Discovery of Novel Inhibitors of BRD4 for Treating Prostate Cancer: A Comprehensive Case Study for Considering Water Networks in Virtual Screening and Drug Design

Discovery of a potent and selective peptide inhibitor with d-amino acids targeting the BRD4 ET domain for renal cancer therapy

Renal cancer is a highly aggressive tumor that poses a serious threat to human health. BRD4, as an important epigenetic regulator, is tightly associated with the development of renal cancer. Given the unique biological stability of d-amino acids, they have shown great potential for application in the field of cancer therapy. Currently, there are no reports on d-amino acid inhibitors targeting the ET domain of BRD4. Herein, we discovered a peptide inhibitor containing d-amino acids (BEP-2) targeting the BRD4 ET domain through virtual screening. BEP-2 showed an excellent binding affinity for BRD4 (Kd = 0.45 ± 0.03 nM). MD simulations demonstrate that BEP-2 can stably bind to the BRD4 ET domain. Moreover, BEP-2 displayed good inhibitory activity against 786-O and ACHN renal cancer cells and maintained high stability in serum. Additionally, BEP-2 inhibited the growth of 786-O cell xenograft tumors in nude mice. In summary, these data imply that BEP-2 is a promising antitumor drug that offers new perspectives for the treatment of renal cancer.

Structural Basis of SARS-CoV-2 Nsp13-Derived Peptide-Mediated NK Cell Activation

As pivotal effectors of antiviral immunity, natural killer (NK) cells are crucial for controlling the spread of COVID-19. The nonstructural protein 13 of SARS-CoV-2 can encode a viral peptide (Nsp13232-240) preventing human leukocyte antigen E (HLA-E) from recognizing inhibitory receptor NKG2A, thereby activating NK cells. The underlying molecular mechanisms of Nsp13232-240 remain unclear. Therefore, we compared the interaction discrepancy between the self-peptide and Nsp13232-240, theoretically predicting its source. Results indicate that electrostatic interaction energy provides the main source of binding, and its attenuation greatly promotes binding affinity differences. Nsp13232-240 disrupts the hydrogen bond network between CD94 and HLA-E, impacting the binding of hot-spot residues, including Q112CD94 and E161HLA-E. Moreover, Nsp13232-240 breaks the salt bridges formed by K217NKG2A and K199NKG2A with HLA-E. Conformational changes induced by Nsp13232-240 lead to diminished atomic contacts and an unstable binding pattern. These findings provide novel insights into the immunomodulatory role of Nsp13232-240 and may inform future NK cell-mediated strategies targeting SARS-CoV-2.

Hit to lead optimization of the 4-trifluoromethylquinoline derivatives as novel SGK1 inhibitors with potent anti-prostate cancer activity

Prostate cancer (PCa) remains a significant health concern for males, and serum/glucocorticoid-regulated kinase-1 (SGK1) plays a crucial role in its pathogenesis. This provides a promising target for the development of novel therapies against PCa. Herein, we reported the structural optimization of the hit compound H1, which was discovered in our previous work as an SGK1 inhibitor. Based on docking research for the active binding conformation of compound H1, a series of novel 4-trifluoromethyl quinoline derivatives were developed by replacing the 6-methoxy group in the quinoline skeleton of compound H1 with a larger aryl ring to occupy the hinge region of SGK1. Among them, compound 12f showed the strongest SGK1 inhibitory potency, with an IC50 value of 0.39 μM, representing a 7.8-fold improvement over compound H1. Molecular docking studies revealed that the 6-methoxyphenylamine moiety of compound 12f effectively extends into the hinge region of SGK1, establishing a crucial hydrogen bonding interaction with Glu183 that enhances its biological potency. In vivo, compound 12f effectively suppressed tumor growth in the PC3 xenograft model in BALB/c nude mice without inducing any observable toxicity. Moreover, mechanistic studies showed that compound 12f hindered PC3 cell migration and invasion, improved the thermal stability of SGK1 protein in PC3 cells, decreased SGK1 protein levels in tumor tissues, and effectively inhibited the phosphorylation of SGK1 and its substrates in PC3 cells in a dose- and time-dependent manner. In summary, the results of this study highlight the potential of 12f as a lead compound for further optimization in the development of new therapies against PCa targeting SGK1.

Design of Selective BRD4 Inhibitors for the Treatment of Autosomal Dominant Polycystic Kidney Disease

Epigenetic modulation plays a pivotal role in restraining tumor progression by governing gene expression and protein function. Autosomal dominant polycystic kidney disease (ADPKD), characterized by neoplastic-like progression, can be managed by inhibiting cyst expansion. Of note, the epigenetic regulator BRD4 has been implicated in ADPKD's development. Our prior research unveiled a class of (pyrazol-3-yl) pyrimidin-4-amine compounds as potent BRD4 inhibitors with additional kinase inhibition, which might induce unwanted biological activities. To address this, this study focused on creating selective BRD4 inhibitors through structure-guided design, minimizing off-target kinase interactions. Specifically, compound 23 emerged as an efficacious and selective BRD4 inhibitor in cellular and embryonic kidney models of ADPKD, along with encouraging outcomes in murine models. Collectively, these results highlight the therapeutic potential of targeted BRD4 inhibition as a safe and efficacious strategy for managing ADPKD.

Docking‑based virtual screening of BRD4 (BD1) inhibitors: assessment of docking methods, scoring functions and in silico molecular properties

To enhance the accuracy of virtual screening for bromodomain-containing protein 4 (BRD4) inhibitors, two docking protocols and seven scoring functions were compared. A total of 73 crystal structures of BRD4 (BD1) complexes were selected for analysis. Firstly, docking was carried out using both the LibDock and CDOCKER methods. The CDOCKER protocol was shown to be more effective based on the root mean square deviation (RMSD) values (in Å) between the docking positions and the co-crystal structures, achieving a docking accuracy rate of 86.3%. Then, among the various scoring functions (LigScore1, LigScore2, PLP1, PLP2, PMF, PMF04 and Ludi3), PMF showed the highest correlation with inhibition constants (r2 = 0.614), while Ludi3 scored lowest (r2 = 0.266). Finally, using ligand descriptors from PubChem, a strong correlation (r2 > 0.5) with inhibition constants for heavy atom count was found. Based on these comprehensive evaluations, the PMF scoring function emerged as the best tool for docking-based virtual screening of potential BRD4 (BD1) inhibitors. And the correlation between molecular properties and BRD4 (BD1) ligands also provided information for future design strategies.

Design, synthesis and FXR partial agonistic activity of anthranilic acid derivatives bearing aryloxy moiety as therapeutic agents for metabolic dysfunction-associated steatohepatitis

Farnesoid X receptor (FXR) is considered a promising therapeutic target for the treatment of metabolic dysfunction-associated steatohepatitis (MASH). Increasing evidence suggests that targeting FXR with full agonists may lead to side effects. FXR partial agonists, which moderately activate FXR signaling, are emerging as a feasible approach to mitigate side effects and address MASH. Herein, a series of novel anthranilic acid derivatives bearing aryloxy moiety were designed and synthesized using a hybrid strategy from the previously identified FXR partial agonists DM175 and AIV-25. Particularly, compound 26 exhibited potent FXR partial agonistic activity in a dual-luciferase reporter gene assay with an EC50 value of 0.09 ± 0.02 µM (75.13 % maximum efficacy relative to OCA). In the MASH mice model, compound 26 significantly ameliorated the pathological features of the liver, including steatosis, inflammation, and fibrosis. In addition, compound 26 displayed high selectivity, good oral bioavailability, high liver distribution, as well as an acceptable safety profile. Molecular simulation studies showed that compound 26 fitted well with the binding site of FXR. Collectively, these findings demonstrated that compound 26 might serve as a promising candidate targeting FXR for MASH treatment.

Discovery of 5-Nitro-N-(3-(trifluoromethyl)phenyl) Pyridin-2-amine as a Novel Pure Androgen Receptor Antagonist against Antiandrogen Resistance

The transformation of clinical androgen receptor (AR) antagonists into agonists driven by AR mutations poses a significant challenge in treating prostate cancer (PCa). Novel anti-AR therapeutics combating mutation-induced resistance are required. Herein, by combining structure-based virtual screening and biological evaluation, a high-affinity agonist E10 was first discovered. Then guided by the representative conformation of State 1 at the free energy landscape, the structural optimization of E10 was performed, and pure AR antagonists EL15 (IC50 = 0.94 μM) and EF2 (IC50 = 0.30 μM) were successfully identified. Both can antagonize wild-type and variant drug-resistant ARs. Therein, EF2 demonstrated potent inhibition of the AR pathway and effectively suppressed tumor growth in a C4-2B xenograft mouse model following oral administration. Further molecular dynamics simulation and mutagenesis studies revealed atomic insights into the mode of action of EF2 which may serve as a novel lead compound for developing therapeutics against AR-driven PCa.

Structural basis of tolvaptan binding to the vasopressin V2 receptor

The vasopressin V2 receptor (V2R) is a validated therapeutic target for autosomal dominant polycystic kidney disease (ADPKD), with tolvaptan being the first FDA-approved antagonist. Herein, we used Gaussian accelerated molecular dynamics simulations to investigate the spontaneous binding of tolvaptan to both active and inactive V2R conformations at the atomic-level. Overall, the binding process consists of two stages. Tolvaptan binds initially to extracellular loops 2 and 3 (ECL2/3) before overcoming an energy barrier to enter the pocket. Our simulations result highlighted key residues (e.g., R181, Y205, F287, F178) involved in this process, which were experimentally confirmed by site-directed mutagenesis. This work provides structural insights into tolvaptan-V2R interactions, potentially aiding the design of novel antagonists for V2R and other G protein-coupled receptors.

Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery

Computational methods constitute efficient strategies for screening and optimizing potential drug molecules. A critical factor in this process is the binding affinity between candidate molecules and targets, quantified as binding free energy. Among various estimation methods, alchemical transformation methods stand out for their theoretical rigor. Despite challenges in force field accuracy and sampling efficiency, advancements in algorithms, software, and hardware have increased the application of free energy perturbation (FEP) calculations in the pharmaceutical industry. Here, we review the practical applications of FEP in drug discovery projects since 2018, covering both ligand-centric and residue-centric transformations. We show that relative binding free energy calculations have steadily achieved chemical accuracy in real-world applications. In addition, we discuss alternative physics-based simulation methods and the incorporation of deep learning into free energy calculations.

Structural Basis for Long Residence Time c-Src Antagonist: Insights from Molecular Dynamics Simulations

c-Src is involved in multiple signaling pathways and serves as a critical target in various cancers. Growing evidence suggests that prolonging a drug's residence time (RT) can enhance its efficacy and selectivity. Thus, the development of c-Src antagonists with longer residence time could potentially improve therapeutic outcomes. In this study, we employed molecular dynamics simulations to explore the binding modes and dissociation processes of c-Src with antagonists characterized by either long or short RTs. Our results reveal that the long RT compound DAS-DFGO-I (DFGO) occupies an allosteric site, forming hydrogen bonds with residues E310 and D404 and engaging in hydrophobic interactions with residues such as L322 and V377. These interactions significantly contribute to the long RT of DFGO. However, the hydrogen bonds between the amide group of DFGO and residues E310 and D404 are unstable. Substituting the amide group with a sulfonamide yielded a new compound, DFOGS, which exhibited more stable hydrogen bonds with E310 and D404, thereby increasing its binding stability with c-Src. These results provide theoretical guidance for the rational design of long residence time c-Src inhibitors to improve selectivity and efficacy.

DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery

Artificial intelligence (AI)-aided drug design has demonstrated unprecedented effects on modern drug discovery, but there is still an urgent need for user-friendly interfaces that bridge the gap between these sophisticated tools and scientists, particularly those who are less computer savvy. Herein, we present DrugFlow, an AI-driven one-stop platform that offers a clean, convenient, and cloud-based interface to streamline early drug discovery workflows. By seamlessly integrating a range of innovative AI algorithms, covering molecular docking, quantitative structure-activity relationship modeling, molecular generation, ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction, and virtual screening, DrugFlow can offer effective AI solutions for almost all crucial stages in early drug discovery, including hit identification and hit/lead optimization. We hope that the platform can provide sufficiently valuable guidance to aid real-word drug design and discovery. The platform is available at https://drugflow.com.

Discovery of potent and novel dual NAMPT/BRD4 inhibitors for efficient treatment of hepatocellular carcinoma

The NAPRT-induced increase in NAD+ levels was proposed as a mechanism contributing to hepatocellular carcinoma (HCC) resistance to NAMPT inhibitors. Thus, concurrently targeting NAMPT and NAPRT could be considered to overcome drug resistance. A BRD4 inhibitor downregulates the expression of NAPRT in HCC, and the combination of NAMPT inhibitors with BRD4 inhibitors simultaneously blocks NAD+ generation via salvage and the PH synthesis pathway. Moreover, the combination of the two agents significantly downregulated the expression of tumor-promoting genes and strongly promoted apoptosis. The present work identified various NAMPT/BRD4 dual inhibitors based on the multitargeted drug rationale. Among them, compound A2, which demonstrated the strongest effect, exhibited potent inhibition of NAMPT and BRD4 (IC50 = 35 and 58 nM, respectively). It significantly suppressed the growth and migration of HCC cells and facilitated their apoptosis. Furthermore, compound A2 also manifested a robust anticancer effect in HCCLM3 xenograft mouse models, with no apparent toxic effects. Our findings in this study provide an effective approach to target NAD+ metabolism for HCC treatment.

Structure-based virtual screening of novel USP5 inhibitors targeting the zinc finger ubiquitin-binding domain

The equilibrium of cellular protein levels is pivotal for maintaining normal physiological functions. USP5 belongs to the deubiquitination enzyme (DUBs) family, controlling protein degradation and preserving cellular protein homeostasis. Aberrant expression of USP5 is implicated in a variety of diseases, including cancer, neurodegenerative diseases, and inflammatory diseases. In this paper, a multi-level virtual screening (VS) approach was employed to target the zinc finger ubiquitin-binding domain (ZnF-UBD) of USP5, leading to the identification of a highly promising candidate compound 0456-0049. Molecular dynamics (MD) simulations were then employed to assess the stability of complex binding and predict hotspot residues in interactions. The results indicated that the candidate stably binds to the ZnF-UBD of USP5 through crucial interactions with residues ARG221, TRP209, GLY220, ASN207, TYR261, TYR259, and MET266. Binding free energy calculations, along with umbrella sampling (US) simulations, underscored a superior binding affinity of the candidate relative to known inhibitors. Moreover, US simulations revealed conformational changes of USP5 during ligand dissociation. These insights provide a valuable foundation for the development of novel inhibitors targeting USP5.