Affinity Kd Research Articles

New High-Affinity Peptide Ligands for Kv1.2 Channel: Selective Blockers and Fluorescent Probes

Advanced molecular probes are required to study the functional activity of the Kv1.2 potassium channel in normal and pathological conditions. To address this, a fully active Kv1.2 channel fused with fluorescent protein mKate2 (K-Kv1.2) was engineered that has high plasma membrane presentation due to the S371T substitution, and hongotoxin 1 (HgTx1) fused with eGFP at the C-terminus (HgTx-G) was produced. HgTx-G and HgTx1 N-terminally labeled with Atto488 fluorophore were shown to be fluorescent probes of Kv1.2 in cells with dissociation constants (Kd) of 120 and 80 pM, respectively. K-Kv1.2 and HgTx-G were used as components of an analytical system to study peptide blockers of the channel and helped to find out that Ce1 and Ce4 peptides from Centruroides elegans venom possess high affinity (Kd of 10 and 30 pM) and selectivity for Kv1.2. Using molecular docking and molecular modeling techniques, the complexes of Kv1.2 with HgTx1, Ce1, and Ce4 were modeled, and determinants of the high affinity binding were proposed. New fluorescent probes and selective blockers of Kv1.2 can be used to resolve Kv1.2-related challenges in neuroscience and neuropharmacology.

Regulation of classical zinc fingers for neuronal signaling in the central nervous system

AbstractZinc finger (ZF) proteins are well‐known for their regulatory functions in the central dogma, and their structural domains serve as promising scaffolds for the study of neurodegenerative diseases. These proteins often contain multiple ZF domains, enabling interactions with target molecules that regulate transcription and translation. The Cys2His2 (C2H2) type ZF domains, found in the brain, are associated with long‐ and short‐term memory, neuronal differentiation and development, and other physiological processes. The classical C‐X2‐C‐X12‐H‐X3‐H type ZF domains have been detected in studies of Parkinson's disease (PD) and are closely linked to biological pathways involved in a wide range of neurodegenerative diseases. In this review, we introduce three ZF proteins expressed in the brain: Parkin‐interacting substrate (PARIS), zinc finger and BTB domain‐containing 20 (ZBTB20), and zinc finger protein 18 (ZNF18). We explore the structural and functional roles of these ZF proteins in the brain. Each of these proteins contains more than four ZF domains, as well as functional domains such as KRAB, BTB, and SCAN, which perform modular roles independently of the ZF domains. Biophysical studies of PARIS have demonstrated that its classical three‐ZF domain, PARIS(ZF2–4), forms hydrogen bonds with insulin response sequences (IRSs) with high specificity (Kd = 38.9 ± 2.4 nM). Metal coordination studies showed that PARIS binds Co2+ with high affinity (Kd = 49.1 ± 7.7 nM), more strongly than other ZF domains, and it also coordinates with other xenobiotic metal ions such as Fe2+ and Ni2+. Although Zn2+–PARIS(ZF2–4) binds specifically to IRSs, Fe2+–, Fe3+– or Co2+–PARIS(ZF2–4) cannot, due to distortions in the ZF domain structure that disrupt hydrogen bonding. These brain‐specific ZF domains exhibit common patterns, with similar numbers of ZF domains and sequence homology at the C‐terminus, whereas both the ZF domains and N‐terminal protein–protein interaction domains contribute to their functional versatility. Elucidating the structure and function of these classical ZF proteins offers promising avenues for the treatment of diverse brain disorders, including Alzheimer's disease, PD, and autism spectrum disorder.

Coordination-Based Site-Specific Labeling Strategy for Electrogenerated Chemiluminescence Biosensing of Matrix Metalloproteinase 2.

Matrix metalloproteinase 2 (MMP-2) is an important biomarker for some diseases. Herein, one first-case coordination-based site-specific labeling strategy is proposed for electrogenerated chemiluminescence (ECL) biosensing of MMP-2 by employing an iridium(III) solvent complex as a signal reagent and a histidine (His)-containing peptide as a molecular recognition substrate. One ECL probe was prepared via coordination labeling of the His-containing peptide with one iridium(III) solvent complex ([(3-(2-pyridyl)benzoic acid)2Ir(DMSO)Cl], Ir1-DMSO). High ECL efficiency and good cleavage ability by MMP-2 were obtained for the ECL probe. By combining the high sensitivity of the ECL method, the good specificity of the peptide, and the simpleness of the magnetic bead-based assay, one "cleavage-magnetic enrichment type" ECL biosensing method was developed to detect MMP-2. MMP-2 can be sensitively detected in the linear range of 1.0-10 ng/mL with a limit of quantification of 1.0 ng/mL and a limit of detection of 0.3 ng/mL. Moreover, the ECL biosensing method was successfully applied for the determination of MMP-2 in serum samples with recoveries from 98.0% ± 8.0% to 108.0% ± 6.0%. Further, high affinity (Kd = 0.11 nM) was obtained for the Ir1-DMSO-labeled His-containing peptide and MMP-2. This work may pave the way for the labeling of His-containing biomolecules with an iridium(III) solvent complex and provides a promising method in point-of-care testing of MMP-2.

Discovery of Propionic Acid Derivatives with a 5-THIQ Core as Potent and Orally Bioavailable Keap1-Nrf2 Protein-Protein Interaction Inhibitors for Acute Kidney Injury.

Keap1 plays a crucial role in regulating the Nrf2-mediated cytoprotective response and is increasingly targeted for oxidative stress-related diseases. Using small molecules to disrupt the Keap1-Nrf2 protein-protein interaction (PPI) has emerged as a new strategy for developing Nrf2 activators. Through extensive structure-activity relationship studies, we identified compound 56, which features a unique 5-tetrahydroisoquinoline scaffold and acts as a potent inhibitor of the Keap1-Nrf2 PPI. Compound 56 exhibited significant inhibitory activity (IC50 = 16.0 nM) and tight Keap1 binding affinity (Kd = 3.07 nM), along with acceptable oral bioavailability (F = 20%). Notably, 56 enhanced antioxidant defenses in HK-2 renal tubular epithelial cells and significantly reduced plasma creatinine and blood urea nitrogen levels in acute kidney injury (AKI) mice. These findings collectively position compound 56 as a promising candidate for the treatment of AKI.

PGE2 Binding Affinity of Hemocyte Membrane Preparations of Manduca sexta and Identification of the Receptor-Associated G Proteins in Two Lepidopteran Species.

Prostaglandin E2 (PGE2) is an eicosanoid that mediates a range of physiological actions in vertebrates and invertebrates, including reproduction and immunity. The PGE2 receptor was identified and functionally assessed in two lepidopteran insects, Manduca sexta and Spodoptera exigua. However, its binding affinity to the receptor has not been reported. The PGE2 receptor is a G-protein coupled receptor (GPCR) although its corresponding G-protein is not identified. PGE2 binding assays were performed with membrane preparations from hemocytes of M. sexta larvae. We recorded an optimal binding in 4 h reactions conducted at pH 7.5 with 12 nM tritium-labeled PGE2. We found that hemocytes express a single population of PGE2 binding sites with a high affinity (Kd = 35 pmol/mg protein), which are specific and saturable. The outcomes of experiments on the influence of purine nucleotides suggested these are functional GPCRs. A bioinformatics analysis led to a proposed trimeric G-protein in the S. exigua transcriptome, in which the Gα subunit is classified into five different types: Gα(o), Gα(q), Gα(s), Gα(12), and Gα(f). After confirming expressions of these five types in S. exigua, individual RNA interference (RNAi) treatments were applied to the larvae using gene-specific double-stranded RNAs. RNAi treatments specific to Gα(s) or Gα(12) gene expression significantly suppressed the cellular immune responses although the RNAi treatments specific to other three Gα components did not. While PGE2 treatments led to elevated hemocyte cAMP or Ca2+ levels, the RNAi treatments specific to Gα(s) or Gα(12) genes led to significantly reduced second messenger levels under PGE2, although the RNAi treatments specific to the other three Gα components did not. These results showed that the PGE2 receptor has high PGE2 affinity in the nanomolar range and binds G-proteins containing a Gα(s) or Gα(12) trimeric component in S. exigua and M. sexta, and likely, all lepidopteran insects.

Nanocatalysis of silver-nanobioprobe based supersensitive electrochemical detection of Salmonella serotypes targeting virulence protein

Herein, we report a supersensitive and specific detection of Salmonella employing nanocatalysis of silver nanoparticle (AgNp). A nanobioprobe was developed employing specific antibody (Ab) that binds to a peptide present in transmembrane protein of Salmonella. We have studied 7 surface-exposed peptide hits from conserved virulence proteins (PagC, ST50, PagN, CdtB and FliC). These peptides were experimentally evaluated by BLI (Bio layer interferometry) for their reactivity towards antisera raised against an admix of major Salmonella serogroups. The most promising peptide was used to generate Ab with binding affinity Kd of 5.6 × 10−9 M. The Ab exhibited high specificity towards entire Salmonella serotypes prevalent in foods, as illustrated by FACS (Fluorescence-activated cell sorting) study. The Ab-AgNp probe was blocked with a dual layer to prevent non-specific interactions, confirmed by employing BLI and TEM (Transmission electron microscopy). For the electrochemical detection, the autonanocatalysis of AgNp in presence of H2O2 was used to generate numerous Ag+ resulting in an amplified signal that could detect 10 cells/mL. The relative standard deviation (RSD) was observed to be 4.5%. The platform achieved recovery of 100–112% calculated for 102 cells/mL. The performance was validated in milk, buffer peptone water (BPW) and tap water by spiking studies. The study highlights the effectiveness of efficiently blocked AgNp-mediated probes for the highly selective and sensitive detection of Salmonella, representing a significant advancement in bacterial sensing.

Dual-labeled anti-GD2 targeted probe for intraoperative molecular imaging of neuroblastoma

BackgroundSurgical resection is integral for the treatment of neuroblastoma, the most common extracranial solid malignancy in children. Safely locating and resecting primary tumor and remote deposits of disease remains a significant challenge, resulting in high rates of complications and incomplete surgery, worsening outcomes. Intraoperative molecular imaging (IMI) uses targeted radioactive or fluorescent tracers to identify and visualize tumors intraoperatively. GD2 was selected as an IMI target, as it is highly overexpressed in neuroblastoma and minimally expressed in normal tissue.MethodsGD2 expression in neuroblastoma cell lines was measured by flow cytometry. DTPA and IRDye® 800CW were conjugated to anti-GD2 antibody to generate DTPA-αGD2-IR800. Binding affinity (Kd) of the antibody and the non-radiolabeled tracer were then measured by ELISA assay. Human neuroblastoma SK-N-BE(2) cells were surgically injected into the left adrenal gland of 3.5-5-week-old nude mice and the orthotopic xenograft tumors grew for 5 weeks. 111In-αGD2-IR800 or isotype control tracer was administered via tail vein injection. After 4 and 6 days, mice were euthanized and gamma and fluorescence biodistributions were measured using a gamma counter and ImageJ analysis of acquired SPY-PHI fluorescence images of resected organs (including tumor, contralateral adrenal, kidneys, liver, muscle, blood, and others). Organ uptake was compared by one-way ANOVA (with a separate analysis for each tracer/day combination), and if significant, Sidak’s multiple comparison test was used to compare the uptake of each organ to the tumor. Handheld tools were also used to detect and visualize tumor in situ, and to assess for residual disease following non-guided resection.Results111In-αGD2-IR800 was successfully synthesized with 0.75-2.0 DTPA and 2–3 IRDye® 800CW per antibody and retained adequate antigen-binding (Kd = 2.39 nM for aGD2 vs. 21.31 nM for DTPA-aGD2-IR800). The anti-GD2 tracer demonstrated antigen-specific uptake in mice with human neuroblastoma xenografts (gamma biodistribution tumor-to-blood ratios of 3.87 and 3.88 on days 4 and 6 with anti-GD2 tracer), while isotype control tracer did not accumulate (0.414 and 0.514 on days 4 and 6). Probe accumulation in xenografts was detected and visualized using widely available operative tools (Neoprobe® and SPY-PHI camera) and facilitated detection ofputative residual disease in the resection cavity following unguided resection.ConclusionsWe have developed a dual-labeled anti-GD2 antibody-based tracer that incorporates In-111 and IRDye® 800CW for radio- and fluorescence-guided surgery, respectively. The tracer adequately binds to GD2, specifically accumulates in GD2-expressing xenograft tumors, and enables tumor visualization with a hand-held NIR camera. These results encourage the development of 111In-αGD2-IR800 for future use in children with neuroblastoma, with the goal of improving patient safety, completeness of resection, and overall patient outcomes.

Fluorescence Turn-ON Displacement Assays with Cucurbit[7]uril-Thiophenylpyridinium Complexes as Host-Dye Reporter Pairs.

The N-methyl-4-thiophenylpyridinium cation (ThioPy) is a high affinity (Kd ca. 5 nM), fast-exchanging fluorescent probe for cucurbit[7]uril (CB7). The CB7/ThioPy complex shows a unique fluorescence turn-ON response upon displacement by an analyte in sensing application. This enabled the development of a real-time fluorescence assay with the MRFA peptide for the protease thermolysin, which is also suitable for the cancer biomarker cathepsin B. Moreover, liposome encapsulation of CB7/ThioPy in large unilamellar vesicles (LUVs) provided mechanistic insight into intravesicular dye displacement reactions.

Unravelling biochemical and molecular mechanism of a carboxylesterase from Dietzia kunjamensis IITR165 reveal novel activities against polyethylene terephthalate

Plastics and plasticizers accumulate in the ecological niches affecting biodiversity, and human and environmental health. Bacteria degrading polyethylene terephthalate (PET) were screened and PETases involved in PET degradation were characterized. Here, we identified a carboxylesterase Dkca1 of 48.44 kDa molecular mass from Dietzia kunjamensis IITR165 shown to degrade amorphous PET film into bis(2-hydroxyethyl) terephthalate (BHET) and terephthalic acid (TPA) formed 64.35 μM and 35.26 μM, respectively within 96 h at 37 °C as revealed by LC-MS analysis showed significant PET hydrolase activity similar to reported PETases. SEM analysis confirms the surface erosion as cavities and holes. Dkca1 also hydrolysed BHET and dibutyl phthalate (DBP) at a concentration of 1 mM within 3 h indicating its versatility. Fluorescence quenching shows Dkca1 protein has a maximum affinity (Kd) towards BHET (86.55 μM) than DBP (134.2 μM). The protein demonstrated high stability under temperatures above 40 °C and at the pH range of 6.0–9.0. Moreover, Amino acid composition showed that the Dkca1 enzyme belongs to family VII carboxylesterase containing conserved catalytic triad of Ser183-Glu289-His378 with pentapeptide motif GXSAG and an oxyanion hole H103GGG106, sharing 37.47 % and 32.44 % similarity with a PET hydrolase TfCa from Thermobifida fusca and PAE hydrolase CarEW from Bacillus sp. K91, respectively. A docking study revealed that ligand PET, BHET, and DBP showed favourable binding in the catalytic pocket of the Dkca1 protein.

Deciphering Pathways and Thermodynamics of Protein Assembly Using Native Mass Spectrometry.

Protein oligomerization regulates many critical physiological processes, and its dysregulation can contribute to dysfunction and diseases. Elucidating the assembly pathways and quantifying their underlying thermodynamic and kinetic parameters are crucial for a comprehensive understanding of biological processes and for advancing therapeutics targeting abnormal protein oligomerization. Established binding assays, with limited mass precision, often rely on simplified models for data interpretation. In contrast, high-resolution native mass spectrometry (nMS) can directly determine the stoichiometry of biomolecular complexes in vitro. However, quantification is hindered by the fact that the relative abundances of gas-phase ions generally do not reflect solution concentrations due to nonuniform response factors. Recently, slow mixing mode (SLOMO)-nMS, which can quantify the relative response factors of interacting species, has been demonstrated to reliably measure the affinity (Kd) of binary biomolecular complexes. Here, we introduce an extended form of SLOMO-nMS that enables simultaneous quantification of the thermodynamics in multistep association reactions. Application of this method to homo-oligomerization of concanavalin A and insulin confirmed the reliability of the assay and uncovered details about the assembly processes that had previously resisted elucidation. Results acquired using SLOMO-nMS implemented with charge detection shed new light on the binding of recombinant human angiotensin-converting enzyme 2 and the SARS-CoV-2 spike protein. Importantly, new assembly pathways were uncovered, and the affinities of these interactions, which regulate host cell infection, were quantified. Together, these findings highlight the tremendous potential of SLOMO-nMS to accelerate the characterization of protein assembly pathways and thermodynamics and, in so doing, enhance fundamental biological understanding and facilitate therapeutic development. https://orcid.org/0000-0002-3389-7112.

Biochemical rationale for transfusion of high titre COVID-19 convalescent plasma

We aimed to model binding of donor antibodies to virus that infects COVID-19 patients following transfusion of convalescent plasma (CCP). An immunosorbent assay was developed to determine apparent affinity (Kd, app). Antibody binding to virus was modelled using antibody concentration and estimations of viral load. Assay and model were validated using reference antibodies and clinical data of monoclonal antibody therapy. A single Kd, app or two resolvable Kd, app were found for IgG in 11% or 89% of CCP donations, respectively. For IgA this was 50%-50%. Median IgG Kd, app was 0.8nM and 3.6nM for IgA, ranging from 0.1-14.7nM and 0.2-156.0nM respectively. The median concentration of IgG was 44.0nM (range 8.4-269.0nM) and significantly higher than IgA at 2.0nM (range 0.4-11.4nM). The model suggested that a double CCP transfusion (i.e. 500 mL) allows for > 80% binding of antibody to virus provided Kd, app was < 1nM and concentration > 150nM. In our cohort from the pre-vaccination era, 4% of donations fulfilled these criteria. Low and mid-range viral loads are found early post exposure, suggesting that convalescent plasma will be most effective then. This study provides a biochemical rationale for selecting high affinity and high antibody concentration CCP transfused early in the disease course.

Influence of PEGylation on HER2-targeting retro A9 peptide analogue

Elevated levels of HER2 receptor in breast cancer can be targeted through receptor-specific peptides for precise detection and therapy by nuclear medicine approach. Previously reported retro analogue of A9 peptide had shown HER2-specificity with promising pharmacokinetic features. Hence, with an aim of further improving the circulation time of rL-A9 radiopeptide, long polyethylene glycol chain (PEG12) was introduced at the N-terminus of the peptide during solid phase synthesis and influence of PEGylation on biological profile was studied. [177Lu]Lu-DOTA-PEG12-rL-A9 demonstrated high specific cellular uptake (5.94 ± 0.09 %) in HER2-expressing human breast carcinoma SKBR3 cells and low nanomolar binding affinity (Kd = 34.58 ± 12.78 nM). Uptake in SKBR3 tumors induced in female SCID mice was higher at all the time points investigated (3, 24, 48 h) in comparison to the non-PEGylated radiopeptide, [177Lu]Lu-DOTA-rL-A9. Blocking studies led to 51 % reduction in accumulation of radioactivity in the tumor indicating specificity of the radiopeptide. Improved tumor-to-stomach and tumor-to-intestine ratios for [177Lu]Lu-DOTA-PEG12-rL-A9 compared to [177Lu]Lu-DOTA-rL-A9 at 48 h shall pave the way for better contrast and delineation of metastatic sites.

Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydroptein pyrophosphokinase: Toward cell permeability

6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a key enzyme in the folate biosynthesis pathway. It catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). HPPK is essential for microorganisms but is absent in mammals. Yet, it is not the target of any existing antibiotics. Hence, this enzyme is an attractive target for developing novel antimicrobial agents. A wealth of structural and mechanistic information has provided solid basis for structure-based design of HPPK inhibitors. Our bisubstrate inhibitors were initially created by linking 6-hydroxymethylpterin to adenosine through 2, 3, or 4 phosphate groups (HPnA, n = 2, 3, or 4), among which HP4A exhibited the highest binding affinity (Kd = 0.47 ± 0.04 μM). Further development was carried out based on high-resolution structures of HPPK in complex with HP4A. Replacing the phosphate bridge with a piperidine linked thioether eliminated multiple negative charges of the bridge. Substituting the pterin moiety with 7,7-dimethyl-7,8-dihydropterin improved the binding affinity. Arming the piperidine ring with a carboxyl group and oxidizing the thioether further enhanced the potency, resulting in a druglike inhibitor of HPPK (Kd = 0.047 ± 0.007 μM). None of these inhibitors, however, exhibits bacterial cell permeability. It is most likely due to the lack of active folate transporters in bacteria. Replacing the pterin moiety with a 7-deazagaunine moiety, we have obtained a novel bisubstrate inhibitor (HP-101) showing observable cell permeability toward a Gram-positive bacterium. Here, we report the in vitro activity of HP-101 and its structure in complex with HPPK, providing a framework for structure-based further development.

ATH434, a promising iron-targeting compound for treating iron regulation disorders.

Cytotoxic accumulation of loosely bound mitochondrial Fe2+ is a hallmark of Friedreich's Ataxia (FA), a rare and fatal neuromuscular disorder with limited therapeutic options. There are no clinically approved medications targeting excess Fe2+ associated with FA or the neurological disorders Parkinson's disease and Multiple System Atrophy. Traditional iron-chelating drugs clinically approved for systemic iron overload that target ferritin-stored Fe3+ for urinary excretion demonstrated limited efficacy in FA and exacerbated ataxia. Poor treatment outcomes reflect inadequate binding to excess toxic Fe2+ or exceptionally high affinities (i.e. ≤10-31) for non-pathologic Fe3+ that disrupts intrinsic iron homeostasis. To understand previous treatment failures and identify beneficial factors for Fe2+-targeted therapeutics, we compared traditional Fe3+ chelators deferiprone (DFP) and deferasirox (DFX) with additional iron-binding compounds including ATH434, DMOG, and IOX3. ATH434 and DFX had moderate Fe2+ binding affinities (Kd's of 1-4 µM), similar to endogenous iron chaperones, while the remaining had weaker divalent metal interactions. These compounds had low/moderate affinities for Fe3+(0.46-9.59µM) relative to DFX and DFP. While all compounds coordinated iron using molecular oxygen and/or nitrogen ligands, thermodynamic analyses suggest ATH434 completes Fe2+ coordination using H2O. ATH434 significantly stabilized bound Fe2+ from ligand-induced autooxidation, reducing reactive oxygen species (ROS) production, whereas DFP and DFX promoted production. The comparable affinity of ATH434 for Fe2+ and Fe3+ position it to sequester excess Fe2+ and facilitate drug-to-protein iron metal exchange, mimicking natural endogenous iron binding proteins, at a reduced risk of autooxidation-induced ROS generation or perturbation of cellular iron stores.

Characterization of a cytochrome P450 that catalyzes the O-demethylation of lignin-derived benzoates

Cytochromes P450 (P450s) are a superfamily of heme-containing enzymes possessing a broad range of monooxygenase activities. One such activity is O-demethylation, an essential and rate-determining step in emerging strategies to valorize lignin that employ carbon-carbon bond cleavage. We recently identified PbdA, a P450 from Rhodococcus jostii RHA1, and PbdB, its cognate reductase, which catalyze the O-demethylation of para-methoxylated benzoates (p-MBAs) to initiate growth of RHA1 on these compounds. PbdA had the highest affinity (Kd = 3.8 ± 0.6 μM) and apparent specificity (kcat/KM = 20 000 ± 3 000 M-1 s-1) for p-MBA. The enzyme also O-demethylated two related lignin-derived aromatic compounds with remarkable efficiency: veratrate and isovanillate. PbdA also catalyzed the hydroxylation and dehydrogenation of p-EB even though RHA1 did not grow on this compound. Atomic-resolution structures of PbdA in complex with p-MBA, p-EB and veratrate revealed a cluster of three residues that form hydrogen bonds with the substrates’ carboxylate: Ser87, Ser237 and Arg84. Substitution of these residues resulted in lower affinity and O-demethylation activity on p-MBA as well as increased affinity for the acetyl analogue, p-methoxyacetophenone. The S87A and S237A variants of PbdA also catalyzed the O-demethylation of an aldehyde analogue of p-MBA, p-methoxy-benzaldehyde, while the R84M variant did not, despite binding this compound with high affinity. These results suggest that Ser87, Ser237 and Arg84 are not only important determinants of specificity but also help to orientate that substrate correctly in the active site. This study facilitates the design of biocatalysts for lignin valorization.

Rapid and ordered cleavage of prothrombin by Hopsarin D in the absence of phospholipid membranes

BackgroundThrombin is produced by the prothrombinase complex, composed of factor (f)Xa and fVa on a phospholipid (PL) membrane surface. Snakes of the Elapidae family have venom versions of these factors that cause coagulopathy in prey. Group C venoms contain both fⅩa and fⅤa orthologues. Group D venoms only contain a fXa orthologue and hijack fⅤa of the prey. Hopsarin D (HopD) is the venom fⅩa of the Stephen’s banded snake (Hoplocephalus stephensii). ObjectivesWe set out to address the following: does HopD bind to human fⅤa with high affinity in the absence of PL? Does it process prothrombin through the meizothrombin pathway? Is the order of cleavage PL-dependent? Can HopD activate fⅤ? MethodsWe produced and characterized full-length and truncated HopD. ResultsHopD is only able to clot plasma that contains fⅤ and competes with human fⅩa for fⅤa binding. HopD binds to both human fⅤa and fⅤ with high affinity (dissociation constant, ∼10 nM), in contrast to fⅩa. HopD processes prothrombin down the meizothrombin route in the absence and presence of PL. Although HopD can bind to fⅤ, conversion to fⅤa is necessary for prothrombin processing. HopD initiates clotting in the blood of prey by activating fⅤ. ConclusionHopD binds to fⅤa with high affinity and rapidly activates prothrombin in the absence of PL, exclusively through the meizothrombin intermediate. HopD binds with high affinity to both fⅤa and fⅤ, suggesting that the B-domain does not sterically block fⅩa binding, but inhibits productive interaction in another way, and additionally prevents prothrombin binding.

Molecular basis and functional consequences of the interaction between the base excision repair DNA glycosylase NEIL1 and RPA

NEIL1 is a DNA glycosylase that recognizes and initiates base excision repair of oxidized bases. The ubiquitous ssDNA binding scaffolding protein, replication protein A (RPA), modulates NEIL1 activity in a manner that depends on DNA structure. Interaction between NEIL1 and RPA has been reported, but the molecular basis of this interaction has yet to be investigated. Using a combination of NMR spectroscopy and isothermal titration calorimetry (ITC), we show that NEIL1 interacts with RPA through two contact points. An interaction with the RPA32C protein recruitment domain was mapped to a motif in the common interaction domain (CID) of NEIL1 and a dissociation constant (Kd) of 200 nM was measured. A substantially weaker secondary interaction with the tandem RPA70AB ssDNA binding domains was also mapped to the CID. Together these two contact points reveal NEIL1 has a high overall affinity (Kd ∼ 20 nM) for RPA. A homology model of the complex of RPA32C with the NEIL1 RPA binding motif in the CID was generated and used to design a set of mutations in NEIL1 to disrupt the interaction, which was confirmed by ITC. The mutant NEIL1 remains catalytically active against a thymine glycol lesion in duplex DNA in vitro. Testing the functional effect of disrupting the NEIL1-RPA interaction in vivo using a Fluorescence Multiplex-Host Cell Reactivation (FM-HCR) reporter assay revealed an unexpected role for NEIL1 in nucleotide excision repair. These findings are discussed in the context of the role of NEIL1 in replication-associated repair.

Repurposing GnRH-A as a Near-Infrared Fluorescent Probe for Diagnosis and Surgical Navigation of Breast Cancer Tumors and Metastases.

Breast cancer, globally the most common cancer in women, presents significant challenges in treatment. Breast-conserving surgery (BCS), a less traumatic and painful alternative to radical mastectomy, not only preserves the breast's appearance but also supports postsurgical functional recovery. However, accurately identifying tumors, precisely delineating margins, and thoroughly removing metastases remain complex surgical challenges, exacerbated by the limitations of current imaging techniques, including poor tumor uptake and low signal contrast. Addressing these challenges, our study developed a series of GnRHR-targeted probes (YQGN-n) for fluorescence imaging and surgical navigation of breast cancer through a drug repositioning strategy. Notably, YQGN-7, with its high cellular affinity (Kd of 217.8 nM), demonstrates exceptional selectivity and specificity for breast cancer tumors, surpassing traditional imaging agents like ICG in tumor uptake and pharmacokinetic properties. Furthermore, YQGN-7's effectiveness in surgical navigation, both for primary breast tumors and metastases, highlights its potential as a revolutionary tool in BCS.

Development and biological evaluation of 68Ga-labeled peptides for potential application in HER2-positive colorectal cancer

Colorectal cancer (CRC) is among the most lethal and prevalent malignancies in the world. Human epidermal growth factor receptor 2 (HER2) is a promising target for the diagnosis and treatment of CRC. In this study, we aimed to design, synthesize and label peptide-based positron emission tomography (PET) tracers targeting HER2-positive CRC, namely [68Ga]Ga-ES-01 and [68Ga]Ga-ES-02. The results show that [68Ga]Ga-ES-01 and [68Ga]Ga-ES-02 possessed hydrophilicity, rapid pharmacokinetic properties and excellent stabilities. [68Ga]Ga-ES-02 demonstrated higher binding affinity (Kd = 24.29 ± 4.95 nM) toward the HER2 in CRC. In HER2-positive HT-29 CRC xenograft mouse model, PET study showed specific tumor uptake after injection of [68Ga]Ga-ES-02 (SUV15min max = 0.87 ± 0.03; SUV30min max = 0.64 ± 0.02). In biodistribution study, the T/M ratios of 68Ga-ES-02 at 30 min after injection reached a maximum of 4.07 ± 0.34. In summary, we successfully synthesized and evaluated two novel peptide-based PET tracers. Our data demonstrate that [68Ga]Ga-ES-01/02 is capable of HER2-positive colorectal cancer, with [68Ga]Ga-ES-02 showing superior imaging effect, enhanced targeting, and increased specificity.

Advancing Cancer Theranostics Through Integrin αVβ3-Targeted Peptidomimetic IAC: From Bench to Bedside.

Introduction: The expression of alpha-five beta-three (αVβ3) integrins is upregulated in various malignancies undergoing angiogenesis. The development of integrin antagonists as diagnostic probes makes the αVβ3 integrin a suitable candidate for targeting tumor angiogenesis. The goal of this study was to optimize the radiolabeling and evaluate the potential of conjugated integrin antagonist carbamate (IAC), a peptidomimetic, as a theranostic radiopharmaceutical for targeting tumor angiogenesis. Methodology: Radiolabeling of DOTAGA [2,2',2"-{10-(2,6-dioxotetrahydro-2H-pyran-3-yl)-1,4,7,10-tetraazacyclododecane-1,4,7-triyl} triacetic-acid]-IAC with [68Ga]Ga, [177Lu]Lu, and [225Ac]Ac was optimized. The binding affinity (Kd) of DOTAGA-IAC for the αVβ3 receptor and cancer cell lines was quantified. The biodistribution studies were conducted in healthy Wistar rats. Dosimetry analysis was performed on [177Lu]Lu-DOTAGA-IAC distribution data. A pilot study of [68Ga]Ga-DOTAGA-IAC and [18F]FDG Positron Emission Tomography (PET/CT) imaging was performed in five patients with histopathologically confirmed breast cancer. PET/CT findings were compared between [68Ga]Ga-DOTAGA-IAC and [18F]FDG in these patients. Results: Radiopharmaceuticals were prepared with high radiochemical purity (>99.9%). Kd and Bmax measurements were 15.02 nM and 417 fmol for αVβ3 receptor protein: 115.7 nM and 295.3 fmol for C6 glioma cells. Biodistribution studies in rats suggested the excretion via kidneys and partially through the hepatobiliary route. The effective dose of [177Lu]Lu-DOTAGA-IAC was found to be 0.17 mSv/MBq. The dynamic study in patients revealed the optimal imaging time to be 30-35 mins postadministration. Out of the cohort, [68Ga]Ga-DOTAGA-IAC detected the primary lesions in all five patients with a mean standard uptake value (SUVmax) of 3.94 ± 0.58 compared with [18F]FDG (SUVmax 13.8 ± 6.53). Conclusion: The study demonstrates that DOTAGA-IAC exhibits strong binding to αVβ3 integrin, positioning it as a promising PET agent for assessing primary and metastatic cancers. The outcomes from the pilot study suggest the potential of [68Ga]Ga-DOTAGA-IAC PET/CT in breast carcinoma diagnosis. While recognizing the theranostic potential of DOTAGA-IAC for αVβ3 integrin-expressing tumors, further clinical investigations are warranted to comprehensively assess therapeutic efficacy.