Structure-activity Relationship Research Articles

A comprehensive review of distribution, traditional use, phytochemistry and anticancer of the genus Goniothalamus.

Natural products (NPs) play a crucial role in drug discovery, with over 30% of recent FDA-approved drugs derived from them. Plants from the genus Goniothalamus, belonging to the Annonaceae family, have garnered significant interest as potential sources of active lead compounds. Over the past five decades, researchers have isolated 357 compounds from Goniothalamus species (GCs), which exhibit a wide range of pharmacological properties, including cytotoxicity, antibacterial, antifungal, antiplasmodial, antioxidant, and other activities. Notably, cytotoxicity stands out as the most prominent characteristic of GCs. This review also summarizes the structure-activity relationship (SAR) studies related to the cytotoxicity of GCs and their underlying mechanisms. In summary, our objective is to provide an overview of the research progress concerning the Goniothalamus genus, aiming to foster further development and utilization of these plants.

Resorcinol-based Bolaamphiphilic Quaternary Ammonium Compounds.

Quaternary ammonium compounds (QACs) play crucial disinfectant roles in healthcare, industry, and domestic settings. Most commercially utilized QACs like benzalkonium chloride have a common architectural theme, leading to a rise in bacterial resistance and urgent need for novel structural classes. Some potent QACs such as chlorhexidine (CHX) and octenidine (OCT) feature a bolaamphiphilic architecture, comprised of two cationic centers at the molecular periphery and a non-polar region connecting them; these compounds show promise to elude bacterial resistance mechanisms. Inspired by such structures, we synthesized a series of 43 biscationic amphiphilic compounds focused on a resorcinol core, featuring flexibility of linker lengths, alkyl tails, and relative substituent positioning, to study their structure activity relationships (SARs). Antibacterial activity evaluation against a panel of gram-positive and gram-negative strains, including ESKAPE pathogens (A. baumannii,P. aeruginosa), were encouraging, with minimum inhibitory concentrations (MICs) of 0.5-4 μM against all tested strains for select compounds. Ten prepared compounds bearing either 17 or 18 total side chain carbons demonstrated uniformly strong antibacterial activity againstP. aeruginosa(MIC 4-16 μM) and 6 other strains (MIC ≤4 μM), irrespective of cationic spacing.These findings promise to further extend the application of bolaamphiphilic QACs as a novel class of disinfectants.

Design and development of pyrazol-5-ylbenzamide derivatives containing chiral oxazoline moiety as fungicides based on molecular docking.

Development of novel chiral antifungal agents for effective control of plant pathogens is urgently needed. In this study, a series of pyrazol-5-yl-benzamide derivatives containing chiral oxazoline moiety were rationally designed and developed based on molecular docking. The in vitro antifungal assay results indicated that compounds (rac)-4h (R1 = Et), (S)-4 h (R1 = S-Et) and (R)-4 h (R1 = R-Et) exhibited remarkable antifungal activities against Valsa mali with median effective concentration (EC50) values of 0.24, 0.06 and 1.08 mg/L, respectively. Preliminary structure-activity relationships (SARs) revealed that the modification of the chiral substituent group at the oxazoline moiety significantly affected the antifungal activities of the target compounds. Furthermore, compounds (S)-4h (87.5%) and (R)-4h (84.3%) exhibited in vivo protective activities comparable to tebuconazole (87.5%) against V. mali. Subsequent molecular docking analysis, succinate dehydrogenase (SDH) enzyme inhibition assays and molecular dynamic (MD) simulations verified that the potential target enzyme of this class of derivatives could be SDH and helped to explain the large difference in antifungal activities of compounds (S)-4h and (R)-4h. Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) observations confirmed that these two compounds severely disrupted the mycelial morphology of V. mali. Theoretical calculation studies provided some insight into the subsequent modification of such pyrazol-5-yl-benzamide derivatives. Resistance frequency studies showed that (S)-4h and (R)-4h treatments were less likely to produce resistant fungal strains than tebuconazole. Meanwhile, compounds (S)-4h and (R)-4h exhibited no apparent toxicity to the Apis mellifera L. Therefore, these derivatives are potential candidates for the development of novel chiral fungicides for crop protection. © 2025 Society of Chemical Industry.

Ionic Liquid Catalysts for Poly(ethylene terephthalate) Glycolysis: Use of Structure Activity Relationships to Combine Activity with Biodegradability

Ionic Liquid Catalysts for Poly(ethylene terephthalate) Glycolysis: Use of Structure Activity Relationships to Combine Activity with Biodegradability

Structure Characterization and Antioxidant Activity of a Novel Polysaccharide from Bacillus natto Fermented Millet Bran

To improve the high-value application of millet bran, a water-soluble polysaccharide was extracted from fermented millet bran (FMBP) by using Bacillus natto fermentation. A neutral polysaccharide, FMBP-1, was separated and purified from FMBP using an anion exchange column. Its structure and antioxidant activity in vitro were characterized and determined. The molecular weight of FMBP-1 was 1.154 × 104 Da, and its molecular weight distribution was relatively uniform. The monosaccharide composition, FT-IR, methylation, and NMR results indicated that FMBP-1 was only composed of glucose and was an α-(1→4)-D-glucan that branched at O-6 with a terminal 1-linked α-D-Glcp as a side chain. In addition, the antioxidant assays indicated that FMBP-1 possessed certain capacities for scavenging free radicals and reducing power, and this was in a concentration-dependent manner. This research will provide fundamental data regarding the structure–activity relationship of millet bran polysaccharides and provide a theoretical foundation for the high-value utilization of millet bran within the food and pharmaceutical industries.

Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors.

The global impact of SARS-CoV-2 highlights the need for treatments beyond vaccination, given the limited availability of effective medications. While Pfizer introduced Paxlovid, an FDA-approved antiviral targeting the SARS-CoV-2 main protease (Mpro), this study focuses on designing new antivirals against another protease, papain-like protease (PLpro), which is crucial for viral replication and immune suppression. NCATS/NIH performed a high-throughput screen of ∼15,000 molecules from an internal molecular library, identifying initial hits with a 0.5% success rate. To improve the hit rate and identify potent inhibitors, machine learning-based virtual screens were applied to ∼150,000 compounds, yielding 125 top predicted hits. Biochemical evaluation revealed 25 promising compounds, with a 20% hit-rate and IC50 values from 1.75 μM to <36 μM across 13 chemotypes. Further analog screening of those chemotypes, as part of the structure-activity relationships, led to 20 additional hits. Additionally, the hit-to-lead optimization of chemotype 7 produced 10 more analogs. These PLpro inhibitors provide promising templates for antiviral development against COVID-19.

Small Molecular Oligopeptides Adorned with Tryptophan Residues as Potent Antitumor Agents: Design, Synthesis, Bioactivity Assay, Computational Prediction, and Experimental Validation.

Tryptophan participates in important life activities and is involved in various metabolic processes. The indole and aromatic binuclear ring structure in tryptophan can engage in diverse interactions, including π-π, π-alkyl, hydrogen bonding, cation-π, and CH-π interactions with other side chains and protein targets. These interactions offer extensive opportunities for drug development. In this letter, we have designed and synthesized a series of linear oligopeptides adorned with tryptophan residues and identified their potential targets through artificial intelligence-assisted technology and experimental verification. In vitro bioactivity assays revealed that the oligopeptides containing Gly-Pro-Trp residues exhibited promising antitumor activity by inducing autophagy and apoptosis. The PharmMapper pharmacophore mapping approach, molecular docking, and molecular dynamics simulations together identified poly(ADP-ribose) polymerase 1 (PARP1), an enzyme associated with chromatin regulation, as the potential target for the designed compounds. Experimental biolayer interferometry (BLI) and enzyme-linked immunosorbent assay (ELISA) have verified that the oligopeptides could bind with PARP1 and influence PARP1 expression levels. A quantitative structure-activity relationship has been established between the chemical structures of the prepared compounds and their IC50 values. In summary, the research presents a feasible approach for exploring oligopeptide-based antitumor agents.

Structure-Based Optimization of Pyridone α-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.

The main protease Mpro is a clinically validated target to treat infections by the coronavirus SARS-CoV-2. Among the first reported Mpro inhibitors was the peptidomimetic α-ketoamide 13b, whose cocrystal structure with Mpro paved the way for multiple lead-finding studies. We established structure-activity relationships for the 13b series by modifying residues at the P1', P3, and P4 sites. Guided by cocrystal structures, we reduced the P1' substituent size to better fill the pocket and added a fluorine substituent to the pyridone ring, enabling a new hydrogen bond with Gln189 in P3. Among 22 novel analogues, 6d and 12d inhibited Mpro with IC50s of 110 nM and 40 nM, improving the potency of 13b by up to 9.5-fold. Compound 6d had pronounced antiviral activity with an EC50 of 1.6 μM and was stable in plasma and microsomes. The study illustrates the potential of structure-based design to systematically improve peptidomimetic α-ketoamides.

Chemical O‐ADP‐Ribosylations: Synthesis and Bioconjugation of ADPr‐Peptides/Proteins from NAD+

AbstractADP‐ribosylation is a complex post‐translational modification involved in key physiological processes and associated with various health and disease states. The growing interest in ADP‐ribosylation necessitates straightforward and efficient synthetic methods for the preparation of ADP‐ribosylated peptides/proteins. In this study, we report a facile reaction between nicotinamide adenine dinucleotide (NAD+) and alcohols promoted by a combination of ionic liquids, yielding up to 94 % with α : β ratios ranging from 88 : 12 to 99 : 1 and a switchable configuration selectivity. This method significantly simplifies the production of ADP‐ribosylated peptides and proteins, enabling diverse applications. It allows detailed investigation of side‐chain structure–activity relationships, facilitates two‐step clickable conjugation of ADP‐ribosyl groups to proteins, and, for the first time, enables non‐enzymatic synthesis of well‐defined ADP‐ribosylated peptides/proteins from natural counterparts and NAD+.

Context-dependent similarity analysis of analogue series for structure-activity relationship transfer based on a concept from natural language processing.

Analogue series (AS) are generated during compound optimization in medicinal chemistry and are the major source of structure-activity relationship (SAR) information. Pairs of active AS consisting of compounds with corresponding substituents and comparable potency progression represent SAR transfer events for the same target or across different targets. We report a new computational approach to systematically search for SAR transfer series that combines an AS alignment algorithm with context-depending similarity assessment based on vector embeddings adapted from natural language processing. The methodology comprehensively accounts for substituent similarity, identifies non-classical bioisosteres, captures substituent-property relationships, and generates accurate AS alignments. Context-dependent similarity assessment is conceptually novel in computational medicinal chemistry and should also be of interest for other applications.Scientific contributionA method is reported to systematically search for and align analogue series with SAR transfer potential. Central to the approach is the assessment of context-dependent similarity for substituents, a new concept in cheminformatics, which is based upon vector embeddings and word pair relationships adapted from natural language processing.

Novel tetracycline hybrids: synthesis, characterization, docking studies and in-vitro evaluation of antibacterial activity

BackgroundThe biggest menace in the world today is the infection caused by pathogenic bacteria in humans, where majority of the available antibiotics fail to provide therapeutic results due to resistance. The discovery of new molecules is the need of the hour and several research groups worldwide are contributing to fight this scare. This work highlights our efforts towards discovering novel tetracycline hybrids that could serve as potent agents against several pathogenic bacterial strains causing infections. In total, ten compounds were synthesized which were chemically conjugates of Minocycline, an age-old tetracycline, and naturally occurring aldehydes and ketones available from the plant sources. Structural characterization of these compounds was done using Mass and 1HNMR. Molecular docking was carried out in order to predict the binding affinity of these compounds to various bacterial enzymes and known protein targets and to establish the structure–activity relationships. Molecular dynamic simulation studies and in silico pharmacokinetic and toxicity prediction studies were done to determine in silico pharmacokinetics and toxicity of compounds. In-vitro antibacterial activities were done using standard protocols against gram positive bacteria like Enterococcus faecalis, Staphylococcus aureus and gram-negative bacteria like Klebsiella pneumoniae, Pseudomonas aeruginosa and Escherichia coli.ResultsPromising results were obtained viz. compound 1,2 and 10 were found to be more potent against Staphylococcus aureus, compound 1 against Enterococcus faecalis, compound 2 and 3 against Escherichia coli, compound 7 and 8 against Pseudomonas aeruginosa and compound 7 against Klebsiella pneumoniae when compared with minocycline as standard compound.ConclusionAll the synthesized compounds were screened for their anti-bacterial activity against gram positive and gram negative microorganisms. Amongst the ten synthesized minocycline hybrids, four minocycline hybrids exhibited potent antibacterial activity as compared to minocycline. These hybrids can serve as a promising lead compound for antibiotic drug discovery.

Synergistic Enhancing of Biological Activity and Natural Light Self-Degradation of Organic-Inorganic Hybrid Nano-organometallic Pesticide-Fused Phenylpyrazole Amine Derivatives with Hollow Box TiO2 by One-pot Microwave Synthesis.

Nano-TiO2 as an antimicrobial inorganic material, can stimulate cells to produce reactive oxygen species and exhibit effective biochemical properties; however, phenylpyrazole derivatives, as organic pesticides, are widely used in agriculture and food. To find novel pesticides with environmental friendliness, combined with three-dimensional quantitative structure-activity relationship (3D-QSAR) prediction analysis, three types of alkaloidal phenylpyrazole amine derivatives (PA) were synthesized by a one-pot microwave method. Based on the dye sensitization strategy, four nano-organometallic pesticides (PT) were prepared by organic-inorganic hybridization. PA and PT showed 2.5 and 5.2 times higher insecticidal activity against P. xylostella than fipronil, and PT had 3.9 times greater antibacterial activity against A. tumefaciens. The synergistic effect realizes the balance of amphiphilicity, enhances the biological activity of PT, improves the phloem fluidity, and promotes the absorption and transportation of substances. In addition, this synergistic effect reduces the band gap width, improves the light absorption capacity, induces cells to produce active reactive oxygen species and free radicals (ROS: ·O2-, ·OH), and destroys the cytomembrane so that PT can better enter the cell, resulting in cell death. PT has excellent natural light self-degradation performance and converts to the phenylpyrazole parent moiety, which enhances biological activity and greatly reduces the environmental residues, implying that nano-organometallic pesticide (PT) provides a new idea for its natural degradation and fluorescence detection of pesticide residues.

Synergistic design and synthesis of O, N Co-doped hierarchical porous carbon for enhanced supercapacitor performance

Carbon-based supercapacitors have emerged as promising energy storage components for renewable energy applications due to the unique combination of various physicochemical characteristics in porous carbon materials (PCMs) that can improve specific capacitance (SC) properties. It is essential to develop a methodical approach that exploits the synergy of these effects in PCMs to achieve superior capacitance performance. In this study, machine learning (ML) provided a clear direction for experiments in the screening of key physicochemical features; SHapley Additive exPlanations analysis on ML indicated that specific surface area and specific doping species had a significant synergistic impact on SC enhancement. Utilizing these insights, an O, N co-doped hierarchical porous carbon (ONPC-900) was synthesized using a synergistic pyrolysis strategy through K2CO3-assisted in-situ thermal exfoliation and nanopore generation. This method leverages the role of carbon nitride (graphite-phase carbon nitride) as an in-situ layer-stacked template and the oxygen (O)-rich properties of the pre-treated lignite, enabling controlled synthesis of graphene-like folded and amorphous hybrid structures engineered for the efficient N and O doping sites and high specific surface area, resulting in an electrode material with enhanced structural adaptability, rapid charge transfer, and diffusion mass transfer capacity. Density functional theory (DFT) calculations further confirmed that pyrrole nitrogen (N-5), carboxyl (-COOH) active sites, and the defect structure formed by pores synergically enhanced the adsorption of electrolyte ions (K+) and electron transfer, improving the SC performance. The optimized ONPC-900 electrode exhibited impressive SC properties of 440 F g-1 (0.5 A g-1), outperforming most coal-based PCMs. This study provides a methodology for designing and synthesizing high SC electrode materials by optimizing the key characteristic parameters of synergism from complex structure-activity relationships through the combination of ML screening, experimental synthesis, and density functional theory validation.

A Simple Machine Learning-Based Quantitative Structure–Activity Relationship Model for Predicting pIC50 Inhibition Values of FLT3 Tyrosine Kinase

Background/Objectives: Acute myeloid leukemia (AML) presents significant therapeutic challenges, particularly in cases driven by mutations in the FLT3 tyrosine kinase. This study aimed to develop a robust and user-friendly machine learning-based quantitative structure–activity relationship (QSAR) model to predict the inhibitory potency (pIC50 values) of FLT3 inhibitors, addressing the limitations of previous models in dataset size, diversity, and predictive accuracy. Methods: Using a dataset which was 14 times larger than those employed in prior studies (1350 compounds with 1269 molecular descriptors), we trained a random forest regressor, chosen due to its superior predictive performance and resistance to overfitting. Rigorous internal validation via leave-one-out and 10-fold cross-validation yielded Q2 values of 0.926 and 0.922, respectively, while external validation on 270 independent compounds resulted in an R2 value of 0.941 with a standard deviation of 0.237. Results: Key molecular descriptors influencing the inhibitor potency were identified, thereby improving the interpretability of structural requirements. Additionally, a user-friendly computational tool was developed to enable rapid prediction of pIC50 values and facilitate ligand-based virtual screening, leading to the identification of promising FLT3 inhibitors. Conclusions: These results represent a significant advancement in the field of FLT3 inhibitor discovery, offering a reliable, practical, and efficient approach for early-stage drug development, potentially accelerating the creation of targeted therapies for AML.

Quantitative Structure–Activity Relationship (QSAR) Modeling of Chiral CCR2 Antagonists with a Multidimensional Space of Novel Chirality Descriptors

The development of chirality descriptors for quantitative chirality structure–activity relationship (QCSAR) modeling has always attracted attention, owing to the importance of chiral molecules in pharmaceutical, agriculture, food, and fragrance industries, and environmental toxicology. The utility of a multidimensional space of novel relative chirality indices (RCIs) in the QCSAR modeling of twenty CCR2 antagonists is reported upon in this paper. The numerical characterization of chirality by the RCI approach gives a large pool of chirality descriptors with different degrees of mutual correlation (the correlation coefficient among the computed descriptors varied from 0.02 to 0.99). In the present study, the final data set contains 198 chirality descriptors for each of the twenty CCR2 antagonist molecules, providing a multidimensional space for modeling. The data reduction using principal component analysis resulted in the extraction of eight principal components (PCs). The linear regression using the principal component scores (PCSs) resulted in a three-predictor prediction model with good statistics: R2 = 0.823; Adj R2 = 0.790. The regression models were rebuilt using the chirality descriptors (RCIs) that are most correlated with each of the scores (PCSs) of the three principal components. The R2 value for the regression models with three RCIs as the predictors is 0.742 and the five-fold cross validation, Rcv2, is 0.839. The new chirality descriptors, namely, the RCIs calculated using a different weighting scheme, provide a multidimensional space of chirality descriptors for a set of chiral molecules, and such a multidimensional chirality space is a powerful tool to build quantitative chiral structure–activity relationship (QCSAR) models.

Computer-guided identification of novel inhibitors of apoptosis-signaling kinase 1 from Spondia mombim bioactive compounds against colorectal cancer

BackgroundApoptosis-signaling kinase 1 is a MAPKKK (mitogen-activated protein kinase) overexpressed in various types of human cancer including colorectal cancer. It mediates inflammation and apoptosis and promotes cell proliferation through the transcription of cyclin D1. 5-Fluorouracil remains one of the primary recommended drugs to manage colorectal cancer. However, this drug often causes various adverse effects, notably diarrhea, vomiting, nausea, and leukopenia. Therefore, a novel treatment is required to eradicate these problems. The clinical implication of apoptosis-signaling kinase 1 in the pathogenicity of colorectal cancer makes it an important drug target in the treatment of colorectal cancer. The use of natural compounds in human cancer treatment continues to gain significant attention in the scientific community due to their therapeutic efficacy.MethodIn this study, computational models such as flexible docking, induced fit docking, and binding free energy calculation were employed to identify small molecule inhibitors from known bioactive compounds of Spondias mombin in reference to 5-fluorouracil (Colorectal cancer standard drug) targeting apoptosis-signaling kinase 1.ResultsMolecular docking studies identified 10 promising candidates which include uvaretin, rutin, isoquercitrin, ellagic acid, quercetin, linalool, acetyl eugenol, tangeretin (-)-catechin, and d-sorbitol based on their favorable binding affinity, with uvaretin having the best score (− 11.328 kcal/mol). The results were further validated with more dependable analysis such as induced fit docking and binding free energy calculation. These compounds showed modest indices for ADMET parameters. Molecular dynamic simulation validated ellagic acid and (-)-catechin with greater binding stability as leading compounds.ConclusionThese compounds showed improved flexible docking results and formed considerable stable interaction with the protein than 5-fluorouracil. They are non-carcinogenic. The oral bioavailability and toxicities of these compounds are promising as compounds obeyed the Lipinski rule of five. The constructed quantitative structure–activity relationship model with a trustworthy R2 coefficient value supports the inhibition prowess of these compounds. The findings from this research confer that these compounds could be considered potent apoptosis-signaling kinase 1 inhibitors, and these could be confirmed experimentally as lead compounds of apoptosis-signaling kinase 1 inhibitors in colorectal cancer.

Structure–Antioxidant Activity Relationship of Polysaccharides Isolated by Microwave/Ultrasonic-Assisted Extraction from Pleurotus ferulae

To investigate the structure–antioxidant activity relationship, Pleurotus ferulae polysaccharides were extracted using ultrasonic (U-PFPS) and microwave/ultrasonic-assisted methods (MU-PFPS). Compared to U-PFPS with a molecular weight of 1.566 × 103 kDa, MU-PFPS exhibited a lower molecular weight of 89.26 kDa. In addition, unlike U-PFPS, which is primarily composed of glucose (Glu:Man:Gal = 91.1:3.5:5.4), MU-PFPS has a more balanced composition of Glu:Man:Gal in the ratio of 39.4:27.8:32.8 and contains more branched chains. Furthermore, antioxidant analysis revealed that high concentration (at concentrations above 600 μg/mL) MU-PFPS demonstrated stronger protective effects against oxidative damage in RAW264.7 cells than U-PFPS did. Collectively, these data suggest that lower molecular weight and higher branching degree of polysaccharides at appropriate concentrations may correlate with enhanced antioxidant enzyme activities. Our work provides a method for isolating polysaccharides with higher antioxidant activity and offers insights into the structure–activity relationship of polysaccharides, laying the foundation for future applications in polysaccharide modification and structural characterization.

Single-atom catalysts for (photo)electrocatalytic biomass valorization to high-value-added chemicals

As a crucial renewable energy resource, biomass can be converted into high-value-added chemicals via unique catalytic routes, which facilitate the reduction of excessive dependency on fossil resources. However, the complex functional groups inherent in biomass and biomass-derived compounds enable considerable difficulties for their selective functionalization. The precise cleavage of special chemical bonds in biomass highly depended on the structure design of catalysts. Single-atom catalysts (SACs) have garnered significant attention in biomass valorization through the electrocatalytic and photoelectrocatalytic processes due to their maximal atom utilization efficiency, unique electronic structure, and tunable coordination environments. The present review outlines the latest research progress in this emerging field, focusing on the (photo)electrocatalytic application of SACs in biomass valorization, including cellulose-derived and hemicellulose-derived compounds and lignin. We also emphasize the innovative design and precise modulation of atomically dispersed metal active sites at the atomic level. Through state-of-the-art catalytic systems, we elaborately discuss the structure-activity relationship and elucidate the mechanisms of the (photo)electrocatalytic processes over SACs. Finally, we provide the prospects of SACs in (photo)electrocatalytic biomass valorization.

Substituted piperazine conjugated to quinoline-thiosemicarbazide as potent α-glucosidase inhibitors to target hyperglycemia

Diabetes mellitus, particularly type 2 diabetes, is a growing global health challenge characterized by chronic hyperglycemia due to insulin resistance. One therapeutic approach to managing this condition is the inhibition of α-glucosidase, an enzyme involved in carbohydrate digestion, to reduce postprandial blood glucose levels. In this study, a series of thiosemicarbazide-linked quinoline-piperazine derivatives were synthesized and evaluated for their α-glucosidase inhibitory activity, to identify new agents for type 2 diabetes management. Structure-activity relationship (SAR) analysis revealed that the nature and position of substituents on the aryl ring significantly impacted the inhibitory potency. Among the synthesized derivatives, the 2,5-dimethoxy phenyl substitution (7j) exhibited the most potent activity with an IC50 value of 50.0 µM, demonstrating a 15-fold improvement compared to the standard drug acarbose. Kinetic studies identified compound 7j as a competitive inhibitor, with a Ki value of 32 µM. Molecular docking simulations demonstrated key interactions between compound 7j and the active site of α-glucosidase, while molecular dynamics simulations confirmed the stability of the enzyme-ligand complex, reflected in low RMSD and RMSF values.

APH Inhibitors that Reverse Aminoglycoside Resistance in Enterococcus casseliflavus.

Aminoglycoside-phosphotransferases (APHs) are a class of bacterial enzymes that mediate acquired resistance to aminoglycoside antibiotics. Here we report the identification of small molecules counteracting aminoglycoside resistance in Enterococcus casseliflavus. Molecular dynamics simulations were performed to identify an allosteric pocket in three APH enzymes belonging to 3' and 2'' subfamilies in which we then screened, in silico, 12,000 small molecules. From a subset of only 14 high-scored molecules tested in vitro, we identified a compound, named here EK3, able to non-competitively inhibit APH(2'')-IVa, an enzyme mediating clinical gentamicin resistance. Structure-activity relationship (SAR) exploration of this hit compound allowed us to identify a molecule with improved enzymatic inhibition. By measuring bacterial sensitivity, we found that the three best compounds in this series restored bactericidal activity of various aminoglycosides, including gentamicin, without exhibiting toxicity to HeLa cells. This work not only provides a basis to fight aminoglycoside resistance but also highlights a proof-of-concept for the search of allosteric modulators by using in silico methods.