Dual Binding Site Research Articles

Novel dopamine-derived carbon modified fe-based metal–organic framework enhanced aptasensor rendering ultrasensitive electrochemical detection of oxytetracycline

In the present work, an aptasensor with dual binding sites based on Au NPs modified with self-polymerized polydopamine (PDA) and Fe-MOF is successfully constructed. In terms of standard electron transfer, the cyclic voltammetry (CV) analysis showcases a rate constant (ks) of 96.0 s−1, signifying an exceptional electron transfer rate of oxytetracycline at the sensor interface of Apt/Au@PDA@NH2-MIL-101(Fe)/GCE. Further deepening the investigation into electrochemical kinetics using chronoamperometry (CA), we investigated the electrocatalytic parameters (Kcat) of Au@PDA@NH2-MIL-101(Fe) in relation to oxytetracycline. The results divulged an impressive average Kcat value of 3.06 × 105 M−1 S-1. This evidence robustly suggests the superior electrocatalytic activity of Au@PDA@NH2-MIL-101(Fe) when it comes to oxytetracycline oxidation. A custom-designed portable rapid detection platform was developed, achieving detection limits of 6.88 nM under static water flow conditions and 5.56 nM under dynamic conditions. Remarkably, the self-polymerization of PDA on Au NPs not only refines their size but also boosts their interaction with biomolecules, thereby promising excellent biocompatibility. Moreover, the abundance of –COOH groups and unsaturated Fe3+ sites on the NH2-MIL-101(Fe) surface furnishes a considerable number of grafting sites for the aptamer. More importantly, the redox interplay between Au@PDA and NH2-MIL-101(Fe) accelerates electron movement, thus amplifying the electrochemical signal and the detection sensitivity for oxytetracycline.

Mechanism of Dual-Site Recognition in a Classic DNA Aptamer.

Nucleic acid aptamers possess unique advantages in specific recognition. However, the lack of in-depth investigation into their dynamic recognition mechanisms has restricted their rational design and potential applications in fields such as biosensing and targeted therapy. We herein utilized enhanced sampling molecular dynamics to address affinities of adenosine monophosphate (AMP) to the dual binding sites in the DNA aptamer, focusing on the dynamic recognition mechanism and pathways. The present results indicate that in addition to the widely known intermolecular interactions, inequivalence of chemical environments of the two binding sites leads to slightly higher stability of AMP binding to the site proximal to the aptamer terminus. In the presence of two AMPs captured by the two sites, each binding free energy is enhanced. In particular, an additional hydrogen bond of AMP to A10 is introduced in the dual-site binding complex, which increases the binding energy from -4.25 ± 0.47 to -9.48 ± 0.33 kcal mol-1 in the site close to the loop. For the dual-site recognition process, the free energy landscape and minimum free energy pathway calculations elucidate the crucial role of electrostatic interactions between the AMP phosphate groups and Na+ ions in positively cooperative binding mechanisms.

Dual client binding sites in the ATP-independent chaperone SurA

The ATP-independent chaperone SurA protects unfolded outer membrane proteins (OMPs) from aggregation in the periplasm of Gram-negative bacteria, and delivers them to the β-barrel assembly machinery (BAM) for folding into the outer membrane (OM). Precisely how SurA recognises and binds its different OMP clients remains unclear. Escherichia coli SurA comprises three domains: a core and two PPIase domains (P1 and P2). Here, by combining methyl-TROSY NMR, single-molecule Förster resonance energy transfer (smFRET), and bioinformatics analyses we show that SurA client binding is mediated by two binding hotspots in the core and P1 domains. These interactions are driven by aromatic-rich motifs in the client proteins, leading to SurA core/P1 domain rearrangements and expansion of clients from collapsed, non-native states. We demonstrate that the core domain is key to OMP expansion by SurA, and uncover a role for SurA PPIase domains in limiting the extent of expansion. The results reveal insights into SurA-OMP recognition and the mechanism of activation for an ATP-independent chaperone, and suggest a route to targeting the functions of a chaperone key to bacterial virulence and OM integrity.

Selective chromogenic nanomolar level sensing of arsenite anions in food samples using dual binding site probes

In the present study, two chromogenic probes, N7R2 and N7R3, each containing two binding sites, were designed and synthesized for the selective detection of arsenite in DMSO/H2O (1:1, v/v). The probes exhibited stability across a pH range spanning from 5 to 12. The lower detection limits of 2.01 ppb (18.86 nM) for N7R2 and 1.79 ppb (16.75 nM) for N7R3, which are much lower than the WHO recommended permissible limit of arsenite, confirmed the superior efficiency of the probes in detecting arsenite. The detection mechanism for arsenite was proposed through UV and 1H NMR titrations, electrochemical studies, and DFT calculations. Practical applications were demonstrated through the fabrication of test strips and molecular logic gates. The probes efficiently recognized arsenite in real water, honey, milk samples, and fruit/vegetable juices. Both N7R2 and N7R3 exhibited excellent recovery rates in the analysis of food samples, demonstrating the probes' usefulness in real sample analysis.

Microwave-Assisted Synthesis of Indoloquinoxaline Derivatives as Promising Anti-Alzheimer agents: DFT and Molecular docking Study

Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline. One of the major pathological features of AD is the degeneration of cholinergic neurons and associated loss of acetylcholine (ACh), a key neurotransmitter involved in memory and cognition. Reduced ACh levels correlate with the severity of cognitive symptoms in AD. Thus, inhibition of acetylcholinesterase (AChE), the enzyme responsible for breaking down ACh, is a leading treatment strategy. This study aimed to synthesize and evaluate novel AChE inhibitors based on an indolo[2,3-b]quinoxaline scaffold. A series of indolo[2,3-b]quinoxaline derivatives were designed by molecular hybridization of indole and quinoxaline privileged structures. Microwave-assisted synthesis improved the efficiency of obtaining the desired compounds. In vitro screening identified several potent AChE inhibitors, with IC50 values down to 0.02 µM. The most active compounds contained electron-withdrawing groups like nitro and benzoyl moieties. DFT calculations provided insights into geometrical, thermal, and electronic properties of the compounds. FMO analysis revealed variations in HOMO and LUMO energies that impact reactivity. Molecular docking elucidated binding modes, highlighting the pi-pi, pi-H, and H-bonding interactions with key amino acids in the catalytic gorge of AChE. Overall, the indole-quinoxaline hybrids represent promising candidates for development of novel dual binding site AChE inhibitors and multifunctional anti-Alzheimer agents.

Podophyllotoxin derivatives-tubulin complex reveals a potential binding site of tubulin polymerization inhibitors in α-tubulin adjacent to colchicine site

The colchicine site of β-tubulin has been proven to be essential binding sites of microtubule polymerization inhibitors. Recent studies implied that GTP pocket of α-tubulin adjacent to colchicine sites is a potential binding site for developing tubulin polymerization inhibitors. However, the structural basis for which type of structural fragments was more beneficial for enhancing the affinity of α-tubulin is still unclear. Here, podophyllotoxin derivatives-tubulin complex crystals indicated that heterocyclic with the highly electronegative and small steric hindrance was conducive to change configuration and enhance the affinity of the residues in GTP pocket of α-tubulin. Triazole with lone-pairs electrons and small steric hindrance exhibited the strongest affinity for enhancing affinity of podophyllotoxin derivatives by forming two hydrogen bonds with αT5 Ser178. Pyrimidine with the secondary strong affinity could bind Asn101 to make the αH7 configuration deflection, which reduces the stability of tubulin result in its depolymerization. Conversely, 4β-quinoline-podophyllotoxin with the weakest affinity did not interact with α-tubulin. The molecular dynamics simulation and protein thermal shift results showed that 4β-triazole-podophyllotoxin-tubulin was the most stable mainly due to two hydrogen bonds and the higher van der Waals force. This work provided a structural basis of the potential binding sites for extending the α/β-tubulin dual-binding sites inhibitors design strategy.

Enhancing efficiency in inverted perovskite solar cells: The role of dual-site binding ligands

Despite the rapid progress in efficiency, PSCs encounter substantial challenges regarding durability and scalability. Inverted p-i-n PSCs provide enhanced long-term operating stability over the conventional n-i-p structures but lag in PCE (Park and Zhu, 2020 [3]). This limitation is mainly due to the interface between the perovskite light-absorbing layer and charge transport materials, where energy band misalignment and energy level pinning hinder PCE. Furthermore, surface defects exacerbate these constraints. In the endeavor to improve performance of PSCs, surface passivation is crucial for reducing nonradiative recombination at the interface. A recent study by Chen et al., published in the journal Science, introduces an innovative interface passivation strategy for p-i-n PSCs that could set a new benchmark for efficiency and stability (Chen et al., 2024 [4]). This commentary assesses the potential impact of dual-site-binding ligands on PSCs and anticipates their transformative effect on the field.

Novel multifunctional tacrine-donepezil hybrids against Alzheimer's disease: Design synthesis and bioactivity studies.

A series of tacrine-donepezil hybrids were synthesized as potential multifunctional anti-Alzheimer's disease (AD) compounds. For this purpose, tacrine and the benzylpiperidine moiety of donepezil were fused with a hydrazone group to achieve a small library of tacrine-donepezil hybrids. In agreement with the design, all compounds showed inhibitory activity toward both acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with IC50 values in the low micromolar range. Kinetic studies on the most potent cholinesterase (ChE) inhibitors within the series showed a mixed-type inhibition mechanism on both enzymes. Also, the docking studies indicated that the compounds inhibit ChEs by dual binding site (DBS) interactions. Notably, tacrine-donepezil hybrids also exhibited significant neuroprotection against H2O2-induced cell death in a differentiated human neuroblastoma (SH-SY5Y) cell line at concentrations close to their IC50 values on ChEs and showed high to medium blood-brain barrier (BBB) permeability on human cerebral microvascular endothelial cells (HBEC-5i). Besides, the compounds do not cause remarkable toxicity in a human hepatocellular carcinoma cell line (HepG2) and SH-SY5Y cells. Additionally, the compounds were predicted to also have good bioavailability. Among the tested compounds, H4, H16, H17, and H24 stand out with their biological profile. Taken together, the proposed novel tacrine-donepezil scaffold represents a promising starting point for the development of novel anti-ChE multifunctional agents against AD.

Sulphated Fucooligosaccharide from Sargassum Horneri: Structural Analysis and Anti-Alzheimer Activity.

In the present study, sulfated polysaccharides were obtained by digestion of Sargassum horneri and preparation with enzyme-assisted extraction using three food-grade enzymes, and their anti- Alzheimer's activities were investigated. The results demonstrated that the crude sulfated polysaccharides extracted using AMGSP, CSP and VSP dose-dependently (25-100µg·mL- 1) raised the spontaneous alternating manner (%) in the Y maze experiment of mice and reduced the escape latency time in Morris maze test. AMGSP, CSP and VSP also exhibited good anti-AChE and moderate anti-BuChE activities. CSP displayed the best inhibitory efficacy against AChE. with IC50 values of 9.77 µM. And, CSP also exhibited good inhibitory selectivity of AChE over BuChE. Next, CSP of the best active crude extract was separated by the preparation type high performance liquid phase to obtain the sulphated fucooligosaccharide section: SFcup (→3-α-L-fucp(2-SO3-)-1→4-α-L-fucp(2,3-SO3-)-1→section), SFcup showed a best inhibitory efficacy against AChE with IC50 values of 4.03 µM. The kinetic research showed that SFcup inhibited AChE through dual binding sites. Moreover, the molecular docking of SFcup at the AChE active site was in accordance with the acquired pharmacological results.

Unveiled the Structure-Selectivity Relationship for Carbon Dioxide Reduction Triggered by Bi-Doped Cu-Based Nanocatalysts.

To investigate synergistic effect between geometric and electronic structures on directing CO2RR selectivity, water phase synthetic protocol and surface architecture engineering strategy are developed to construct monodispersed Bi-doped Cu-based nanocatalysts. The strongly correlated catalytic directionality and Bi3+ dopant can be rationalized by the regulation of [*COOH]/[*CO] adsorption capacities through the appropriate doping of Bi3+ electronic modulator, resulting in volcano relationship between FECO/TOFCO and surface EVBM values. Spectroscopic study reveals that the dual-site binding mode ([Cu─μ─C(═O)O─Bi3+]) enabled by Cu1Bi3+ 2 motif in single-phase Cu150Bi1 nanocatalyst drives CO2-to-CO conversion. In contrast, the study of dynamic Bi speciation and phase transformation in dual-phase Cu50Bi1 nanocatalyst unveils that the Bi0-Bi0 contribution emerges at the expense of BOC phase, suggesting metallic Bi0 phase acting as [H]˙ formation center switches CO2RR selectivity toward CO2-to-HCOO- conversion via [*OCHO] and [*OCHOK] intermediates. This work provides significant insight into how geometric architecture cooperates with electronic effect and catalytic motif/phase to guide the selectivity of electrocatalytic CO2 reduction through the distinct surface-bound intermediates and presents molecular-level understanding of catalytic mechanism for CO/HCOO- formation.

Structurally diverse brefeldin A derivatives as potent and selective acetylcholinesterase inhibitors from an endophytic fungus Penicillium brefeldianum F4a

Nine previously undescribed brefeldin A (BFA) derivatives (1–9), together with one known compound 4-epi-brefeldin A (10), were isolated from an endophytic fungus Penicillium brefeldianum F4a. The chemical structures were elucidated using NMR and HRESIMS. ECD analysis and Mosher's method were used to confirm the absolute configurations of 1–9. The inhibitory activity of all isolated BFA derivatives (1–10) on acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) was evaluated in vitro. The bioassay results suggested that neobrefeldin (1) and brefeldin H (2) exhibited higher potent and selective AChE inhibitory activity (IC50 = 0.12 and 0.28 μM) than the therapeutic drug galantamine for Alzheimer's disease (AD) (IC50 = 0.66 µM), whereas only neobrefeldin (1) displayed weak inhibitory activity against BuChE (IC50 = 175.04 µM). Moreover, a molecular docking analyses was performed and showed compounds 1 and 2 were dual binding site AChE inhibitors. It is worth noting that neobrefeldin (1) showed a better binding affinity with the peripheral anionic site through the hydrogen bonding interaction with Tyr124 than brefeldin H (2), resulting in better AChE inhibitory activity. These findings not only provide a promising AChE inhibitor neobrefeldin (1) for developing agents against early AD, but also provide a valuable perspective for better understanding its AChE inhibition activity.

Novel Lawsone-Quinoxaline Hybrids as New Dual Binding Site Acetylcholinesterase Inhibitors.

A new family of lawsone-quinoxaline hybrids was designed, synthesized, and evaluated as dual binding site cholinesterase inhibitors (ChEIs). In vitro tests revealed that compound 6d was the most potent AChEI (IC50 = 20 nM) and BChEI (IC50 = 220 nM). The compound 6d did not show cytotoxicity against the SH-SY5Y neuronal cells (GI50 > 100 μM). In silico and enzyme kinetic experiments demonstrated that compound 6d bound to both the catalytic anionic site and the peripheral anionic site of HuAChE. The lawsone-quinoxaline hybrids exhibited potential for further development of potent acetylcholinesterase inhibitors for the treatment of Alzheimer's disease.

In-situ construction of N-doped hollow carbon polyhedral cage anchored Co-Ni dual binding sites as nanoreactor for efficient real lignin oil hydrodeoxygenation

Rational design multifunctional nanoreactor with high activity under H2-free/low-H2 conditions for lignin hydrodeoxygenation reaction (HDO) is attractive for sustainable energy conversion. Here, strategy for in-situ assembly-etching was proposed to prepare N-doped hollow carbon polyhedral cage anchored Co-Ni dual binding sites as nanoreactors (CoxNiy/NC). Its unique and controllable hollow structure exhibits high content of pyridine-N as Lewis-base site for adsorption of substrate, and in adjacent nitrogen defect sites as active metal anchors enabled the Co2Ni1/NC to perform perfect the hydrodeoxygenation of real lignin oil. The conversion of lignin pyrolytic oil to cycloalkane products was achieved under 0.2 MPa H2 and 3 h, the yield of total liquid product and the cyclohexane were 87.8 wt% and 53.4 wt%, respectively. This research provides a novel way for upgrading raw bio-oil to high-value products under low energy consuming conditions.

A fully π-conjugated covalent organic framework with dual binding sites for ultrasensitive detection and removal of divalent heavy metal ions

Covalent organic frameworks (COFs) have become a promising candidate for the remediation of heavy metal pollution. However, researches on COF adsorbents still have challenges on maintaining good optical properties and adsorption performance under harsh conditions. Herein, a fully π-conjugated COF with dual binding sites (Bpy-sp2c-COF) is reported for rapid fluorescence recognition and enhanced adsorption towards divalent heavy metal ions. The vinylene-linkage lattice shows strong luminescence and excellent stability in both strong acidity and basicity. Bpy-sp2c-COF demonstrates not only nanomolar-scale detection of divalent heavy metal ions, but also good adsorption capacity (Hg2+ 718.48, Ni2+ 278.64, Cu2+ 260.11, and Co2+ 126.23 mg/g). Experimental and theoretical studies reveal the intramolecular charge transfer as the fluorescence quenching mechanism. Further simulation results demonstrate the cyano and bipyridine groups on the lattice can act as dual binding sites for divalent heavy metal ions. Experimental results confirmed the adsorption capacity of Bpy-sp2c-COF superior to that of COFs with either cyano groups (Hg2+ 415.34, Ni2+ 165.60, Cu2+ 160.55, and Co2+ 73.14 mg/g), or bipyridine groups (Hg2+ 369.25, Ni2+ 133.41, Cu2+ 133.32, and Co2+ 69.23 mg/g). Besides, robust regeneration of the adsorbent could be achieved over 10 cycles. The fully π-conjugated COF with dual binding sites provides a new approach for designing next-generation sensors and adsorbents with excellent performances.

General Strategy for Specific Fluorescence Imaging of Homocysteine in Living Cells and In Vivo.

The aberrantly changed level of homocysteine (Hcy) triggers a variety of pathological symptoms and subsequently Hcy-related diseases. Direct and selective visualization of Hcy in biological systems is pivotal to understanding the pathological functions of Hcy at the molecular level. Herein, a general strategy was developed for the specific fluorescence imaging of Hcy through the combination of dual-binding sites and the introduction of a nitro group at the 6-position of the 7-diethylaminocoumarin fluorophore. Also, a series of novel fluorescent probes were exploited for monitoring Hcy with excellent selectivity, high sensitivity, and far-red/near-infrared fluorescence emission. Furthermore, fluorescence imaging of endogenous Hcy dynamics in living cells and in vivo was achieved, providing direct and solid evidence for the increasement of endogenous Hcy in type 2 diabetes mellitus and Alzheimer's disease. This research will greatly advance the development and understanding of the molecular nexus between the Hcy metabolism cascade and the root causes of diseases related to Hcy.

In Silico Design of New Dual Inhibitors of SARS-CoV-2 MPRO through Ligand- and Structure-Based Methods.

The viral main protease is one of the most attractive targets among all key enzymes involved in the life cycle of SARS-CoV-2. Considering its mechanism of action, both the catalytic and dimerization regions could represent crucial sites for modulating its activity. Dual-binding the SARS-CoV-2 main protease inhibitors could arrest the replication process of the virus by simultaneously preventing dimerization and proteolytic activity. To this aim, in the present work, we identified two series' of small molecules with a significant affinity for SARS-CoV-2 MPRO, by a hybrid virtual screening protocol, combining ligand- and structure-based approaches with multivariate statistical analysis. The Biotarget Predictor Tool was used to filter a large in-house structural database and select a set of benzo[b]thiophene and benzo[b]furan derivatives. ADME properties were investigated, and induced fit docking studies were performed to confirm the DRUDIT prediction. Principal component analysis and docking protocol at the SARS-CoV-2 MPRO dimerization site enable the identification of compounds 1b,c,i,l and 2i,l as promising drug molecules, showing favorable dual binding site affinity on SARS-CoV-2 MPRO.

ATG16L1 adopts a dual-binding site mode to interact with WIPI2b in autophagy.

Macroautophagy plays crucial roles in the regulation of cellular physiology and requires de novo synthesis of double-membrane autophagosomes, which relies on a specific interaction between autophagy-related 16L1 (ATG16L1) and WD repeat domain phosphoinositide-interacting protein 2b (WIPI2b). However, the molecular mechanism governing the interaction of ATG16L1 with WIPI2b remains elusive. Here, we find that ATG16L1 has two distinct binding sites for interacting with WIPI2b, the previously reported WIPI2b-binding site (WBS1) and the previously unidentified site (WBS2). We determine the crystal structures of WIPI2b with ATG16L1 WBS1 and WBS2, respectively, and elucidate the molecular mechanism underpinning the recruitment of ATG16L1 by WIPI2b. Moreover, we uncover that ATG16L1 WBS2 and its binding mode with WIPI2b is well conserved from yeast to mammals, unlike ATG16L1 WBS1. Last, our cell-based functional assays demonstrate that both ATG16L1 WBS1 and WBS2 are required for the effective autophagic flux. In conclusion, our findings provide mechanistic insights into the key ATG16L1/WIPI2b interaction in autophagy.

Pyridine based dual binding site aromatase (CYP19A1) inhibitors.

Aromatase (CYP19A1) inhibitors are the mainstay therapeutics for the treatment of hormone dependant breast cancer, which accounts for approximately 70% of all breast cancer cases. However, increased resistance to the clinically used aromatase inhibitors, including letrozole and anastrazole, and off target effects, necessitates the development of aromatase inhibitors with improved drug profiles. The development of extended 4th generation pyridine based aromatase inhibitors with dual binding (haem and access channel) is therefore of interest and here we describe the design, synthesis and computational studies. Cytotoxicity and selectivity studies identified the pyridine derivative (4-bromophenyl)(6-(but-2-yn-1-yloxy)benzofuran-2-yl)(pyridin-3-yl)methanol (10c) as optimal with CYP19A1 IC50 0.83 nM (c.f. letrozole IC50 0.70 nM), and an excellent cytotoxicity and selectivity profile. Interestingly, computational studies for the 6-O-butynyloxy (10) and 6-O-pentynyloxy (11) derivatives identified an alternative access channel lined by Phe221, Trp224, Gln225 and Leu477, providing further insight into the potential binding mode and interactions of the non-steroidal aromatase inhibitors.

Overview of Research into mTOR Inhibitors.

The mammalian target of rapamycin (mTOR) is a serine/threonine kinase that belongs to the phosphoinositide 3-kinase (PI3K)-related kinase (PIKK) family. The kinase exists in the forms of two complexes, mTORC1 and mTORC2, and it participates in cell growth, proliferation, metabolism, and survival. The kinase activity is closely related to the occurrence and development of multiple human diseases. Inhibitors of mTOR block critical pathways to produce antiviral, anti-inflammatory, antiproliferative and other effects, and they have been applied to research in cancer, inflammation, central nervous system diseases and viral infections. Existing mTOR inhibitors are commonly divided into mTOR allosteric inhibitors, ATP-competitive inhibitors and dual binding site inhibitors, according to their sites of action. In addition, there exist several dual-target mTOR inhibitors that target PI3K, histone deacetylases (HDAC) or ataxia telangiectasia mutated and Rad-3 related (ATR) kinases. This review focuses on the structure of mTOR protein and related signaling pathways as well as the structure and characteristics of various mTOR inhibitors. Non-rapalog allosteric inhibitors will open new directions for the development of new therapeutics specifically targeting mTORC1. The applications of ATP-competitive inhibitors in central nervous system diseases, viral infections and inflammation have laid the foundation for expanding the indications of mTOR inhibitors. Both dual-binding site inhibitors and dual-target inhibitors are beneficial in overcoming mTOR inhibitor resistance.

Oxygen-Plasma-Treated Fe–N–C Catalysts with Dual Binding Sites for Enhanced Electrocatalytic Polysulfide Conversion in Lithium–Sulfur Batteries

Oxygen-Plasma-Treated Fe–N–C Catalysts with Dual Binding Sites for Enhanced Electrocatalytic Polysulfide Conversion in Lithium–Sulfur Batteries