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European Journal of Medicinal Chemistry

○ Elsevier BV

Preprints posted in the last 90 days, ranked by how well they match European Journal of Medicinal Chemistry's content profile, based on 17 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
Synthesis of substituted oxabicyclic phenol derivatives with increased affinity and activity for the classical estrogen receptor ERα

Pepermans, R. A.; Tenorio, A. J.; Saxon, T.; Talipov, M. R.; Maio, W. A.; Ramesh, C.; Prossnitz, E. R.; Arterburn, J. B.

2026-10-01 pharmacology and toxicology 10.64898/2026.09.25.754525 medRxiv
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The classical estrogen receptor (ER) is a steroid hormone receptor known for its role in both health and disease. ER, like its counterpart ER{beta}, acts as a receptor for its endogenous ligand 17{beta}-estradiol (E2) and is capable of binding a diverse set of natural and synthetic small molecules. Several screening campaigns have identified various ER ligands, based on the oxabicyclo[3.3.1]-nonene scaffold, that act as ER agonists. One such campaign extensively characterized an oxabicyclic ER agonist, termed AB-1. Herein, we report the synthesis of a series of analogs based on the scaffold of AB-1 (herein termed 1), focusing on the enhancement of their binding to ER and functional potencies in ER mediated assays. We identify a new substituted compound 9 that achieves subnanomolar potencies for ER binding (IC50= 0.45 nM) and ER dependent transcription (EC50= 0.37 nM) and proliferation (EC50= 0.03 nM), with potencies approaching those of E2. The high potency of 9 provides a promising scaffold for the potential development of new ER-targeted therapeutics.

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Development of Potent G Protein Pathway-Biased GPR183 Agonists

Bhuskute, K. R.; Manandhar, A.; Kjaer, V. M. S.; Casartelli, F.; Koutsaki, M. I.; Sathyanarayanan, U.; Hjortkilde, E.; Turcio, R.; Rosenkilde, M. M.; Ulven, T.; Ulven, E. R.

2026-07-30 pharmacology and toxicology 10.64898/2026.07.27.740726 medRxiv
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GPR183 is an oxysterol-sensing GPCR predominantly expressed in lymphoid organs and tissues. Activation of the receptor by oxysterol 7,25-OHC leads to Gi protein-mediated signaling as well as {beta}-arrestin2 recruitment. GPR183/oxysterol signaling modulates localization of lymphoid cells, consequently the receptor is associated with several inflammation-associated diseases and is an interesting potential drug target. Previously, we reported the discovery of moderately potent G protein-biased partial agonists for GPR183 from a virtual screening based on the scaffold of the antagonist NIBR189. Herein, we present the detailed structure-activity investigations and optimizations, which led to the identification of full agonists for GPR183 with complete bias for Gi protein signaling and low nanomolar potency, including 63 (TUG-2604) with potency and efficacy similar to 7,25-OHC. Notably, 63 was unable to induce migration of human dendritic cells but inhibited migration induced by 7,25-OHC. This compound will be valuable for further explorations of the signaling-specific function and drug target potential of GPR183.

3
3-Hydroxypropanamidines: from antiplasmodial leads to a novel antibacterial scaffold

Kaufmann, L.-S.; Schultz, A.; Wladarz, N.; Gangnus, T.; Lungerich, B.; Knaab, T. C.; Haase, A.; Joswig, L.; Dressler, F.; Dietze, P.; Benndorf, R.; Burckhardt, B. B.; Kurz, T.; Bandow, J. E.

2026-09-21 microbiology 10.64898/2026.09.20.752996 medRxiv
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Arylamino alcohols constitute an established class of antimalarial agents. While this class is best known for its potent antiplasmodial activity, selected members, most notably mefloquine, have also been reported to exhibit antibacterial activity. Structurally related 3-hydroxypropanamidines were developed as highly potent antimalarial agents. Here, we explored the antibacterial activity of three 3-hydroxypropanamidines (4 (BLK278), 5 (BLK280), and 6 (TKK088)) against clinically relevant Gram-positive and Gram-negative bacteria and investigated their cytotoxicity, in vitro pharmacokinetic properties, and proteome-based bacterial response to treatment. We observed good antibacterial activity against Staphylococcus aureus, with 6 (TKK088) displaying the highest activity against multidrug-resistant MRSA and VISA strains. 5 (BLK280) demonstrated the greatest spectrum of activity acting also against clinically relevant Gram-negative strains of Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Klebsiella aerogenes, and Shigella sonnei. In cytotoxicity assays with HUVEC and HAOSMC cells, 4 (BLK278) and the previously reported 7 (TKK129) showed the most favourable overall profiles among the investigated 3-hydroxypropanamidines. The selectivity indices for S. aureus were below 2.5 with clear cell-type-dependent differences for all compounds including mefloquine, suggesting that improving antibacterial selectivity is an important objective for further optimization. In vitro pharmacokinetics showed high plasma protein binding and good human microsomal and plasma stability for all three 3-hydroxypropanamidines. Gel-based proteomic responses revealed a strong impact on the bacterial cell envelope. The observed acute proteomic responses reflect pleiotropic effects and are consistent with earlier reports implicating F0F1-ATPase as a potential molecular target of mefloquine in Streptococcus pneumoniae.

4
Rationally Engineered, Chemically Stable Tunicamycin Analogues Decouple DPAGT1 Inhibition from Non-Selective Toxicity

Kurosu, M.; Mitachi, K.; Sanchez-Ruiz, A.; Mingle, D.; Cheng-Sanchez, I.; Kirsh, J. M.; Sarabia, F.; Clemons, W. M.

2026-07-29 biochemistry 10.64898/2026.07.28.741246 medRxiv
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Tunicamycins are potent inhibitors of dolichyl-phosphate N-acetylglucosamine phosphotransferase (DPAGT1) but are unsuitable for therapeutic development due to non-selective cytotoxicity, acid-labile glycosidic linkages, and poor physicochemical properties. Although prior structural modifications reduced the promiscuous toxicity of tunicamycins, the intrinsic 11'-{beta}-1''- trehalose-type glycosidic linkage remains chemically unstable, limiting biological durability. Here, we report a rationally engineered scaffold-stabilization strategy in which the acid-labile linkage is replaced with a chemically robust cyclitol framework, enabling the concise synthesis of chemically stable and water-soluble tunicamycin analogues in only 12 synthetic steps. From this platform, TM-Cy-TBPA (4) was identified as a lead DPAGT1 inhibitor that potently suppresses the proliferation of breast cancer cells by inducing G2-phase arrest followed by apoptosis, while exhibiting minimal cytotoxicity toward nontransformed cells. The compound shows improved solubility, and favorable pharmacokinetic exposure. These results establish tunicamycin cyclitol analogues as a structurally distinct class of selective DPAGT1-targeted anticancer agents and demonstrate that stabilization of the glycosidic linkage is an effective strategy for enhancing pharmacological selectivity, improving in vivo performance, and simplifying the synthetic route.

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Discovery of Bavachin as a Dual Trk-A/Trk-B Agonist via Integrated Computational Screening and Experimental Validation

Patil, S. P.; Kuehn, B.; Schlosser, R.; Samohod, J.

2026-09-16 neuroscience 10.64898/2026.09.10.750759 medRxiv
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Neurotrophins regulate neuronal survival, differentiation, and synaptic plasticity through activation of tropomyosin receptor kinase (Trk) receptors, and their dysregulation is strongly implicated in neurodegenerative disorders, including Alzheimer's disease. However, the therapeutic application of recombinant neurotrophins remains limited by poor bioavailability, rapid degradation, and inadequate blood brain barrier permeability. Here, we report the discovery of Bavachin as a dual Trk-A/Trk-B neurotrophin mimetic via an integrated computational screening and experimental validation approach. Structure-based virtual screening of a bioactive natural product library derived from Traditional Chinese Medicine, combined with a novel consensus-ranking strategy, enabled the identification of flavonoid scaffolds targeting neurotrophin-binding sites of Trk receptors. Among these, Bavachin demonstrated robust, dose-dependent activation of both Trk-A and Trk-B receptors, but not Trk-C, indicating receptor selectivity. Induced-fit docking and molecular dynamics simulations revealed stable binding of Bavachin within conserved and receptor-specific ligand-binding pockets, consistent with its dual agonist activity. Collectively, this study identifies Bavachin as a putative small-molecule neurotrophin mimetic and establishes an integrated computational and experimental framework for the discovery of dual Trk-A/Trk-B agonists for neurodegenerative disease therapeutics.

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Discovery and optimization of the next generation of cell active Protein Kinase Novel 3 (PKN3) inhibitors

Georgiou, E.; Laitinen, T.; Poso, A.; Heino, R.; Asquith, C. R. M.

2026-08-20 pharmacology and toxicology 10.64898/2026.08.20.745975 medRxiv
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Protein Kinase Novel 3 (PKN3) understudied kinase with a diverse array of biological functions that are yet to be fully defined. Here, we report the design and development of a novel advanced functional chemical tool inhibitor for PKN3. A pyridyl imidazole series has been synthesized and evaluated against PKN3 in vitro and in cells. These efforts led to the discovery of 6e (URS03-06), a submicromolar cell active functional inhibitor with a narrow kinome spectrum, to enable the elucidation and interrogation of PKN3 cellular biology.

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IKKβ as a putative non-covalent and quinone-mediated covalent target of 4-methylcatechol in RANKL/NF-κB signaling: a combined computational and experimental analysis

Xie, C.; Zhang, L.; Bao, X.; Li, X.; Ding, Y.; Tabandeh, M.; Basit, F.; Velez, H.; Kumar, S.; Deepak, V.

2026-08-04 pharmacology and toxicology 10.64898/2026.07.29.741661 medRxiv
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Excessive osteoclast activity contributes to pathological bone loss in osteoporosis, rheumatoid arthritis, and osteolytic malignancies. The effects of small catechol derivatives on receptor activator of nuclear factor-{kappa}B ligand (RANKL)-induced osteoclastogenesis remain poorly understood. This study investigated the effects of 4-methylcatechol (4-MC) on RANKL-induced NF-{kappa}B activation and osteoclast differentiation. 4-MC reduced RANKL-induced NF-{kappa}B luciferase activity in HEK-293T/RANK cells. 4-MC also suppressed RANKL-induced TRAP activity in RAW264.7 cells in a concentration-dependent manner and reduced the number of TRAP-positive multinucleated osteoclasts, without affecting cell viability. Molecular docking predicted non-covalent binding of 4-MC within the ATP-binding hinge region of IKK{beta} (PDB: 4KIK), forming a close polar contact with Glu97, predicted hydrogen bonds with Cys99, and a hydrophobic contact with Ile165, within the pocket occupied by the co-crystallized inhibitor K252a. Covalent docking predicted that the oxidized quinone form of 4-MC engages Cys179 in the IKK{beta} activation loop. Quantum chemical calculations confirmed a markedly higher electrophilicity index for the oxidized quinone than for the parent catechol, supporting this mechanism. In silico ADMET profiling indicated favorable drug-likeness and safety. These findings identify IKK{beta} as a plausible molecular target of 4-MC through both non-covalent and covalent mechanisms. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/741661v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@35a0d3org.highwire.dtl.DTLVardef@d19458org.highwire.dtl.DTLVardef@1623fadorg.highwire.dtl.DTLVardef@1429e8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

8
Cellular uptake of folate-olaparib conjugates via folate receptor-mediated endocytosis: Potential for selective delivery of DNA damage response inhibitors into tumour cells

Bavetsias, V.; Pickard, L.; Diaz-Sanchez, S.; Gowan, S.; Wood, F.; Ruddle, R.; Wong, C.; Sharif, H.; Raynaud, F.; Burke, R.; Wang, A.; Blagg, J.; Kirkin, V.; Rossanese, O.; Banerji, U.

2026-09-24 biochemistry 10.64898/2026.09.23.752340 medRxiv
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The folate receptor (FR) is overexpressed in a range of human tumours including ovarian cancer cells. We propose that the overexpression of the FR on the surface of ovarian tumour cells could be exploited for the selective delivery of a DNA damage response inhibitor (DDRi) in the form of an intact folate drug conjugate (FDC). This approach would improve the therapeutic index of the parent DDRi facilitating combination studies of the DDRi-based FDC with DNA damaging chemotherapy. FR-mediated cellular uptake of the proposed folate drug conjugates is requisite for FDC selective delivery into tumours. In this study, we synthesised a series of olaparib-based folate conjugates that maintained the biochemical PARP1 inhibition associated with olaparib and showed binding affinity for the folate receptor. Significantly, we identified compounds 10b and 11 that selectively enter FR overexpressing tumour cells via folate receptor-mediated endocytosis in their intact form and engage with their target as demonstrated by the potent inhibition of PARylation (KB cells, PARylation IC50 = 5.7 and 3.9 nM; respectively).

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Computational and Structure-Guided E-Pharmacophore-Based Virtual Screening for the Identification of Novel NEK2 Kinase Inhibitors as Potential Anticancer Agents

Rehman, H. M. M.; Latif, A.; Hammad, H. M.; Sajjad, M.

2026-08-06 bioinformatics 10.64898/2026.07.31.742111 medRxiv
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Cancer is a serious public health problem, and is becoming more common, with a projected increase in deaths and more than 25 million new cases in coming decades. A number of molecular mechanisms are involved in the tumoral process, with one of them, never in mitosis A-related kinase 2 (NEK2), a serine/threonine protein kinase, being a frequent target of amplification in various malignancies that is responsible for chromosomal instability, aneuploidy and activation of several oncogenic pathways. Available kinase inhibitors are not yet optimized in terms of their pharmacokinetic properties for clinical use, and current therapies, such as chemotherapeutic agents or immunotherapies are often limited by their resistance. In silico methods represent an effective tool to search for novel potent inhibitors, before testing in animals, with time constraints and limited resources. To find new inhibitors of NEK2, we used E pharmacophore-based modeling and structure based virtual screening in this study. NEK2 was chosen as the target for therapeutic intervention and an energy optimized pharmacophore model was employed to screen the Enamine REAL library of millions of compounds. Pharmacodynamic and Pharmacokinetic properties of the Top hits were tested using ADMET profiling. These were further screened using molecular docking (standard precision and extra precision) and virtual screening to obtain three lead compounds 1, 2, and 3 which have docking score of -7.414, -8.037 and -7.562 respectively. MM-GBSA calculations were used to estimate the binding free energies for these complexes, which were determined to be -54.92, -54.18 and -49.23 kcal/mol. Lastly, 100 ns molecular dynamics simulations have been run to evaluate complex stability in dynamic situations. The overall results of the MD showed the overall stability of the NEK2-ligand complexes, and thus these three compounds are promising NEK2 inhibitor candidates and could be further validated in vitro and in vivo for clinical application. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/742111v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@14e9cfeorg.highwire.dtl.DTLVardef@24ec78org.highwire.dtl.DTLVardef@20be75org.highwire.dtl.DTLVardef@1b80c02_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Deep reinforcement learning-driven discovery of a MsbA-targeted small-molecule antibiotic for the treatment of Acinetobacter baumannii infection

Wang, L.; Jing, B.; Liu, Q.; Zhong, J.; Han, Z.; Yang, Y.; Jin, H.; Li, Y.; Peng, L.; Wu, S.; Xia, J.

2026-09-15 biochemistry 10.64898/2026.09.12.751098 medRxiv
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Antibiotics with new mechanisms are highly pursued to address the threat of infections caused by drug-resistant Gram-negative bacteria. Targeting MsbA, a key protein of the lipopolysaccharide biosynthesis pathway, represents a promising strategy to discover new classes of antibiotics. However, currently available MsbA-targeted molecules either lack sufficient potency or have unfavorable properties, necessitating expansion of chemical space. In this study, we chose the most promising cerastecin Cpd 4 as the template, and used two Artificial Intelligence (AI)-based tools, i.e. Link-INVENT and AutoMolDesigner for molecular design, performed chemical derivatization and antibacterial activity evaluation, which led to the discovery of Y-11 (MIC for A. baumannii: 0.5 g/mL). Encouragingly, Y-11 showed equivalent potency to Cpd4 for carbapenem-resistant A. baumannii, and less cytotoxicity and hemolysis as well as lower spontaneous resistance frequency. In vivo efficacy study demonstrated that Y-11 could effectively reduce bacterial loads in the mice infected by A. baumannii. The following mechanism study including molecular dynamics simulation, biochemical assay, and transmission electron microscope (TEM) analysis suggested that Y-11 inhibited the transport of lipooligosaccharide and impaired the formation of outer membrane, probably by competitively binding to the substrate binding site of MsbA and modulating ATPase activity. Taken together, we have discovered a MsbA-targeted small molecule Y-11 via AI-driven drug design, which provides a foundation for future antibiotic development.

11
Discovery and Optimization of Imidazothiazole Carboxamides as Novel Anti-Tuberculosis Agents

Meng, L.; Grant, D.; Xie, H.; Ford, R.; Webb, J.; McNamara, C. W.; Sukheja, P.; Yang, B.; Chatterjee, A. K.

2026-09-24 microbiology 10.64898/2026.09.21.753226 medRxiv
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Screening of the open-access CRESTdb small-molecule library identified the imidazothiazole carboxamide sCQG200 (1) as an initial hit, with activity against H37Rv and Erdman Mycobacterium tuberculosis strains in cholesterol-containing medium (MIC90= 6.88 uM and 4.48 uM, respectively) and against intracellular Mtb (EC50= 3.80 uM). sCQG200 retained activity against drug-resistant Mtb strains, including clinical MDR/XDR isolates. SAR optimization led to analogs 21 and 24 with substantially improved antimycobacterial potency. Mouse pharmacokinetic studies following oral and intravenous administration showed 62.1% and 29.5% oral bioavailability for 21 and 24, respectively. This structurally differentiated chemotype provides a promising starting point for further optimization as antitubercular agent.

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Computer-Assisted Systematic Chemical-Space Mapping of a First-in-Class Peripherally Restricted α2AAR Agonist through Scaffold-Seeded Enumeration

Moore, C.; Zhu, L.; Cheng, Z.

2026-09-24 pharmacology and toxicology 10.64898/2026.09.16.751790 medRxiv
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CC10137 is a first-in-class peripherally restricted 2A-adrenergic receptor (2AAR) agonist with broad-spectrum analgesic efficacy and a favorable safety profile. Systematic exploration of the chemical space surrounding first-in-class leads is important for defining series boundaries and guiding continued optimization, but conventional analogue-by-analogue medicinal chemistry samples only a small fraction of the accessible structural space. Here, we used a scaffold-seeded enumeration strategy to expand the chemical space surrounding CC10137 from four SAR-informed seed compounds comprising CC10137 and three closely related structural variants. Application of predefined medicinal chemistry transformation rules in StarDrop generated a virtual library of 16,601,163 unique structures. Morgan fingerprint-based principal component analysis indicated that the library occupied a highly multidimensional structural space involving variation in scaffold substitution, peripheral functional groups, and side-chain composition. A retrospective comparison set of 43 compounds independently designed and experimentally characterized in the earlier CC10137 program represented only approximately 0.00026% of the 16.6-million-member library, yet all 43 were recovered as exact structural matches. Three compounds selected directly from the virtual library retained 2AAR binding affinity and agonist potency below 25 nM. Five representative compounds further showed significant anti-allodynic effects in the in vivo spared nerve injury model, with inhibition rates ranging from 39.3% to 55.7%. These findings support scaffold-seeded computational enumeration as a practical strategy for systematic chemical-space mapping around a first-in-class lead and for identifying additional pharmacologically active structural regions for further optimization.

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MeFluHyA: a novel fluorescent screening tool for high-throughput identification of HDAC6-selective inhibitors

Klingl, Y. E.; Goethals, J.; Sicart, A.; Borgarelli, C.; Van Lindt, J.; Prior, R.; Ismalaj, E.; De Borggraeve, W.; Van Damme, P.; Hooker, J. M.; Curcio, M.; Verhelst, S.; Schönberger, M.; Van Den Bosch, L.

2026-07-27 biochemistry 10.64898/2026.07.24.740064 medRxiv
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The cytosolic histone deacetylase 6 (HDAC6) plays a key role not only in cancer but also in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) peripheral neuropathies. Pharmacological inhibition as well as genetic silencing of HDAC6 is able to rescue several defects. Therefore, developing pharmacological compounds targeting this enzyme is of crucial interest. Here, we report the design, synthesis, and characterization of Methyl Fluorescent Hydroxamic Acid (MeFluHyA), a novel fluorescent HDAC6-selective probe designed for cell imaging. By integrating a Cy5 fluorophore into a phenyl hydroxamic acid scaffold, MeFluHyA shows binding to the catalytically active CD2 domain of HDAC6 without significantly inhibiting its deacetylating function in the sub-micromolar range. Biochemical enzymatic activity assays confirmed its selectivity over other HDAC isoforms. Fluorescent imaging studies in HeLa cells demonstrated strong colocalization with HDAC6-eGFP and a commercial HDAC6 antibody. Competitive binding assays revealed that MeFluHyA effectively identifies known HDAC6 inhibitors, with reduced probe-binding serving as a readout for successful target engagement. MeFluHyA is a cell-permeable, fast and easy to use probe that can be added organism-independent, and its red-shifted fluorophore makes it compatible with multiplex, live and fixed imaging. Overall, we provide a novel tool for screening platforms aimed at identifying novel HDAC6-targeting inhibitors.

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In-silico Exploration of Drug Leads Targeting Mycobacterial Ag85C

Singh, K. R.; Anuradha, D. C. M.; Suresh kumar, D. C.

2026-10-01 bioinformatics 10.64898/2026.09.26.754622 medRxiv
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This study aims to identify potential inhibitors of the Ag85C enzyme from Mycobacterium tuberculosis through primary docking, pharmacophore modelling, and ADME/pharmacokinetics analysis. Delamanid and Pretomanid emerged as the top hits in primary docking, demonstrating strong binding affinities and interactions with key active site residues. A robust pharmacophore model was developed, identifying essential features for binding and used to screen 4254 antituberculotic compounds, yielding three promising candidates: F0314-0040, F0398-0505, and F0349-2716. These compounds exhibited high binding affinities in major docking studies. ADME and pharmacokinetics analysis revealed favorable Drug likeness and absorption profiles, supporting their potential as effective antituberculotic agents. The integration of computational methods provided a comprehensive approach for rational drug design.

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Discovery of a molecular glue inhibitor that stabilises a non-productive Kalirin-Rac1 complex

Gray, J. L.; Callens, M. C.; Henley, A.; Zaidman, D.; Jimenez Antunez, C.; Thompson, A. P.; Lei, Z.; Skyner, R.; Miller, M.; Williams, E. P.; Robinson, A.; Seupal, R.; Fry, M. T.; Filep, M.; von Delft, F.; Willis, M. P.; von Delft, A. R.; London, N.; Brennan, P. E.

2026-09-11 biochemistry 10.64898/2026.09.08.749156 medRxiv
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Rho guanosine triphosphatases (GTPases) are molecular-switches implicated in neurodegenerative diseases, yet targeting them through competitive inhibition remains a challenge due to their high affinity for guanine nucleotides. Guanine nucleotide exchange factors (GEFs) catalyse GDP-to-GTP nucleotide exchange to activate GTPases, providing an alternative opportunity for GTPase modulation. Herein, we describe a complex-targeted strategy to inhibit nucleotide exchange with covalent molecular glues that engage the Kalirin-Rac1 GEF-GTPase complex at the nucleotide binding site are sequester the GEF Kalirin. Fragment hits were identified through XChem and in silico screening, and a fragment merging approach resulted in the generation of covalent inhibitors RS-009 and MC-278. Multiple analyses demonstrate our compounds inhibit nucleotide exchange both through competition with the nucleotides and by stabilising a ternary inhibitor-Rac1-Kalirin complex, thereby trapping Kalirin in a non-productive state and reducing GEF turnover. Biochemical selectivity screening and cellular activity-based protein profiling (ABPP) show that selectivity can be achieved across distinct GEF-GTPase complexes, which may result in improved spatiotemporal control over targeting the GTPase alone. This work provides evidence for targeting GTPase signalling via stabilization of the GEF-GTPase complex in a unique covalent molecular glue mechanism and provides the basis of a chemical probe or therapeutic.

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Discovery and Structure Activity Relationship Optimization of a Novel Rv1625c Agonist Chemotype with Antitubercular Activity

Xie, H.; Sukheja, P.; Tolentino, K.; Webb, J.; Woods, A.; Chi, V.; Kathayat, D.; Montague, C. R.; VanderVen, B. C.; Winneroski, L.; Durst, G.; Mendel, D.; Hipskind, P.; Henry, K.; McNamara, C. W.; Yang, B.; Chatterjee, A. K.

2026-09-19 microbiology 10.64898/2026.09.17.752203 medRxiv
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Rv1625c/Cya has emerged as a promising target for the development of treatment-shortening therapies for tuberculosis. Screening of an Enamine compound library identified sBQQ004 as an initial hit, and rapid hit optimization led to compound 1, which was subsequently confirmed as an Rv1625c/Cya agonist. Structure activity relationship studies identified lead compound 25 with potent activity against Mycobacterium tuberculosis H37Rv under cholesterol-dependent growth conditions (MIC = 0.27 uM) and strong intramacrophage activity (EC50 = 0.079 uM). Compounds 1 and 25 showed oral bioavailabilities of 84.5% and 51.9% in mice, respectively. Repeat BID dosing of compound 1 resulted in a dose- and time-dependent decrease in systemic exposure. Despite this pharmacokinetic limitation, the potency and overall profile of this chemotype encouraged continued optimization.

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Identification of novel HDAC11 inhibitors: In silico & in vitro studies

Paul, M.; Kumar, D. S.; Mishra, S.; Kalle, A. M.

2026-08-27 bioinformatics 10.64898/2026.08.24.746593 medRxiv
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Histone deacetylases (HDACs) are pivotal epigenetic regulators that modulate diverse cellular pathways by removing acetyl groups from lysine residues on both histone and non-histone proteins. Histone deacetylase 11 (HDAC11), the sole member of class IV HDACs, exhibits both deacetylation and fatty acid deacylation activities. Accumulating evidence implicates HDAC11 as a key epigenetic regulator of fundamental cellular processes, including metabolism, immune responses, and tissue development. Dysregulation of HDAC11 activity has been associated with inflammatory diseases, metabolic disorders, neurodegenerative conditions, and cancer, highlighting its potential as a therapeutic target. Although several HDAC11-specific inhibitors have been identified, none have progressed to clinical development. In this study, we aimed to discover HDAC11-selective inhibitors by integrating in silico and in vitro validation approaches. Homology modelling of the HDAC11 structure was conducted, followed by model validation, structure-based virtual screening, molecular dynamics (MD) simulations, and binding free energy calculations. We identified and validated three lead compounds and their intermediates using biochemical and cell-based assays. Fluorescence-based and HPLC-based enzymatic assays demonstrated potent inhibition of both the deacetylase and deacylase activities of HDAC11, with Inhibitor 6 and Inhibitor 3 exhibiting the strongest effects among the six compounds tested. Further, a decrease in lipid accumulation, reduced stability of the HDAC11 substrate SHMT2, as determined by immunoblot analysis and decreased cell viability, as assessed by MTT assay, confirmed HDAC11 inhibition in cellular models. The study shows that new HDAC11 inhibitors significantly reduce the viability of breast cancer cells and induce apoptosis; inhibitor 6, in particular, showed high potency, similar to the reference compound SIS-17. Flow cytometry showed that treated MDA-MB-231 cells exhibited cell-cycle arrest and increased apoptosis, a finding further confirmed by Annexin V/PI staining. Molecular analysis showed that BAX increased while BCL2 decreased, indicating that apoptotic pathways were activated in novel compound-treated MDA-MB-231 cells. The results suggest that inhibiting HDAC11 is an effective way to induce cancer cell death and provide a basis for further assessment of these compounds as potential treatments for breast cancer. Collectively, this study identifies novel zinc-chelating HDAC11 inhibitors containing a nitro-sp2 group, providing promising candidates for further therapeutic development.

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KPB82 potently and selectively inhibits ACER2 and protects tumor and primary cells from doxorubicin-induced cytotoxicity

Devi, A.; Xu, R.; Szulc, Z.; Kim, I.; Salama, M.; Bhabak, K. P.; Arenz, C.; Canals, D.; Hannun, Y. A.; Mao, C.

2026-10-02 biochemistry 10.64898/2026.09.29.754712 medRxiv
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Alkaline ceramidase 2 (ACER2) catalyzes the hydrolysis of ceramides into sphingosine and free fatty acids, playing crucial roles in regulating various biological processes, including but not limited to cell proliferation, survival, and the DNA damage response. However, a pharmacological tool that regulates its catalytic and signaling functions remains to be developed. In this study, N-[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]dodecane-1-sulfonamide (KPB82) was identified as a potent and selective ACER2 inhibitor. In vitro enzymatic assays showed that KPB82 inhibited ACER2 with an IC50 of 190 nM, while displaying minimal activity against acid and neutral ceramidases (IC50> 100 {micro}M) and no significant inhibition of alkaline ceramidase 1 or alkaline ceramidase 3. Enzymatic kinetic studies revealed that KPB82 is a competitive inhibitor of ACER2. The three-dimensional structure of ACER2 was modeled in the AlphaFold3 server, revealing key Zn2+-coordinating histidine residues and a substrate-binding pocket. Molecular docking studies demonstrated that KPB82 binds ACER2 within this pocket, forming hydrogen bonds with the catalytically important amino residues, Asp93 and His215, and interacting with several hydrophobic residues. Lactate dehydrogenase release assays revealed that KPB82 significantly reduced cytotoxicity in HeLa cells overexpressing ACER2, as well as in HCT116 cells, RT4 cells, and human umbilical vein endothelial cells treated with the DNA-damaging agent doxorubicin. Lipidomic analysis showed that KPB82 inhibited sphingosine production in response to ACER2 overexpression or doxorubicin treatment. Collectively, these findings demonstrate that KPB82 is a potent and selective ACER2 inhibitor capable of suppressing ACER2-dependent biological processes and highlight its potential as a tool for studying ceramide metabolism and ACER2-mediated signaling pathways.

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Integrated Computational and Spectroscopic Analyses to unravel the Role of Cu(II) Coordination in Modulating Doxorubicin-DNA Binding

Pattanayak, D. R.; Kurdekar, A. D.; Sai Manohar, C.; Sarojini, R.; Dharmaraj, R.

2026-09-14 biophysics 10.64898/2026.09.11.750536 medRxiv
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Doxorubicin (DOX) is a clinically important anthracycline whose anticancer activity is closely associated with DNA binding. However, the structural basis by which metal coordination modulates DOX-DNA association remains poorly understood. Here, an integrated computational and spectroscopic approach was employed to elucidate the role of Cu(II)-coordination in modulating the structure of DOX and its DNA binding. DFT, molecular docking, and molecular dynamics simulations established a stable intercalative association of DOX with DNA. At the same time, DFT-based characterization of Cu(II)-DOX revealed coordination induced structural and electronic changes consistent with reduced conformational freedom and increased rigidity. This led to the hypothesis that Cu(II) coordination may favor an intercalation-compatible configuration of DOX. UV-Vis and competitive fluorescence studies experimentally supported Cu(II)-dependent modulation of DOX-DNA association, with UV-Vis analysis indicating a substantial tenfold increase in apparent DNA-binding affinity and fluorescence measurements confirming pronounced perturbation of DNA-associated ethidium bromide. Collectively, the findings establish a coherent relationship between Cu(II) coordination, DOX conformational modulation, and DNA recognition, highlighting metal coordination as a potential strategy for tuning the biomolecular interactions of anthracycline therapeutics.

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Repurposing dopamine D3 receptor fluorescent ligands for D2 receptor

Ots, K.; Laasfeld, T.; Hollo, K.; Ilisson, M.; Ortigueira Noya, S.; Grassl, F.; Tousi, D.; Allas, H.-R.; Majellaro, M.; Enkvist, E.; Heinrich, M. R.; Sotelo, E.; Allikalt, A.

2026-10-09 biochemistry 10.64898/2026.10.07.756687 medRxiv
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The dopamine D2 receptor is a principal target of antipsychotic and antiparkinsonian drugs, yet well-characterized fluorescent ligands for the D2 receptor remain scarce compared with its relative, the D3 receptor. Here we show that fluorescent ligands developed for the D3 subtype can be repurposed as tools for studying the D2 receptor pharmacology. Using a machine-learning-assisted, live-cell fluorescence microscopy assay, we screened twelve fluorescent probes and identified eight ligands that bound specifically to the D2 receptor at 10 nM. Four ligands exhibited classical saturable binding, yielding Kd in the nanomolar range, whereas the remaining probes displayed unsaturated, time-dependent binding profiles. Kinetic analyses revealed substantial differences in association and dissociation behavior, highlighting the importance of time-resolved measurements. Competition binding with dopamine and haloperidol yielded affinity estimates consistent with literature values. These results expand the toolkit of validated D2 receptor fluorescent probes and support cross-receptor repurposing as a strategy for fluorescent ligand development.