Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries

Identification of novel plant cysteine oxidase inhibitors from a yeast chemical genetic screen

Hypoxic responses in plants involve Plant Cysteine Oxidases (PCOs). They catalyze the N-terminal cysteine oxidation of Ethylene Response Factors VII (ERF-VII) in an oxygen-dependent manner, leading to their degradation via the cysteine N-degron pathway (Cys-NDP) in normoxia. In hypoxia, PCO activity drops, leading to the stabilization of ERF-VIIs and subsequent hypoxic gene upregulation. Thus far, no chemicals have been described to specifically inhibit PCO enzymes. In this work, we devised an in vivo pipeline to discover Cys-NDP effector molecules. Budding yeast expressing AtPCO4 and plant-based ERF-VII reporters was deployed to screen a library of natural-like chemical scaffolds and was further combined with an Arabidopsis Cys-NDP reporter line. This strategy allowed us to identify three PCO inhibitors, two of which were shown to affect PCO activity in vitro. Application of these molecules to Arabidopsis seedlings led to an increase in ERF-VII stability, induction of anaerobic gene expression, and improvement of tolerance to anoxia. By combining a high-throughput heterologous platform and the plant model Arabidopsis, our synthetic pipeline provides a versatile system to study how the Cys-NDP is modulated. Its first application here led to the discovery of at least two hypoxia-mimicking molecules with the potential to impact plant tolerance to low oxygen stress.

Hybrid curcumin compounds: a new strategy for cancer treatment

Cancer is a multifactorial disease that requires treatments able to target multiple intracellular components and signaling pathways. The natural compound, curcumin, was already described as a promising anticancer agent due to its multipotent properties and huge amount of molecular targets in vitro. Its translation to the clinic is, however, limited by its reduced solubility and bioavailability in patients. In order to overcome these pharmacokinetic deficits of curcumin, several strategies, such as the design of synthetic analogs, the combination with specific adjuvants or nano-formulations, have been developed. By taking into account the risk-benefit profile of drug combinations, as well as the knowledge about curcumin's structure-activity relationship, a new concept for the combination of curcumin with scaffolds from different natural products or components has emerged. The concept of a hybrid curcumin molecule is based on the incorporation or combination of curcumin with specific antibodies, adjuvants or other natural products already used or not in conventional chemotherapy, in one single molecule. The high diversity of such conjugations enhances the selectivity and inherent biological activities and properties, as well as the efficacy of the parental compound, with particular emphasis on improving the efficacy of curcumin for future clinical treatments.

Are natural products still the best source for antibacterial discovery? The bacterial entry factor

BACKGROUND

One of the reasons for the low output of new antibacterial agents from recent discovery efforts has been the reliance on synthetic chemicals in screening for inhibitors of new bacterial targets. As the bulk of antibacterials are natural product-derived, is a return to natural products for screening warranted?

OBJECTIVE

As bacterial entry is required for inhibition of many targets, this review concentrates on the potential for natural products and compounds from synthetic libraries to enter and be retained in the bacterial cytoplasm.

METHODS

Papers investigating the physicochemical nature of synthetic libraries, natural products and antibacterials were reviewed; the requirements for entry into the bacterial cytoplasm were delineated.

RESULTS/CONCLUSION

Until rules for cytoplasmic entry are developed and routinely used for design of synthetic libraries, natural products still provide a rich resource for antibacterial discovery.

Osthole: A Promising Lead Compound for Drug Discovery from a Traditional Chinese Medicine (TCM)

Natural products have always been important resources either as therapeutic agents or as lead compounds for the production of pharmaceutical compounds. Osthole, 7-methoxy-8-(3-methyl-2-butenyl) coumarin, an ingredient of a Traditional Chinese Medicine(TCM), has received considerable attention recently because of its significant and diverse pharmacological activities, including anticancer, antisteoporotic, and antiproliferative, which make it a very promising natural lead compound for new drug discovery. The present work summarizes the related biological information on osthole and its analogues and proposes the possibility of its development as a promising lead compound for drug discovery.

New aspects of natural products in drug discovery

During the past 15 years, most large pharmaceutical companies have decreased the screening of natural products for drug discovery in favor of synthetic compound libraries. Main reasons for this include the incompatibility of natural product libraries with high-throughput screening and the marginal improvement in core technologies for natural product screening in the late 1980s and early 1990 s. Recently, the development of new technologies has revolutionized the screening of natural products. Applying these technologies compensates for the inherent limitations of natural products and offers a unique opportunity to re-establish natural products as a major source for drug discovery. Examples of these new advances and technologies are described in this review.

A Cheminformatic Toolkit for Mining Biomedical Knowledge

PURPOSE

Cheminformatics can be broadly defined to encompass any activity related to the application of information technology to the study of properties, effects and uses of chemical agents. One of the most important current challenges in cheminformatics is to allow researchers to search databases of biomedical knowledge, using chemical structures as input.

MATERIALS AND METHODS

An important step towards this goal was the establishment of PubChem, an open, centralized database of small molecules accessible through the World Wide Web. While PubChem is primarily intended to serve as a repository for high throughput screening data from federally-funded screening centers and academic research laboratories, the major impact of PubChem could also reside in its ability to serve as a chemical gateway to biomedical databases such as PubMed.

CONCLUSION

This article will review cheminformatic tools that can be applied to facilitate annotation of PubChem through links to the scientific literature; to integrate PubChem with transcriptomic, proteomic, and metabolomic datasets; to incorporate results of numerical simulations of physiological systems into PubChem annotation; and ultimately, to translate data of chemical genomics screening efforts into information that will benefit biomedical researchers and physician scientists across all therapeutic areas.

One pot synthesis of oxygenated tri-heterocycles as anti-microbial agents

A one pot synthesis of an array of angularly linked tri-heterocycles with coumarin, benzofuran and furan rings is described. This high yielding synthesis is achieved by the reaction of various 4-bromomethylcoumarins with furyl o-hydroxyphenyl ketones involving benzylic nucleophilic displacement and intramolecular aldolization. All the compounds have been tested in vitro for their anti-microbial activity against Micrococcus aureus, Pseudomonas chinchori, Asperigillus fumigatus and Penicillium wortmanni at 100, 50, and 25 microg ml(-1) concentrations. Chloro groups in the benzofuran ring enhanced the activity.

Natural products as a hunting ground for combinatorial chemistry

Natural products have a long history of success as biologically active leads for therapeutic agents. The ability to prepare analogues and to discover structure-activity relationships is necessary to truly harness the potential of natural products. Recently, combinatorial chemistry has risen to this challenge, and even fairly complex natural products can be targeted for parallel synthesis. Academic and industrial efforts have employed natural products from the peptide, alkaloid, polyketide, and terpenoid and steroid classes in combinatorial chemistry approaches for the production of medicinally important compounds.

Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates

MOTIVATION

To gather information about available databases and chemoinformatics methods for prediction of properties relevant to the drug discovery and optimization process.

RESULTS

We present an overview of the most important databases with 2-dimensional and 3-dimensional structural information about drugs and drug candidates, and of databases with relevant properties. Access to experimental data and numerical methods for selecting and utilizing these data is crucial for developing accurate predictive in silico models. Many interesting predictive methods for classifying the suitability of chemical compounds as potential drugs, as well as for predicting their physico-chemical and ADMET properties have been proposed in recent years. These methods are discussed, and some possible future directions in this rapidly developing field are described.

Libraries from natural product-like scaffolds

Natural products are an attractive source of varied structures that exhibit potent biological activities, and desirable pharmacological profiles. Since the relatively recent advent of high-throughput organic synthesis in the drug discovery process, several design approaches have been applied to the construction of screening libraries. Libraries of natural-product derivatives, natural-product-like compounds prepared by total synthesis, and libraries derived from natural-products are several types that have been reported.

Computational design strategies for combinatorial libraries

Medicinal chemistry principles are being increasingly applied to the design of smaller, high purity, information-rich libraries. Recent computational advances in statistical methodology, the design of libraries to reduce ADMET problems, targeting protein families and revisiting natural products as sources of inspiration for scaffolds and reagents are all areas of progressive research.

Evaluation of similarity measures for searching the dictionary of natural products database

Similarity searches using combinations of seven different similarity coefficients and six different representations have been carried out on the Dictionary of Natural Products database. The objective was to discover if any special methods of searching apply to this database, which is very different in nature from the many synthetic databases that have been the subject of previous studies of similarity searching. Search effectiveness was assessed by a recall analysis of the search outputs from sets of pharmacologically active target structures. The different target sets produce exceptional but contradictory results for the Russell-Rao and Forbes coefficients, which have been shown to be due to a dependence on molecular size; these are the coefficients of choice in the case of large and small structures, respectively. Rankings from these results have been combined using a data fusion scheme and some small gains in performance were normally obtained by using substructural fingerprints and molecular holograms in combination with the Squared Euclidean or Tanimoto coefficients.