Abstract Although the gastrin-releasing peptide receptor (GRPR) is an established theranostic target across multiple cancers, many GRPR-targeting peptides undergo rapid renal clearance, limiting tumor uptake and therapeutic exposure. Albumin-binding moieties (ABMs) reversibly interact with serum albumin, prolonging systemic exposure and increasing the opportunity for tumor uptake. To examine how ABM structure and placement affect this behavior, we prepared four DOTA-functionalized GRPR-targeting conjugates, varying both ABM lipophilicity and position relative to the DOTA chelator. The conjugates were radiolabeled with lutetium-177 in radiochemical yields and purities of >98%. All radioconjugates retained GRPR-mediated uptake in PC-3 cells, exhibited subnanomolar receptor affinity and enhanced blood retention. [177Lu]Lu-CA6356, bearing a 4-(p-iodophenyl)butyric acid-derived ABM, achieved the highest tumor uptake in PC-3 xenografts at 4 h pi (12 ± 2% IA/g), which increased by approximately 30% 24 h pi. These findings show that ABM identity and placement can modulate systemic exposure and tumor uptake in GRPR-targeting radioligands.
Abstract Skeletal muscle atrophy is driven in part by unrestrained myostatin (MSTN) signaling. We designed all-d tripeptide prodrug mimetics of the MSTN prodomain minimum active 23-mer fragment. Compounds 1 (H-d-Arg-d-Leu-d-Ala-OiPr) and 2 (H-d-Arg-d-Abu-d-Ala-OiPr) inhibited MSTN-induced myotube atrophy with sub-micromolar potency, while free-acid analogues (3, 4) and scrambled control (scr) were less active. All-d configuration conferred proteolytic stability exceeding 24 h. In vivo, compound 1 increased soleus mass and grip strength in mice. This work establishes compound 1 as a lead prodrug for MSTN antagonism in muscle atrophy.
Abstract The increasing emergence of antimicrobial resistance (AMR) is reducing the effectiveness of existing antibiotics against bacterial infections, including tuberculosis (TB), a deadly disease caused by Mycobacterium tuberculosis (M.tb). Approximately 90% of infected individuals develop latent tuberculosis infection, for which current treatment options are limited. Latent tuberculosis infection is characterised by the formation of hypoxic granulomas, which restrict oxygen and drug penetration, highlighting the need for therapies effective under hypoxic conditions. In this study, a hypoxia-activated prodrug (HAP) strategy was employed to improve selective drug delivery of promising anti-tuberculosis drugs bedaquiline, TBAJ-587 and TBAJ-876 (sorfequiline) to hypoxic TB granulomas. Thirty-six nitroimidazole-based hypoxia-activated prodrugs (HAPs) were successfully synthesized and evaluated for antitubercular activity. The HAPs exhibited potent in vitro activity under both oxic and hypoxic conditions, with consistently lower MIC values observed in the hypoxic assays. Assessment of hypoxic selectivity demonstrated enhanced trigger cleavage under hypoxic conditions, providing strong evidence for the hypoxia-selective activation of these compounds. Collectively, these findings highlight the therapeutic potential of hypoxia-mediated strategies for the treatment of latent tuberculosis, particularly within hypoxic niches that drive disease persistence and prolonged treatment regimens.
Abstract The SARS-CoV-2 main protease (Mpro) and host cysteine protease cathepsin L (CatL) are both attractive targets for antiviral intervention. Herein we describe the rational design and synthesis of dual Mpro/CatL inhibitors derived from the previously reported leads SM141 and SM142. Optimization focused on replacement of the acrylate ester warhead in SM141 and SM142 with a nitrile, modifying the P2, P3, and P4 capping groups, and variation of the P1 lactam ring size. In addition, conformational restriction was achieved through macrocyclization between the P1 and P4 side chains to enhance binding affinity. These efforts identified multiple dual-target inhibitors with nanomolar potency against both Mpro and CatL and potent antiviral activity as well as selective Mpro inhibitors with strong enzymatic activity. Targeting both a viral protease and a host factor may provide more durable antiviral efficacy by reducing susceptibility to resistance arising from viral evolution of Mpro.
Abstract Design time prioritization of central nervous system (CNS) drug candidates remains a challenge due to the restrictive nature of the blood–brain barrier (BBB) governing brain exposure. Although various multiparameter optimization (MPO) strategies have guided CNS medicinal chemistry for over a decade, existing frameworks rely heavily on heuristic cutoffs and offer limited interpretability across chemically diverse scaffolds. Here, we introduce a next generation CNS-MPO framework─Aragen-iMPO, (A-iMPO)─which was developed using 5,129 curated compounds through an integrated workflow combining explainable machine learning, rigorous descriptor selection, and low-dimensional discriminant mapping. This yielded six chemically intuitive features capturing polarity, ionization, size, rigidity, and electronic distribution. The resulting score provides a transparent discriminant function enabling direct compound prioritization through a simple threshold rule. Across internal and external validation sets, A-iMPO outperformed established CNS-focused scoring methods while maintaining mechanistic interpretability, providing a practical and design ready tool for CNS drug discovery.
Abstract Selective stabilization of complexes formed by the hub protein 14-3-3 represents an emerging mechanism for the modulation of therapeutically relevant targets. In this letter, we describe a hit-finding campaign designed to identify small molecule stabilizers of the interaction between 14-3-3σ and the estrogen receptor alpha (ERα). Four structurally distinct hits were identified and validated using a combination of biochemical assays and biophysical techniques. Ternary complex crystal structures revealed that all four hit compounds form a covalent bond with Cys38 of 14-3-3σ via four different electrophilic warheads. Structure-based optimization of the most promising hit compound 9 led to dramatic improvements in stabilization activity and selectivity that exceeded the complex natural product fusicoccin A.
On the basis of an X-ray cocrystal structure of our previously disclosed monosaccharide-derived galectin-3 inhibitor 3 with human galectin-3 protein, we envisioned that galectin-3 could be an appropriate target for targeted protein degradation as a potential novel drug discovery strategy. The identification and studies of a series of potent, metabolically stable, cell permeable, and noncytotoxic galectin-3 degraders, represented by 5 and 6, are herein reported. These compounds were highly effective in inducing galectin-3 degradation in normal human lung fibroblast (NHLF), A549, and LL29 cells with a degradation half effective concentration (DC50) value of 4 nM for 5 in NHLF cells. Global proteomics analysis of 6 revealed that the galectin-3 degrader was exquisitely selective for galectin-3 over >7800 other proteins quantified that include galectin family members. To the best of our knowledge, targeted protein degradation of galectin-3 or any other lectin has not been reported in the past.
Malaria, caused by Plasmodium parasites, remains a major global health challenge, exacerbated by the widespread emergence of drug-resistant plasmodium strains. Subtilisin-like serine protease SUB1 triggers escape of the parasite from the red cell via a process called egress, rendering the enzyme a prospective antimalarial drug target. While several SUB1 inhibitors have been developed, irreversible covalent inhibition has not been explored so far. In this work, we report our studies of peptidic inhibitors bearing covalent serine traps such as β-lactam, β-lactone, epoxide, and diaryl phosphonate. Out of these, peptidic diaryl phosphonates were found to be irreversible PfSUB1 inhibitors, with the best inhibitor 3b showing a PfSUB1 inhibitory potency (IC50) of 167 nM.
Fluorination is a powerful yet highly context-dependent strategy in medicinal chemistry. The F-DrugDatabase comprising 1,789 fluorinated small molecules was constructed, including 430 FDA-approved or marketed drugs. Using Bemis-Murcko scaffold analysis and a matched molecular pair (MMP) "defluorination-hydrogenation" approach, we reveal that 87.7% of fluorinated drugs contain only 1-3 fluorine atoms, with benzene scaffolds dominating (63.5%). Quantitative MMP analysis indicated that the -CF3 group was associated with an increase in predicted elimination half-life (average Δt1/2 = +12.24 h, P < 0.01), whereas -CH2F showed less favorable and more variable predicted effects. Based on these insights, we propose F_RO5, a fluorination-adapted drug-likeness guideline (MW ≤ 800 Da, cLogP ≤ 7, and TPSA ≤ 200 Å2) that covers 94.2% of marketed fluorinated drugs, providing broader coverage than the conventional Lipinski Rule-of-Five (68.2%). This data-driven framework provides quantitative guidelines for rational fluorination and early stage candidate prioritization.
Cyclin-dependent kinase 2 (CDK2) has emerged as a critical oncogenic driver in cancers characterized by cyclin E amplification and resistance to existing cell-cycle therapies. A recent patent disclosure describes heterobifunctional degraders that selectively induce CDK degradation by recruiting E3 ligases. By eliminating rather than inhibiting CDK2, these compounds offer a promising approach to suppress tumor proliferation and overcome therapeutic resistance in cyclin E-dependent malignancies.
Abstract Provided herein are novel compounds as TREM2 agonists, pharmaceutical compositions, use of such compounds in treating Parkinson’s disease, Alzheimer’s disease, amyotrophic lateral sclerosis, frontotemporal dementia, Nasu-Hakola disease, and stroke, and processes for preparing such compounds.
Salt-inducible kinases (SIK1/2/3) belong to the AMPK family of serine/threonine kinases, and SIK inhibition has been identified as a promising strategy for therapeutic intervention in oncology and immunology. Herein, we describe the use of parallel chemistry approaches to facilitate the development of novel SIK inhibitors. From these efforts, potent pan-SIK inhibitors were identified, as well as compounds which demonstrated biased isoform selectivity toward SIK3, and possessed attractive in vitro ADME properties. To validate the most promising compounds as high-quality chemical tools, cellular target engagement was assessed using NanoBRET assays, and selectivity was investigated across the wider kinome. Finally, the pharmacological effects of several compounds were studied using cellular models of acute myeloid leukemia, resulting in the identification of potent antiproliferative agents. The compounds reported represent high-quality chemical tools of potential value for target validation studies and could serve as effective starting points for a lead optimization campaign.
Provided herein are novel compounds as orexin 2 receptor agonists, pharmaceutical compositions, use of such compounds in treating narcolepsy, and processes for preparing such compounds.
To address the pharmacokinetic limitations and moderate potency of current prostanoid IP receptor agonists for treating pulmonary arterial hypertension, we developed a series of conformationally constrained diphenylpyrazinyl amino cycloalkoxy acetic acids. By replacing the flexible side chain of MRE-269 with a rigid cyclic framework, we locked the bioactive conformation, identifying 7a-5 and its deuterated analog 7a-19. Compound 7a-19 exhibited potent antiaggregatory activity (IC50 = 0.97 μM), a 7-fold enhancement over MRE-269 (IC50 = 7.4 μM). Crucially, leveraging the deuterium kinetic isotope effect in rats, 7a-19 demonstrated an 11-fold increase in systemic exposure (AUC o‑t = 26.7 h μg/mL), a prolonged half-life (t 1/2 = 12.0 h), and excellent oral bioavailability (F = 47.3%). Combined with a clean safety profile in the Mini-Ames assay and a lack of hERG inhibition (IC50 = 143.1 μM), 7a-19 stands out as a robust, long-acting lead candidate for PAH therapy.
Provided herein are novel compounds as SARS-CoV-2-related 3C-like protease (3CLPRO) inhibitors, pharmaceutical compositions, use of such compounds in treating coronavirus infections, and processes for preparing such compounds.
Abstract METTL1 is the human RNA methyltransferase that catalyzes the methylation of N7-guanosine in RNA. Overexpression of METTL1 has been linked to cancer, and increasing evidence supports the therapeutic potential of METTL1 inhibition in oncology. In this study, we have optimized a series of adenosine 5′-carboxamide derivatives as METTL1 inhibitors through structure-guided modifications of a previously discovered hit compound. The advanced inhibitor B22 shows an IC50 of 1 μM in an enzymatic assay, which is a 178-fold improvement with respect to the initial hit. The crystal structure of the des-methyl analogue of B22 (compound B19, IC50 = 0.4 μM) provides evidence that the benzylpiperazine moiety is accommodated within the guanosine-binding subsite of METTL1. The inhibitor B22 shows high solubility and metabolic stability and is selective against a panel of seven histone methyltransferases and the RNA-methyltransferase METTL3/METTL14.
Abstract The convergence of oxidative stress and inflammation drives neurodegeneration and cancer, positioning NADPH oxidases (NOXs) as critical therapeutic targets. Starting from the polyfunctional thiadiazolopyrimidine hit 1, we systematically truncated its peripheral arms to map minimum pharmacophoric requirements. While extensive clipping compromised activity, strategic optimization yielded the streamlined analogue 5. In silico, 5 acted as a competitive NADPH mimic; in cell-free assays, it maintained multi-isoform potency, inhibiting NOX1 and NOX5 at low-micromolar concentrations. In rat brain subcellular fractions, 1 and 5 demonstrated concentration-dependent neuroprotective and antioxidant efficacy (1–10 μM) by suppressing lipid peroxidation and preserving mitochondrial and synaptosomal viability. Notably, chemical profiling proved that 5 successfully stripped away the pro-oxidant liabilities and radical-scavenging artifacts inherent to 1. In cancer, 1 displayed some antiproliferative activity, mainly in hematological malignancies. Compound 5, although aqueous solubility issues limited its cellular antiproliferative performance, represents a specific, artifact-free architectural starting point for future selective NOX inhibitor development.
Abstract The investigational drug zervimesine (CT1812) is an allosteric small molecule modulator of the sigma-2 receptor (S2R), known as transmembrane protein 97 (TMEM97), currently in clinical development for Alzheimer’s disease and dementia with Lewy bodies. In Phase 2 trials, consistent favorable trends across outcome measures were observed for Alzheimer’s disease (NCT03507790), dementia with Lewy Bodies (NCT05225415), and another indication, dry AMD (NCT05893537). The crystal structure of S2R complexed with zervimesine to 2.74 Å resolution reveals this investigational therapeutic bound in the binding site of S2R analogous to that seen previously with other S2R ligands, and is consistent with binding affinity data from a S2R competition assay. The structural interactions by which zervimesine binds with S2R are illuminated, which may shed light on the potential structure–function relationship underlying the favorable effects of zervimesine seen preclinically and clinically, and may foster the design of future S2R modulators for neurodegenerative conditions.
Abstract Spindlin1 (SPIN1) is an epigenetic reader involved in oncology, whose third Tudor domain remains largely underexplored. Here, we applied a minimalist pruning strategy to the 26-mer peptide DOCpep3 to identify the core pharmacophore for SPIN1 Tudor 3 domain binding. This yielded truncated linear peptide analogues (e.g., 1, 3, and 4) displaying low nanomolar affinities, significantly outperforming the parent peptide. Orthogonal biophysical validation (MST and SPR) confirmed competitive target engagement. Furthermore, circular dichroism spectroscopy revealed that these pruned ligands induce distinct structural rearrangements in SPIN1, establishing high-affinity chemical probes for drug discovery.
We employed structure-based drug design to target the V-region of Streptococcus mutans antigen I/II (VAgI/II) and identified inhibitors of S. mutans (SM) - C. albicans (CA) dual-species biofilms. The lead compound, SN195, inhibited SM single-species biofilms and SM-CA dual-species biofilms at IC50 values of 49.9 and 23.6 μM, respectively, without affecting the planktonic growth of either microbe. SN195 at 100 μM did not affect the growth of the tested oral commensals. The X-ray cocrystal structure of SN195 bound to VAgI/II revealed crucial interactions in the vicinity of the conserved Ca2+ ion in the binding pocket. Structure activity relationship studies resulted in the development of more potent dual-species biofilm inhibitors, 1b and 1j, with IC50 values of 12.9 μM and 0.41 μM, respectively. In a dual-species gnotobiotic rat caries model coinfected with SM and CA, treatment with SN195, 1b, or 1j significantly reduced buccal and sulcal caries scores compared to infected and untreated control rats.
