Frank E. Koehn

The evolving role of natural products in drug discovery

Natural products and their derivatives have historically been invaluable as a source of therapeutic agents. However, in the past decade, research into natural products in the pharmaceutical industry has declined, owing to issues such as the lack of compatibility of traditional natural-product extract libraries with high-throughput screening. However, as discussed in this review, recent technological advances that help to address these issues, coupled with unrealized expectations from current lead-generation strategies, have led to a renewed interest in natural products in drug discovery.

Binding of rapamycin analogs to calcium channels and FKBP52 contributes to their neuroprotective activities

Rapamycin is an immunosuppressive immunophilin ligand reported as having neurotrophic activity. We show that modification of rapamycin at the mammalian target of rapamycin (mTOR) binding region yields immunophilin ligands, WYE-592 and ILS-920, with potent neurotrophic activities in cortical neuronal cultures, efficacy in a rodent model for ischemic stroke, and significantly reduced immunosuppressive activity. Surprisingly, both compounds showed higher binding selectivity for FKBP52 versus FKBP12, in contrast to previously reported immunophilin ligands. Affinity purification revealed two key binding proteins, the immunophilin FKBP52 and the β1-subunit of L-type voltage-dependent Ca2+ channels (CACNB1). Electrophysiological analysis indicated that both compounds can inhibit L-type Ca2+ channels in rat hippocampal neurons and F-11 dorsal root ganglia (DRG)/neuroblastoma cells. We propose that these immunophilin ligands can protect neurons from Ca2+-induced cell death by modulating Ca2+ channels and promote neurite outgrowth via FKBP52 binding.

Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate

The macrocyclic polyketides FK506, FK520, and rapamycin are potent immunosuppressants that prevent T-cell proliferation through initial binding to the immunophilin FKBP12. Analogs of these molecules are of considerable interest as therapeutics in both metastatic and inflammatory disease. For these polyketides the starter unit for chain assembly is (4R,5R)-4,5-dihydroxycyclohex-1-enecarboxylic acid derived from the shikimate pathway. We show here that the first committed step in its formation is hydrolysis of chorismate to form (4R,5R)-4,5-dihydroxycyclohexa-1,5-dienecarboxylic acid. This chorismatase activity is encoded by fkbO in the FK506 and FK520 biosynthetic gene clusters, and by rapK in the rapamycin gene cluster of Streptomyces hygroscopicus. Purified recombinant FkbO (from FK520) efficiently catalyzed the chorismatase reaction in vitro, as judged by HPLC-MS and NMR analysis. Complementation using fkbO from either the FK506 or the FK520 gene cluster of a strain of S. hygroscopicus specifically deleted in rapK (BIOT-4010) restored rapamycin production, as did supplementation with (4R,5R)-4,5-dihydroxycyclohexa-1,5-dienecarboxylic acid. Although BIOT-4010 produced no rapamycin, it did produce low levels of BC325, a rapamycin analog containing a 3-hydroxybenzoate starter unit. This led us to identify the rapK homolog hyg5 as encoding a chorismatase/3-hydroxybenzoate synthase. Similar enzymes in other bacteria include the product of the bra8 gene from the pathway to the terpenoid natural product brasilicardin. Expression of either hyg5 or bra8 in BIOT-4010 led to increased levels of BC325. Also, purified Hyg5 catalyzed the predicted conversion of chorismate into 3-hydroxybenzoate. FkbO, RapK, Hyg5, and Bra8 are thus founder members of a previously unrecognized family of enzymes acting on chorismate.

Discovery and Assembly Line Biosynthesis of the Lymphostin Pyrroloquinoline Alkaloid Family of mTOR Inhibitors in Salinispora Bacteria

The pyrroloquinoline alkaloid family of natural products, which includes the immunosuppressant lymphostin, has long been postulated to arise from tryptophan. We now report the molecular basis of lymphostin biosynthesis in three marine Salinispora species that maintain conserved biosynthetic gene clusters harboring a hybrid nonribosomal peptide synthetase-polyketide synthase that is central to lymphostin assembly. Through a series of experiments involving gene mutations, stable isotope profiling, and natural product discovery, we report the assembly-line biosynthesis of lymphostin and nine new analogues that exhibit potent mTOR inhibitory activity.

Rapid cloning and heterologous expression of the meridamycin biosynthetic gene cluster using a versatile Escherichia coli-streptomyces artificial chromosome vector, pSBAC.

Expression of biosynthetic pathways in heterologous hosts is an emerging approach to expedite production improvement and biosynthetic modification of natural products derived from microbial secondary metabolites. Herein we describe the development of a versatile Escherichia coli-Streptomyces shuttle Bacterial Artificial Chromosomal (BAC) conjugation vector, pSBAC, to facilitate the cloning, genetic manipulation, and heterologous expression of actinomycetes secondary metabolite biosynthetic gene clusters. The utility of pSBAC was demonstrated through the rapid cloning and heterologous expression of one of the largest polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) biosynthetic pathways: the meridamycin biosynthesis gene cluster (mer). The entire mer gene cluster ( approximately 90 kb) was captured in a single pSBAC clone through a straightforward restriction enzyme digestion and cloning approach and transferred into Streptomyces lividans. The production of meridamycin (1) in the heterologous host was achieved after replacement of the original promoter with an ermE* promoter and was enhanced by feeding with a biosynthetic precursor. The success of heterologous expression of such a giant gene cluster demonstrates the versatility of BAC cloning technology and paves the road for future exploration of expression of the meridamycin biosynthetic pathway in various hosts, including strains that have been optimized for polyketide production.

Antiproliferative and immunosuppressive properties of microcolin A, a marine-derived lipopeptide

The immunosuppressive effects of microcolin A, a lipopeptide extracted from the marine blue green alga Lyngbya majuscula were investigated. Microcolin A suppressed concanavalin A (IC50 = 5.8 nM), phytohemagglutinin (IC50 = 12.5 nM) and lipopolysaccharide (IC50 = 8.0 nM) induced proliferation of murine splenocytes. Mixed lymphocyte reaction (IC50 = 5.0 nM), anti-IgM (mu-chain specific) (IC50 = 10.0 nM), and phorbol 12-myristate 13-acetate plus ionomycin (IC50 = 5.8 nM) stimulation of murine splenocytes were all similarly suppressed by microcolin A. The inhibitory activity of microcolin A was time-dependent and reversible and was not associated with a reduction in cell viability. Moreover, microcolin A not only inhibited IL-2 production and IL-2 receptor expression by concanavalin A activated splenocytes, but also suppressed in vitro antibody responsiveness to keyhole limpet hemocyanin. These results indicate that microcolin A is a potent immunosuppressive and antiproliferative agent.

WEINBERSTEROL DISULFATES A AND B, ANTIVIRAL STEROID SULFATES FROM THE SPONGE PETROSIA WEINBERGI

Abstract Weinbersterol disulfates A (1) and B (2), two new sulfated tetrahydroxy steroids with an unprecedented cyclopropane-containing side chain, were isolated from the sponge Petrosia weinbergi. Both compounds are active in vitro against feline leukemia virus, and 1 is also active in vitro against HIV. The structures of these two compounds were assigned mainly on the basis of spectral data.

New Strategies and Methods in the Discovery of Natural Product Anti-Infective Agents : The Mannopeptimycins

Greater than 25% of deaths worldwide are directly related to infectious disease, and much of this mortality is due to infections arising from resistant organisms. Clearly, there is an urgent need to discover and develop new anti-infective agents possessing novel mechanism of action and enhanced activity profile. However, the past 3 decades have seen only two new classes of antibiotics introduced into clinical use, represented by the natural product daptomycin and the oxazolidinone linezolid. During the past 10 years, only nine antibiotic NMEs or new indications for antibiotics have been approved by the FDA, and only a half-dozen key antibacterials are currently in late stage clinical development. Natural products have been the mainstay of antibiotics discovery since the beginning of the field in the 1940s. There are compelling reasons why natural products derived from microorganisms should continue to be a rich source of novel antimicrobial agents, for it can be argued that the methods employed and environments explored so far in the search for anti-infectives and other agents have uncovered only a minor fraction of the potential biological and chemical diversity. Furthermore, advances in biosynthetic engineering of natural products, particularly polyketides and nonribosomal peptides, are at the stage where significant, unique structural transformations can be achieved on these very complex structures. Why then are there so few new anti-infectives? The answer lies partly in the aggressive timelines now imposed upon natural products discovery programs and in an unfavorable commercial and regulatory atmosphere. This Miniperspective provides a viewpoint that is focused on the chemical challenges surrounding today’s natural products-based antibiotic discovery programs and presents chemical and biological strategies to meet those challenges. The discovery of the mannopeptimycins, a promising new class of potent anti-infective agents, is provided as an example of one of these strategies.

Halitunal, an unusual diterpene aldehyde from the marine alga Halimeda tuna

Abstract Halituna( 1 ), a novel diterpene aldehyde possessing a unique cyclopentadieno[c]pyran ring system, has been isolated from the marine alga Halimeda tuna. The structure of 1 was elucidated by spectroscopic techniques. Halitunal shows antiviral activity against murine coronavirus A59 in-vitro.

Cytotoxic Spliceostatins from Burkholderia sp. and Their Semisynthetic Analogues

The spliceostatin class of natural products was reported to be potent cytotoxic agents via inhibition of the spliceosome, a key protein complex in the biosynthesis of mature mRNA. As part of an effort to discover novel leads for cancer chemotherapy, we re-examined this class of compounds from several angles, including fermentation of the producing strains, isolation and structure determination of new analogues, and semisynthetic modification. Accordingly, a group of spliceostatins were isolated from a culture broth of Burkholderia sp. FERM BP-3421, and their structures identified by analysis of spectroscopic data. Semisynthesis was performed on the major components 4 and 5 to generate ester and amide derivatives with improved in vitro potency. With their potent activity against tumor cells and unique mode of action, spliceostatins can be considered potential leads for development of cancer drugs.