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Journal of Medicinal Chemistry

American Chemical Society (ACS)

Preprints posted in the last 90 days, ranked by how well they match Journal of Medicinal Chemistry's content profile, based on 77 papers previously published here. The average preprint has a 0.06% match score for this journal, so anything above that is already an above-average fit.

1
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.

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Development of GS-441524 Derivatives as Potent SARS-CoV-2 Mac1 Inhibitors via a Direct-to-Biology Approach

Peng, K.; Chakraborty, S.; Wallace, S. D.; Noll, J. C. G.; Shang, J.; Lu, X.; Choi, A.; Whittaker, G.; Fromme, J. C.; Lin, H.

2026-06-25 pharmacology and toxicology 10.64898/2026.06.24.734322 medRxiv
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Targeting viral macrodomains (Mac) has emerged as a promising strategy for antiviral drug development, especially after the outbreak of COVID-19 that claimed millions of lives worldwide. Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mac1 inhibitors have been reported in the past few years. In the present work, we converted GS-441524 (IC50 of [~]10 M for SARS-CoV-2 Mac1) to KP-S54 (18c), a potent inhibitor of both SARS-CoV-2 Mac1 (IC50: 44 nM) and Middle East respiratory syndrome coronavirus (MERS-CoV) Mac1 (IC50: 91 nM) through an iterative direct-to-biology approach. This approach leverages efficient amide-coupling reaction and the mix-and-read fluorescence polarization (FP) assays where reaction mixtures could be screened directly without purification. Cocrystal structure of a selected derivative (12p) binding to SARS-CoV-2 Mac1 revealed the binding mode, which will guide future drug development against viral macrodomains.

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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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Glycosylation of anandamide and other bioactive N-acylethanolamines in mammalian cells and tissues

Stevens, A. F.; Peter, R. E. A.; Gagestein, B.; Ferraz, M.; Been, E.; Vleeshouwer, T.; Ttofi, I.; van den Berg, R. J. B. H. N.; van der Wel, T.; de Paus, L.; Deuschle, C.; van der Horst, C.; Heitman, L. H.; Artola, M. E.; Piomelli, D.; Grande, M. T.; Romero, J.; Overkleeft, H. S.; Brockmann, K.; Gasser, T.; Aerts, J. M. F. G.; van der Stelt, M.

2026-07-17 biochemistry 10.64898/2026.07.16.738921 medRxiv
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N-acylethanolamines (NAEs), including the endocannabinoid anandamide, are bioactive fatty acid amides that are normally hydrolyzed by fatty acid amide hydrolase (FAAH) or N-acyl acid amidohydrolase (NAAA). Strikingly, when canonical NAE degradation is blocked, NAE levels do not increase indefinitely but instead reach a plateau. This apparent metabolic ceiling suggests that additional, underexplored pathways contribute to NAE homeostasis. Identifying these pathways is essential to determine whether NAEs are converted into inactive metabolites or products with distinct biological properties. Here, we identify NAE glycosylation as a metabolic pathway that links endocannabinoid-related lipid metabolism to glycosphingolipid turnover. We synthesized glycosylated NAEs and their isotope-encoded standards and developed targeted LC-MS/MS assays to monitor their enzymatic processing and quantify their abundance in mouse and human cells, tissues, and plasma. We show that non-lysosomal glucosylceramidase GBA2 transfers glucose or galactose to anandamide, N-oleoylethanolamine and N-palmitoylethanolamine, and lysosomal glucosylceramidase GCase hydrolyses {beta}-Glycosylated-NAEs ({beta}-Glyco-NAE) back to their parent NAEs. {beta}-Glyco-NAEs occur endogenously in macrophages and neuronal cells, increase when canonical NAE degradation is impaired, and accumulate in human samples with GCase deficiency, including Gaucher disease and GBA1-associated Parkinsons disease. {beta}-Glyco-NAEs do not engage the cannabinoid receptors, TRPV1, or PPAR, and potentiate inflammatory cytokine release, including IL6 and TNF, from microglia. Based on these findings, we pose that GBA2-dependent NAE glycosylation may constitute an overflow lipid-remodeling pathway that connects NAE metabolism to lysosomal dysfunction, inflammation and neurodegeneration.

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Targeting the Myeloid Immune Checkpoint ILT3 (LILRB4) with Small Molecules Enables Reprogramming of Suppressive Tumor Immunity

Abdel-Rahman, S.; Monari, A.; Miclot, T.; Barbault, F.; Gabr, M.

2026-06-09 pharmacology and toxicology 10.64898/2026.06.05.730341 medRxiv
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Cancer immunotherapy has transformed cancer treatment; however, durable responses remain limited by suppressive myeloid populations within the tumor microenvironment. Leukocyte immunoglobulin-like receptor B4 (LILRB4/ILT3) is an emerging myeloid immune checkpoint implicated in immune evasion and resistance to immunotherapy, yet small molecule targeting of ILT3 remains largely unexplored. Here, we report the discovery of small molecule ILT3 modulators identified using a Dianthus-based temperature-related intensity change (TRIC) screening platform. Screening of an 8,961-member Enamine Library identified multiple direct ILT3 binders, with lead compound ICB-7 demonstrating high-affinity binding to recombinant human ILT3 by microscale thermophoresis and robust cellular target engagement in CETSA assays. Molecular docking and molecular dynamics simulations revealed a stable hydrophobic binding pocket within the D2 domain of ILT3. Functionally, ICB-7 disrupted the ILT3-SCG2 interaction and inhibited downstream SHP1, SHP2, and STAT3 signaling. In patient-derived colorectal cancer and acute myeloid leukemia co-culture models, ICB-7 enhanced cytotoxic T-cell activity, and reduced tumor-cell viability. The compound also demonstrated favorable pharmacokinetic and safety properties together with significant anti-tumor efficacy in the CT26 syngeneic colorectal carcinoma model. Collectively, these findings establish ILT3 as a tractable target for small-molecule immunomodulation and support pharmacological targeting of suppressive myeloid checkpoints as a promising cancer immunotherapy strategy.

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Direct Small Molecule Modulation of LILRB4 (ILT3) Restores Anti-Tumor Immunity In Vivo and in Patient-Derived Cells

Abdel-Rahman, S.; Mariam, Z.; Deganutti, G.; Gabr, M.

2026-06-11 pharmacology and toxicology 10.64898/2026.06.10.731269 medRxiv
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Small molecule targeting of suppressive myeloid immune checkpoints remains a major challenge in cancer immunotherapy, particularly for non-enzymatic receptors lacking conventional druggable active sites. Leukocyte immunoglobulin-like receptor B4 (LILRB4/ILT3) is an immunosuppressive myeloid checkpoint implicated in tumor immune evasion, T-cell dysfunction, and resistance to immunotherapy across both solid and hematologic malignancies. Here, we report the discovery and characterization of GL-4512, a direct small molecule modulator of LILRB4 identified through a Dianthus-based temperature-related intensity change (TRIC) screening platform. Orthogonal biophysical studies, including microscale thermophoresis, surface plasmon resonance, and cellular thermal shift assays, confirmed direct target engagement with nanomolar affinity. Extensive microsecond molecular dynamics simulations combined with site-directed mutagenesis identified a previously unrecognized ligandable pocket within the flexible extracellular domain of LILRB4. Functionally, GL-4512 disrupted the immunosuppressive LILRB4-SCG2 signaling axis and suppressed downstream SHP1/SHP2 and STAT3 signaling. In patient-derived colorectal cancer and acute myeloid leukemia co-culture systems, pharmacological inhibition of LILRB4 restored anti-tumor immune activity, enhanced IFN-{gamma} and IL-2 production, increased cytotoxic T-cell activation, and reduced tumor-cell viability. GL-4512 additionally demonstrated favorable pharmacokinetic and safety properties supporting oral in vivo administration. In immunocompetent CT26 syngeneic colorectal tumors, once-daily oral treatment significantly suppressed tumor growth and enhanced intratumoral immune activation. Collectively, these findings establish LILRB4 as a tractable target for direct small molecule immunomodulation and support therapeutic targeting of suppressive myeloid immune checkpoints for cancer using non-biologic modalities.

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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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Selective covalent-allosteric tools to dissect Akt2

Quambusch, L.;D\'Angelo, G.;Kirschner, T.;Beerbaum, M.;Depta, L.;Schnecke, F.;Niggenaber, J.;Brandherm, S.;Weisner, J.;Mueller, M.;Dehmelt, L.;Rauh, D.

2026-06-19 Cancer Biology 10.64898/2026.06.15.732341 medRxiv
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The protein kinase Akt and its isoforms play a crucial role in various diseases. Unique functions of the individual isoforms (Akt1, Akt2, Akt3) might be essential for survival in malignancies. Particularly for Akt2, it was reported that a knock-out led to diabetic phenotype and might be correlated with clinically adverse hyperglycemic effects observed in pan Akt-treatment. Enduring failure of Akt inhibitors in the clinic indicates the necessity for a thorough understanding of the underlying biology, preferably by using highly isoform-selective small molecules. Here we report the structure-guided development of Akt2-selective covalent-allosteric probe molecules, that can be successfully modified within a complex environment using biorthogonal chemistry. Thus, enabling first Akt2-specific pull-down studies and the use in functional studies, such as selective fluorescent labeling in cellular systems. These chemical probes expand our toolbox to dissect the critical questions of Akt2s function in health and disease, thereby paving the way for novel therapeutic strategies based on thorough mechanistic insights.

9
Discovery of a pathway-selective platelet P2Y1R inverse agonist that suppresses inflammation while preserving hemostasis

Pitchford, S. C.; Nahar, K.; Pan, D.; Sisk, C. M.; Al-Adhami, T.; Ekinci, K.; Amison, R. T.; Gargate, N.; Saji, A.; Wills, E.; Page, C. P.; Ladds, G.; Rahman, K. M.

2026-06-24 pharmacology and toxicology 10.64898/2026.06.19.732319 medRxiv
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The platelet P2Y1 receptor (P2Y1R) is necessary for inflammation, signalling via Rho-GTPase pathways to elicit functions that are distinct from aggregation (PLC-dependent canonical signalling pathway). Whether these distinct platelet inflammatory functions can be selectively suppressed to preserve hemostasis through the rational design of P2Y1R antagonists has not been explored. In silico molecular docking analysis examined biased nucleotide interactions within the P2Y1R binding pocket. The identified possible key amino acid residues guided rational design to synthesize compounds for pathway selective inhibition, evolving from nucleotide to non-nucleotide structures. The nucleotide analogue KMR-82-13 was predicted to engage distinct regions of the binding pocket and selectively inhibited platelet chemotaxis while preserving aggregation. These findings informed the design of a non-nucleotide compound KSN-159-27, aiming to retain key KMR-82-13-like interactions while improving drug-like properties. Docking and molecular dynamics simulation supported a stable but dynamic binding mode for KSN-159-27 within the P2Y1R pocket, consistent with pathway-selective inhibition. KSN-159-27 displayed characteristics of a pathway selective inverse agonist at P2Y1R towards G12/13-mediated pathways, but not those associated by Gq activation in P2Y1R-transfected HEK293T cells. KSN-159-27 showed functionally selective inhibition for platelet P2Y1R-mediated functions. In vivo, KSN-159-27 suppressed inflammatory cell recruitment, whilst preserving bleeding time and ADP-induced thromboembolic responses, in contrast to the neutral P2Y1R antagonist MRS2500. This first demonstration for the rational design of a pathway selective inverse agonist at platelet P2Y1Rs has significant implications for novel therapeutic strategies developed to safely target platelet activation during inflammation, in contrast to current anti-platelet drugs used in the prevention of thrombosis. Key PointsO_LIBiased inverse platelet P2Y1R agonists selectively supress inflammation whilst preserving hemostasis and the ability of platelets to aggregate. C_LIO_LIBiased inverse agonism selectively inhibited P2Y1R G12/13 (Rho-GTPAse functions) but not Gq activities (PLC functions). C_LI

10
Chemoselective Halogenation of Premarineosin A for Next-Generation Antimalarial Development

Harris, N. R.; Amin, S.; Curtis, B. J.; Teklemichael, A. A.; Dranchak, P.; McBride, C. M.; Verhey-Henke, L.; Warrell, C. J.; Dulaney, W. M.; Oliphant, E. N.; Inglese, J.; Su, X.-z.; Sherman, D. H.; Pereira, F.

2026-06-17 biochemistry 10.64898/2026.06.16.732709 medRxiv
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Premarineosin A undergoes rapid, chemoselective C12 halogenation under mild conditions, providing brominated, chlorinated, fluorinated, and iodinated analogs. These derivatives retained potent antiplasmodial activity against both chloroquine-sensitive and -resistant Plasmodium falciparum strains and displayed smaller reductions in potency against the resistant strain than the parent compound.

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Screening of Stereochemically Defined 2,5-Diketopiperazines Identifies Autophagy Inducers without mTORC1 Suppression

Yano, S.; Uchida, S.; Karakama, S.; Suzuki, S.; Kino, K.; Hara, T.

2026-08-13 biochemistry 10.64898/2026.08.12.744315 medRxiv
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Modulating autophagy has emerged as a potential strategy for treating age-related diseases. However, commonly used pharmacological approaches to induce autophagy, particularly inhibition of mechanistic target of rapamycin complex 1 (mTORC1), can be associated with adverse effects, including immunosuppression and insulin resistance. This has prompted interest in autophagy modulators that act without directly inhibiting mTORC1. 2,5-Diketopiperazines (DKPs) are bioactive cyclic dipeptide scaffolds with diverse biological activities. However, systematic evaluation of their structure-activity relationships has been hindered by racemization during conventional chemical synthesis, leaving the contribution of stereochemistry to autophagy regulation poorly understood. Here, we used a stereoselective one-pot chemoenzymatic synthesis based on the adenylation domain of tyrocidine synthetase A to generate a DKP library with defined stereochemistry. Phenotypic screening in Caco-2 cells stably expressing the GFP-LC3-RFP autophagic flux probe identified four DKPs that increased autophagic flux: c(DW-DP), c(DW-LP), c(DF-DP), and c(DM-LP). Structure-activity analysis revealed stereochemistry-dependent effects associated with amino acid side-chain properties: D-configured residues were favored among DKPs containing aromatic amino acids or methionine, whereas L-configured residues were favored among those containing branched-chain amino acids. Substitution of the proline residue further altered activity, with glycine substitution tending to increase autophagic flux in some DKP scaffolds. Importantly, the active DKPs did not detectably reduce the phosphorylation of the mTORC1 downstream targets p70 S6K and 4EBP1, indicating that their autophagy-inducing effects do not require detectable suppression of canonical mTORC1 signaling. These findings establish stereochemically defined DKPs as candidate scaffolds for the development of autophagy inducers that act through mechanisms distinct from direct mTORC1 inhibition.

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AI-Guided Discovery of Small Molecule LILRB4 (ILT3) Inhibitors Reprograms Microglia and Reduces Amyloid Pathology

Abdel-Rahman, S.; Gabr, M.

2026-06-16 pharmacology and toxicology 10.64898/2026.06.12.731845 medRxiv
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The inhibitory microglial receptor LILRB4 (ILT3) suppresses amyloid-beta clearance in Alzheimers disease (AD) through ApoE-dependent signaling but remains undrugged by small molecules. Here, we report the AI-guided discovery of small molecule inhibitors that directly disrupt the LILRB4-ApoE interaction. Ultralarge-scale screening of [~]500 million compounds identified small molecules that bind LILRB4 with nanomolar affinity and competitively block ApoE engagement, as validated across orthogonal biophysical assays. Structural and mutational analyses define a tractable interdomain pocket that mediates ligand recognition. In human iPSC-derived microglia, LILRB4 inhibition suppresses SHP1/2-dependent signaling, attenuates NF-{kappa}B activation, and restores A{beta} uptake. The lead compound exhibits favorable pharmacokinetics with robust brain penetration and, upon oral administration, improves cognitive performance, reduces amyloid burden, and dampens neuroinflammation in the 5xFAD mouse model. These findings establish LILRB4 as a druggable neuroimmune checkpoint and demonstrate that small molecule disruption of inhibitory microglial signaling can restore disease-relevant function in vivo.

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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

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Computational Design of Two Novel BRAF V600E Inhibitors: Exploiting Sulfoximine Bioisosterism and Chiral Constraints to Evade Paradoxical Activation

Yu, Z. H.; Siegel, J. B.; Morrow, E. R.

2026-06-30 pharmacology and toxicology 10.64898/2026.06.25.734343 medRxiv
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Metastatic melanoma is an aggressive cutaneous malignancy frequently driven by the oncogenic V600E mutation within the BRAF kinase. While first-generation Type IS BRAF inhibitors, such as dabrafenib, are currently prescribed to target this specific molecular vulnerability, paradoxical MAPK pathway activation, and acquired drug resistance necessitate the continuous development of structurally optimized lead molecules. In this study, chemical intuition, bioisosteric replacement, and computational molecular docking were employed to propose two novel BRAFV600E drug candidates. The proposed therapeutics, engineered to incorporate constrained sp3-hybridized aliphatic rings and a sulfoximine bioisostere, demonstrated thermodynamically superior docking scores within the mutant catalytic cleft compared to dabrafenib. Lastly, a homology analysis determined that Mus musculus is a suitable model organism for future preclinical studies and confirmed crucial structural selectivity against microbial off-target kinases.

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Induced alanine auxotrophy as a therapeutic strategy against Mycobacterium tuberculosis

Shalaby, M.-A. W.; Beeralingappa, N. C.; Shrinidhi, A.; Makafe, G. G.; Nece, E.; Patwardhan, A.; Low-Beer, T.; Kuki, A.; Sheinerman, F.; Weinrick, B.; Flaherty, D. P.; Chojnacki, M.

2026-06-16 pharmacology and toxicology 10.64898/2026.06.12.731178 medRxiv
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New antitubercular agents acting through previously unexploited mechanisms are urgently needed. Using a drug-repurposing platform, we identified TI-374, a hydroxamic acid containing compound that inhibits Mycobacterium tuberculosis (Mtb) with sub-micromolar potency. Systems analysis, resistance mapping, supplementation assays, and biochemical studies showed that TI-374 inhibits two PLP-dependent aminotransferases, AlaA and HisC1. However, its activity is driven primarily by irreversible inhibition of AlaA, whereas HisC1 inhibition is only partially reversible, revealing differential reversibility between the two targets. Optimization yielded TI-801, a low-nanomolar AlaA inhibitor. Both compounds remained active against intracellular Mtb in a macrophage infection model, where alanine supplementation did not rescue growth, indicating that host-derived alanine is unlikely to bypass AlaA inhibition. Genetic deletion of alaA attenuated Mtb survival in a murine infection model. Together, these findings support AlaA as a host-relevant metabolic vulnerability in Mtb and TI-801 as a mechanistic chemical probe for its validation as an antitubercular target.

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Cereblon on Steroids: Beyond the Canonical Ligand Space

Herrmann, A.; Heim, C.; Maiwald, S.; Boichenko, I.; Neuenschwander, M.; Oder, A.; Hernandez Alvarez, B.; Lupas, A. N.; von Kries, J. P.; Hartmann, M. D.

2026-08-31 biochemistry 10.64898/2026.08.28.747849 medRxiv
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Cereblon (CRBN) is widely used in targeted protein degradation, but its ligand space has remained dominated by a narrow set of cyclic imide chemotypes. Here, we show that the accessible CRBN ligand space extends substantially beyond this canonical space. A high-throughput screen of > 40,000 compounds, followed by orthogonal biophysical validation, X-ray crystallography and SAR analyses, identified several chemically distinct ligand classes. These include linear acetyl-based motifs, a phthalide-derived scaffold, steroidal compounds, and a range of bicyclic ligands. They engage CRBN through distinct recognition modes, several of which deviate from the canonical hydrogen-bonding pattern. Steroidal scaffolds were particularly notable: cortisone binds the human CRBN thalidomide-binding domain with an affinity comparable to thalidomide, with its A-ring occupying the tri-tryptophan pocket in a glutarimide-like orientation despite lacking the canonical imide NH donor. SAR within this series showed substantial tolerance for chemical modification and scaffold simplification, raising the possibility that endogenous steroidal metabolites may contribute to the physiological ligand landscape of CRBN. Bicyclic lactams additionally provided synthetically accessible scaffolds with tunable affinity and promising sites for linker attachment. Across the identified ligand classes, none of the tested representatives induced detectable degradation of canonical CRBN neosubstrates, and several showed largely clean proteomic profiles. Together, these findings broaden the chemical, mechanistic and potential physiological landscape of CRBN recognition and provide diverse starting points for alternative, potentially neosubstrate-sparing CRBN recruiters.

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Discovery of ILT3 (LILRB4) Small Molecule Inhibitors by Affinity Se-lection-Mass Spectrometry Reveals Druggability of a Neuroimmune Checkpoint in Alzheimers Disease

Abdel-Rahman, S.; Murugan, N.; Gabr, M.

2026-06-09 pharmacology and toxicology 10.64898/2026.06.05.730337 medRxiv
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Leukocyte immunoglobulin-like receptor B4 (LILRB4/ILT3) is an emerging neuroimmune checkpoint that restricts microglial activation and amyloid clearance in Alzheimers disease (AD) through ApoE-dependent signaling. Here, we establish ILT3 as a tractable small molecule target using affinity selection-mass spectrometry (AS-MS) to identify direct binders. Biophysical validation confirmed high-affinity engagement, with LT12 exhibiting nanomolar binding by MST and SPR. Computational modeling and mutagenesis defined a discrete ILT3 binding pocket, revealing a distributed interaction network critical for ligand engagement. Targeting ILT3 disrupted the ILT3-ApoE interaction, with LT12 showing potent inhibition in orthogonal biochemical assays. In human iPSC-derived microglia, ILT3 modulation attenuated SHP1/2 signaling, suppressed NF-{kappa}B activation, reduced IL-1{beta} secretion, and restored A{beta} uptake. In vivo, pharmacological targeting of ILT3 improved cognition, reduced amyloid burden, and attenuated neuroinflammation in 5xFAD mice. Together, these findings validate ILT3 as a druggable neuroimmune checkpoint and support its therapeutic targeting in AD.

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AlfaDAX-Derived ActRIIA/B Antibody with Semaglutide Enhances Fat Loss and Improves Weight-Loss Quality in DIO Mice

Zhang, N.; Long, Y.; Xu, Z.; Chen, G.; Wang, A.; Chen, W.; Chen, Z.; Liang, Z.; Leung, k.; chen, l.

2026-07-13 pharmacology and toxicology 10.64898/2026.07.09.737400 medRxiv
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GLP-1 receptor agonists achieve weight loss but are associated with clinically significant reductions in lean mass. Activin type II receptors (ActRIIA and ActRIIB) mediate signaling of myostatin and activin A, both of which negatively regulate muscle growth, suggesting that dual blockade of these receptors may preserve or increase lean mass while promoting fat loss. In this study, we developed anti-ActRIIA/B antibodies using AI-driven platforms (AlfaDAX) and selected the lead candidate AB130-165 based on in vitro binding, functional blocking, and developability assessments. Compared with a laboratory-prepared bimagrumab analog, AB130-165 exhibited potent dual inhibition of ActRIIA/B signaling, with a 9.5-fold higher functional blocking activity against activin A-induced SMAD signaling and 1054-fold improvements in binding affinity for ActRIIA (KD = 0.204 pM), 10-fold for ActRIIB (KD = 0.243 pM), respectively. In diet-induced obese mice, combination therapy with AB130-165 and semaglutide resulted in a 33.4% body weight reduction, which was superior to semaglutide monotherapy (-24.3%) and the bimagrumab combination group (-25.5%). Moreover, the combination significantly improved body composition, reducing fat mass percentage by 77.8% (vs. 65.0% in the bimagrumab combination group) and increasing the lean-to-body weight ratio to 67.3% (vs. 62.3%), demonstrating superior fat loss with better preservation of lean mass. Collectively, these findings establish AB130-165 as a differentiated anti-ActRII antibody that enables high-quality weight loss, and its combination with semaglutide shows superior efficacy over bimagrumab-based regimens. With favorable developability and potential for long-acting subcutaneous administration, AB130-165 represents a promising next-generation therapeutic candidate for obesity and muscle-sparing weight management.

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From DNA-Encoded Library (DEL) Screening to In Vivo Validation: LILRB4 (ILT3)-Targeted Small Molecules Reprograms Myeloid Immune Suppression

Abdel-Rahman, S.; Gabr, M.

2026-06-12 pharmacology and toxicology 10.64898/2026.06.10.731267 medRxiv
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Alzheimers disease (AD) remains a major unmet clinical challenge, with limited therapeutic strategies capable of effectively modulating neuroimmune dysfunction. Leukocyte immunoglobulin-like receptor B4 (LILRB4/ILT3) has recently emerged as an inhibitory microglial immune checkpoint implicated in ApoE-mediated suppression of amyloid-{beta} (A{beta}) clearance and inflammatory signaling, supporting its potential as a therapeutic target in AD. Here, we applied DNA-encoded library (DEL) screening of approximately 3.6 billion compounds to identify small molecule binders of LILRB4. Biophysical validation identified APX1 as a direct LILRB4 ligand with submicromolar affinity, which was further confirmed by cellular thermal shift assay (CETSA). Docking-guided mutagenesis studies defined a discrete ligand-binding interface involving key hotspot residues required for stable target engagement. Functionally, APX1 disrupted the LILRB4-ApoE interaction in orthogonal ELISA and biolayer interferometry assays. In human iPSC-derived microglia, APX1 suppressed SHP1/2 phosphorylation, attenuated NF-{kappa}B activation and IL-1{beta} secretion, and restored A{beta}42 uptake under ApoE-driven inflammatory conditions. APX1 further demonstrated favorable in vitro developability, metabolic stability, and CNS exposure properties. In the 5xFAD mouse model of AD, oral administration of APX1 improved cognitive performance, reduced cortical and hippocampal A{beta}42 burden, suppressed neuroinflammatory cytokines, and decreased activated microglial populations. Collectively, these findings establish APX1 as a promising small molecule modulator of the LILRB4-ApoE signaling axis and support pharmacological targeting of neuroimmune checkpoints as a therapeutic strategy for AD.

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Expanding the Ligandable Chemical Space of OTUB1 through Discovery of a Four-Membered-Ring Recruiter Chemotype

Wu, Q.; Song, X.; Chen, L.; Inuzuki, H.; Atkins, J.; Qi, Y.; Xiong, Y.; Wei, W.; Jin, J.

2026-08-27 biochemistry 10.64898/2026.08.26.747398 medRxiv
Top 0.1%
14.8%
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Deubiquitinase-targeting chimeras (DUBTACs) have emerged as a promising strategy for targeted protein stabilization, but their broader application remains limited by the scarcity of ligandable deubiquitinase recruiters. Here, we report a previously unexplored four-membered-ring OTUB1 recruiter chemotype. Through systematic structure-activity relationship studies, we identified compound 21 (MS2159) as a potent and selective covalent OTUB1 ligand. Biochemical and intact protein mass spectrometric analyses demonstrated that MS2159 selectively engages the non-catalytic C23 residue of OTUB1, shows minimal reactivity toward other tested proteins, and preserves OTUB1 deubiquitinase activity. Conjugation of MS2159 with the CFTR ligand lumacaftor yielded compound 25 (MS2134), which effectively stabilized {Delta}F508-CFTR. Collectively, these findings establish a new OTUB1 recruiter scaffold, expand the ligandable chemical space of OTUB1, and provide additional opportunities for developing next-generation DUBTACs.