Virtual Screening and In Vitro Evaluation of PD-1 Dimer Stabilizers for Uncoupling PD-1/PD-L1 Interaction from Natural Products

Genetic mutations accumulated overtime could generate many growth and survival advantages for cancer cells, but these mutations also mark cancer cells as targets to be eliminated by the immune system. To evade immune surveillance, cancer cells adopted different intrinsic molecules to suppress immune response. PD-L1 is frequently overexpressed in many cancer cells, and its engagement with PD-1 on T cells diminishes the extent of cytotoxicity from the immune system. To resume immunity for fighting cancer, several therapeutic antibodies disrupting the PD-1/PD-L1 interaction have been introduced in clinical practice. However, their immunogenicity, low tissue penetrance, and high production costs rendered these antibodies beneficial to only a limited number of patients. PD-L1 dimer formation shields the interaction interface for PD-1 binding; hence, screening for small molecule compounds stabilizing the PD-L1 dimer may make immune therapy more effective and widely affordable. In the current study, 111 candidates were selected from over 180,000 natural compound structures through virtual screening, contact fingerprint analysis, and pharmacological property prediction. Twenty-two representative candidates were further evaluated in vitro. Two compounds were found capable of inhibiting the PD-1/PD-L1 interaction and promoting PD-L1 dimer formation. Further structure optimization and clinical development of these lead inhibitors will eventually lead to more effective and affordable immunotherapeutic drugs for cancer patients.     

Biphenyl Ether Analogs Containing Pomalidomide as Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Cell Death-Ligand 1 Interaction

New biphenyl-based chimeric compounds containing pomalidomide were developed and evaluated for their activity to inhibit and degrade the programmed cell death-1/programmed cell death- ligand 1 (PD-1/PD-L1) complex. Most of the compounds displayed excellent inhibitory activity against PD-1/PD-L1, as assessed by the homogenous time-resolved fluorescence (HTRF) binding assay. Among them, compound 3 is one of the best with an IC₅₀ value of 60 nM. Using an ex vivo PD-1/PD-L1 blockade cell line bioassay that expresses human PD-1 and PD-L1, we show that compounds 4 and 5 significantly restore the repressed immunity in this co-culture model. Western blot data, however, demonstrated that these anti-PD-L1/pomalidomide chimeras could not reduce the protein levels of PD-L1.     

Structural Characterization of a Macrocyclic Peptide Modulator of the PD-1/PD-L1 Immune Checkpoint Axis

The clinical success of PD-1/PD-L1 immune checkpoint targeting antibodies in cancer is followed by efforts to develop small molecule inhibitors with better penetration into solid tumors and more favorable pharmacokinetics. Here we report the crystal structure of a macrocyclic peptide inhibitor (peptide 104) in complex with PD-L1. Our structure shows no indication of an unusual bifurcated binding mode demonstrated earlier for another peptide of the same family (peptide 101). The binding mode relies on extensive hydrophobic interactions at the center of the binding surface and an electrostatic patch at the side. An interesting sulfur/π interaction supports the macrocycle-receptor binding. Overall, our results allow a better understanding of forces guiding macrocycle affinity for PD-L1, providing a rationale for future structure-based inhibitor design and rational optimization.     

Novel Inhibitors of Nicotinamide-N-Methyltransferase for the Treatment of Metabolic Disorders

Nicotinamide-N-methyltransferase (NNMT) is a cytosolic enzyme catalyzing the transfer of a methyl group from S-adenosyl-methionine (SAM) to nicotinamide (Nam). It is expressed in many tissues including the liver, adipose tissue, and skeletal muscle. Its expression in several cancer cell lines has been widely discussed in the literature, and recent work established a link between NNMT expression and metabolic diseases. Here we describe our approach to identify potent small molecule inhibitors of NNMT featuring different binding modes as elucidated by X-ray crystallographic studies.     

Aryl Extensions of Thienopyrimidinones as Fibroblast Growth Factor Receptor 1 Kinase Inhibitors

Optimization of thienopyrimidinone derivatives as FGFR1 kinase inhibitors is being pursued. The present results confirm predictions of computational modeling that an aryl substituent can be introduced at the 2-position in structure 3. The substituent is anticipated to project deeper into the binding site and provide opportunities for enhanced activity and selectivity. The most potent analog reported herein, 13, has a 4-hydroxyphenyl substituent and yields an IC₅₀ of 6 μM for inhibition of phosphorylation by FGFR1 kinase. It was also found that the western anisole-containing substituent in 3 can be replaced by a propionic acid group with no loss in potency and with potentially significant gains in pharmacologically relevant properties.     

Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors

A new type of berberine derivatives was obtained by the reaction of berberrubine with aliphatic sulfonyl chlorides. The new polycyclic compounds have a sultone ring condensed to C and D rings of a protoberberine core. The reaction conditions were developed to facilitate the formation of sultones with high yields without by-product formation. Thus, it was shown that the order of addition of reagents affects the composition of the reaction products: when sulfochlorides are added to berberrubine, their corresponding 9-O-sulfonates are predominantly formed; when berberrubine is added to pre-generated sulfenes, sultones are the only products. The reaction was shown to proceed stereo-selectively and the cycle configuration was confirmed by 2D NMR spectroscopy. The inhibitory activity of the synthesized sultones and their 12-brominated analogs against the DNA-repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1), an important target for a potential antitumor therapy, was studied. All derivatives were active in the micromolar and submicromolar range, in contrast to the acyclic analogs and 9-O-sulfonates, which were inactive. The significance of the sultone cycle and bromine substituent in binding with the enzyme was confirmed using molecular modeling. The active inhibitors are mostly non-toxic to the HeLa cancer cell line, and several ligands show synergy with topotecan, a topoisomerase 1 poison in clinical use. Thus, novel berberine derivatives can be considered as candidates for adjuvant therapy against cancer.     

氨基乙内酰脲类BACE1抑制剂的特征结构与作用机制

对BACE1抑制剂的研究与开发已成为目前治疗阿尔兹海默症的主要研究方向之一。本文选取105个氨基乙内酰脲类BACE1抑制剂作为研究对象,借助比较分子相似性指数(Comparative Molecular Similarity Index, CoMSIA)和分子对接方法,建立定量构效关系预测模型,研究影响化合物抑制活性的特征结构信息,揭示该类抑制剂与靶标之间的作用模式。结果表明,模型(Q_²=0.45, R_²ncv=0.87, R_²pre=0.85)具有较强的预测能力,抑制剂主要占据了靶标的S3、S1和S2"位点,其主要作用力类型为氢键力。实验所得模型和信息可为日后研究开发新型高效的BACE1抑制剂提供一定的理论指导,节省研究时间与费用。     

Novel Complex of PD-L1 Aptamer and Albumin Enhances Antitumor Efficacy In Vivo

The PD-1/PD-L1 pathway blockade can generate a good clinical response by reducing immunosuppression and provoking durable antitumor immunity. In addition to antibodies, aptamers can also block the interaction between PD-1 and PD-L1. For the in vivo application, however, free aptamers are usually too small in size and quickly removed from blood via glomerular filtration. To avoid renal clearance of aptamer, we conjugated the PD-L1 aptamer to albumin to form a larger complex (BSA-Apt) and evaluated whether BSA-Apt would enhance the in vivo antitumor efficacy. The PD-L1 aptamer was thiol-modified and conjugated to the amino group of BSA via a SMCC linker. The average size of BSA-Apt was 11.65 nm, which was above the threshold for renal clearance. Functionally, BSA-Apt retained the capability of the PD-L1 aptamer to bind with PDL1-expressing tumor cells. Moreover, both the free aptamer and BSA-Apt augmented the PBMC-induced antitumor cytotoxicity in vitro. Furthermore, BSA-Apt generated a significantly stronger antitumor efficacy than the free PD-L1 aptamer in vivo without raising systemic toxicity. The results indicate that conjugating the PD-L1 aptamer to albumin may serve as a promising strategy to improve the in vivo functionality of the aptamer and that BSA-Apt may have application potential in cancer immunotherapy.     

基于虚拟筛选策略发现新型潜在JAK3小分子抑制剂

利用已知活性的分子采用基于配体的策略构建药效团模型,通过基于类药规则、药效团模型、多种精度的分子对接算法、MM/GBSA结合能预测以及ADMET筛选手段对含约250万个分子的数据库进行虚拟筛选。发现5种JAK3抑制剂的新型骨架,其中6个以1-苯基咪唑烷-2-酮为骨架的分子在与JAK3激酶的结合能以及分子的ADMET性质评价方面均表现优异,具备高JAK3抑制剂潜力,被认为是虚拟筛选的命中分子。     

Discovery of Novel Dual Extracellular Regulated Protein Kinases (ERK) and Phosphoinositide 3-Kinase (PI3K) Inhibitors as a Promising Strategy for Cancer Therapy

Concomitant inhibition of MAPK and PI3K signaling pathways has been recognized as a promising strategy for cancer therapy, which effectively overcomes the drug resistance of MAPK signaling pathway-related inhibitors. Herein, we report the scaffold-hopping generation of a series of 1H-pyrazolo[3,4-d]pyrimidine dual ERK/PI3K inhibitors. Compound 32d was the most promising candidate, with potent inhibitory activities against both ERK2 and PI3Kα which displays superior anti-proliferative profiles against HCT116 and HEC1B cancer cells. Meanwhile, compound 32d possessed acceptable pharmacokinetic profiles and showed more efficacious anti-tumor activity than GDDC-0980 and the corresponding drug combination (BVD-523 + GDDC-0980) in HCT-116 xenograft model, with a tumor growth inhibitory rate of 51% without causing observable toxic effects. All the results indicated that 32d was a highly effective anticancer compound and provided a promising basis for further optimization towards dual ERK/PI3K inhibitors.     

Structure-Based Virtual Screening towards the Discovery of Novel ULK1 Inhibitors with Anti-HCC Activities

There is an urgent need to develop new effective therapies for HCC. Our previous study identified ULK1 as the potential target for HCC therapy and screened the compound XST-14 as a specific inhibitor of ULK1 to suppress HCC progression. However, the poor manufacturability of XST-14 impeded the process of its clinical translation. In this study, we first generated pharmacophore models of ULK1 based on the X-ray structure of UKL1 in complex with ligands. We then screened the Specs chemical library for potential UKL1 inhibitors. By molecular docking, we screened out the 19 compounds through structure-based virtual screening. Through CCK8 activity screening on HCC cells, we found that ZZY-19 displayed obvious cell killing effects on HCC cells. SPR assay indicated that ZZY-19 had a higher binding affinity for ULK1 than XST-14. Moreover, ZZY-19 induced the effects of anti-proliferation, anti-invasion and anti-migration in HCC cells. Mechanistically, ZZY-19 induces autophagy inhibition by reducing the expression of ULK1 on HCC cells. Especially, the combination of ZZY-19 with sorafenib synergistically suppresses the progression of HCC in vivo. Taken together, ZZY-19 was a potential candidate compound that targeted ULK1 and possessed promising anti-HCC activities by inhibiting autophagy.     

抗肿瘤缺氧诱导因子-1的小分子抑制剂

肿瘤的缺氧微环境与其增殖、分化、血管生成、能量代谢、耐药性的发生以及患者预后状况密切相关。缺氧诱导因子1(Hypoxia-inducible factor 1, HIF-1)是细胞适应缺氧环境的重要转录因子和调控蛋白,通过调控下游靶基因如EPO、VEGF、GLUT等的表达,促进血管新生及有氧糖酵解以适应缺氧的环境,进而影响肿瘤细胞代谢、血管生成和肿瘤转移等。因此,开发以HIF-1为靶标的小分子抑制剂药物有望成为一种有效的肿瘤治疗方法。本文就HIF-1小分子抑制剂在肿瘤学研究中的进展进行综述,旨在为靶向HIF-1抗肿瘤药物的研发提供新思路。     

PD-1与单克隆抗体残基特异性结合机制的计算丙氨酸扫描研究

通过分子动力学模拟检测了2种程序性细胞死亡蛋白(PD-1)/单克隆抗体(Pembrolizumab和Nivolumab)复合物,并使用高效的计算丙氨酸扫描方法预测了单抗与PD-1的结合热点,将它们与对PD-1/PD-L1结合重要的热点残基进行对比分析.结果显示, Pembrolizumab以类似于PD-L1的方式与PD-1结合,而Nivolumab则以不同的方式与PD-1结合. 2个PD-1/mAb复合物中共有的热点只有PD-1K131.同时发现,与PD-1K131结合的单抗的关键残基通常都受范德华(vdW)能量控制. 2种单克隆抗体上热点的自由能贡献都以vdW能量为主,这表明在下一代PD-1新抗体的设计中需要提高静电型热点残基的数量.     

Assessing the Inhibitory Potential of Kinase Inhibitors In Vitro: Major Pitfalls and Suggestions for Improving Comparability of Data Using CK1 Inhibitors as an Example

Phosphorylation events catalyzed by protein kinases represent one of the most prevalent as well as important regulatory posttranslational modifications, and dysregulation of protein kinases is associated with the pathogenesis of different diseases. Therefore, interest in developing potent small molecule kinase inhibitors has increased enormously within the last two decades. A critical step in the development of new inhibitors is cell-free in vitro testing with the intention to determine comparable parameters like the commonly used IC₅₀ value. However, values described in the literature are often biased as experimental setups used for determination of kinase activity lack comparability due to different readout parameters, insufficient normalization or the sheer number of experimental approaches. Here, we would like to hold a brief for highly sensitive, radioactive-based in vitro kinase assays especially suitable for kinases exhibiting autophosphorylation activity. Therefore, we demonstrate a systematic workflow for complementing and validating results from high-throughput screening as well as increasing the comparability of enzyme-specific inhibitor parameters for radiometric as well as non-radiometric assays. Using members of the CK1 family of serine/threonine-specific protein kinases and established CK1-specific inhibitors as examples, we clearly demonstrate the power of our proposed workflow, which has the potential to support the generation of more comparable data for biological characterization of kinase inhibitors.     

From Myricetin to the Discovery of Novel Natural Human ENPP1 Inhibitors: A Virtual Screening,Molecular Docking,Molecular Dynamics Simulation,and MM/GBSA Study

It was recently revealed that naturally occurring myricetin can inhibit ectonucleotidase ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which, in turn, can treat ischemic cardiac injury. However, due to myricetin’s poor druggability, its further developments are relatively limited, which necessitates the discovery of novel ENPP1-inhibiting myricetin analogs as alternatives. In this study, the binding model of myricetin with ENPP1 was elucidated by molecular docking and molecular dynamics studies. Subsequently, virtual screening on the self-developed flavonoid natural product database (FNPD), led to the identification of two flavonoid glycosides (Cas No: 1397173-50-0 and 1169835-58-8), as potential ENPP1 inhibitors. Docking scores and MM/GBSA binding energies predicted that they might have higher inhibitory effects than myricetin. This study provides a strong foundation for the future development of ischemic cardiac injury drugs.     

新型吡咯并三嗪酮类PARP-1抑制剂的设计、合成及生物活性

分别以5-溴-2-氟苯甲腈(1a)和3-溴苯甲腈(1b)为原料,经Sonogashira偶联,脱三甲基硅基保护基,三分子偶联及水解等5步反应制得中间体2-氟-5-［(4-氧代-3,4-二氢吡咯［1,2-d］［1,2,4］三嗪-1-基)甲基］苯甲酸（6a)和3-[(4-氧代-3,4-二氢吡咯［1,2-d］［1,2,4］三嗪-1-基)甲基］苯甲酸（6b）。环烷基甲酸经酰氯化,缩合和脱Boc保护基3步反应制得环烷基哌嗪-1-基甲酮(7a~7c)。 6a与NCS（1 eq.）反应制得5-［(6-氯-4氧代-3,4二氢吡咯［1,2-d］［1,2,4］三嗪-1-基)甲基］-2氟 苯甲酸(6c); 6a与NCS(2 eq.)反应制得5-［(6,7-二氯-4氧代-3,4二氢吡咯［1,2-d］［1,2,4］三嗪-1-基)甲基］-2氟-苯甲酸(6d)。 6a~6d, 6a~6c分别与7a~7c和1-（2-嘧啶基）哌嗪在TBTU（缩合剂）,DIPEA（碱）的作用下合成了13个新型吡咯并三嗪酮类PARP-1抑制剂(8a~8m),其结构经¹HNMR和MS(ESI)表征。采用Alarm blue法研究了8a~8m对肿瘤细胞MDA-MB-436的抑制活性(IC₅₀)。结果表明：8f, 8g, 8i和8j对MDA-MB-436有较强的抑制活性（IC₅₀=30.5~69.3 nmol·L^-1）。     

新型吲唑类PARP-1抑制剂的合成及其生物活性评价

以3-甲基-2-硝基苯甲酸甲酯为起始原料,经两步反应制得中间体1H-吲唑-7-甲酸甲酯(3); 3分别与三氯氧磷、液溴和碘单质反应制得3的3-位卤代产物(4b~4d); 4d与氟试剂或氰化锌反应制得3-氟(氰基)-3(4a和4e); 4d与苯硼酸或甲基硼酸在四三苯基磷钯催化下反应制得3-甲基(苯基)-3(5a和5b);以氢化钠为碱,3, 4a~4c, 4e, 5分别与4-甲烷磺酰氧基哌啶或3-甲烷磺酰氧基四氢吡咯经缩合反应制得3的2,3-位取代产物(6a～6n); 6a～6n在甲醇中氨解,随后采用氯化氢气体脱去Boc保护基合成了14个新型吲唑类PARP-1抑制剂(7a～7n),其结构经¹H NMR和ESI-MS表征。生物活性评价结果显示,有7个目标化合物对PARP-1酶活性抑制IC₅₀低于30 nmol·L^-1,其中2-(四氢吡咯-4-基)-2H-吲唑-7-甲酰胺(7e)和3-氟-2-(四氢吡咯-4-基)-2H-吲唑-7-甲酰胺(7f)的IC₅₀分别为4.2 nmol·L^-1和4.6 nmol·L^-1。