FFLOM: A Flow-Based Autoregressive Model for Fragment-to-Lead Optimization.

Recently, deep generative models have been regarded as promising tools in fragment-based drug design (FBDD). Despite the growing interest in these models, they still face challenges in generating molecules with desired properties in low data regimes. In this study, we propose a novel flow-based autoregressive model named FFLOM for linker and R-group design. In a large-scale benchmark evaluation on ZINC, CASF, and PDBbind test sets, FFLOM achieves state-of-the-art performance in terms of validity, uniqueness, novelty, and recovery of the generated molecules and can recover over 92% of the original molecules in the PDBbind test set (with at least five atoms). FFLOM also exhibits excellent potential applicability in several practical scenarios encompassing fragment linking, PROTAC design, R-group growing, and R-group optimization. In all four cases, FFLOM can perfectly reconstruct the ground-truth compounds and generate over 74% of molecules with novel fragments, some of which have higher binding affinity than the ground truth.

Preventing Morphine-Seeking Behavior through the Re-Engineering of Vincamine's Biological Activity.

Innovative discovery strategies are essential to address the ongoing opioid epidemic in the United States. Misuse of prescription and illegal opioids (e.g., morphine, heroin) has led to major problems with addiction and overdose. We used vincamine, an indole alkaloid, as a synthetic starting point for dramatic structural alterations of its complex, fused ring system to synthesize 80 diverse compounds with intricate molecular architectures. A select series of vincamine-derived compounds were screened for both agonistic and antagonistic activities against a panel of 168 G protein-coupled receptor (GPCR) drug targets. Although vincamine was without an effect, the novel compound 4 (V2a) demonstrated antagonistic activities against hypocretin (orexin) receptor 2. When advanced to animal studies, 4 (V2a) significantly prevented acute morphine-conditioned place preference (CPP) and stress-induced reinstatement of extinguished morphine-CPP in mouse models of opioid reward and relapse. These results demonstrate that the ring distortion of vincamine offers a promising way to explore new chemical space of relevance to opioid addiction.

PRMT5 as a druggable target for glioblastoma therapy.

Background: In spite of standard multimodal therapy consisting of surgical resection followed by radiation and concurrent chemotherapy, prognosis for glioblastoma (GBM) patients remains poor. The identification of both differentiated and undifferentiated "stem cell like" populations in the tumor highlights the significance of finding novel targets that affect the heterogeneous tumor cell population. Protein arginine methyltransferase 5 (PRMT5) is one such candidate gene whose nuclear expression correlates with poor survival and has been reported to be required for survival of differentiated GBM cells and self-renewal of undifferentiated GBM cells. In the current study we screened the specificity and efficacy of 4 novel PRMT5 inhibitors in the treatment of GBM. Methods: Efficacies of these inhibitors were screened using an in vitro GBM neurosphere model and an in vivo intracranial zebrafish model of glioma. Standard molecular biology methods were employed to investigate changes in cell cycle, growth, and senescence. Results: In vitro and in vivo studies revealed that among the 4 PRMT5 inhibitors, treatment of GBM cells with compound 5 (CMP5) mirrored the effects of PRMT5 knockdown wherein it led to apoptosis of differentiated GBM cells and drove undifferentiated primary patient derived GBM cells into a nonreplicative senescent state. Conclusion: In vivo antitumor efficacy combined with the specificity of CMP5 underscores the importance of developing it for translation.

Synthesis and biological evaluation of largazole zinc-binding group analogs.

Histone acetylation is an extensively investigated post-translational modification that plays an important role as an epigenetic regulator. It is controlled by histone acetyl transferases (HATs) and histone deacetylases (HDACs). The overexpression of HDACs and consequent hypoacetylation of histones have been observed in a variety of different diseases, leading to a recent focus of HDACs as attractive drug targets. The natural product largazole is one of the most potent natural HDAC inhibitors discovered so far and a number of largazole analogs have been prepared to define structural requirements for its HDAC inhibitory activity. However, previous structure-activity relationship studies have heavily investigated the macrocycle region of largazole, while there have been only limited efforts to probe the effect of various zinc-binding groups (ZBGs) on HDAC inhibition. Herein, we prepared a series of largazole analogs with various ZBGs and evaluated their HDAC inhibition and cytotoxicity. While none of the analogs tested were as potent or selective as largazole, the Zn2+-binding affinity of each ZBG correlated with HDAC inhibition and cytotoxicity. We expect that our findings will aid in building a deeper understanding of the role of ZBGs in HDAC inhibition as well as provide an important basis for the future development of new largazole analogs with non-thiol ZBGs as novel therapeutics for cancer.

ERK Activation Globally Downregulates miRNAs through Phosphorylating Exportin-5.

MicroRNAs (miRNA) are mostly downregulated in cancer. However, the mechanism underlying this phenomenon and the precise consequence in tumorigenesis remain obscure. Here we show that ERK suppresses pre-miRNA export from the nucleus through phosphorylation of exportin-5 (XPO5) at T345/S416/S497. After phosphorylation by ERK, conformation of XPO5 is altered by prolyl isomerase Pin1, resulting in reduction of pre-miRNA loading. In liver cancer, the ERK-mediated XPO5 suppression reduces miR-122, increases microtubule dynamics, and results in tumor development and drug resistance. Analysis of clinical specimens further showed that XPO5 phosphorylation is associated with poor prognosis for liver cancer patients. Our study reveals a function of ERK in miRNA biogenesis and suggests that modulation of miRNA export has potential clinical implications.

Indole-based allosteric inhibitors of HIV-1 integrase.

Employing a scaffold hopping approach, a series of allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) have been synthesized based on an indole scaffold. These compounds incorporate the key elements utilized in quinoline-based ALLINIs for binding to the IN dimer interface at the principal LEDGF/p75 binding pocket. The most potent of these compounds displayed good activity in the LEDGF/p75 dependent integration assay (IC50=4.5µM) and, as predicted based on the geometry of the five- versus six-membered ring, retained activity against the A128T IN mutant that confers resistance to many quinoline-based ALLINIs.

Hydrolysis of casein catalyzed by papain in n-propanol/NaCl two-phase system.

Enzymatic hydrolysis of casein to produce free amino acids by papain was performed in a kind of novel two-phase system, which was composed of n-propanol, NaCl and water. The phase diagram of the two-phase system was plotted. In this system, top phase contained more n-propanol and bottom phase contained more NaCl and water. Papain and casein were mainly distributed in bottom phase, and free aromatic amino acids (tyrosine, tryptophan and phenylalanine) produced by enzymatic hydrolysis were mainly in top phase. When the two-phase system consisted of 44% n-propanol, 60g/l NaCl, 0.15g/l papain and 13g/l casein at 55°C and pH 5.6, the transformation yield was 99.5%, which was higher than those of n-propanol/water single phase, aqueous single phase, n-hexane/water two-phase system and PEG/phosphate two-phase system. The novel two-phase system is practically applicable to some enzymatic reaction, if the substrates and products have different partition coefficients.