing methods for synthesizing N-functionalized lactams often require harsh conditions, toxic reagents, or complex catalytic systems. Here, we report a mild and efficient photochemical approach for generating N-centered radicals, enabling straightforward N-heteroarylation of lactams. This versatile method enables the synthesis of a range of N-(het)arylated lactams and is effective even in aqueous media, facilitating the functionalization of biomolecules. Furthermore, the photochemical reaction is easily scalable under continuous flow conditions, making it highly suitable for large-scale applications.

A Mechanochromic Rotaxane that Releases Azetidine-Trityl-Maleimide, a Versatile Fluorescent Probe

Force sensing at the molecular level has enabled the study of materials failure and it offers great promises for the investigation of mechanobiological processes. Traditional force probes rely on the reversible or irreversible activation of mechanochromic precursors to assess transient or permanent changes in polymer networks. A promising approach involves force-controlled release of sensing molecules, as the accumulation of chromic molecules at specific sites would enable the recording of deformation histories. However, many fluorescent probes are limited by environmental sensitivity, specific release conditions, or low release efficiency. Maleimide-based dyes, especially amino maleimides, offer a robust alternative due to their small size, structural versatility, and tuneable fluorescence properties. Here, we present a mechanochromic rotaxane device that releases an azetidine-trityl-maleimide (ATM) fluorescent probe via a retro-[4+2] cycloaddition reaction. ATM is a rigidochromic, chemically stable, and environmentally insensitive probe, generated exclusively through rotaxane actuation, underscoring the unique mechanochemical properties of rotaxanes. This device holds potential for applications in material science and biology, such as the investigation of polymer networks and active tissues.

Determining the Multivalent Effects of d-Peptide-Based Radiotracers

Dextrorotary (d) peptides, composed of d-amino acids, are hyper-resistant to proteolytic hydrolysis, making them valuable ligands with excellent in vivo stability for radiopharmaceutical development. Multimerization is a well-established strategy for enhancing the in vivo performance of l-peptide-based radiopharmaceuticals. However, the effect of multimerization on the in vivo fate of d-peptide-based radiopharmaceuticals remains largely unexplored. Here, we synthesized the d-peptide DPA, which targets PD-L1, along with its dimer (DP2) and trimer (DP3). PET/CT imaging and ex vivo biodistribution studies were performed to delineate the pharmacokinetics and target interactions of [68Ga]DPA, [68Ga]DP2, and [68Ga]DP3 in both normal and tumor-bearing mice. Our results revealed that tumor uptake and kidney retention increased with higher valency ([68Ga]DP3 > [68Ga]DP2 > [68Ga]DPA). No significant differences were observed in the liver, heart, lung, spleen, intestine, or bone among the three radiotracers. Interestingly, a significant reduction of radioactivity in the bloodstream was detected for the [68Ga]DP3-treated group compared to the other two groups. Data analysis revealed that chiral configuration of amino acids and the linking chemistry used in multimerization are the two dominant factors in the in vivo fate of d-peptide multimers. These findings indicate that d-peptide multimerization exerts a distinct influence on in vivo profiles compared to l-peptide multimerization. This study deepens our understanding of how mirror-imaged peptides/proteins interact with the living systems, paving the way for the development of radiopharmaceuticals that harness d-peptides as targeting moieties.

Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening

Structured RNAs play a crucial role in regulating gene expression, which includes both protein synthesis and RNA processing. Dysregulation of these processes is associated with various conditions, including viral and bacterial infections, as well as cancer. The unique tertiary structures of structured RNAs provide an opportunity for small molecules to directly modulate such processes, making them promising targets for drug discovery. Although small-molecule inhibitors targeting RNA have shown early success, in silico strategies like structure-based virtual screening remain underutilized for RNA-targeted drug discovery. In this study, we developed a virtual screening scheme targeting the structural ensemble of EV-A71 IRES SL II, a noncoding viral RNA element essential for viral replication. We subsequently optimized the experimentally validated hit compound IRE-03 from virtual screening through an "analog-by-catalog" search. This led to the identification of a more potent IRES inhibitor, IRE-03-3, validated through biochemical and functional assays with an EC50 value of 11.96 μM against viral proliferation. Our findings demonstrate that structure-based virtual screening can be effectively applied to RNA targets, providing exciting new opportunities for future antiviral drug discovery.

A biorthogonal chemistry approach for high-contrast antibody imaging of lymphoma at early time points

BACKGROUND

Monoclonal antibodies are highly specific for their targets making them effective for cancer therapy. However, their large molecular weight causes slow blood clearance, often requiring weeks to be removed from circulation. This limitation affects companion nuclear imaging and antibody-based diagnostics, necessitating delayed imaging. We report the expansion of a methodology improving positron emission tomography (PET) contrast of the lymphoma biomarker CD20 at early time points after radiolabeled antibody administration. Intact radioimmunoconjugates are allowed to stay in circulation long enough to accumulate in tumors, and then, using a chemical trigger, we induced rapid clearance of the radioactivity from non-target tissues by cleaving the linker between the antibody and the radioactivity. For brevity, we refer to the this as the Tetrazine KnockOut (TKO) method which uses the transcyclooctene-tetrazine (TCO-Tz) reaction, wherein an antibody is conjugated with linker containing TCO and a radioisotope.

RESULTS

We optimized the TCO linker with several different radioisotopes and evaluated the ability of tetrazines to knockout radioactivity from circulating antibodies. We explored several cell types and antibodies with varying internalization rates, to characterize the parameters of TKO and tested [89Zr]Zr-DFO-TCO-rituximab in a lymphoma model with PET imaging after Tz or vehicle administration. Treatment with Tz induced > 70% cleavage of the TCO linker in vitro within 30 min. Internalizing radioimmunoconjugates exhibited similar cellular uptake with Tz compared to vehicle, whereas decreased uptake was seen with slowly internalizing antibodies. In rodents, Tz rapidly liberated the radioactivity from the antibody, cleared from the blood, and accumulated in the bladder. TKO resulted in > 50% decreased radioactivity in non-target organs following Tz injection. No decrease in tumor uptake was observed when rate of antibody internalization is higher in a lymphoma model, and the target-to-background ratio increased by > twofold in comparison with Tz nontreated groups at 24 h.

CONCLUSION

The TKO approach potentiates early imaging of rituximab radioimmunoconjugates and has translational potential for lymphoma imaging.

Effect of selective COX-2 inhibitors and non-selective non-steroidal anti-inflammatory drugs on severity of acute pancreatitis: A systematic review and meta-analysis

BACKGROUND

It's been suggested that non-steroidal anti-inflammatory drugs (NSAIDs) may reduce the inflammatory response and severity of acute pancreatitis (AP). In this systematic review and meta-analysis, we aimed to explore the impact of selective COX-2 and non-selective NSAIDs compared to non-NSAID options on the severity of AP.

METHODS

We searched MEDLINE, EMBASE, and Cochrane Central, from database inception through September 2023. We included RCTs and observational studies comparing NSAIDs with non-NSAID controls. The primary outcome was the development of severe acute pancreatitis (SAP) characterized by persistent organ failure lasting >48 h. Secondary outcomes included mortality, pancreatic necrosis, length of stay (LOS), pain relief, and requirement for rescue analgesia. Meta-analysis was conducted separately for selective COX-2 inhibitors and non-selective NSAIDs.

RESULTS

Eleven studies met eligibility criteria including 1830 patients with AP. Of 3 studies that used selective NSAIDs (1 RCT and 2 observational), COX-2 inhibitors significantly reduced SAP (OR = 0.38; 95 %CI 0.27-0.52; p < 0.001; I2 = 0 %), pancreatic necrosis (OR = 0.48; 95 %CI 0.29-0.78; p = 0.003; I2 = 0 %), LOS by 5.51 days (95 %CI -10.80 to -0.22; p = 0.04; I2 = 97 %), and rescue opioids (OR = 0.32; 95 %CI 0.24-0.45; p < 0.001; I2 = 0 %). However, the certainty of the evidence was graded as low to very low using GRADE methodology. There was no significant effect of COX-2 inhibitors on mortality. Of 8 studies (all RCTs) that compared non-selective NSAIDs and non-NSAIDs, there was no difference in clinical outcomes, pain relief, and need for rescue analgesia.

CONCLUSIONS

Selective COX-2 inhibitors potentially mitigate disease severity and shorten hospitalization in patients with AP, while non-selective NSAIDs lack this benefit. Confirmatory large-scale RCTs are warranted to validate these findings.

Positive Charge in an Antimalarial Compound Unlocks Broad-Spectrum Antibacterial Activity

In this study, we synthesized a library of eNTRy-rule-compliant compounds by introducing ionizable nitrogen atoms to an antimalarial compound. These positively charged derivatives gained activity against both Gram-negative and -positive bacteria, Mycobacterium tuberculosis, and boosted Plasmodium falciparum inhibition to the double-digit nanomolar range. Overcoming and remaining inside the cell envelope of Gram-negative bacteria (GNB) is one of the major difficulties in antibacterial drug discovery and development. The eNTRy rules (N = ionizable nitrogen, T = low three-dimensionality, R = rigidity) can be a useful structural guideline to improve accumulation of small molecules in GNB. With the aim of unlocking Gram-negative activity, we added amines and (cyclic) N-alkyl guanidines to an already flat and rigid pyrazole-amide class as a representative example for our investigation. To test their performance, we compared these eNTRy-rule-compliant compounds to closely related noncompliant ones through phenotypic screening of various pathogens (P. falciparum, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, and M. tuberculosis), obtaining a handful of broad-spectrum hits. The results support the working hypothesis and even extend its applicability. The studied pyrazole-amide class adheres to the eNTRy rules; noncompliant compounds do not kill any of the bacteria tested, while compliant compounds largely showed growth inhibition of Gram-negative, -positive, and M. tuberculosis bacteria in the single-digit micromolar range.