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Acta Pharmaceutica Sinica B

Elsevier BV

Preprints posted in the last 90 days, ranked by how well they match Acta Pharmaceutica Sinica B's content profile, based on 11 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit.

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Discovery of Semicarbazone and Thiosemicarbazone Analogs as Competitive SARS-CoV-2 Virus Main Protease (Mpro) Inhibitors

Barreto, L. V.; Lourenco, E. M. G.; da Silva, E. B.; de Godoy, M. O.; Martins, L. C.; Laureano de Souza, M.; Almeida, R. G.; Cunha, V. L. S.; Pires, M. C.; Lavorato, S. N.; de Souza, T. B.; Bretas, A. C. O.; Ottoni, F. M.; Junior, E. N. S.; Oliva, G.; Alves, R. J.; de Oliveira, R. B.; Guido, R. V. C.; Ferreira, R. S.

2026-03-12 biochemistry 10.64898/2026.03.11.711159 medRxiv
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Despite the development of vaccines and antivirals, coronavirus disease 2019 (COVID-19) continues to affect populations worldwide. Given the high mutation rate of the SARS-CoV-2 virus and reports of drug resistance, there is a continued need for new therapeutic options. SARS-CoV-2 main protease (Mpro) is essential for viral replication and is a conserved target among coronaviruses. Most known Mpro inhibitors target the active site, although allosteric sites have already been identified. In this study, we conducted a virtual screening of 2,060 compounds targeting an allosteric site of SARS-CoV-2 Mpro. From this screen, 41 computational hits and analogs were selected and evaluated using biochemical assays against SARS-CoV-2 Mpro. Among them, compound 25, a semicarbazone, demonstrated a half-maximal inhibitory concentration (IC50) of 99 M. Additionally, two thiosemicarbazone analogs (compounds 50 and 51) inhibited SARS-CoV-2 Mpro with IC50 values of 61 M and 70 M. Biochemical assays suggest that these compounds act as noncovalent competitive inhibitors of SARS-CoV-2 Mpro. Molecular dynamics simulations revealed that compound 25 is unstable at the allosteric site of SARS-CoV-2 Mpro but forms stable and favorable interactions at the active site, supporting its potential as a competitive inhibitor, a finding subsequently confirmed by biochemical assays. Our structure-based computational and biochemical approach identified semicarbazone and thiosemicarbazone scaffolds as promising candidates for the development of reversible SARS-CoV-2 Mpro inhibitors.

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Discovery of dual thiobarbiturate-indole scaffold as a selective inhibitor targeting chikungunya virus nsP3 macrodomain through a cryptic binding pocket

Duong, M. T. H.; Parviainen, T. A. O.; Thiruvaiyaru, A.; Ahola, T.; Heiskanen, J. P.; Lehtiö, L.

2026-03-12 biochemistry 10.64898/2026.03.10.710793 medRxiv
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The chikungunya virus (CHIKV) outbreak imposes a significant burden on healthcare systems and raises an urgent need for effective antiviral therapies. So far there are no specific drugs against CHIKV. A CHIKV macrodomain is critical for virulence and counteracts the host immune response, representing a promising antiviral drug target. Here, we describe small molecule inhibitors targeting the CHIKV macrodomain. Compound 1 (MDOLL-0273) was identified through a high-throughput screening using a fluorescence resonance energy transfer (FRET)-based assay, and its inhibitory activity was validated through multiple orthogonal assays. Compound 1 has a dual thiobarbiturate-indole scaffold and exhibits an IC50 of 8.9 {micro}M. X-ray crystallography revealed that the inhibitor occupies an adenine binding site of the macrodomain and extends into a novel cryptic pocket. Notably, the inhibitor shows high selectivity for the CHIKV macrodomain over a panel of human and viral ADP-ribosyl binding and hydrolyzing proteins. Structure-activity relationship studies and medicinal chemistry efforts provide a promising starting point for further hit optimization.

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A High-throughput Fluorescence Polarization Assay for Screening Sirtuin Inhibitors

Peng, K.; Chakraborty, S.; Jin, Y.; Lin, H.

2026-04-17 biochemistry 10.64898/2026.04.06.716694 medRxiv
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Sirtuins (SIRTs), which remove protein lysine acyl modifications, play crucial roles in diverse cellular processes, including metabolism, gene transcription, DNA damage repair, cell survival, and stress response. Several sirtuins are considered non-oncogene addiction of cancer cells and promising targets for anticancer drug development. High-throughput screening (HTS) methods for sirtuins are critical for the development of potent and isoform-selective sirtuin inhibitors, which are needed to validate the therapeutic potential. Herein, we designed and synthesized a fluorescent polarization (FP) tracer, KP-SC-1. Using this high-affinity tracer, we developed a robust, high-throughput FP competition assay for screening SIRT1-3 inhibitors. The assay was validated by testing known SIRT1-3 inhibitors. The assay can detect NAD+-independent SIRT1-3 inhibitors, as well as NAD+-dependent inhibitors, such as Ex-527 and TM. Finally, our assay showed satisfactory stability and outstanding performance in a pilot library screening. Compared to previous assays, the FP assay uses much less SIRT1-3 enzymes, a feature important for high-throughput library screening. We believe that the FP assay developed here will accelerate the discovery and development of SIRT1-3 inhibitors.

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Stable isotope-assisted computational mass spectrometry reveals root-specific alkaloids in Glycyrrhiza species

Sawai, K.; Todoroki, Y.; Nakamukai, S.; Matsuzawa, Y.; Noguchi, K.; Kato, T.; Mori, T.; Rai, A.; Hirai, M. Y.; Tsugawa, H.

2026-05-08 biochemistry 10.64898/2026.05.05.722977 medRxiv
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Licorice (Glycyrrhiza) is a medicinal plant widely used in approximately 70% of traditional Japanese Kampo formulations and is known to produce a wide array of specialized metabolites with diverse pharmacological properties. Although hundreds of metabolites have been reported, the overall chemical diversity of Glycyrrhiza remains poorly characterized. Here, using mass spectrometry data obtained from fully 13C-labeled leaves and roots of Glycyrrhiza uralensis and Glycyrrhiza glabra, we determined the carbon number, followed by molecular formula and substructure prediction in combination with MS/MS similarity-based molecular networking. After excluding redundant ions, including isotopic peaks, adducts, and in-source fragments, we extracted 3,060 unique metabolite features with assigned carbon numbers. Among these, substructure information was assigned to 1,015 features (33%) across the four plant tissues, revealing the tissue-specific metabolome profiles. Furthermore, we discovered five previously unreported alkaloids, homopipecolic acid-conjugated flavonoids, in the roots of G. uralensis and G. glabra, and Glycine max, another member of the Fabaceae family. Two of these structures were validated using nuclear magnetic resonance spectroscopy. We further proposed a biosynthetic route involving a spontaneous reaction between 1-piperideine and malonyl glycoside substrates and confirmed the formation of the conjugated product using authentic standards.

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An Integrated Computational-Experimental Strategy For the Prediction of Small Molecules as GLP-1R Agonists

Murcia Garcia, E.; Tian, N.; Alonso Fernandez, J. R.; Cai, X.; Yang, D.; Hernandez Morante, J. J.; Perez Sanchez, H.

2026-04-01 bioinformatics 10.64898/2026.03.30.715288 medRxiv
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The glucagon-like peptide-1 receptor (GLP-1R) plays a central role in metabolic regulation and is a major therapeutic target for obesity and diabetes. Peptide agonists, like semaglutide, targeting the GLP-1R remain among the most effective regulators of glucose metabolism and appetite. Nonetheless, recent reports about weight regain have limited the effectiveness of GLP1R peptide agonists, sustaining the interest in expanding the chemical diversity of GLP-1R ligands through drug discovery strategies. However, the structural complexity and conformational plasticity of class B1 GPCRs make conventional single-method virtual screening approaches prone to bias and limited chemotype recovery. Using an integrated ligand- and structure-based virtual screening pipeline, explicitly combining complementary ligand-based descriptors, multi-fingerprint similarity, electrostatic similarity, pharmacophore modeling, and multi-conformation docking under a consensus-driven selection strategy, we were able to identify three chemically distinct classes of GLP-1R agonist candidates: GQB47810, a non-peptidic molecule; neuromedin C, a peptide, and 2,5-Pen-enkephalin (DPDPE), a small peptide. From all of them, DPDPE showed the greatest effectiveness, reaching values similar to those of GLP-1, although with lower potency. Further in vitro characterization confirmed that pen-enkephalin behaved as a full agonist and exhibited dual GLP-1R/GIPR agonistic activity. These findings establish a consensus-driven and transferable computational framework for chemotype-diverse agonist discovery at conformationally flexible GPCR targets, and revealed a pentapeptide with GLP-1-like efficacy as a promising lead for next-generation small peptide therapeutics.

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A Fragment Screen Identifies Acrylamide Covalent Inhibitors of the TEAD/YAP Protein-Protein Interaction

Bum-Erdene, K.; Ghozayel, M. K.; Zhang, M. J.; Gonzalez-Gutierrez, G.; Meroueh, S. O.

2026-03-20 biochemistry 10.64898/2026.03.18.712694 medRxiv
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TEA domain (TEAD) proteins bind co-activator Yes-associated protein (YAP) to regulate the expression of target genes of the Hippo pathway. The TEAD*YAP protein-protein interaction is not druggable, but TEADs possess a unique and deep palmitate pocket with a highly conserved cysteine located outside the TEAD*YAP protein-protein interaction interface. Here, we screen a fragment library of acrylamide electrophiles and identify a fragment that forms an adduct with the conserved palmitate pocket cysteine and inhibits TEAD4 binding to YAP. Synthesis of a focused set of derivatives and time- and concentration-dependent studies with four TEADs provide reaction rates and binding constants. Co-crystal structures of fragments bound to TEAD2 and TEAD3 reveal reaction at the conserved palmitate pocket cysteine but also at another less conserved cysteine located in the palmitate pocket of TEAD2 closer to the TEAD*YAP interface. These fragments provide a starting point for the development of allosteric acrylamide small-molecule covalent TEAD*YAP inhibitors.

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Identification of key Y4R residues enables the discovery of selective non-peptide small-molecule agonists

Beck-Sickinger, A. G.; Pelczyk, T.; Schuss, C.; Sklodowski, M.; Liessmann, F.; Jordan, D.; Ehrlich, V.; Eisenhuth, P.; Stichel, J.; Gattor, A. O.; Keller, M.; Meiler, J.

2026-05-01 biochemistry 10.64898/2026.04.27.721169 medRxiv
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G protein-coupled receptors (GPCRs) are central regulators of human physiology and disease, classifying them as relevant targets for therapeutic interventions. As transmembrane proteins, they convert extracellular signals into intracellular responses through agonist-induced conformational changes. Understanding how agonists stabilize active receptor conformations is decisive for rational drug design. In this study, we used the endogenous ligand pancreatic polypeptide (PP) and the cyclic hexapeptides UR-AK95c and UR-AK86c as molecular tools to determine key interactions critical for Y4R activation, which plays a crucial role in metabolic diseases. Guided by molecular docking, we systematically replaced Y4R residues and assessed activation. The in vitro and in silico studies delineated a key Y4R activation interface centered around the conserved C-terminal RXRY-NH2 motif of the peptides and, separately, identified receptor residues with distinct peptide-specific functional effects. Next, we performed an ultra-large library screening (ULLS) and experimentally validated three predicted hits as selective Y4R agonists that engage in a substantial subset of the identified critical receptor contacts. This study demonstrates how GPCR activation interface knowledge can be translated into the discovery of novel small-molecule agonists and outlines a general strategy for advanced GPCR drug discovery.

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Computational Design of Novel Selective Phosphodiesterase 4B Inhibitors from Natural Products: An Integrated Machine Learning and Structure-Based Drug Discovery Approach

Oni, S. A.; Oyemomi, M. D.; Osho, A.; Abdulfatai, A.

2026-05-19 bioinformatics 10.64898/2026.05.16.725619 medRxiv
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Selective inhibition of phosphodiesterase 4B (PDE4B) remains a promising strategy for preserving the anti-inflammatory benefit of PDE4 inhibition in chronic obstructive pulmonary disease while reducing PDE4D-associated tolerability liabilities. This study integrated SHAP-interpretable machine learning, natural product virtual screening, hierarchical docking, post-docking MM-GBSA, isoform cross-docking, binding-pocket comparison, ADMET prediction, and 100 ns molecular dynamics simulations to identify PDE4B-selective inhibitors from the LOTUS natural product database. A Random Forest classifier trained on curated ChEMBL PDE4B bioactivity data achieved an external performance with AUC-ROC = 0.955, accuracy = 0.893, F1-score = 0.896, MCC = 0.785, and prioritized 119,698 predicted actives from 276,518 LOTUS compounds. SHAP analysis identified BertzCT and TPSA as major contributors to predicted activity. Sequential Lipinski, PAINS, and QED filtering retained 14,210 candidates for structure-based evaluation. Extra precision docking identified four leads with PDE4B docking scores of -9.123 to -12.080 kcal/mol, all outperforming roflumilast (-7.658 kcal/mol). Cross-docking and post-docking MM-GBSA supported preferential PDE4B binding for three candidates. The top lead, LTS0048837, maintained a stable PDE4B-bound pose during simulation, with comparatively stronger interaction persistence than its PDE4D complex and the roflumilast reference. These findings nominate LTS0048837 as a computationally prioritized PDE4B-selective natural product lead requiring experimental enzyme, cellular, and pharmacokinetic validation.

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The discovery of missing taxane C13α-O-deacetylases re-delineates the biosynthetic pathway of paclitaxel

Li, C.; Sun, X.; Chen, R.; Xie, K.; Chen, D.; Liu, J.; Dai, J.

2026-04-30 biochemistry 10.64898/2026.04.28.721278 medRxiv
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The prevalence of naturally occurring C13-acetoxy taxanes, together with the presence of a native C13-acetyltransferase in yew trees, suggests that the natural biosynthetic pathway for paclitaxel may involve a cryptic C13-O-deacetylation step. However, whether a putative taxane C13-O-deacetylase (T13dA) acts in the pathway of paclitaxel biosynthesis remains elusive. Here we functionally characterized two novel taxane C13-O-deacetylases (T13dA1 and T13dA2) from Taxus x media cell cultures, providing experimental evidence for the molecular and biochemical plausibility of C13-O-deacetylation in paclitaxel biosynthesis in Taxus species. Also, we identified a previously uncharacterized bifunctional taxane C7{beta}-O-, C9-O-deacetylase, designated T79dA, which demonstrates the functional promiscuity by enabling stepwise deacetylation at taxane C7{beta} and C9 positions in a single enzymatic reaction. Furthermore, T7dA1, a novel taxane C7{beta}-O-deacetylase with higher activity than the reported T7dA was discovered and characterized here. Moreover, we reconstituted two new pathways (an 18-gene and a 19-gene pathway) enabled by the integration of a C13-O-acetylation-deacetylation module for the de novo biosynthesis of baccatin III in Nicotiana benthamiana leaves. These pathways with the previously established 17-gene baccatin III pathway, further allow paclitaxel biosynthesis to be a network. Our reconstituted 19-gene pathway achieves a baccatin III yield of up to 23 g g-1 dried weight (DW) in N. benthamiana leaves, which is comparable to the yield reported for the 17-gene pathway. This work facilitates a better understanding, elucidation and reconstruction of metabolic network of paclitaxel biosynthetic pathway, and provides new enzymes and strategies for artificial pathway reconstruction and efficiently bio-chemical production of paclitaxel.

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Elucidation of the anti-inflammatory mechanism of isoliquiritigenin from Glycyrrhiza uralensis using activity-based protein profiling

Sakai, H.; Chung, M. H.; Nakaya, T.; Ohbuchi, K.; Isobe, Y.; Arita, M.; Tsumagari, K.; Imami, K.; Hirokawa, T.; Tsugawa, H.

2026-05-08 biochemistry 10.64898/2026.05.05.722967 medRxiv
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Glycyrrhiza uralensis is a widely used medicinal plant present in more than 70% of Kampo formulations in Japan owing to its diverse pharmacological activities, including immunomodulatory, antitumor, and antioxidant effects. Isoliquiritigenin (ILG), a major chalcone constituent of G. uralensis, exhibits anti-inflammatory activity; however, its molecular mechanism remains unclear. Here, we employed an activity-based protein profiling approach to identify the molecular targets of ILG. Given that the ,{beta}-unsaturated carbonyl moiety of ILG can covalently react with reactive cysteine residues via nucleophilic addition, we used an iodoacetamide-based probe to globally profile cysteine-reactive proteomes. The comparative analysis between ILG- and vehicle-treated RAW 264.7 macrophages identified cysteine 65 (Cys65) of lipocalin-type prostaglandin D2 synthase (L-PGDS) as a potential covalent target. ILG treatment did not alter L-PGDS expression levels, indicating that reduced probe labeling reflects direct covalent competition rather than changes in expression. Consistently, ILG significantly suppressed prostaglandin D2 (PGD2) production, comparable to the selective L-PGDS inhibitor AT-56. Although both ILG and AT-56 reduced interleukin-6 expression, ILG exerted a stronger inhibitory effect. Our results demonstrate that covalent inhibition of L-PGDS and subsequent suppression of PGD2 production represent a key mechanism underlying the anti-inflammatory activity of ILG.

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The multifaceted role of acetamide derivative of Chalcone: Anti-inflammatory Action and Impact on Osteoclastogenesis, insights on NF-kB and MAPK pathways.

Anjum, S.; Akram, T.; Sharma, U.; Manhas, O.; Anal, J. M. H.; Kour, G.; Ahmed, Z.

2026-03-23 immunology 10.64898/2026.03.20.713114 medRxiv
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Inflammation serves as a vital physiological process essential for preserving health and countering illness. Yet, persistent inflammation drives osteoclastogenesis and ongoing bone erosion in rheumatoid arthritis (RA), mainly via macrophage activation and overproduction of pro-inflammatory cytokines like TNF-, IL-1{beta}, and IL-6. Limitations of prolonged conventional treatments underscore the need for safer small-molecule inhibitors that address both inflammation and osteoclast formation. Chalcones, natural plant defense compounds, exhibit diverse pharmacological properties including anti-inflammatory, anticancer, antibacterial, antifungal, and antiparasitic actions, owing to their characteristic reactive , {beta}- unsaturated carbonyl moiety. This study assessed chalcone derivative 7a for its anti-inflammatory effects in vitro and in vivo, alongside its capacity to modulate osteoclast differentiation, offering the inaugural demonstration of its dual anti-inflammatory and anti-osteoclastogenic properties. In LPS-stimulated macrophages, 7a substantially curtailed nitric oxide production, curbed pro-inflammatory cytokines (TNF-, IL-1{beta}, IL-6), and concentration-dependently diminished iNOS and COX-2 expression while inhibiting reactive oxygen species levels. In vivo, oral 7a dosing potently alleviated carrageenan-evoked paw swelling and restored serum lactate dehydrogenase and C-reactive protein to normalcy. In LPS-exposed mice, it further lowered systemic cytokines and rectified dysregulated biomarkers such as LDH, ALP, ALT, AST, creatinine, and urea. Moreover, in RANKL-stimulated osteoclast cultures, 7a markedly suppressed osteoclastogenesis by downregulating pivotal markers like tartrate-resistant acid phosphatase (TRAP) and matrix metalloproteinase-9 (MMP-9). Derivative 7a also enhances antioxidant defense--superoxide dismutase and catalase--via blockade of NF-{kappa}B and MAPK pathways. Overall, chalcone derivative 7a displays robust anti-inflammatory and anti-osteoclastogenic activity, positioning it as a compelling candidate for RA therapy.

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Host cell plasma membrane-derived vesicles efficiently inhibit in vitro Influenza A virus infection in a size-dependent manner

Qazi, B.; Vishwakarma, V.; Kumar, V.; Pant, G.; Mitra, K.; Tripathi, R. K.; Haldar, S.

2026-05-04 biochemistry 10.64898/2026.05.03.722494 medRxiv
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The influenza virus poses a significant global health threat due to its continuous evolution, immune evasion, and zoonotic spillover. The rise of drug resistance, reduced susceptibility to existing antiviral medications, and the limited effectiveness of annual vaccines underscore the need for new antiviral strategies. To infect, the influenza virus binds to sialic acid (SA)-containing molecules on host cell membranes through hemagglutinin (HA). Blocking this interaction represents a promising antiviral approach. Herein, we report that SA containing plasma membrane-derived vesicles (PMV) efficiently inhibits in vitro Influenza A virus (IAV) infection. Using orthogonal methods, we demonstrate that PMV derived from A549, MDCK, and HEK cells competitively bind to H1N1 (WSN) and H3N2 (X-31) IAV strains, block entry and infection in human respiratory epithelial cells in a dose-dependent manner, without causing significant toxicity. When the size of the vesicles was reduced through extrusion, the antiviral activity was enhanced, and this was found to be correlated with a size-dependent increase in hemagglutination inhibition and reduced IAV internalisation. Plasma membrane-derived vesicles may serve as a novel antiviral strategy against influenza virus infections due to their simple production method and conserved SA binding site on HA.

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Discovery of Selective Nrf2 Activators from Natural Products: AComputational Screening Approach to Minimize Off-Target Effects on PXR and CYP2D6

Wang, Y.; Gong, Y.; Li, R.; Li, Z.; Cai, H.; Fan, L.; Ma, H.

2026-04-15 bioinformatics 10.64898/2026.04.12.718057 medRxiv
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Nuclear factor erythroid 2-related factor 2 (Nrf2) is a central regulator of cellular antioxidant responses and a highly promising therapeutic target for a range of oxidative stress-related diseases. However, the clinical translation of Nrf2 activators has been hampered by significant off-target effects--notably unintended activation of the pregnane X receptor (PXR) and inhibition of cytochrome P450 2D6 (CYP2D6)--which can lead to dangerous drug-drug interactions and metabolic complications. To overcome this critical barrier, we conducted the first large-scale computational screening of 628,898 natural products from the COCONUT database, integrating molecular docking with a rigorous three-tier selectivity strategy designed to prioritize compounds that strongly bind KEAP1 (the primary Nrf2 repressor) while minimizing interactions with PXR and CYP2D6. Our innovative approach identified 10 ultraselective candidates that demonstrate potent KEAP1 affinity, negligible PXR engagement, and only moderate CYP2D6 binding--achieving up to 12.29-fold selectivity for Nrf2 pathway activation. These top hits are structurally novel, enriched in lipid-like and nucleoside-inspired scaffolds, and exhibit promising drug-like properties. By providing both a curated set of chemically diverse, selectivity-optimized leads and a publicly accessible screening dataset, this work establishes a new foundation for the rational development of safer, more precise Nrf2-targeted therapies, bridging a crucial gap between target potential and clinical viability. By prioritizing compounds with minimal off-target effects on PXR and CYP2D6, our approach offers a scalable template for reducing drug development failures and advancing safer therapeutics for oxidative stress-related diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/718057v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@13c6c79org.highwire.dtl.DTLVardef@1f5a078org.highwire.dtl.DTLVardef@fa4f4borg.highwire.dtl.DTLVardef@16bc881_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

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The gut microbiota metabolite Urolithin A mitigates JAK signaling to suppress cytokine-mediated autoimmune diseases

Geng, S.; Tang, R.-C.; Yu, H.; Zhang, A.; Yu, S.-S.; Zhang, L.; Zhang, J.

2026-05-12 immunology 10.64898/2026.05.08.723914 medRxiv
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Aberrant activation of type I interferon (IFN-I) is closely related to the development of autoimmune diseases. The metabolic regulation of cytokine signaling is essential for immune homeostasis. In this study, we characterized Urolithin A(UA), a natural gut-derived metabolite, as an inhibitor of Janus kinase (JAK) signaling. UA was found to broadly dampen JAK phosphorylation and the downstream signaling induced by cytokines such as type I interferons (IFN-I), type II interferons (IFN-II), and interleukin-6 (IL-6). UA can directly bind to JAK1 JH1 domain and treatment with UA attenuated autoimmune pathogenesis in Trex1-KO mice, IMQ-induced SLE and psoriasis models. Our findings unveil that UA is an anti-inflammatory metabolite that promotes immune homeostasis and could be used to treat inflammatory and autoimmune diseases.

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The inner nuclear membrane protein SUN1 regulates cullin-3 neddylation to maintain insulin signaling

Upadhyay, K. K.; Yang, Y.; Shah, A.; Basrur, V.; Nesvizhskii, A. I.; Brady, G. F.

2026-04-20 physiology 10.64898/2026.04.16.718478 medRxiv
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Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease and strongly linked to obesity and insulin resistance. We previously reported that the common nuclear envelope variant rs6461378 (g.842031C>T; SUN1 H118Y) associated with MASLD and related traits including insulin resistance. To gain insight into how wild-type (WT) and H118Y SUN1 might differentially impact insulin signaling, we performed affinity purification-mass spectrometry (AP-MS) in human liver-derived cells stably expressing WT or H118Y SUN1. Unbiased AP-MS revealed a novel SUN1-CUL3 interaction, with comparative analysis showing that WT SUN1 interacted robustly with CUL3, while CUL3 interaction was markedly diminished with H118Y SUN1. Cells in which SUN1 was silenced via siRNA, or in which H118Y SUN1 was ectopically expressed, showed increased CUL3 neddylation, which is required for cullin RING ligase (CRL)-mediated ubiquitination of insulin receptor substrate (IRS) proteins. Inhibition of neddylation restored IRS-1 levels and insulin signaling in H118Y SUN1-expressing cells. Together, our findings provide a potential mechanism of H118Y SUN1-driven insulin resistance and a viable therapeutic approach for its reversal.

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Integrating targeted genome mining and structure-guided modeling reveals unexplored 7-deazapurine-containing pathways

Cediel-Becerra, J. D. D.; Chevrette, M. G.; de Crecy-Lagard, V.; Dias, R.

2026-04-19 bioinformatics 10.64898/2026.04.15.718813 medRxiv
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7-deazapurines are nucleoside analogs that play key roles in nucleic acid modification and can serve as building blocks for diverse, bioactive secondary metabolites. Despite their biological significance, their biosynthetic diversity, distribution, and enzymatic determinants of structural diversification remain poorly understood. Here, we leverage large-scale targeted genome mining, phylogenetic, and network analysis to explore 7-deazapurine-containing pathways across [~]2 million bacterial genomes. We identified over 900 candidate biosynthetic gene clusters (BGCs), grouped into more than 100 families, most of which remain uncharacterized. These GATOR-GC-predicted BGCs were predominantly found in Streptomyces. We then examined enzyme-substrate interactions in three representative pathways: (i) peptidyl-deazapurines, (ii) huimycin, and (iii) dapiramicin A. Molecular docking and molecular dynamics (MD) simulations recapitulated known enzyme-substrate interactions and highlighted candidate catalytic residues governing amide bond formation, methylation, and glycosylation. Using this genome- and structure-guided framework, we identified a candidate BGC for dapiramicin A and proposed tailoring steps, including scaffold methylation and deoxy-sugar formation. These findings expand the known diversity of 7-deazapurine-containing BGCs and demonstrate how integrating genome mining with structural modeling can link BGCs to chemical function, providing a foundation for discovering and characterizing 7-deazapurine-containing secondary metabolites. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/718813v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@c00feforg.highwire.dtl.DTLVardef@156468forg.highwire.dtl.DTLVardef@1326e90org.highwire.dtl.DTLVardef@1f8d57b_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Potent and Broad HIV-1 Neutralization by a Bispecific CD4-CD4i Fusion Protein based on Single-Domain CD4-D1 and X5 CD4i antibody

Chu, X.; Shetler, C.; Sun, Z.; Perrone, C.; Feng, Z.; Penrose, K. J.; Jones, R. B.; Mellors, J. W.; Dimitrov, D. S.; Li, W.

2026-04-25 molecular biology 10.64898/2026.04.22.719690 medRxiv
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Human immunodeficiency virus (HIV) infection remains a global health threat. Although antiretroviral therapy (ART) has significantly transformed HIV into a manageable chronic disease, emergence of drug resistance to current ART is a continuing concern. Broadly neutralizing antibodies, as well as reagents containing both a soluble CD4 mimetic and an HIV co-receptor inhibitor--such as CD4-CD4i antibodies--are promising strategies for the prevention and treatment of HIV infection. We previously developed a CD4 D1mimetic (mD1.22) with enhanced neutralization potency, surpassing that of the clinically validated sCD4-D1D2 mimetic. We also previously identified a novel CD4i antibody (X5) that targets the conserved coreceptor binding site on the gp120 core and recognizes an epitope partially overlapping with 17b monoclonal antibody binding site. X5 binding to gp120 was augmented by CD4 and modestly enhanced by CCR5. To leverage these favorable interactions, we designed and optimized sCD4-X5 bispecific antibodies by computational structure-aided modification of antibody size and fusion linkers between the two binding moieties. The bispecific D1X5, with a (G4S)7 long linker between D1 and X5 (IgG1-LL D1X5), exhibited broad neutralization against 11 diverse HIV subtypes across B, C, G clades and AC, BC recombinants. The TZM-bl cell neutralization assay showed IgG1-LL D1X5 neutralization geometric mean IC50 and IC80 are 0.6 g/mL and 3.4 g/mL respectively, which are within the range of potent bnAbs. This work has identified a novel single domain soluble CD4 based CD4-CD4i bispecific antibody with broad HIV-1 neutralization.

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The redesign of the molecular scaffold of viral ion channel blockers

Zsido, B.; Mernyak, E.; Földes, F.; Kopasz, Z.; Leiner, K.; Madai, M.; Zana, B.; Kuczmog, A.; Hetenyi, C.

2026-05-06 pharmacology and toxicology 10.64898/2026.04.30.721843 medRxiv
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The rise of new, rapidly mutating viruses presents increasing challenges for drug developers. Traditional methods, such as high-throughput screening and drug repurposing against mutagenic viral targets, have recently shown their limitations. Our current rational molecular engineering approach offers a sustainable solution by targeting viral ion channels, which generally have low mutation rates. First, extending the amantadine molecule led to the development of new compounds that better match the alternating hydrophobic and hydrophilic patterns of the inner walls of ion channels--a common feature across many viruses. Then, simplifying the structure yielded a cyclohexylamine-based minimalist scaffold that effectively blocks the ion channel and demonstrates improved antiviral activity compared to well-known agents such as amantadine and arterolane. SARS-CoV-2 variants served as test systems in laboratory experiments. The new molecular scaffolds presented here provide a strong foundation for designing potent, broad-spectrum viral ion channel blockers.

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Orally Bioavailable SARS-CoV-2 Protease Inhibitors Bearing a Hydroxymethyl Ketone Warhead

Elshan, N. G. R. D.; Wolff, K. C.; Weiss, F.; Ghorai, S.; Grabovyi, G.; Wilson, K.; Riva, L.; Woods, A. K.; Pedroarena, J.; Nazarian, A.; Liu, Y.; Mazumdar, W.; Song, L.; Okwor, N.; Malvin, J.; Bakowski, M. A.; Kirkpatrick, M. G.; Gebara-Lamb, A.; Huang, E.; Nguyen-Tran, V. T. B.; Chi, V.; Li, S.; Lee, K.-J.; McNamara, C. W.; Gupta, A. K.; Rahimi, A.; Chen, J. J.; Joseph, S. B.; Schultz, P. G.; Chatterjee, A. K.

2026-05-18 pharmacology and toxicology 10.64898/2026.05.15.725542 medRxiv
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The use of covalent warheads targeting the catalytic cysteine has been a cornerstone in coronavirus main protease (Mpro) inhibitor development, where various electrophilic motifs have been used including aldehydes, nitriles, ketoamides, and hydroxymethyl ketones (HMKs). Recent efforts have been mostly centered around nitrile warheads, given the success of compounds like Nirmatrelvir and Ensitrelvir in the clinic. However, finding and advancing alternative chemotypes with differentiating chemical and pharmacological profiles is essential for future pandemic preparedness. Among such alternatives, HMKs hold special interest because they balance reduced intrinsic electrophilicity with an excellent selectivity profile. Nevertheless, early HMK-based compounds, such as the clinical-stage Mpro inhibitor PF-00835231, suffered from poor oral bioavailability and therefore required intravenous administration, with or without prodrug derivatization of the hydroxyl group. Here, we describe our efforts in advancing the HMK field via the discovery of mCMX110, a lead that has superior potency, increased unbound exposure in vivo, and favorable oral bioavailability in preclinical studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/725542v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@abe1c9org.highwire.dtl.DTLVardef@746a08org.highwire.dtl.DTLVardef@dd5861org.highwire.dtl.DTLVardef@1d572c7_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Mosquito-directed PROTACs to block malaria transmission

Rawat, N.; Singhal, J.; Goyal, B.; Parveen, N.; Tupe, C.; Gupta, K.; Chakraborti, S.; Pandey, K. C.; singh, s.

2026-04-17 molecular biology 10.64898/2026.04.16.719026 medRxiv
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The mosquito stage of the Plasmodium falciparum life cycle is an attractive target for intervention since it is crucial for the sexual reproduction and transmission of parasites to human host. Mosquito determinants crucial for parasite infection and growth pose as lucrative targets for transmission blockers. Owing to the fact that p38 MAPK has role in immune response and vector competence, we have evaluated the potential of PROTAC molecule (NR-7h) to degrade Anopheles stephensi p38 MAPK (Asp38 MAPK), a conserved serine/threonine kinase involved in stress reactions, midgut homeostasis, and parasite survival. PROTAC-mediated degradation of Asp38 MAPK led to the disrupted development of the parasite, suggesting its crucial function in vector competence. Furthermore, NR-7h-treated mosquitoes showed higher expression of immune genes such Rel-2, TEP1, APL1, and NOS, suggesting that p38 MAPK regulates host immunity in a way that promotes parasite persistence. PROTAC-mediated degradation of target proteins, provides a more persistent and resistance-proof therapeutic effect than traditional kinase inhibitors. Our findings establish PROTACs as a novel vector-targeted strategy for the development of endectocides to limit malaria transmission.