Charting, navigating, and populating natural product chemical space for drug discovery

Natural products are a heterogeneous group of compounds with diverse, yet particular molecular properties compared to synthetic compounds and drugs. All relevant analyses show that natural products indeed occupy parts of chemical space not explored by available screening collections while at the same time largely adhering to the rule-of-five. This renders them a valuable, unique, and necessary component of screening libraries used in drug discovery. With ChemGPS-NP on the Web and Scaffold Hunter two tools are available to the scientific community to guide exploration of biologically relevant NP chemical space in a focused and targeted fashion with a view to guide novel synthesis approaches. Several of the examples given illustrate the possibility of bridging the gap between computational methods and compound library synthesis and the possibility of integrating cheminformatics and chemical space analyses with synthetic chemistry and biochemistry to successfully explore chemical space for the identification of novel small molecule modulators of protein function.The examples also illustrate the synergistic potential of the chemical space concept and modern chemical synthesis for biomedical research and drug discovery. Chemical space analysis can map under explored biologically relevant parts of chemical space and identify the structure types occupying these parts. Modern synthetic methodology can then be applied to efficiently fill this “virtual space” with real compounds.From a cheminformatics perspective, there is a clear demand for open-source and easy to use tools that can be readily applied by educated nonspecialist chemists and biologists in their daily research. This will include further development of Scaffold Hunter, ChemGPS-NP, and related approaches on the Web. Such a “cheminformatics toolbox” would enable chemists and biologists to mine their own data in an intuitive and highly interactive process and without the need for specialized computer science and cheminformatics expertise. We anticipate that it may be a viable, if not necessary, step for research initiatives based on large high-throughput screening campaigns,in particular in the pharmaceutical industry, to make the most out of the recent advances in computational tools in order to leverage and take full advantage of the large data sets generated and available in house. There are “holes” in these data sets that can and should be identified and explored by chemistry and biology.     

Axitinib, a novel anti-angiogenic drug with promising activity in various solid tumors

Axitinib is an oral inhibitor of the VEGF, PDGF and colony stimulating factor-1 receptor tyrosine kinases and is currently in development by Pfizer Inc for the potential treatment of various solid tumors. Phase II trials with this agent alone or in combination with chemotherapeutic drugs were reported in several types of malignancy, with activity observed in thyroid, pancreatic, lung, renal, breast and colorectal cancers, melanoma and other carcinomas. Although frequent side effects have included fatigue, hypertension, diarrhea, hand-foot syndrome and proteinuria, axitinib was well tolerated overall. Larger, randomized phase II/III studies were ongoing at the time of publication.     

Waixenicin A,a marine-derived TRPM7 inhibitor: a promising CNS drug lead

Ion channels are the third largest class of targets for therapeutic drugs. The pharmacology of ion channels is an important research area for identifying new treatment options for human diseases. The past decade or so has seen increasing interest in an ion channel protein belonging to the transient receptor potential (TRP) family, namely the melastatin subfamily member 7 (TRPM7), as an emerging drug target. TRPM7 is a bifunctional protein with a magnesium and calcium-conducting divalent ion channel fused with an active kinase domain. TRPM7 is ubiquitously expressed in human tissues, including the brain, and regulates various cell biology processes such as magnesium and calcium homeostasis, cell growth and proliferation, and embryonic development. TRPM7 provides a link between cellular metabolic status and intracellular calcium homeostasis in neurons due to TRPM7’s unique sensitivity to fluctuating intracellular Mg·ATP levels. Thus, the protein plays a key role in ischemic and hypoxic neuronal cell death and brain injury, and is one of the key nonglutamate mechanisms in cerebral ischemia and stroke. Currently, the most potent and specific TRPM7 inhibitor is waixenicin A, a xenicane diterpenoid from the Hawaiian soft coral Sarcothelia edmondsoni. Using waixenicin A as a pharmacological tool, we demonstrated that TRPM7 is involved in promoting neurite outgrowth in vitro. Most recently, we found that waixenicin A reduced hypoxic–ischemic brain injury and preserved long-term behavioral outcomes in mouse neonates. We here suggest that TRPM7 is an emerging drug target for CNS diseases and disorders, and waixenicin A is a viable drug lead for these disorders.     

Carfilzomib:从天然产物到药物的研发历程

天然产物及其衍生物是药物的重要来源。Carfilzomib是一个以天然产物为先导通过结构优化得到的用于治疗多发性骨髓瘤的药物,其先导化合物Epoxomicin是从微生物中发现的具有抗癌活性的环氧酮肽类天然产物,能够选择性地抑制蛋白酶体,其环氧酮结构以独特的两步反应和蛋白酶体共价结合,因此克服了同类药物的脱靶缺点。以Epoxomicin为先导,通过结构优化得到活性更强、成药性性更好的Carfilzomib,作为新一代蛋白酶体抑制剂于2012年上市。     

Mining the microbial metabolome: a new frontier for natural product lead discovery

Traditionally, natural products have been important sources of new leads for the pharmaceutical industry, but with discovery rates of novel structural classes in decline, the need to bioprospect alternate sources of chemical diversity is evident. Microbial genome sequencing projects have revealed the presence of 'silent' biosynthetic gene clusters where there is no current detectable product. Likewise, culture-independent techniques have provided access to the collective genomes of environmental microflora. Both sources of molecular diversity could encode potentially valuable metabolites. The ability to measure the entire complement of metabolites within microorganisms that are used as surrogate hosts to express such gene clusters will be crucial to the exploitation of these yet untapped reservoirs of metabolic diversity for future natural product drug discovery.     

Plant-derived natural product research aimed at new drug discovery

Many important bioactive compounds have been discovered from natural sources using bioactivity-directed fractionation and isolation (BDFl) [Balunas MJ, Kinghorn AD (2005) Drug discovery from medicinal plants. Life Sci 78:431–441]. Continuing discovery has also been facilitated by the recent development of new bioassay methods. These bioactive compounds are mostly plant secondary metabolites, and many naturally occurring pure compounds have become medicines, dietary supplements, and other useful commercial products. Active lead compounds can also be further modified to enhance the biological profiles and developed as clinical trial candidates. In this review, the authors will summarize research on many different useful compounds isolated or developed from plants with emphasis placed on those recently discovered by the authors’ laboratories as antitumor and anti-HIV clinical trial candidates. Antitumor Agents 263 and Anti-AIDS Agents 74.     

Rho kinase, a promising drug target for neurological disorders

Rho kinases (ROCKs), the first Rho effectors to be described, are serine/threonine kinases that are important in fundamental processes of cell migration, cell proliferation and cell survival. Abnormal activation of the Rho/ROCK pathway has been observed in various disorders of the central nervous system. Injury to the adult vertebrate brain and spinal cord activates ROCKs, thereby inhibiting neurite growth and sprouting. Inhibition of ROCKs results in accelerated regeneration and enhanced functional recovery after spinal-cord injury in mammals, and inhibition of the Rho/ROCK pathway has also proved to be efficacious in animal models of stroke, inflammatory and demyelinating diseases, Alzheimer's disease and neuropathic pain. ROCK inhibitors therefore have potential for preventing neurodegeneration and stimulating neuroregeneration in various neurological disorders.     

Pure compound libraries; a new perspective for natural product based drug discovery

What often distinguishes the leaders in drug discovery and development from the rest is the quality of their compound libraries and the ease of access that they have to the information within those libraries. The screening of natural products can provide greater structural diversity than standard synthetic chemistry and offers significant opportunities for finding novel low molecular weight lead compounds. However, which strategy is the best for natural-product-based drug discovery? Two well established but relatively time consuming approaches are the screening of crude extracts and pre-fractionated extracts. This case study describes a third, pure-compound-screening approach, and discusses its benefits and pitfalls.     

An intensely sweet dihydroflavonol derivative based on a natural product lead compound

The dihydroflavonol dihydroquercetin 3-acetate (1) was isolated as a sweet constituent of the young shoots of Tessaria dodoneifolia (Hook. & Arn.) Cabrera (Compositae). Compound 1 and dihydroquercetin 3-acetate 4'-(methyl ether) (2), a novel synthetic analogue of this natural product lead compound, were rated by a taste panel as being 80 and 400 times sweeter than a 2% w/v sucrose solution, respectively. Synthetic dihydroquercetin 4'-(methyl ether) (3) showed a reduced sweetness intensity when compared to 2, while (+)-dihydroquercetin (4) was devoid of sweetness. Dihydroflavonol derivatives 1-3 represent a new class of potentially noncaloric and noncariogenic intense sweeteners.     

Artemisinin,a novel antimalarial drug: biochemical and molecular approaches for enhanced production

Artemisinin, a sesquiterpene lactone containing an endoperoxide bridge, has been isolated from the aerial parts of Artemisia annua L. plants. It is effective against both drug-resistant and cerebral malaria-causing strains of Plasmodium falciparum. The relatively low yield (0.01-0.8 %) of artemisinin in A. annua is a serious limitation to the commercialization of the drug. Therefore, the enhanced production of artemisinin either in cell/tissue culture or in the whole plant of A. annua is highly desirable. It can be achieved by a better understanding of the biochemical pathway leading to the synthesis of artemisinin and its regulation by both exogenous and endogenous factors. Furthermore, genetic engineering tools can be employed to overexpress gene(s) coding for enzyme(s) associated with the rate limiting step(s) of artemisinin biosynthesis or to inhibit the enzyme(s) of other pathway competing for its precursors. These aspects which may be employed to enhance the yield of artemisinin both in vitro and in vivo are discussed in this review.     

The bacterial ribosome,a promising focus for structure-based drug design

Recent crystal structures of the bacterial ribosome have identified the complex molecular interactions involved in antibiotic-ribosome recognition. Insights into the binding of aminoglycosides, macrolides, tetracyclines and other antibiotics provide opportunities for computational, structure-based approaches to be used in the design of appropriate modifications to existing antibiotics as well as in the discovery of completely new drug classes.     

Dopaminergic pharmacology and antioxidant properties of pukateine, a natural product lead for the design of agents increasing dopamine neurotransmission

The dopaminergic and antioxidant properties of pukateine [(R)-11-hydroxy-1,2-methylenedioxyaporphine, PUK], a natural aporphine derivative, were analyzed in the rat central nervous system. At dopamine (DA) D1 ([3H]-SCH 23390) and D2 ([3H]-raclopride) binding sites, PUK showed IC50 values in the submicromolar range (0.4 and 0.6 microM, respectively). When the uptake of tritiated dopamine was assayed by using a synaptosomal preparation, PUK showed an IC50 = 46 microM. In 6-hydroxydopamine unilaterally denervated rats, PUK (8 mg/kg but not 4 mg/kg) elicited a significant contralateral circling, a behavior classically associated with a dopaminergic agonist action. When perfused through a microdialysis probe inserted into the striatum, PUK (340 microM) induced a significant increase in dopamine levels. In vitro experiments with a crude rat brain mitochondrial suspension showed that PUK did not affect monoamine oxidase activities, at concentrations as high as 100 microM. PUK potently (IC50 = 15 microM) and dose-dependently inhibited the basal lipid peroxidation of a rat brain membrane preparation. As a whole, PUK showed a unique profile of action, comprising an increase in extracellular DA, an agonist-like interaction with DA receptors, and antioxidant activity. Thus, PUK may be taken as a lead compound for the development of novel therapeutic strategies for Parkinson disease.     

Aquaporins: a promising target for drug development

Aquaporins (AQPs) are a family of small hydrophobic, integral membrane proteins that are expressed in all living organisms and play critical roles in controlling the water flow into and out of cells. So far, 13 different AQPs have been identified in mammals (AQP 0 – 12). AQPs have recently been implicated in various diseases such as cancer, cataract, brain oedema, gallstone disease and nephrogenic diabetes insipidus, as well as in the development of obesity and polycystic kidney disease. Interfering with the expression of AQPs will undoubtedly have therapeutic applications. Hence, in this review, the authors look at each AQP and its association with various pathological conditions in humans and demonstrate that they form potential targets for the treatment of such diseases.     

Aquaporins: a promising target for drug development

Aquaporins (AQPs) are a family of small hydrophobic, integral membrane proteins that are expressed in all living organisms and play critical roles in controlling the water flow into and out of cells. So far, 13 different AQPs have been identified in mammals (AQP 0-12). AQPs have recently been implicated in various diseases such as cancer, cataract, brain oedema, gallstone disease and nephrogenic diabetes insipidus, as well as in the development of obesity and polycystic kidney disease. Interfering with the expression of AQPs will undoubtedly have therapeutic applications. Hence, in this review, the authors look at each AQP and its association with various pathological conditions in humans and demonstrate that they form potential targets for the treatment of such diseases.     

Strontium ranelate,a promising disease modifying osteoarthritis drug

Introduction: The articular cartilage and subchondral bone may have potential crosstalk in the development and progression of osteoarthritis (OA). Strontium ranelate (SrR) has the ability to dissociate the bone remodeling process and to change the balance between bone resorption and bone formation. Its effect on subchondral bone makes it a potential disease- modifying osteoarthritis drug (DMOAD) in the treatment of OA. The aim of the current review is to summarize up-to-date pharmacological and clinical data of SrR for OA treatment.

Areas covered: A literature search was performed on PubMed and European Medicines Agency (EMA) website for all publications and documents related to SrR and OA. References of related studies were searched by hand. Treatment with SrR, especially at the dosage of 2 g/day, was associated with reduced radiographic knee OA progression, and with meaningful clinical improvement. It was also significantly associated with decreased MRI-assessed cartilage volume loss (CVL) and bone marrow lesions (BMLs).

Expert opinion: SrR could be a promising DMOAD particularly for OA patients with bone phenotypes. The clinical efficacy and side effects of SrR for OA treatment need to be further investigated in future clinical trials before clinical application.     

Bacterial hosts for natural product production

Four bacterial hosts are reviewed in the context of either native or heterologous natural product production. E. coli, B. subtilis, pseudomonads, and Streptomyces bacterial systems are presented with each having either a long-standing or more recent application to the production of therapeutic natural compounds. The four natural product classes focused upon include the polyketides, nonribosomal peptides, terpenoids, and flavonoids. From the perspective of both innate and heterologous production potential, each bacterial host is evaluated according to biological properties that would either hinder or facilitate natural product biosynthesis.     

Self-assembled small molecule natural product gel for drug delivery: a breakthrough in new application of small molecule natural products

Natural products, as a gift of nature to humanity, have long been used as drugs or pharmacological actives to help people cure various diseases. Yet we still know comparatively little about their ability to be materials. In recent years, some small molecule natural products isolated from traditional Chinese medicines have been found to have new features, namely, self-assembly to form gels (i.e., natural product gels, NPG). However, the application development of these natural products is seriously lacking, which greatly weakens their practical value and delays the maturity of the field. Here, a series of self-assembled triterpenoid natural products are used as materials (gel scaffolds) to construct drug delivery systems. Surprisingly, these NPG not only exhibit the excellent self-healing, controlled gelation, good safety and sustained release, but also achieve synergistic treatment of tumors through bioactive natural products. Compared with non-bioactive gel scaffolds, NPG scaffolds show great advantages in tumor therapy, including optimal tumor inhibition, preferable health, better body recovery, stronger immune function, less toxic side effects and longer survival. The successful construction of NPG scaffolds not only takes full advantage of the self-assembled natural products, but also takes an important step in the development of new applications for natural products.