Combinatorial biosynthesis in plants: a (p)review on its potential and future exploitation

Combinatorial biochemistry, also called combinatorial biosynthesis, comprises a series of methods that establish novel enzyme-substrate combinations in vivo and, in turn, lead to the biosynthesis of new, natural product-derived compounds that can be used in drug discovery programs. Plants are an extremely rich source of bioactive natural products and continue to possess a huge potential for drug discovery. In this review, we discuss the state-of-the-art in combinatorial biosynthesis methods to generate novel molecules from plants. We debate on the progress and potential in biotransformation, mutasynthesis, combinatorial metabolism in hybrids, activation of silent plant metabolism and synthetic biology in plants to create opportunities for the combinatorial biosynthesis of plant-derived natural products, and, ultimately, for drug discovery. The therapeutic value of two classes of natural products, the terpenoid indole alkaloids and the triterpene saponins, is particularly highlighted.     

Factors Determining the Selection of Organic Reactions by Medicinal Chemists and the Use of These Reactions in Arrays (Small Focused Libraries)

Synthetic organic reactions are a fundamental enabler of small‐molecule drug discovery, and the vast majority of medicinal chemists are initially trained—either at universities or within industry—as synthetic organic chemists. The sheer breadth of synthetic methodology available to the medicinal chemist represents an almost endless source of innovation. But what reactions do medicinal chemists use in drug discovery? And what criteria do they use in selecting synthetic methodology? Why are arrays (small focused libraries) so powerful in the lead‐optimization process? In this Minireview, we suggest some answers to these questions and also describe how we have tried to expand the number of robust reactions available to the medicinal chemist.     

Late-Stage Formal Double C−H Oxidation of Prenylated Molecules to Alkylidene Oxetanes and Azetidines by Strain-Enabled Cross-Metathesis

Prenylation is a ubiquitous late-stage modification in nature that often confers significantly improved bioactivity for secondary metabolites. While this lipophilic modification renders enhanced potency, the lipophilic tag(s) can diminish bioavailability and adversely alter drug transportation and metabolism. Thus, a functional-group-tolerant, mild, and selective late-stage C−H functionalization of prenyl tags would present a great potential in drug discovery programs but could also impact other fields, such as agrochemistry and chemical biology. Herein we report an exocyclic-strain-driven cross-metathesis reaction of prenyl tags, a formal double C−H oxidation protocol, that can be used for the selective late-stage derivatization of prenylated compounds and natural products. This methodology avoids the need for prefunctionalization of target molecules and affords ready access to an unprecedented library of oxo- and aza-prenylated complex molecules. Thus, in a broader context, this methodology extends late-stage functionalization beyond that available to nature.     

An optical DNA-based biosensor for the analysis of bioactive constituents with application in drug and herbal drug screening

The efficient and rapid detection of bioactive compounds in complex matrices of different origins (natural or synthetic) is a key step in the discovery of molecules with potential application in therapy. Among them, molecules able to interact with nucleic acids can represent important targets.In this study, an optical DNA biosensor, based on surface plasmon resonance (SPR) transduction, has been studied in its potential application as new analytical device for drug screening. This device was applied to the analysis of pure synthetic or natural molecules and also to some fractions obtained by chromatographic separation of an extract of Chelidonium majus L. (great celandine), a plant containing benzo[c]phenanthridinium alkaloids having intercalating properties.The ability of these molecules to interact with the double stranded nucleic acid (dsDNA) immobilised on the sensor surface has been investigated. The optical sensing relies on the SPR-based bench instrument Biacore X™ and represents an example of multiuse sensor. The results obtained demonstrate the potential application of this device for the rapid screening of bioeffective compounds. The characteristics of the biosensor offer the possibility to be coupled to chemical analysis as in hyphenated technologies.     

Recent developments in the combinatorial synthesis of nitrogen heterocycles using solid phase technology

Recognizing the potential of combinatorial chemistry to accelerate drug discovery and development, most pharmaceutical and related industries are seriously looking toward combinatorial synthesis of compounds in order to facilitate the identification of 'lead' molecules. In particular, solid phase synthesis is the core technology for combinatorial chemistry and is widely used for generating libraries of structurally related compounds. Since many drugs contain the nitrogen heterocyclic component and since heterocycles possess a high order of structural diversity, a precise overview of recent progress in the combinatorial synthesis of nitrogen heterocycles using solid phase methodology would be useful. Since the progress in solid phase synthesis of organic molecules has been reviewed regularly from 1992 to 1998, only the development of solid phase combinatorial synthetic approaches of small nitrogen heterocycles since 1999 will be reviewed here. This review describes the solid phase synthesis of azepanes, benzodiazepines, benzimidazoles, benzothiazepines, cinnolines, indolizines, beta lactams, oxazepins, oxazoles including benzisooxazoles, hydantoins, piperidines, pyrimidines, pyrazolones, quinolones, trizolopyridazines and thiazoles.     

Stereoselective synthesis of macrocyclic peptides via a dual olefin metathesis and ethenolysis approach

Macrocyclic compounds occupy an important chemical space between small molecules and biologics and are prevalent in many natural products and pharmaceuticals. The growing interest in macrocycles has been fueled, in part, by the design of novel synthetic methods to these compounds. One appealing strategy is ring-closing metathesis (RCM) that seeks to construct macrocycles from acyclic diene precursors using defined transition-metal alkylidene catalysts. Despite its broad utility, RCM generally gives rise to a mixture of E- and Z-olefin isomers that can hinder efforts for the large-scale production and isolation of such complex molecules. To address this issue, we aimed to develop methods that can selectively enrich macrocycles in E- or Z-olefin isomers using an RCM/ethenolysis strategy. The utility of this methodology was demonstrated in the stereoselective formation of macrocyclic peptides, a class of compounds that have gained prominence as therapeutics in drug discovery. Herein, we report an assessment of various factors that promote catalyst-directed RCM and ethenolysis on a variety of peptide substrates by varying the olefin type, peptide sequence, and placement of the olefin in macrocycle formation. These methods allow for control over olefin geometry in peptides, facilitating their isolation and characterization. The studies outlined in this report seek to expand the scope of stereoselective olefin metathesis in general RCM.     

Diversity-oriented synthesis; a challenge for synthetic chemists

The efficient, simultaneous synthesis of structurally diverse compounds, better known as diversity-oriented synthesis (DOS), is not obvious, and remains a challenge to synthetic chemistry. This personal account details why DOS has such enormous implications for the discovery of small molecules with desired properties, such as catalysts, synthetic reagents, biological probes and new drugs, Also, I describe the evolution behind the current state-of-play of DOS.     

Multicomponent reactions and combinatorial chemistry

Multi-component reactions (MCRs) constitute a methodology to shorter syntheses of natural products or complex molecules for drug discovery. Due to the large number of accessible compounds, this type of chemistry has become very popular between scientists who are working in the area of combinatorial chemistry. Over the last decade combinatorial chemistry has evolved from the synthesis of great quantity of simple compounds to the parallel synthesis of complex molecules with a widely varied structure. MCRs are ideally suited for this trend, being free of limitations of a traditional multistep synthesis. The close connection and interference of multicomponent reactions and combinatorial chemistry are discussed in this review.     

Making priors a priority

When we build a predictive model of a drug property we rigorously assess its predictive accuracy, but we are rarely able to address the most important question, “How useful will the model be in making a decision in a practical context?” To answer this requires an understanding of the prior probability distribution (“the prior”) and hence prevalence of negative outcomes due to the property being assessed. In this perspective, we illustrate the importance of the prior to assess the utility of a model in different contexts: to select or eliminate compounds, to prioritise compounds for further investigation using more expensive screens, or to combine models for different properties to select compounds with a balance of properties. In all three contexts, a better understanding of the prior probabilities of adverse events due to key factors will improve our ability to make good decisions in drug discovery, finding higher quality molecules more efficiently.     

Synthesis of Pyrazole Derivatives Possessing Anticancer Activity: Current Status

Pyrazole is a versatile lead compound to design potent bioactive molecules for drug discovery and development, particularly in cancer therapy. The aim of this review is to present the most recent deeds in the field of synthetic route made for functionalized pyrazole derivatives active against cell proliferation disease. The review article covers the synthesis of 1H-pyrazole, synthesis of N-substituted pyrazoles, synthesis of pyrazolopyrazoles, and synthesis of pyrazoles fused with a naturally occurring moiety. Some of these reported compounds have passed the preclinical or initial-phase clinical trials for their anticancer activity.     

Property distributions: differences between drugs,natural products,and molecules from combinatorial chemistry

The differences between three different compound classes, natural products, molecules from combinatorial synthesis, and drug molecules, were investigated. The major structural differences between natural and combinatorial compounds originate mainly from properties introduced to make combinatorial synthesis more efficient. These include the number of chiral centers, the prevalence of aromatic rings, the introduction of complex ring systems, and the degree of the saturation of the molecule as well as the number and ratios of different heteroatoms. As drug molecules derive from both natural and synthetic sources, they cover a joint area in property space of natural and combinatorial compounds. A PCA-based scheme is presented that differentiates the three classes of compounds. It is suggested that by mimicking certain distribution properties of natural compounds, combinatorial products might be made that are substantially more diverse and have greater biological relevance.     

High Throughput and High Speed Organic Synthesis in Drug Discovery: An Integration of Chemistry and Technology

Drug discovery is a complicated process that involves multiple synthetic chemistry tasks. Among them, lead generation and optimization is the core business in the discovery research. During the stage of lead generation, a large library of many thousands individual compounds will be screened against a biological target to identify a set of hits that showed desirable activity. Once a hit has been identified, analog synthesis and development of SAR around this hit and establishment of relationsh…     

Pharmacophore features distributions in different classes of compounds

A pharmacophore analysis approach was used to investigate and compare different classes of compounds relevant to the drug discovery process (specifically, drug molecules, compounds in high throughput screening libraries, combinatorial chemistry building blocks and nondrug molecules). The distributions for a set of pharmacophore features including hydrogen bond acceptors, hydrogen bond donors, negatively ionizable centers, positively ionizable centers and hydrophobic points, were generated and examined. Significant differences were observed between the pharmacophore profiles obtained for the drug molecules and those obtained for the high-throughput screening compounds, which appear to be closely related to the nondrug pharmacophore distribution. It is suggested that the analysis of pharmacophore profiles could be used as an additional tool for the property-based optimization of compound selection and library design processes, thus improving the odds of success in lead discovery projects.     

Molecular complexity and its impact on the probability of finding leads for drug discovery.

Using a simple model of ligand-receptor interactions, the interactions between ligands and receptors of varying complexities are studied and the probabilities of binding calculated. It is observed that as the systems become more complex the chance of observing a useful interaction for a randomly chosen ligand falls dramatically. The implications of this for the design of combinatorial libraries is explored. A large set of drug leads and optimized compounds is profiled using several different properties relevant to molecular recognition. The changes observed for these properties during the drug optimization phase support the hypothesis that less complex molecules are more common starting points for the discovery of drugs. An extreme example of the use of simple molecules for directed screening against thrombin is provided.     

Molecular Design in Practice: A Review of Selected Projects in a French Research Institute That Illustrates the Link between Chemical Biology and Medicinal Chemistry

Chemical biology and drug discovery are two scientific activities that pursue different goals but complement each other. The former is an interventional science that aims at understanding living systems through the modulation of its molecular components with compounds designed for this purpose. The latter is the art of designing drug candidates, i.e., molecules that act on selected molecular components of human beings and display, as a candidate treatment, the best reachable risk benefit ratio. In chemical biology, the compound is the means to understand biology, whereas in drug discovery, the compound is the goal. The toolbox they share includes biological and chemical analytic technologies, cell and whole-body imaging, and exploring the chemical space through state-of-the-art design and synthesis tools. In this article, we examine several tools shared by drug discovery and chemical biology through selected examples taken from research projects conducted in our institute in the last decade. These examples illustrate the design of chemical probes and tools to identify and validate new targets, to quantify target engagement in vitro and in vivo, to discover hits and to optimize pharmacokinetic properties with the control of compound concentration both spatially and temporally in the various biophases of a biological system.     

Synthesis of tricyclic 4-chloro-pyrimido[4,5-b][1,4]benzodiazepines

[reaction: see text] A novel methodology was developed for the efficient synthesis of 4-chloro-pyrimido[4,5-b][1,4]benzodiazepines. The key is the intramolecular Friedel-Crafts cyclization of 5-amino-4-(N-substituted)anilino-6-chloropyrimidine with either a carboxylic acid or its derivatives to construct the 4-chloro-pyrimido[4,5-b][1,4]benzodiazepine core. Subsequent nucleophilic substitution allows the introduction of one more diversity point in the target molecules. This strategy provides an efficient method to access a library of compounds based on privileged substructures that are of great interest in drug discovery.     

Can we really do computer-aided drug design?

In this article, we discuss what we mean by ‘design’ and contrast this with the application of computational methods in drug discovery. We suggest that the predictivity of the computational models currently applied in drug discovery is not yet sufficient to permit a true design paradigm, as demonstrated by the large number of compounds that must currently be synthesised and tested to identify a successful drug. However, despite the uncertainties in predictions, computational methods have enormous potential value in narrowing the range of compounds to consider, by eliminating those that have negligible chance of being a successful drug, while focussing efforts on chemistries with the best likelihood of success. Applied appropriately, computational approaches can support decision-makers in achieving multi-parameter optimisation to guide the selection and design of compounds with the best chance of achieving an appropriate balance of properties for a drug discovery project’s objectives. Finally, we consider some approaches that may contribute over the next 25 years to improve the accuracy and transferability of computational models in drug discovery and move towards a genuine design process.     

New Methods for the Synthesis of Spirocyclic Cephalosporin Analogues

Spiro compounds provide attractive targets in drug discovery due to their inherent three-dimensional structures, which enhance protein interactions, aid solubility and facilitate molecular modelling. However, synthetic methodology for the spiro-functionalisation of important classes of penicillin and cephalosporin β-lactam antibiotics is comparatively limited. We report a novel method for the generation of spiro-cephalosporin compounds through a Michael-type addition to the dihydrothiazine ring. Coupling of a range of catechols is achieved under mildly basic conditions (K₂CO₃, DMF), giving the stereoselective formation of spiro-cephalosporins (d.r. 14:1 to 8:1) in moderate to good yields (28−65%).