Benzylidene-thiazolidinedione derivatives (SA01-SA12) were designed and synthesized using structure-based 3D-QSAR (R² = 0.819, Q² = 0.537) and pharmacophore modeling techniques to discover potent ALR2 inhibitors. Molecular docking analyses revealed that...
Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine salvage pathway that has recently emerged as a potential therapeutic target in cancer. While its role in hematological malignancies is relatively well established, its contribution to solid tumors, particularly breast cancer, remains insufficiently defined. This review aims to critically evaluate the role of PNP in breast cancer progression, with a focus on its involvement in metabolic reprogramming, tumor aggressiveness, and immune modulation, in addition to therapeutic targeting potential. Current evidence indicates that PNP overexpression supports nucleotide homeostasis, promotes proliferation, and contributes to metastatic phenotypes through metabolites such as hypoxanthine. Structural and computational studies have facilitated the development of diverse PNP inhibitors; however, their clinical translation into breast cancer therapy remains limited. A major research gap lies in the lack of mechanistic integration between PNP-driven metabolism, tumor-immune interactions, and subtype-specific breast cancer biology, as well as insufficient in vivo and clinical validation of candidate inhibitors in solid tumors. To address these limitations, future research should focus on integrating multi-omics approaches, advanced computational modeling, and patient-derived models to elucidate PNP-centered metabolic-immune networks. In parallel, the rational design of selective inhibitors with improved pharmacokinetic profiles, combined with biomarker-driven patient stratification and combination therapy strategies, establishes a strong rationale for the development of clinically effective PNP-targeted therapies for breast cancer.
PNP-mediated metabolic and immune reprogramming in breast cancer: mechanisms and therapeutic strategies.
CBX7 plays an important role in the epigenetic regulation of aggressive malignancies. The discovery of small-molecule and drug-like inhibitors is key to studying this protein's biological function and in the development of therapeutics. Herein we report the campaign that led to the cell-active and potent CBX7 small-molecule inhibitor EC134. From an initial high throughput screen, a 2-pyridone compound class was identified and 30 structural analogs were made through a convergent synthetic route that allowed for easy diversification. Multiple regions of the scaffold were modified including the 2-pyridone, a piperazine core and a terminal aromatic group. An SAR was established identifying key substituents necessary for binding, and most intriguing was the positioning of methyl groups around a pyridine-aryl bond, showing a sharp line between potency and inactivity that we explored using molecular docking studies. This work resulted in four hit compounds with potent IC50 values (<60 μM) and provides important insight in the development of small-molecule inhibitors for CBX7.
Peptides are promising candidates for targeting unconventional drug targets involving large interaction interfaces, such as protein-protein interactions (PPIs), historically considered undruggable. However, when removed from their native protein context, short peptides are flexible, resulting in an entropic penalty upon binding and poor pharmacological properties. A wide variety of design strategies have therefore been developed, making the selection of the most appropriate protein mimicry approach far from trivial. In this review, we provide an overview of the main approaches, focusing on the well-established p53-hDM2 interaction, which has been widely used as a model system in the field. This model enables a direct comparison between the different design strategies and highlights their respective impact on conformational stability, target affinity, and pharmacological properties, including proteolytic stability, cell permeability, and toxicity, ultimately governing biological activity. Overall, this comparison aims to guide the rational selection of design strategies for the development of new proteomimetics targeting challenging PPIs.
Macrocyclic peptides and peptidomimetics (MPPs) have emerged as a powerful therapeutic class in peptide-based drug discovery, uniquely positioned to modulate challenging protein-protein interactions (PPIs). While dysregulated PPIs drive diverse human pathologies, including cancer, metabolic disorders, neurodegenerative proteinopathies, inflammatory conditions, and microbial infections, targeting them remains difficult. Traditional small molecules lack the surface area to bind large, flat PPI interfaces, whereas linear peptides suffer from rapid proteolytic degradation and poor cell permeability. MPPs overcome these limitations by bridging the gap between small molecules and biologics. Their cyclic architecture provides conformational rigidity minimizing entropic penalties and maximizing binding affinity and selectivity. This structural pre-organization also enhances metabolic robustness, protease resistance, and cellular permeability. This review comprehensively examines the biological significance of PPIs in human disease and details how MPPs effectively modulate historically undruggable targets. We highlight current synthetic strategies, peptide engineering platforms, and the clinical and preclinical status of leading MPP candidates, while weighing their operational advantages and limitations. Finally, we analyze the contemporary market trajectory and emerging commercial opportunities, positioning MPPs as next-generation, PPI-targeting therapeutics.
In this study, a series of oridonin (ORI 1) derivatives were synthesized, and their antiproliferative activities were evaluated against colorectal cancer (CRC) cell lines. Structure-activity relationship (SAR) analysis revealed that aromatic and heteroaromatic substitutions significantly enhanced the antiproliferative potency compared to the parent compound. Among the synthesized derivatives, difuroate enmein-type compound 11b emerged as the most interesting candidate (IC50 = 0.49 μM), displaying a favorable balance between anticancer activity and cytotoxicity toward normal colon cells. Mechanistic studies revealed that compound 11b significantly inhibited the proliferation of SW620 cells, increased the doubling time, and induced S and G2/M cell cycle arrest. In addition, treatment with this compound reduced intracellular ROS levels, decreased the expression of CDK1 and CDK6, and attenuated mTOR signaling. Collectively, these findings identify compound 11b as a valuable scaffold for further development of novel anticancer agents targeting CRC.
Chalcones, pyrazolines, and pyrazoles constitute a uniquely powerful discovery pipeline in which each is a privileged scaffold with distinct applications, while also serving as the synthetic precursor to the next. Despite a theoretical chalcone library exceeding 680 000 unique structures accessible from commercial starting materials alone, fewer than 5140 examples have been reported in the literature-representing just 0.8% of this chemical space. Combining this precursor library with the downstream pyrazoline and pyrazole chemical spaces yields a combined landscape conservatively estimated to exceed 7.5 million unique structures, which remains largely unexplored. This review examines leading examples from 1990 to 2025 across all three scaffold classes, with particular emphasis on the most promising applications of this pipeline: anti-cancer, anti-inflammatory, anti-viral, and fluorescent sensing applications. We explore how pharmacophore hybridisation is further expanding this pipeline. Whereas previous reviews have focused on individual scaffold classes in isolation, this review takes an integrated, systematic approach that unifies all three into a single coherent discovery pipeline. We conclude with a roadmap on how the convergence of design of experiments, automated synthesis, high-throughput screening, and machine learning will unlock the potential of this vastly unexplored chemical space.
Bromodomain adjacent to zinc finger 2A and 2B (BAZ2A/B) are regulatory subunits of imitation switch (ISWI) chromatin remodelling complexes. Despite their implication in diverse pathologies, BAZ2A/B remain poorly understood, largely due to the lack of chemical probes capable of discriminating between these homologues or targeting their multiple domains. To address this challenge, we recently disclosed two first-in-class PROTACs: dBAZ2, which degrades both BAZ2A and BAZ2B, and the BAZ2B-selective degrader dBAZ2B. Here, we describe the medicinal chemistry campaign that led to their discovery. In addition, we report here an optimized synthesis of the BAZ2A/B bromodomain (BRD) ligand BAZ2-ICR enabling two different attachment points for linker incorporation and demonstrate that BAZ2A/B degradation is more readily achieved through recruitment of VHL than CRBN. We also identify a third degrader, 8, which employs an alternative linkage vector to BAZ2-ICR compared to dBAZ2 and dBAZ2B, adding to the structural diversity of BAZ2 PROTACs. Cooperativity assays and the BAZ2B-BRD:8:VHL-EloC-EloB co-crystal structure reflect the ability of 8 to degrade both BAZ2A and BAZ2B. In contrast, dBAZ2B achieves selectivity through preferential ternary complex formation with BAZ2B. Finally, we demonstrate the utility of dBAZ2/dBAZ2B as chemical probes: dBAZ2 induces expression of BAZ2A-regulated genes more strongly than dBAZ2B or BAZ2-ICR, and the BAZ2B selectivity of dBAZ2B is maintained across multiple cell lines. Collectively, this work delivers new chemical tools to interrogate BAZ2A/B biology and establishes a platform for developing heterobifunctional molecules targeting these understudied yet disease-relevant proteins.
The development of innovative treatment medicines that can overcome drug resistance and intracellular persistence is necessary since tuberculosis (TB) continues to be a significant worldwide health burden. In this work,...
In the ongoing search to target Alzheimer's disease, the inhibitory potential of novel oxoisoindoline derivatives against two key enzymes, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), was investigated. The structures of all...
SARS-CoV-2 main protease (MPro) is a proven target for drug discovery of small-molecule antiviral agents due to its crucial role in viral polyprotein processing, high structural conservation across numerous divergent variants, and the lack of similar human enzymes. Unlike covalent compounds, noncovalent inhibitors of MPro do not modify the enzyme's active site, and may offer improved safety profiles, greater chemical tractability, and better oral bioavailability without the need for pharmacokinetic enhancement. In this study, we designed, synthesized and characterized thirteen noncovalent nonpeptidic SARS-CoV-2 MPro inhibitors clustered into two series (KK and KB) of compounds. The inhibitors were designed based on our recently discovered Mcule-5948770040 and its analogue HL-3-68 designed through the structure-activity relationship study. To obtain atomic details of the inhibitors' binding we solved room-temperature X-ray structures of the MPro/inhibitor complexes, and to quantify their binding and antiviral properties we performed in vitro DSF and ITC measurements and TCID50 antiviral assays. In addition, a room-temperature neutron structure of the MPro/KB-5 complex allowed direct determination of hydrogen positions, mapping intermolecular interactions and directly visualizing the protonation states and hydrogen bonding. Improved binding affinities of KK-7 and KB-3 through KB-6 could be attributed to the observed nonconventional S-H⋯F hydrogen bond and an additional conventional hydrogen bond between the carboxamide moieties and Q189. Our study provides binding details for the designed compounds and demonstrates the feasibility of our joint X-ray/neutron structure-assisted drug design approach to generate more potent noncovalent nonpeptidic MPro inhibitors.
Breast cancer is the most frequently occurring cancer worldwide and has become the second primary cause of cancer-associated fatalities among females. It mainly arises from the abnormal proliferation of epithelial cells in the breast tissue and differs in prognosis, biological behaviour and treatment. The study of quinazolinone derivatives has gained attention as promising anti-breast cancer agents by suppressing tumor cell growth and progression. The presence of a carbonyl group and a nitrogen atom in the quinazolinone scaffold contributes to hydrogen bonding with amino acid residues of target proteins indicating strong and specific target binding affinities of these compounds. This review highlights the structure-activity relationship (SAR) of different quinazolinone derivatives along with their binding interactions which indicate that the electronic and lipophilic characteristics of substituents on different positions of the quinazolinone core significantly affect their activity in breast cancer. The incorporation of electron-donating and electron-withdrawing groups on the phenyl ring at the third position of the quinazolinone ring can affect cellular permeability and interaction with biological targets. The introduction of different substituents to the quinazolinone moiety can improve selectivity and potency across breast cancer cell lines. Recent studies have suggested that quinazolinone derivatives act as promising therapeutic candidates for breast cancer therapy. Further optimization through SAR studies and detailed mechanistic investigations could facilitate the design of highly effective and selective anti-breast cancer agents with low toxicity.
Autophagy plays a central role in cellular degradation and recycling pathways, and the LC3B protein is essential for this process. Dysregulation of LC3B has been implicated in oncogenesis. In this study, we used a computational approach to design a novel peptide nucleic acid (PNA) targeting the RNA-binding domain of LC3B, with the aim of inhibiting its function. The RNA AAUAAA polyadenylation signal was used as a starting point to design new PNAs with high affinity for LC3B. Molecular dynamics simulations and binding free-energy calculations on the RNA-AAUAAA/LC3B complex enabled the identification of promising PNA analogues. The lead candidate, a PNA with the sequence AATAAA, was synthesized, and its biological activity was investigated through biophysical and cellular assays. Cell viability was evaluated in the human prostate cell lines PNT1A and PNT2, as well as in the prostate cancer cell lines PC3 and DU145, while its efficacy in inhibiting autophagy was assessed in PC3 cells. The combined computational, biophysical and cellular results support AATAAA-PNA as an LC3B-binding hit whose cellular effects are consistent with modulation of LC3B-associated autophagy and mRNA-decay pathways. Overall, this study presents an in silico strategy for the design and development of LC3B inhibitors based on the RNA AAUAAA motif. The designed PNA represents a promising hit compound for further optimization in cancer therapy.
The orexin system, acting through OX1R and OX2R receptors, plays a key role in the regulation of sleep, motivation, and reward-related processes, making it a promising therapeutic target. While dual OXR antagonists are approved for the treatment of insomnia, the selective modulation of individual receptor subtypes remains poorly understood. In particular, the role of OX1R in neuropsychiatric disorders is still largely unexplored. In this study, we combined fragment-based and structure-based drug design approaches to investigate the structural determinants of underlying subtype selectivity in orexin receptor ligands. Through the exploration of novel aryl(amine) moieties, the modulation of aza-cyclic linker geometry, and the optimization of aryl amide cores, we identified key conformational features and substitution patterns governing receptor selectivity. This approach led to the discovery of antagonists with >10-30-fold selectivity for OX1R, and/or >30-100-fold selectivity for OX2R, as demonstrated by radioligand binding and Gq-mediated functional assays (IP1 and Ca2+ signaling). Given the close interplay among the orexin, dopamine and opioid systems in reward and motivation pathways, herein we further highlight the compatibility of dopaminergic and opioid-related scaffolds in expanding the chemical space for OXR ligand design.
The Nod-like receptor protein 3 (NLRP3) inflammasome, a critical component of the innate immune system, governs the release of pro-inflammatory cytokines such as interleukin-1β (IL-1β) and IL-18 and thereby plays...
PROTACs are heterobifunctional molecules that modulate protein levels through targeted degradation, eliminating both physiological and pathophysiological functionality. Photoswitchable PROTACs (or PHOTACs) expand on this technology by enabling spatial and temporal...
Novel ligands for the ifenprodil binding site of NMDA receptors with GluN2B subunit were designed, synthesized and pharmacologically evaluated. Derived from potent negative allosteric modulators, the γ-amino alcohol pharmacophore was conformationally restricted by embedding it into a 1-benzoxepine ring. Furthermore, the phenolic OH moiety was replaced bioisosterically by a primary or secondary amino moiety as well as by amido groups. The 7- to 9-step synthesis started with 4-aminosalicylic acid comprising a Dieckmann condensation of diester 7 and aminolysis of β-keto esters 8 as key steps. Membrane fragments of mouse fibroblast cells stably transfected with GluN1-1a and GluN2B subunits of the NMDA receptor and [3H]ifenprodil were used in radioligand receptor binding studies. In the benzylpiperidine d-series, the affinity towards GluN2B subunit-containing NMDA receptors increased from benzylamine 11d to primary amine 12d to formamide 13d (K i = 278 nM). Larger acyl moieties reduced the NMDA receptor affinity. Removal of the benzylic OH moiety led to allylamines 18b and 18d with considerable GluN2B affinity. However, their σ1 affinity was even higher than their GluN2B affinity. It was concluded that the benzylic OH moiety is not essential for high GluN2B affinity, but is important for selectivity over σ1 receptors. The novel class of 1-benzoxepine-based negative allosteric modulators of the NMDA receptor revealed promising lipophilicity (e.g., 13b: log D 7.4 = 1.99). Binding at human serum albumin correlated with the lipophilicity (e.g., 13b: PPB = 81%). Most of the 1-benzoxepines showed more than 65% metabolic stability during incubation with mouse liver microsomes and NADPH for 90 min.
Novel 5N-sulfonyl-1,5-benzodiazepin-2-one derivatives (2b, d) with strong inhibition of neutrophil elastase have been developed. The atropisomers of 2d, based on the rotation of the two interlocking sp2-sp2 (Ar-N) axes [(aR, aR) and (aS, aS)], were stably isolated at room temperature by HPLC using a chiral column. A significant difference was observed in the inhibitory activity between the atropisomers [(+)-2d, (-)-2d, and (±)-2d], and the eutomer was revealed to be (+)-2d. The X-ray analysis revealed that the configuration of the eutomer (+)-2d was (aR, aR). The eutomer exhibited approximately 10-fold higher inhibitory activity than the currently used lead compound sivelestat (ONO-0546) (1), indicating its potential as a treatment for acute lung injury. Docking studies with target proteins supported our hypothesis of high activity.
This study identifies and characterizes compound 24 (HA-218-6-31-80), a novel small-molecule NEDD8-activating enzyme (NAE) inhibitor. Discovered from a high-throughput screening, followed by structure-guided optimization, compound 24 possesses a distinct spirocyclic amide chemical core entirely different from the clinical-stage NAE inhibitor MLN4924. Biochemical assays confirm that compound 24 directly binds NAE and suppresses its catalytic activity, blocks the formation of E2-NEDD8 thioesters, and reduces the neddylation of CUL1 and CUL5 in purified protein systems. In human lung cancer cells, it potently suppresses neddylation of multiple CUL family members, leading to the accumulation of CRL substrates including p27 and NOXA. Functionally, it triggers G1-phase arrest and NOXA-dependent apoptosis, inhibiting lung cancer cell proliferation and survival. In A549 xenograft models, it significantly suppresses tumor growth without obvious systemic toxicity. Collectively, 24 (HA-218-6-31-80) represents a promising NAE inhibitor, offering a potential therapeutic candidate for lung cancer and a novel scaffold for neddylation targeted drug discovery.
