Using natural products for drug discovery: the impact of the genomics era

Introduction: Evolutionarily selected over billions of years for their interactions with biomolecules, natural products have been and continue to be a major source of pharmaceuticals. In the 1990s, pharmaceutical companies scaled down their natural product discovery programs in favor of synthetic chemical libraries due to major challenges such as high rediscovery rates, challenging isolation, and low production titers. Propelled by advances in DNA sequencing and synthetic biology technologies, insights into microbial secondary metabolism provided have inspired a number of strategies to address these challenges.

Areas covered: This review highlights the importance of genomics and metagenomics in natural product discovery, and provides an overview of the technical and conceptual advances that offer unprecedented access to molecules encoded by biosynthetic gene clusters.

Expert opinion: Genomics and metagenomics revealed nature’s remarkable biosynthetic potential and her vast chemical inventory that we can now prioritize and systematically mine for novel chemical scaffolds with desirable bioactivities. Coupled with synthetic biology and genome engineering technologies, significant progress has been made in identifying and predicting the chemical output of biosynthetic gene clusters, as well as in optimizing cluster expression in native and heterologous host systems for the production of pharmaceutically relevant metabolites and their derivatives.     

Gamma irradiation of medicinally important plants and the enhancement of secondary metabolite production

Purpose: The profitable production of some important plant-based secondary metabolites (ginsenosides, saponins, camptothecin, shikonins etc.) in vitro by gamma irradiation is a current area of interest. We reviewed different types of secondary metabolites, their mode of synthesis and effect of γ-radiation on their yield for different plants, organs and in vitro cultures (callus, suspension, hairy root). Special effort has been made to review the biochemical mechanisms underlying the increase in secondary metabolites. A comparison of yield improvement with biotic and abiotic stresses was made.

Results: Phenolic compounds increase with γ-irradiation in whole plants/plant parts; psoralen content in the common herb babchi (Psoralea corylifolia) was increased as high as 32-fold with γ-irradiation of seeds at 20 kGy. The capsaicinoids, a phenolic compound increased about 10% with 10 kGy in paprika (Capsicum annum L.). The in vitro studies show all the three types of secondary metabolites are reported to increase with γ-irradiation. Stevioside, total phenolic and flavonoids content were slightly increased in 15?Gy-treated callus cultures of stevia (Stevia rebaudiana Bert.). In terpenoids, total saponin and ginsenosides content were increased 1.4- and 1.8-fold, respectively, with 100?Gy for wild ginseng (Panax ginseng Meyer) hairy root cultures. In alkaloids, camptothecin yield increased as high as 20-fold with 20?Gy in callus cultures of ghanera (Nothapodytes foetida). Shikonins increased up to 4-fold with 16?Gy in suspension cultures of purple gromwell (Lithospermum erythrorhizon S.). The enzymes associated with secondary metabolite production were increased with γ-irradiation of 20?Gy; namely, phenylalanine ammonia-lyase (PAL) for phenolics, chalcone synthase (CHS) for flavonoids, squalene synthase (SS), squalene epoxidase (SE) and oxidosqualene cyclases (OSC) for ginsenosides and PHB (p-hydroxylbenzoic acid) geranyl transferase for shikonins.

Conclusions: An increase in secondary metabolites in response to various biotic and abiotic stresses is compared with ionizing radiation. A ～5- to 20-fold increase is noted with ～20?Gy irradiation dose. It increases the yield of secondary metabolites by enhancing the activity of certain key biosynthetic enzymes. Identification of the optimum dose is the important step in the large-scale production of secondary metabolites at industrial level.     

深海细菌Psychrobacter submarinus 1A01998的次级代谢产物研究

目的 对来自深海沉积物中的海洋细菌Psychrobacter submarinus1 A01998的次级代谢产物进行研究.方法 采用大孑L吸附树脂、硅胶、ODS和Sephadex LH-20凝胶等柱层析色谱分离方法,对海洋细菌Psychrobacter submarinus1 A01998进行次级代谢产物的分离纯化,根据1H NMR、13C NMR和MS等波谱数据分析并结合相关文献对化学结构进行鉴定.结果 从深海细菌Psychrobacter submarinus 1A01998的发酵粗提物中分离得到4个化合物,分别鉴定为环(L-脯氨酸-L-酪氨酸)(1)、环(D-脯氨酸-L-酪氨酸)(2)、3-吲哚甲醛(3)、2'-O-甲氧基尿嘧啶核苷(4).结论 化合物1～4均为首次从该属中分离得到,其中化合物1、2为环二肽类化合物.     

海洋微生物次级代谢产物抗菌作用研究进展

海洋微生物次级代谢产物种类繁多，具有丰富的结构多样性和不同的抗菌功能。其中以抗菌活性物质最为突出，已经成为近年来新药筛选的重要资源，在药品开发应用中具有良好的发展前景。本文结合近年关于海洋微生物次级代谢产物的报道，分析海洋微生物次级代谢产物的结构和功能；并对海洋微生物次级代谢产物在抗菌方面的作用及其抗菌作用机制的研究进展进行总结。     

特殊生境真菌来源的新结构活性物质研究

真菌的物种与生态多样性导致了其次生代谢产物结构与活性的多样性，是药物先导化合物的重要来源之一。常规真菌来源活性物质的研究多是针对普通资源的盲筛，尽管通过高通量筛选能提高效率，但发现新活性物质的几率较低，成为制约先导化合物发现的瓶颈。由于特殊生境真菌资源的收集、整理以及培养的难度较大，制约了相关的研究，因而挖掘其代谢潜力对发现先导化合物、解析探索真菌的互作与环境适应机制都具有重要的意义。本课题组主要选择生存环境及互作关系独特的内生菌与冬虫夏草定殖真菌进行研究，高效发现新结构活性次生代谢产物。本文主要介绍近4年来我们在这方面研究中取得的进展。     

中国南海软体动物及其食源生物的化学、化学生态学和生物活性研究

海洋软体动物色彩艳丽、行动缓慢,主要依赖次生代谢产物形成的化学防御机制对抗天敌的捕食.多数软体动物可以通过选择适当的食物并将其中有用的代谢物质经过进一步的生物转化或积累到身体的特定部位而用作化学防御物质,以保护自己不受天敌的捕食;少数软体动物能够生物合成自身所需要的化学物质,从而建立起化学防御体系.研究软体动物及其食源生物的化学组成可以揭示它们之间的食物链关系,并进一步阐明这些化学物质的生态学作用.同时,这种进化的化学防御体系也能为我们提供一种从自然界寻找生物活性物质的新方法.近年来,我们研究小组对中国南海软体动物及其相关食源生物海绵、珊瑚和海藻等常见海洋生物物种之间的食物链关系进行了系统研究,获得了这些海洋生物的化学及生物学等方面的知识,并对这些化学物质的药理活性进行了系统考察,为更加系统、深入地开展中国海洋天然产物研究、开发具有自主知识产权的海洋新药打下了坚实的基础.     

杜仲内生真菌EL09次生代谢产物的研究

目的对杜仲内生真菌EL09次生代谢产物进行研究。方法采用色谱技术进行分离纯化内生真菌EL09的代谢产物,理化性质及波谱分析技术确定化合物的结构,通过最小抑菌浓度法测定化合物的抑菌活性。结果从杜仲内生真菌EL09次生代谢产物中分离并鉴定了6个化合物,分别是麦角甾醇(1),5-hydroxymethylfuran-3-carboxylic acid(2),fumiquina-zoline C(3),赤藓醇(4),D-甘露醇(5),尿嘧啶(6)。结论次生代谢产物中化合物2对黄瓜枯萎病菌有效。     

诱导子对百里香中次生代谢产物的影响差异

 目的 研究不同浓度诱导子对不同增殖阶段百里香中次生代谢产物积累的影响。方法 以1/2 MS为基本培养基，培养百里香至20、30和40 d后，分别用外源诱导子茉莉酸甲酯（MeJA）、水杨酸(SA)和壳聚糖(Chs)对百里香进行诱导；采用萃取法对有效成分进行提取，用气相色谱-质谱联用仪检测不同增殖阶段诱导子对次生代谢产物积累的影响。结果 在提取液中检测到46种化合物，其中对比分析了含量大于1%的12种化合物，发现3种诱导子对以百里香酚为代表的芳香族化合物作用效果较为明显，对1-甲基-3-（1-甲基乙基）苯和1-甲基-4-4（1-甲基乙基）-1，4-环己烯为代表的氧化萜类化合物和萜烯类化合物效果十分明显。结论 不同的诱导子对百里香中次生代谢产物含量有显著差异。     

不同氮源对丹参和藏丹参毛状根有效成分积累的影响

目的氮素是中药材有效成分积累的重要影响元素,为探讨不同氮源对丹参Salviamiltiorrhiza和藏丹参Salvia castanea毛状根生长和活性成分积累的影响。方法分别采用硝酸铵、水解乳蛋白、蛋白胨、牛肉浸膏、酪蛋白和酵母提取物6种氮源处理对丹参和藏丹参毛状根的影响,分析毛状根生长及活性成分积累的变化。结果硝酸铵最有利于2种丹参毛状根的生长。水解乳蛋白能够显著促进丹酚酸类成分的积累,与硝酸铵对照相比,丹参迷迭香酸和丹酚酸B含量分别提高了2.94倍和3.27倍,藏丹参二者含量分别提高了13.74倍和2.01倍。酵母提取物对2种丹参毛状根二氢丹参酮Ι和隐丹参酮积累的促进效果最为显著,水解乳蛋白能显著促进丹参根中丹参酮IIA的积累,牛肉浸膏则对藏丹参中丹参酮IIA积累的促进作用最为显著。结论硝酸铵是2种丹参毛状根生长的最佳氮源,水解乳蛋白是丹酚酸积累的最佳氮源,不同氮源对4种丹参酮的影响不一致,丹参和藏丹参对不同氮源的响应也不一致。该研究不仅对丹参毛状根规模化培养及活性成分工业化生产具有一定指导意义,也对藏丹参资源的开发利用提供了借鉴作用。     

Chronic pelvic pain syndrome: Highlighting medicinal plants toward biomolecules discovery for upcoming drugs formulation

Chronic pelvic pain syndrome (CPPS) can be triggered by a various types of gynecological, gastrointestinal, urological, and musculoskeletal disorders. Recently, the role of the central nervous system has proven to be an integral part on the development of any chronic pain syndrome, including CPPS. However, owing to the complex and heterogeneous etiology and pathophysiology of CPPS, the establishment of effective therapeutic interventions remains challenging for both physicians and patients. Nonetheless, recent studies have pointed that medicinal plants and their secondary metabolites can be effectively used in CPPS therapy, besides contributing to restore the patients' quality of life and potentiate the conventional CPPS management. In this sense, this review aims to provide a careful overview on the biomedical data for the use of medicinal plants use and their secondary metabolites on CPPS management.