Volume 79, Issue 4

The natural products theme is deeply rooted in the culture of IUPAC, and the first International Symposium on the Chemistry of Natural Products (ISCNP) on 15-25 August 1960 with Sir Alexander Todd (later, Lord Todd) as President, can claim particular credit in the history of the Union. Not only did it take an early bold step toward the truly global reach that characterizes IUPAC conferences in the modern era, but it was the harbinger of numerous sponsored or Union-initiated series devoted to other areas of specialization in the chemical sciences. International delegates to the inaugural event undertook the then nontrivial journey to Melbourne, Canberra, and Sydney, Australia with an excursion to New Guinea, to participate in a scientific program, in which structural elucidation and synthesis were dominant themes, and most familiar modern tools and techniques were still in their infancy. Natural products lore still celebrates the names of certain pioneers who contributed to that first program. As a series, this hardy biennial has since been hosted throughout the world, and has faithfully served a huge international community of scientists engaged in every conceivable aspect of natural products chemistry. The terms of reference for the ISCNP series have recently been adapted following a decision to merge with the younger series of International Conferences on Biodiversity (ICOB). This step was inaugurated with ISCNP-24/ICOB-4, which was held in New Delhi, India on 26-31 January 2004; <http://www.iupac.org/publications/pac/2005/7701/index.html>. The change exemplifies the evolving nature of the subject, and its ongoing appeal to scientists engaged in exploring and developing less familiar disciplinary interfaces, as well as traditional mainstream areas. It is thus unsurprising that natural products should feature as a Special Topic theme for a second time in the recent history of Pure and Applied Chemistry (PAC); see <http://www.iupac.org/publications/pac/2003/7502/ index.html> for a collection of papers based upon presentations at ISCNP-23, held in Florence, Italy on 28 July-02 August 2002. That program featured fresh insights into proteomics, genetics, and molecular biology, in a trend that ISCNP-25/ICOB-5 has continued to develop, with coverage of related and new features of bioactivity at the molecular level and chemical biological themes, whilst also paying homage to enduring favorites such as structure and synthesis. What is a Special Topic? The concept was introduced as a device to publicize and promote new and emerging principles and practice in all branches of chemical sciences, through the pages of PAC; <http://www.iupac.org/publications/pac/index.html#si>. Themes may be selected from inaugural events or special IUPAC projects, but equally, may identify themselves as dynamic and widely practiced areas of science presently covered by regular IUPAC-sponsored series. Important criteria obviously include relevance, topicality, and readership expectations. Publication projects arising from the Special Topics initiative generally continue to achieve gratifyingly favourable citation profiles, and thereby support the view that they fulfil an important need. It is noteworthy that the Kyoto meeting represents the third occasion that the series has been hosted in Japan, the home of some quite extraordinary manifestations of natural products and biodiversity, as well as some of the outstanding practitioners of the subject. The program of ISCNP-25/ICOB-5 rightly captures some of this local character, but is also a fully representative expression of the international participation and appeal that traditionally characterizes the series. It is a pleasure to acknowledge the able and enthusiastic support of the Conference Editor, Prof. Hideo Kigoshi, in preparing this Special Topic issue of 27 topical papers based upon program presentations. The collection aspires to offer an enduring archival record of a subject that continues to reinvent itself, and to astound and challenge its practitioners with the apparently boundless molecular riches of the biosphere. James R. Bull Scientific Editor

Natural products chemistry primarily involves research on organic compounds produced by plants, animals, and microorganisms, and focuses not only on the determination of chemical structures and biosynthesis, but also on chemical synthesis and the development of stereoselective chemical reactions. In recent years, developments have spread to the field of molecular biology in particular, as indicated by the investigation of the relationship between the structure and activity of biologically active substances, in addition to the elucidation of the mechanisms of biological effects at the molecular level. These achievements have facilitated corresponding progress in other related sciences, and have contributed significantly to developments in pharmaceutical, agrochemical, and other industries. Meanwhile, the science of biodiversity focuses on objectives such as the search for active ingredients in organisms and the preservation of species and diversity, from a scientific perspective. These two fields are closely related in their respective focuses on the diversity of organisms and the diversity of metabolic products, and it is for this reason that the respective conferences on biodiversity and natural products chemistry have come to be merged, starting with the preceding event in the series, held in India. I believe that this joint approach is highly beneficial, and sincerely hope that this conference has provided opportunities for exchange of a diverse range of information between the respective researchers and has contributed to further global development of these fields. This conference was held at the Kyoto International Conference Hall on 23-28 July 2006, and was officially sponsored by IUPAC and hosted by the Science Council of Japan jointly with the Chemical Society of Japan, the Pharmaceutical Society of Japan, and the Japan Society for Bioscience, Biotechnology, and Agrochemistry. In addition to 17 plenary speakers, lectures were also delivered by 77 invitees of various generations, and 580 posters were presented, primarily by younger delegates, of which 72 were supplemented by oral presentations. In order to broadly examine various topics relating to each aspect of the field of natural products chemistry, discussions were conducted by classifying this diverse field into the following eight themes, thereby promoting interactions between researchers and cooperation between related fields. - Isolation and Structure Elucidation of Natural Products - Synthesis of Natural Products and their Models - Biosynthesis and Genetic Engineering on Natural Products - Spectroscopy in Natural Products Chemistry - Molecular Mode of Action on Natural Products and Drugs - Chemical Biology and Related Areas - Chemistry and Biochemistry Related to Biodiversity - Drug Diversity and Developments Approximately 1200 participants from 31 countries and regions attended this conference, and exhibits from a total of 26 companies were presented in the concurrently held exhibition. In addition, pre- and post-symposia were held in Nagoya, Tokushima, Sapporo, Sendai, Fukuoka, and Tokyo, and the 48th Symposium of a regular series on the Chemistry of Natural Products (in Sendai) also took advantage of the opportunity to promote more diverse and closer interactions. I would like to express my deepest gratitude to the aforementioned hosts, co-hosts, and many other organizations and individuals for their support, without which this conference would not have been possible. Finally, it is my sincere hope that this conference has provided opportunities for the future advancement of natural products chemistry and biodiversity science. Daisuke Uemura Chairman, Organizing Committee

Recent studies have proved that huperzine A (HupA) possesses different pharmacological actions other than the inhibition of hydrolysis of ACh. These noncholinergic roles, for instance, the antagonist effect on NMDA receptor, the protection of neuronal cells against β-amyloid, free radicals, and hypoxia-ischemia-induced injury, could be important too in Alzheimer's disease (AD) treatment. The therapeutic effects of HupA are probably based on a multitarget mechanism. By targeting dual active sites of AChE, a series of bis- and bifunctional HupB compounds with various lengths of tether were designed, synthesized, and tested for the inhibition and selectivity of AChE. The most potent bis-HupB compound exhibited increase by three orders of magnitude in AChE inhibition and two orders of magnitude in selectivity for AChE than its parent HupB.

Oxylipins are important signal transduction molecules widely distributed in animals and plants where they regulate a variety of events associated with physiological and pathological processes. The family embraces several different metabolites that share a common origin from the oxygenase-catalyzed oxidation of polyunsaturated fatty acids. The biological role of these compounds has been especially studied in mammalians and higher plants, although a varied and very high concentration of these products has also been reported from marine macroalgae. This article gives a summary of our results concerning the oxylipin chemistry of marine diatoms, a major class of planktonic microalgae that discourage predation from their natural grazers, zooplanktonic copepods, using chemical warfare. These apparently harmless microscopic cells produce a plethora of oxylipins, including short-chain unsaturated aldehydes, hydroxyl-, keto-, and epoxyhydroxy fatty acid derivatives, that induce reproductive failure in copepods through abortions, congenital malformations, and reduced larval growth. The biochemical process involved in the production of these compounds shows a simple regulation based on decompartmentation and mixing of preexisting enzymes and requires hydrolysis of chloroplast-derived glycolipids to feed the downstream activities of C 16 and C 20 lipoxygenases.

A large variety of unique heterocyclic natural marine products, without terrestrial counterparts, have been isolated from marine invertebrates, mainly sponges, ascidians, and soft corals. Many of these compounds display interesting biological activity. In this review, we report our recent studies on nitrogen-containing heterocyclic compounds ("alkaloids"), as well as some containing sulfur and oxygen, which have been isolated from Red Sea and Indo-Pacific organisms, and discuss progress on the synthesis of these natural products and structural analogs.

The secretion from the hippopotamus' skin changes its color from colorless to red, and then brown by polymerization of its pigments. The responsible pigments for the coloring reaction were isolated and denoted as hipposudoric acid (the red pigment) and norhipposudoric acid (the orange pigment). The syntheses of these pigments and the related derivatives were performed, and the latter were of use to elucidate the structures of these pigments including their tautomeric structures in aprotic and protic solvents. These pigments were estimated to be medicines for the hippopotamus, having the effect of both protecting the skin from sunburn and preventing infection by some microbes.

The bioorganic basis of plant movement in two plant systems is described in this article: the circadian rhythmic leaf movement known as nyctinasty and trap movement in the Venus flytrap. The bioactive substances responsible for plant movement, the chemical mechanism of the rhythm, and studies on the key protein controlling nyctinasty are presented. The nyctinastic leaf movement is induced by a pair of leaf-movement factors, and one of each pair is a glucoside. There are two key proteins that are involved in the control of nyctinasty. One is β-glucosidase: a biological clock regulates the activity of β-glucosidase, which deactivates the glucoside-type leaf-movement factor, controlling the balance in the concentrations of the leaf-closing and -opening factors. The other is the specific receptor for each leaf-movement factor: the genuine target cell for each leaf-movement factor is confirmed to be a motor cell from leaflet pulvini, and the specific receptors that regulate the turgor of motor cells are localized in the membrane fraction. The article also discusses the isolation of the "memory" substance from the Venus flytrap and presents a mechanism for this action.

The chemistry of members of the family Piperaceae is of great interest owing to the variety of biological properties displayed. A survey of structural diversity and bioactivity reveals that groups of species specialize in the production of amides, phenylpropanoids, lignans and neolignans, benzoic acids and chromenes, alkaloids, polyketides, and a plethora of compounds of mixed biosynthetic origin. Bioassays against Cladosporium cladosporioides and C. sphaerospermun have resulted in the characterization of various amides, prenylated phenolic compounds, and polyketides as potential classes of antifungal agents. Studies on the developmental process in seedlings of Piper solmsianum have shown that phenylpropanoid are produced instead of the tetrahydrofuran lignans found in adult plants. In suspension cultures of P. cernuum and P. crassinervium , phenylethylamines and alkamides predominate, whereas in the adult plants prenylpropanoids and prenylated benzoic acids are the respective major compound classes. Knowledge of the chemistry, bioactivity, and ecology of Piperaceae species provides preliminary clues for an overall interpretation of the possible role and occurrence of major classes of compounds.

Two new natural products incorporating a phenylpropyl subunit ("phenylpropanoids"), [4-(prop-2-enyl)phenyl angelate and 4-(3-methyloxiranyl)phenyl 2-methylbutyrate], one new bisabolene-type sesquiterpenoid [1-methyl-4-(6-methylhepta-1,5-dien-2-yl)-7-oxabicyclo[4.1.0]heptane ("aureane")], and one new trinorsesquiterpene [4-(6-methylbicyclo[4.1.0]hept-2-en-7yl)butan-2-one ("traginone")] have been isolated from the essential oils of Pimpinella species occurring in Turkey, together with nine known phenylpropanoids and other natural products. Six of the known compounds are newly reported for Umbelliferae, whilst one is newly reported for Pimpinella species. Compound structures were determined by 1D and 2D NMR analysis. Isolated compounds were evaluated for antimalarial, antimicrobial, estrogenic, and aphidicidal activities. Pure compounds were also tested for antifungal activity against strawberry anthracnose-causing fungal plant pathogens Colletotrichum acutatum , C. fragariae , and C. gloeosporioides using direct bioautography and microdilution broth assays.

Liverworts produce a great variety of lipophilic terpenoids, aromatic compounds, and acetogenins. Many of these constituents have characteristic scents, pungency, and bitterness, and display a quite extraordinary array of bioactivities and medicinal properties. These expressions of biological activity are summarized and discussed, and examples are given of the potential of certain lead compounds for structure-activity studies and synthesis.

Our long-standing and continual screening of microorganisms, especially for antiparasitic agents, has produced a wide variety of compounds of global importance, such as the avermectins. Recent discoveries include nafuredin, atpenins, argifin, and argadin. Nafuredin is a helminth-specific inhibitor of electron-transport enzyme, complex I, which exhibits anthelmintic activity against Haemonchus contortus in sheep. The atpenins are the most potent complex II inhibitors ever reported. Co-crystallization study of atpenin A5 and E. coli complex II indicated the binding mechanism of ubiquinone to complex II. Argifin and argadin are the first cyclic peptides to inhibit chitinase at low concentration. Though structurally similar, their chitinase inhibition mechanisms are quite different.

A new cytotoxic and linear peptide (IC 50 460 nM to NCI-H460 human lung tumor cells) was isolated from the marine cyanobacterium Geitlerinema sp. The planar structure of mitsoamide was deduced by 1D and 2D NMR experiments in combination with MS analyses. The structure of mitsoamide contains an unusual polyketide unit (3,7-dimethoxy-5-methyl-nonanedioic acid, DMNA), incorporates a homolysine (HomoLys) residue and possesses a highly unusual piperidine aminal moiety. The configurations of the relatively common amino acids present in mitsoamide (Ala, Ile, N -Me-Ile, Phe, Val) were determined by chiral HPLC analysis of the acid hydrolysate.

FR901379, which is a novel, water-soluble, echinocandin-like lipopeptide, was isolated from a microbial culture broth. It showed potent in vivo antifungal activity against Candida albicans and inhibits the synthesis of 1,3-β-glucan. However, this compound had hemolytic activity and was also less active against Aspergillus fumigatus . To overcome these shortcomings, we synthesized FR131535 bearing an octyloxybenzoyl acyl side chain instead of a fatty acid. FR131535 retained the original activity displayed by FR901379, acquired potent anti- Aspergillus activity, and its hemolytic activity was significantly reduced. Further extensive chemical modification of FR901379 has led to the discovery of micafungin (FK463), which is effective against Candida and Aspergillus spp. Micafungin has been marketed in Japan and the United States as a candin-class parenteral antifungal agent for life-threatening mycoses.

Studies in our laboratory are focused on structural development studies of biological response modifiers (BRMs), including nuclear receptor (NR) ligands, which act directly on cells at the gene expression level, and thalidomide (and related molecules), which modulates a variety of physiological processes. Our studies on the molecular design of ligands for retinoic acid receptor (RAR), androgen receptor (AR), vitamin D receptor (VDR), farnesoid X receptor (FXR), and peroxisome proliferator-activated receptor (PPAR) are reviewed.

Palladium-catalyzed transformations are of great importance in modern synthetic organic chemistry. The vast number of reactions that can be catalyzed by Pd 0 - as well as Pd 2+ -complexes in combination with the relative stability of the intermediates offers the intriguing opportunity of carrying out multiple consecutive bond-forming processes. They can be even performed in a domino fashion and in the presence of chiral ligands to allow the efficient preparation of almost enantiopure compounds. In this article, the use of double Heck, Tsuji-Trost-Heck, and Wacker-Heck reactions for the total syntheses of estradiol, spinosyn A analogs, cephalotaxine, and vitamin E is described.

The zoanthamine alkaloids, a type of heptacyclic marine alkaloid isolated from colonial zoanthids of the genus Zoanthus sp., have distinctive biological and pharmacological properties as well as their unique chemical structures with stereochemical complexity. Namely, norzoanthamine can suppress the loss of bone weight and strength in ovariectomized mice and has been considered a promising candidate for an antiosteoporotic drug, whereas zoanthamine has exhibited potent inhibitory activity toward phorbol myristate-induced inflammation in addition to powerful analgesic effects. Recently, norzoanthamine derivatives were demonstrated to inhibit strongly the growth of P-388 murine leukemia cell lines, in addition to their potent antiplatelet activities on human platelet aggregation. These distinctive biological properties, combined with novel chemical structures, make this family of alkaloids extremely attractive targets for chemical synthesis. However, the chemical synthesis of the zoanthamine alkaloids has been impeded owing to their densely fuctionalized complex stereostructures. We report here the first and highly stereoselective total syntheses of norzoanthamine and zoanthamine, which involves stereoselective synthesis of the requisite triene for intramolecular Diels-Alder reaction via three-component coupling reactions, a key intramolecular Diels-Alder reaction, and subsequent crucial bis-aminoacetalization as the key steps.

Progress toward a total synthesis of spirastrellolide A, a 38-membered marine macrolide, is reported. Syntheses of two diastereomers of the C1-C25 region, and an evolving Sharpless dihydroxylation strategy toward a C26-C40 fragment, are described. The syntheses exploit boron-mediated aldol chemistry to install key stereocenters, and feature late-stage thermodynamically controlled spiroacetalizations.

An analog of mycothiazole and pseudotrienic acid B were synthesized efficiently by using ring-closing metathesis or cross-metathesis as key reactions.

The novel polyketide (+)-discodermolide was isolated in very small quantities from sponge extracts. This compound is one of several microtubule stabilizers showing promise as novel chemotherapeutic agents for the treatment of cancer. The clinical evaluation of this and similar compounds is hampered by lack of material, and at present, the only way to obtain the necessary quantities is total chemical synthesis.

An efficient enantioselective construction of quaternary carbons including spiro carbons is an area of intense interest due to the importance of these units as components of biologically active natural products. Prominent methods are presented for the synthesis of chiral, nonracemic quaternary carbon centers by (i) stereospecific rearrangement of optically active epoxides, (ii) enzyme-catalyzed resolution, and (iii) hypervalent iodine reagent-induced ipso -substitution of para -substituted phenol derivatives. These methods were applied to the total syntheses of fredericamycin A and discorhabdin A.

The effect of C-terminal amidation on the antimicrobial and hemolytic activities of antimicrobial peptides was studied using three cationic peptides which form amphiphilic α-helices when bound to membranes. The natural antimicrobial peptide PGLa, the designer-made antibiotic MSI-103, and the cell-penetrating "model amphipathic peptide" (MAP) are all amidated in their original forms, and their biological activities were compared with the same sequences carrying a free C-terminus. It was found that, in general, a free COOH-terminus reduces both the antimicrobial activity and the hemolytic side effects of the peptides. The only exception was observed for MSI-103, whose antimicrobial activity was not decreased in the acid form. Having shown that the therapeutic index (TI) of this novel peptide is significantly higher than for the other tested peptides, with high antibiotic activity and little undesired effects, we suggest that it could be a useful starting point for further development of new peptide antibiotics.

Earlier reports from our laboratory established the acetyl transferase function of calreticulin (CRT), enabling CRT to transfer acetyl groups from the acetoxy groups of polyphenolic acetates (PAs) to certain receptor proteins. We have in this paper documented the ability of CRT to catalyze the possible transfer of acetyl moiety from 7-acetamido-4-methylcoumarin (7-N-AMC) to the proteins, glutathione S-transferase (GST), and NADPH cytochrome c reductase, leading to the modification of their catalytic activities. 7-Acetoxy-4-methylthiocoumarin (7-AMTC) compared to 7-acetoxy-4-methylcoumarin (7-AMC) when used as a substrate for calreticulin transacetylase (CRTAase) yielded significantly higher catalytic activity. PM3-optimized geometries suggested that the availability of electrons on the sulfur atom of the thiocarbonyl group of the thiocoumarin may render the substrate binding more favorable to the active site of the enzyme as compared to its oxygen analog. Further CRTAase activity was characterized in the human blood lymphocytes. There was no appreciable difference in CRTAase activity of lymphocytes of asthmatic patients as compared to those of normal subjects. The results presented here highlight for the first time the irreversible inhibition of human blood lymphocytes protein kinase C (PKC) by 7,8-diacetoxy-4-methylcoumarin (DAMC) possibly by way of acetylation. The activity of PKC in lymphocytes of asthmatic patients was found to proportionally increase with the severity of the disease. When PA was incubated with lymphocytes of normal patients, PKC was inhibited marginally. On the other hand, lymphocyte PKC of severe asthmatic patients was inhibited drastically. Several PAs inhibited PKC of asthmatic patients in tune with their specificity to CRTAase. DAMC was found to exert maximum inhibitory action on PKC, while 7,8-dihydroxy-4-methylcoumarin (DHMC), the deacetylated product of DAMC, failed to inhibit PKC. These observations clearly describe DAMC as the novel irreversible inhibitor of PKC, and DAMC may be found useful in the control of inflammation and may serve as a potential drug candidate in the therapy of asthma.

The long-overlooked methylerythritol phosphate (MEP) pathway represents an alternative to the mevalonate route for the formation of isoprene units. It is found in most bacteria as well as in the plastids of all phototrophic organisms. A selection of significant steps of its discovery and elucidation are presented in this contribution, as well as a complete hypothetical biogenetic scheme for the last reduction step.

The development of a total synthetic approach for the antimitotic disorazole C 1 and the design of a peptide isostere linked to the reactive oxygen scavenger 2,2,6,6-tetramethylpiperidine- N -oxyl (TEMPO) demonstrate established as well as novel strategies for mining the therapeutic potential of natural products.

In many countries today, the number of students selecting chemistry for higher studies is decreasing. At the same time, interest in the environmental aspects of chemistry, green chemistry, and sustainable use of natural products is increasing among the young generation of students. By modernizing and renewing a venerable proven science, pharmacognosy would have a strategic position to connect biology and chemistry. This multidisciplinary subject is important for discovery of novel and unique molecules with drug potential, and for revealing unknown targets, by studying evolutionary structure-activity optimization in nature. In this paper, the overall aim and strategies of our research are presented and exemplified by three different research projects. Natural products are involved in scientific issues important for a sustainable society, and a multidisciplinary subject such as pharmacognosy can, therefore, be useful in increasing future interest in both chemistry and biology.

Pheromonal signals received by the vomeronasal organ (VNO) have been shown to elicit various behavioral and physiological responses that are typically stereotyped and preprogrammed. Recently, we found a novel male-specific peptide, named exocrine gland-secreting peptide 1 (ESP1), that is secreted in tear fluid and stimulates the VNO in mice. Excreted ESP1 appears to be transferred to the female VNO, where it induces c-Fos expression and elicits an electrical response in a small subset of vomeronasal sensory neurons (VSNs). We report here the identification of molecular components expressed in ESP1-stimulated VSNs by double-staining with c-Fos. We found that the c-Fos-induced cells were localized amongst the Gαo-expressing VSNs. Furthermore, the ESP1 signal was received by VSNs expressing a single type of vomeronasal receptor type 2 (V2Rp5). Finally, double in situ hybridization of the V2Rp5 and various members of the M1 and M10 families of major histocompatibility complex (MHC) class Ib molecules revealed that V2Rp5-expressing VSNs can express multiple MHC molecules. These results suggest that a V2R rather than MHC molecule is mainly responsible for the recognition of ESP1. The identification of the putative sex-pheromone ESP1 and its cognate receptor therefore will help clarify the molecular mechanisms underlying pheromone recognition in the mouse vomeronasal system.

Changing the sugar structures and glycosylation patterns of natural products is an effective means of altering the biological activity of clinically useful drugs. Several recent strategies have provided researchers with the opportunity to manipulate sugar structures and to change the sugar moieties attached to these natural products via a biosynthetic approach. In this review, we explore the utility of contemporary in vivo and in vitro methods to achieve natural product glycodiversification. This study will focus on recent progress from our laboratory in elucidating the biosynthesis of D-desosamine, a deoxysugar component of many macrolide antibiotics, and will highlight how we have engineered the D-desosamine biosynthetic pathway in Streptomyces venezuelae through targeted disruption and heterologous expression of the sugar biosynthetic genes to generate a variety of new glycoforms. The in vitro exploitation of the substrate flexibility of the endogenous D-desosamine glycosyltransferase (GT) to generate many non-natural glycoforms will also be discussed. These experiments are compared with recent work from other research groups on the same topics. Finally, the significance of these studies for the future prospects of natural product glycodiversification is discussed.

Molecular systems containing two or more interacting porphyrins show remarkable spectroscopic features that allow for a very sensitive detection of conformational changes on the microscale level by different methods, such as fluorescence and electronic circular dichroism (ECD). Covalent porphyrin-DNA assemblies can provide a CD profile (exciton couplet) within the porphyrin Soret band region which is very diagnostic for DNA conformational changes. Additionally, covalently linked porphyrins have been shown to function as DNA molecular caps and to stabilize the non-self-complementary non-Watson-Crick guanine-adenine DNA sequence via their strong π-π stacking.

The completion of the whole genome sequence of Arabidopsis thaliana has made it possible to explore the phytochemical genomics in this species by determining gene-to-metabolite correlation through the comprehensive analysis of metabolite accumulation and gene expression. In this study, flavonoid profiling of wild-type plants and T-DNA insertion mutants was analyzed using ultra-performance liquid chromatography (UPLC)/photodiode array detection (PDA)/electrospray ionization (ESI)/multiple-stage mass spectrometry (MS n ). Detailed analysis of the metabolite changes in the mutants suggested the functions of genes that have been mutated. In silico coexpression analysis of genes involved in flavonoid metabolism in Arabidopsis was performed using a publicly available transcriptome database of DNA microarrays. We inferred a coexpression framework model of the genes involved in the pathways of flavonol, anthocyanin, and proanthocyanidin synthesis, suggesting specific functions and coregulation of the genes of pathway enzymes and transcription factors. The metabolic profiling of the omt1 mutant lacking a methyltransferase gene narrowed down by the coexpression analysis showed that AtOMT1 (At5g54160) is involved not only in the production of lignins and sinapoyl esters but also in the methylation of flavonols forming isorhamnetin. These results suggest that the functional genomics approach by detailed target-metabolite profiling with transcriptome coexpression analysis provides an efficient way of identifying novel gene functions involved in plant metabolism.