Protein Binding Research Articles

Does Age Influence Immunosuppressant Drug Pharmacokinetics in Kidney Transplant Recipients?

The pharmacokinetics of immunosuppressant drugs may change with advancing age, potentially affecting patient outcomes. To characterise the effects of age on the pharmacokinetic and exposure parameters of tacrolimus, mycophenolate, and prednisolone. Pharmacokinetic profiling, involving whole blood tacrolimus, total and free plasma mycophenolic acid (MPA), total plasma mycophenolic acid glucuronide (MPAG), and total and free plasma prednisolone, was performed in an older and younger adult cohort. Thirteen samples were drawn on a single occasion, pre-oral dose and then at 0.25, 0.5, 0.75, 1, 1.25, 1.5, 2, 3, 4, 6, 9, and 12h post-dose. Non-compartmental analysis was conducted using the PKNCA package, and pharmacokinetic and exposure parameters were compared between age groups using a Mann-Whitney test. A regression analysis was conducted for free MPA and MPAG using significant variables of interest. This exploratory study included 21 older and 18 younger adults. Dose-adjusted tacrolimus, total MPA and free prednisolone pharmacokineticparameters were not different between age groups; however, for free MPA and MPAG, older recipients had significantly greater minimum and maximum concentrations, trough concentrations, and half-life. There was a two-fold increase in free MPA exposure in older adults (median dose-adjusted AUC0-12: 1284 vs. 684μgh/L, p<0.0001); MPAG exposure similarly increased. Age was significantly associated with free MPA and MPAG exposure, and free MPA exposure was associated with haematocrit (p<0.05). Differences in MPA were found with advancing age and may be due to altered kidney function, haematocrit, plasma protein binding and/or drug absorption. Future research should explore specific covariate contributions to this further.

Pharmacokinetic Profile of Ceftriaxone and Meropenem in Dogs

The principal aim of the study was evaluating the pharmacokinetic of ceftriaxone and meropenem in dogs, eight healthy male dogs were used for this experiment. A microbiological assay was used to determine the pharmacokinetic indices of ceftriaxone and meropenem given intravenously. The values were then fitted to a two-compartment pharmacokinetic open model in order to assess the factors related to distribution and excretion. The obtained results showed that the half-life, volume of distribution, and total body clearance to the samples of plasma of ceftriaxone and meropenem were recorded (0.83 h., 0.35 L/kg and 0.28 L/hr/kg), (0.86 h., 0.48 L/kg and 0.33 L/hr/kg), and the ratio of plasma protein binding were 16.67 %; 9.58 %, respectively. In conclusion, through the pharmacokinetic characteristics of meropenem and ceftriaxone in dogs, they possess an efficacious profile against K. pneumonia as same as other sensitive bacteria which were qualified to be a potential candidate to be one of the most commonly used parenterally administered antibacterial medicines in the treatment of acute bacterial cases that need to be treated quickly in veterinary therapy. However, the differences in the pharmacokinetic profile proved that the effectiveness of meropenem was more than ceftriaxone.

The Development and Application of Tritium-Labeled Compounds in Biomedical Research.

With low background radiation, tritiate compounds exclusively emit intense beta particles without structural changes. This makes them a useful tool in the drug discovery arsenal. Thanks to the recent rapid progress in tritium chemistry, the preparation and analysis of tritium-labeled compounds are now much easier, simpler, and cheaper. Pharmacokinetics, autoradiography, and protein binding studies have been much more efficient with the employment of tritium-labeled compounds. This review provides a comprehensive overview of tritium-labeled compounds regarding their properties, synthesis strategies, and applications.

Label-free, real-time monitoring of membrane binding events at zeptomolar concentrations using frequency-locked optical microresonators

G-protein coupled receptors help regulate cellular function and communication, and are targets of small molecule drug discovery efforts. Conventional techniques to probe these interactions require labels and large amounts of receptor to achieve satisfactory sensitivity. Here, we use frequency-locked optical microtoroids for label-free characterization of membrane interactions in vitro at zeptomolar concentrations for the kappa opioid receptor and its native agonist dynorphin A 1-13, as well as big dynorphin (dynorphin A and dynorphin B) using a supported biomimetic membrane. The measured affinity of the agonist dynorphin A 1-13 to the κ-opioid receptor was also measured and found to be 3.1 nM. Radioligand assays revealed a dissociation constant in agreement with this value (1.1 nM). The limit of detection for the κOR/DynA 1-13 was calculated as 180 zM. The binding of Cholera Toxin B-monosialotetrahexosyl ganglioside was also monitored in real-time and an equilibrium dissociation constant of 1.53 nM was found. Our biosensing platform provides a method for highly sensitive real-time characterization of membrane embedded protein binding kinetics that is rapid and label-free, for drug discovery and toxin screening among other applications.

Comprehensive study of plasma polymerization parameters on thiol-coated LDPE films for effective fibronectin adsorption targeting biomedical applications

In the realm of biomedical applications, biocompatible materials with optimized surface properties are crucial for facilitating cellular interactions. To attain the perfect balance of these properties, surface modification of non-toxic and stable bulk materials is often required. Within this context, this research aimed to improve the physiochemical and cell-responsive properties of a low-density polyethylene film. This was achieved by depositing thiol-rich coatings using a dielectric barrier discharge plasma reactor operating at medium pressures, with 1-propanethiol serving as polymerization precursor. The study systematically investigated the impact of key plasma polymerization parameters, including DBD chamber pressure, treatment time, and the combination of precursor flow rate and discharge power represented by the Yasuda parameter, to identify optimal plasma processing conditions for the formation of thiol-rich coatings. To characterize the coating thickness, hydrophilicity and surface chemical composition, atomic force microscopy, water contact angle measurements, and X-ray photoelectron spectroscopy were employed. The findings indicated that reducing the chamber pressure to 10 kPa led to more hydrophilic and thicker deposits possessing a higher sulphur content. Deposition time (5 to 15 min) also significantly impacted coating thickness and surface chemistry, where long times increased thickness, but also led to a reduced sulphur and increased oxygen content because of more pronounced etching. The optimal deposition time was therefore set at 10 min resulting in the deposition of dense coatings possessing a high number of sulphur-containing functionalities. The Yasuda parameter (W/FM) analysis demonstrated optimal thiol incorporation in combination with high coating stability at an intermediate W/FM value of 72 MJ/kg. Following the determination of the optimal plasma polymerization parameters, the effectiveness of thiol plasma polymerization and subsequent fibronectin immobilization for enhancing cell adhesion and proliferation was investigated. The thiol-coated substrates were found to exhibit superior protein immobilization, because of the high affinity for protein binding of the available thiol groups. To assess cellular responses, Schwann cells were cultured on uncoated and coated samples before and after fibronectin immobilization. The results revealed a superior cellular response of the thiol-coated samples after fibronectin immobilization, showing the highest cell viability and significantly enhanced cell adhesion and proliferation. Collectively, these results underscore the synergistic effect of thiol plasma polymerization and fibronectin immobilization in promoting the cellular response of LDPE substrates, thus highlighting their potential as a surface modification strategy of biomaterials.

YAP1 regulates thrombopoiesis by binding to MYH9 in immune thrombocytopenia

Immune thrombocytopenia (ITP) is a complicated bleeding disease characterized by sharp platelet reduction. As a dominating element involved in ITP, megakaryocytes (MKs) are responsible for thrombopoiesis. However, the mechanism underlying the dysregulation of thrombopoiesis that occurs in ITP remains unidentified. In this study, we examined the role of yes-associated protein 1 (YAP1) in thrombopoiesis during ITP. We observed a reduced YAP1 expression with cytoskeletal actin misalignment in MKs from ITP patients. By using an experimental ITP mouse model, we showed that reduced YAP1 expression induced aberrant MK distribution, reduced the percentage of late MKs among total MKs, and caused submaximal platelet recovery. Mechanistically, YAP1 upregulation by binding of GATA binding protein 1 (GATA1) to its promoter promoted MK maturation. Phosphorylated YAP1 promoted cytoskeletal activation by binding of its WW2 domain to myosin heavy chain 9 (MYH9), facilitating thrombopoiesis. Targeting YAP1 by its activator XMU-MP-1 was sufficient to rescue cytoskeletal defects and thrombopoiesis dysregulation in YAP1+/- mice with ITP and patients. Taken together, these results demonstrate a crucial role for YAP1 in thrombopoiesis, providing a potential for the development of diagnostic markers and therapeutic options for ITP.

RNA nanotherapeutics with fibrosis overexpression and retention for MASH treatment

Metabolic dysfunction-associated steatohepatitis (MASH) poses challenges for targeted delivery and retention of therapeutic proteins due to excess extracellular matrix (ECM). Here we present a new approach to treat MASH, termed “Fibrosis overexpression and retention (FORT)”. In this strategy, we design (1) retinoid-derivative lipid nanoparticle (LNP) to enable enhanced mRNA overexpression in fibrotic regions, and (2) mRNA modifications which facilitate anchoring of therapeutic proteins in ECM. LNPs containing carboxyl-retinoids, rather than alcohol- or ester-retinoids, effectively deliver mRNA with over 10-fold enhancement of protein expression in fibrotic livers. The carboxyl-retinoid rearrangement on the LNP surface improves protein binding and membrane fusion. Therapeutic proteins are then engineered with an endogenous collagen-binding domain. These fusion proteins exhibit increased retention in fibrotic lesions and reduced systemic toxicity. In vivo, fibrosis-targeting LNPs encoding fusion proteins demonstrate superior therapeutic efficacy in three clinically relevant male-animal MASH models. This approach holds promise in fibrotic diseases unsuited for protein injection.

Preclinical pharmacokinetic studies and prediction of human PK profiles for Deg-AZM, a clinical-stage new transgelin agonist.

Deglycosylated azithromycin (Deg-AZM), a newly developed Class I drug with good therapeutic effects on slow transit constipation, is a small-molecule transgelin agonist that has been approved for clinical trials in 2024. The preclinical pharmacokinetic profile of Deg-AZM was investigated to support further development. A LC-MS/MS method was established and validated to detected the concentration of Deg-AZM in various biological samples. In vivo tests such as pharmacokinetic studies in rats and dogs, tissue distribution studies in rats, and extraction studies in rats were conducted to investigated the preclinical pharmacokinetic behaviors of Deg-AZM comprehensively. The plasma protein rate of Deg-AZM was determined by rapid equilibrium dialysis method in vitro. The metabolic stability and metabolite profile of Deg-AZM was assessed using pooled mice, rats, dogs, monkeys and humans microsomes in vitro. The PK profiles of Deg-AZM in human was predicted based on physiologically based pharmacokinetic (PBPK) models. The plasma protein binding rates of Deg-AZM were lower in mice and rats, higher in dogs, and moderate in humans. The metabolic process of Deg-AZM was similar in rat and human liver microsomes. From Pharmacokinetic studies in rats and dogs, Deg-AZM was rapidly absorbed into the blood and then quickly eliminated. Plasma exposure of Deg-AZM was dose dependent with no accumulation after continuous gavage administration. In addition, there is no significant gender difference in the pharmacokinetic behavior of Deg-AZM. Deg-AZM was widely distributed in the tissues without obvious accumulation, and mainly excreted from the urinary excretion pathway. Furthermore, the pharmacokinetic profiles of Deg-AZM in humans showed dose dependency. The pharmacokinetic profiles of Deg-AZM was fully explored, these results could provide valuable information to support the first-in-human dosage prediction and phase I clinical design.

Spectral Characteristics, In Silico Perspectives, Density Functional Theory (DFT), and Therapeutic Potential of Green-Extracted Phycocyanin from Spirulina.

Phycocyanin (PC) is a naturally occurring green pigment in Spirulina. It was extracted by ultrasonic extraction using green technology, and its structure was studied using IR- and NMR-spectroscopy. Spectral data confirmed the PC structure. This study also involves an in silico assessment of the diverse applications of green pigment PC. Utilizing QSAR, PreADME/T, SwissADME, and Pro-Tox, this study explores the safety profile, pharmacokinetics, and potential targets of PC. QSAR analysis reveals a favorable safety profile, with the parent structure and most metabolites showing no binding to DNA or proteins. PreADME/T indicates low skin permeability, excellent intestinal absorption, and medium permeability, supporting oral administration. Distribution analysis suggests moderate plasma protein binding and cautious blood-brain barrier permeability, guiding formulation strategies. Metabolism assessments highlight interactions with key cytochrome P450 enzymes, influencing drug interactions. Target prediction analysis unveils potential targets, suggesting diverse therapeutic effects, including cardiovascular benefits, anti-inflammatory activities, neuroprotection, and immune modulation. Based on the in silico analysis, PC holds promise for various applications due to its safety, bioavailability, and potential therapeutic benefits. Experimental validation is crucial to elucidate precise molecular mechanisms, ensuring safe and effective utilization in therapeutic and dietary contexts. DFT calculations, including geometry optimization, MEP analysis, HOMO-LUMO energy surface, and quantum reactivity parameters of the PC compound, were obtained using the B3LYP/6-311G(d,p) level. This integrated approach contributes to a comprehensive understanding of PC's pharmacological profile and informs future research directions.

Biosynthesis of silver nanoparticles using green tea aqueous leaf extract and their biological and chemotherapeutic activity

Green tea leaf extract-mediated silver nanoparticles (GT-AgNPs) were synthesized and characterized for their biological and chemotherapeutic activity. The synthesis process involved the reduction of silver ions by green tea leaf extract (GTLE), resulting in the formation of GT-AgNPs. Characterization techniques including UV–Vis spectroscopy, Fourier-transform infrared spectroscopy (FTIR), X-ray diffractometry (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS), and zeta potential analysis were employed to study the physicochemical properties of GT-AgNPs. The GT-AgNPs exhibited a characteristic color change and a noticeable shift in the surface plasma resonance (SPR) absorption peak at 458 nm, confirming their successful formation of nanoparticles. XRD analysis indicated a cubic structure with a crystallite size of 9 ± 1 nm. Both SEM and TEM images revealed that the spherical shape and size of the synthesized nanoparticles. The SEM analysis confirmed that the average grain size of GT-AgNPs is 20.27 ± 1 nm, while the TEM analysis determined the average particle size of 9 ± 0.025. GT-AgNPs have a negative zeta potential of -19.7 mV indicating a hydrodynamic diameter of 140.90 nm with a polydispersity index (PDI) of 25.8 %. XPS confirmed the oxidation state of Ag0/+1 in GT-AgNPs. The energy band gap (Eg) value of GT-AgNPs is 3.38 eV, indicating semiconducting properties, while fluorescence activity was observed at 506.17 nm. CT-DNA and BSA protein binding studies demonstrated the formation of CT-DNA-GT-AgNPs and BSA-GT-AgNPs complexes with binding constants of 1.366×1010 M−1 and 6.77×109 M−1, respectively. GT-AgNPs exhibited exceptional anti-oxidant activity by effectively scavenging stable 2, 2ʹ - diphenyl-1-picryl hydroxyl (DPPH) radicals. Cytotoxicity assays using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) demonstrate moderate activity against KB3 and AGS cancer cells while showing no detectable cytotoxicity in Caco-2 cells. This indicates a safe therapeutic window for human eukaryotic cells.

Research Progress on Saccharide Molecule Detection Based on Nanopores.

Saccharides, being one of the fundamental molecules of life, play essential roles in the physiological and pathological functions of cells. However, their intricate structures pose challenges for detection. Nanopore technology, with its high sensitivity and capability for single-molecule-level analysis, has revolutionized the identification and structural analysis of saccharide molecules. This review focuses on recent advancements in nanopore technology for carbohydrate detection, presenting an array of methods that leverage the molecular complexity of saccharides. Biological nanopore techniques utilize specific protein binding or pore modifications to trigger typical resistive pulses, enabling the high-sensitivity detection of monosaccharides and oligosaccharides. In solid-state nanopore sensing, boronic acid modification and pH gating mechanisms are employed for the specific recognition and quantitative analysis of polysaccharides. The integration of artificial intelligence algorithms can further enhance the accuracy and reliability of analyses. Serving as a crucial tool in carbohydrate detection, we foresee significant potential in the application of nanopore technology for the detection of carbohydrate molecules in disease diagnosis, drug screening, and biosensing, fostering innovative progress in related research domains.

Role of PQBP1 in Pathogen Recognition-Impact on Innate Immunity.

The intrinsically disordered polyglutamine-binding protein 1 (PQBP1) has been linked to various cellular processes including transcription, alternative splicing, translation and innate immunity. Mutations in PQBP1 are causative for neurodevelopmental conditions collectively termed as the Renpenning syndrome spectrum. Intriguingly, cells of Renpenning syndrome patients exhibit a reduced innate immune response against human immunodeficiency virus 1 (HIV-1). PQBP1 is responsible for the initiation of a two-step recognition process of HIV-1 reverse-transcribed DNA products, ensuring a type 1 interferon response. Recent investigations revealed that PQBP1 also binds to the p17 protein of avian reovirus (ARV) and is affected by the ORF52 of Kaposi's sarcoma-associated herpesvirus (KSHV), possibly also playing a role in the innate immune response towards these RNA- and DNA-viruses. Moreover, PQBP1-mediated microglia activation in the context of tauopathies has been reported, highlighting the role of PQBP1 in sensing exogenous pathogenic species and innate immune response in the central nervous system. Its unstructured nature, the promiscuous binding of various proteins and its presence in various tissues indicate the versatile roles of PQBP1 in cellular regulation. Here, we systematically review the available data on the structure of PQBP1 and its cellular functions and interactome, as well as possible implications for innate immune responses and neurodegenerative disorders.

Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction.

Protein and nucleic acid binding site prediction is a critical computational task that benefits a wide range of biological processes. Previous studies have shown that feature selection holds particular significance for this prediction task, making the generation of more discriminative features a key area of interest for many researchers. Recent progress has shown the power of protein language models in handling protein sequences, in leveraging the strengths of attention networks, and in successful applications to tasks such as protein structure prediction. This naturally raises the question of the applicability of protein language models in predicting protein and nucleic acid binding sites. Various approaches have explored this potential. This paper first describes the development of protein language models. Then, a systematic review of the latest methods for predicting protein and nucleic acid binding sites is conducted by covering benchmark sets, feature generation methods, performance comparisons, and feature ablation studies. These comparisons demonstrate the importance of protein language models for the prediction task. Finally, the paper discusses the challenges of protein and nucleic acid binding site prediction and proposes possible research directions and future trends. The purpose of this survey is to furnish researchers with actionable suggestions for comprehending the methodologies used in predicting protein-nucleic acid binding sites, fostering the creation of protein-centric language models, and tackling real-world obstacles encountered in this field.

Highly efficient synthesis of isoxazolones and pyrazolones using g-C3N4·OH nanocomposite with their in silico molecular docking, pharmacokinetics and simulation studies

An environmentally friendly, versatile multicomponent reaction for synthesizing isoxazol-5-one and pyrazol-3-one derivatives has been developed, utilizing a freshly prepared g-C3N4·OH nanocomposite as a highly efficient catalyst at room temperature in aqueous environment. This innovative approach yielded all the desired products with exceptionally high yields and concise reaction durations. The catalyst was well characterized by FT-IR, XRD, SEM, EDAX, and TGA/DTA studies. Notably, the catalyst demonstrated outstanding recyclability, maintaining its catalytic efficacy over six consecutive cycles without any loss. The sustainability of this methodology was assessed through various eco-friendly parameters, including E-factor and eco-score, confirming its viability as a green synthetic route in organic chemistry. Additionally, the gram-scale synthesis verifies its potential for industrial applications. The ten synthesized compounds were also analyzed via a PASS online tool to check their several pharmacological activities. The study is complemented by in silico molecular docking, pharmacokinetics, and molecular dynamics simulation studies. These studies discover 5D as a potential candidate for drug development, supported by its favorable drug-like properties, ADMET studies, docking interaction, and stable behavior in the protein binding cavity.

Capturing RAS oligomerization on a membrane

RAS GTPases associate with the biological membrane where they function as molecular switches to regulate cell growth. Recent studies indicate that RAS proteins oligomerize on membranes, and disrupting these assemblies represents an alternative therapeutic strategy. However, conflicting reports on RAS assemblies, ranging in size from dimers to nanoclusters, have brought to the fore key questions regarding the stoichiometry and parameters that influence oligomerization. Here, we probe three isoforms of RAS [Kirsten Rat Sarcoma viral oncogene (KRAS), Harvey Rat Sarcoma viral oncogene (HRAS), and Neuroblastoma oncogene (NRAS)] directly from membranes using mass spectrometry. We show that KRAS on membranes in the inactive state (GDP-bound) is monomeric but forms dimers in the active state (GTP-bound). We demonstrate that the small molecule BI2852 can induce dimerization of KRAS, whereas the binding of effector proteins disrupts dimerization. We also show that RAS dimerization is dependent on lipid composition and reveal that oligomerization of NRAS is regulated by palmitoylation. By monitoring the intrinsic GTPase activity of RAS, we capture the emergence of a dimer containing either mixed nucleotides or GDP on membranes. We find that the interaction of RAS with the catalytic domain of Son of Sevenless (SOScat) is influenced by membrane composition. We also capture the activation and monomer to dimer conversion of KRAS by SOScat. These results not only reveal the stoichiometry of RAS assemblies on membranes but also uncover the impact of critical factors on oligomerization, encompassing regulation by nucleotides, lipids, and palmitoylation.

Integrated CRISPR/Cas12a with terminal protection strategy for homogeneous protein assay

Developing appropriate protein assay methods is necessary, as protein assays play an important role in molecular diagnosis, drug screening, and biomedical research. This article presents a universal homogeneous method based on the CRISPR/Cas12a system and the terminal protection strategy for protein assays. Initially, a single-stranded DNA (ssDNA) labeled with a small molecule at its 3’-end was designed to respond to the target protein and serve as an activator of Cas12a. In the absence of the target protein, small-molecule-linked ssDNA was effectively cleaved using exonuclease I (Exo I). The lack of the activator resulted in the trans-cleavage inactivity of Cas12a, leading to low fluorescence in the detection solution. However, in the presence of the target protein, the specific binding of the target protein to the small molecules on the activator protected the activator against digestion by Exo I. The remaining intact activator triggered the trans-cleavage activation of Cas12a, producing strong fluorescence. Based on this principle, our method achieved fluorescence enhanced detection of the target protein. After experimental condition optimization, our method achieved highly sensitive and specific protein detection in two models: folate receptor and streptavidin. The excellent performance of the fluorescence method highlights the applicability and effectiveness of the CRISPR/Cas12a system in protein assays, and broadening its application scope.

Galectin-3 induces pathogenic immunosuppressive macrophages through interaction with TREM2 in lung cancer

BackgroundHigh infiltration of tumor-associated macrophages (TAMs) is associated with tumor promotion and immunosuppression. The triggering receptor expressed on myeloid cells 2 (TREM2) is emerged as a key immunosuppressive regulator for TAMs, however, how TREM2-expressing TAMs are recruited and what ligands TREM2 interacts with to mediate immunosuppression is unknown.MethodsFlow cytometry and single-cell RNA sequencing were used to analyze TREM2 expression. Mechanistically, mass spectrometry and immunoprecipitation were employed to identify proteins binding to TREM2. Phagocytosis and co-culture experiments were used to explore the in vitro functions of galectin3-TREM2 pair. Establishment of TREM2f/f-Lyz2-cre mice to validate the role of TREM2 signaling pathway in lung carcinogenesis. GB1107 were further supplemented to validate the therapeutic effect of Galectin3 based on TREM2 signaling regulation.ResultsThis study identified that abundant TREM2+ macrophages were recruited at the intra-tumor site through the CCL2-CCR2 chemotactic axis. Galectin-3 impaired TREM2-mediated phagocytosis and promoted the conversion of TREM2+ macrophages to immunosuppressive TAMs with attenuated antigen presentation and co-stimulatory functions both in vitro both in vivo, and galectin-3 is a potential ligand for TREM2. Genetic and pharmacological blockade of TREM2 and galectin-3 significantly inhibited lung cancer progression in subcutaneous and orthotopic cancer models by remodeling the tumor immune microenvironment.ConclusionOur findings revealed a previously unknown association between galectin-3 and TREM2 in TAMs of lung cancer, and suggested simultaneous inhibition of galectin3 and TREM2 as potent therapeutic approach for lung cancer therapy.Graphical

Predicting monoclonal antibody binding sequences from a sparse sampling of all possible sequences

Previous work has shown that binding of target proteins to a sparse, unbiased sample of all possible peptide sequences is sufficient to train a machine learning model that can then predict, with statistically high accuracy, target binding to any possible peptide sequence of similar length. Here, highly sequence-specific molecular recognition is explored by measuring binding of 8 monoclonal antibodies (mAbs) with specific linear cognate epitopes to an array containing 121,715 near-random sequences about 10 residues in length. Network models trained on resulting sequence-binding values are used to predict the binding of each mAb to its cognate sequence and to an in silico generated one million random sequences. The model always ranks the binding of the cognate sequence in the top 100 sequences, and for 6 of the 8 mAbs, the cognate sequence ranks in the top ten. Practically, this approach has potential utility in selecting highly specific mAbs for therapeutics or diagnostics. More fundamentally, this demonstrates that very sparse random sampling of a large amino acid sequence spaces is sufficient to generate comprehensive models predictive of highly specific molecular recognition.

Interactome of the HIV-1 proteome and human host RNA

The human immunodeficiency virus (HIV-1) is highly dependent on a variety of host factors. Beside proteins, host RNA molecules are reported to aid HIV-1 replication and latency maintenance. Here, we implement multiple workflows of native RNA immunoprecipitation and sequencing (nRIPseq) to determine direct host RNA interaction partners of all 18 HIV-1 (poly)proteins. We identify 1,727 HIV-1 protein – human RNA interactions in the Jurkat cell line and 1,558 interactions in SupT1 cells for a subset of proteins, and discover distinct cellular pathways that seem to be used or controlled by HIV-1 on the RNA level: Tat binds mRNAs of proteins involved in the super elongation complex (AFF1-4, Cyclin-T1). Correlation of the interaction scores (based on binding abundancy) allows identifying the highest confidence interactions, for which we perform a small-scale knockdown screen that leads to the identification of three HIV-1 protein binding RNA interactors involved in HIV-1 replication (AFF2, H4C9 and RPLP0).

SARS-CoV-2 seroprevalence in people living with HIV in South Sudan

ObjectivesThe burden of SARS-CoV-2 infection in people living with HIV (PLHIV) in South Sudan is unknown. MethodsWe conducted a cross-sectional seroprevalence survey of SARS-CoV-2 immunoglobulin (Ig) G antibodies and other diseases of public health importance (strongyloidiasis, toxoplasmosis) in PLHIV in South Sudan during April 1, 2020-April 30, 2022. We used a multiplex SARS-CoV-2 immunoassay to detect IgG antibodies targeting the SARS-CoV-2 spike, receptor binding domain, and nucelocapsid (N) proteins, and antigens for other pathogens (Strongyloides stercoralis and Toxoplasma gondii). ResultsAmong 3518 samples tested, seroprevalence of IgG antibodies to SARS-CoV-2 spike protein and receptor binding domain 591 and nucleocapsid ranged from 1.4% (95% confidence interval [CI]: 0.9-2.1%) in April-June 2020 to 53.3% (95% CI: 49.5-57.1%) in January-March 2022. The prevalence of S. stercoralis IgG ranged between 27.3% (95% CI: 23.4-31.5%) in October-December 2021 and 47.2% (95% CI: 37.8-56.8%) in July-September 2021, and, for T. gondii IgG, prevalence ranged from 15.5% (95% CI: 13.3-17.9%) in April-June 2020 to 36.2% (95% CI: 27.4-46.2%) July-September 2021. ConclusionsBy early 2022, PLHIV in South Sudan had high rates of SARS-CoV-2 seropositivity. Surveillance of diseases of global health concern in PLHIV is crucial to estimate population-level exposure and inform public health responses.