Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.

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The re-emergence of natural products for drug discovery in the genomics era

https://www.cell.com/cell/pdf/S0092-8674(13)00288-2.pdf

Lessons from the cancer genome.

Nine genes that are mutated at significant frequencies were identified, including four with established roles in chronic lymphocytic leukemia ( TP53 in 15% of patients, ATM in 9%, MYD88 in 10%, and NOTCH1 in 4%) and five with unestablished roles (SF3B1, ZMYM3, MAPK1, FBXW7, and DDX3X). SF3B1, which functions at the catalytic core of the spliceosome, was the second most frequently mutated gene (with muta tions occurring in 15% of patients). SF3B1 mutations occurred primarily in tumors with deletions in chromosome 11q, which are associated with a poor prognosis in patients with chronic lymphocytic leukemia. We further discovered that tumor sam ples with mutations in SF3B1 had alterations in pre–messenger RNA (mRNA) splicing. Conclusions Our study defines the landscape of somatic mutations in chronic lymphocytic leuke mia and highlights pre-mRNA splicing as a critical cellular process contributing to chronic lymphocytic leukemia.

/pdf/sf3b1-and-other-novel-cancer-genes-in-chronic-lymphocytic-3aqjd7cvrz.pdf

SF3B1 and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia

Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leukemia (CLL), the most frequent leukemia in adults in Western countries. We found 1,246 somatic mutations potentially affecting gene function and identified 78 genes with predicted functional alterations in more than one tumor sample. Among these genes, SF3B1, encoding a subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP), is somatically mutated in 9.7% of affected individuals. Further analysis in 279 individuals with CLL showed that SF3B1 mutations were associated with faster disease progression and poor overall survival. This work provides the first comprehensive catalog of somatic mutations in CLL with relevant clinical correlates and defines a large set of new genes that may drive the development of this common form of leukemia. The results reinforce the idea that targeting several well-known genetic pathways, including mRNA splicing, could be useful in the treatment of CLL and other malignancies.

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.

Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA-protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA-RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions.

/pdf/mechanisms-and-regulation-of-alternative-pre-mrna-splicing-30gwnxjpdd.pdf

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

The removal of intervening sequences from transcripts is catalyzed by the spliceosome, a multicomponent complex that assembles on the newly synthesized pre-mRNA. Pre-mRNA translation in the cytoplasm leads to the generation of aberrant proteins that are potentially harmful. Therefore, tight control to prevent undesired pre-mRNA export from the nucleus and its subsequent translation is an essential requirement for reliable gene expression. Here, we show that the natural product FR901464 (1) and its methylated derivative, spliceostatin A (2), inhibit in vitro splicing and promote pre-mRNA accumulation by binding to SF3b, a subcomplex of the U2 small nuclear ribonucleoprotein in the spliceosome. Importantly, treatment of cells with these compounds resulted in leakage of pre-mRNA to the cytoplasm, where it was translated. Knockdown of SF3b by small interfering RNA induced phenotypes similar to those seen with spliceostatin A treatment. Thus, the inhibition of pre-mRNA splicing during early steps involving SF3b allows unspliced mRNA leakage and translation.

Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA.

Six GEX1 compounds, GEX1A/herboxidiene and its related 5 novel compounds, were isolated from a culture broth of Streptomyces sp. GEX1 compounds induced both G1 and G2/M arrest in a human normal fibroblast cell line, WI-38. All six compounds up-regulated luciferase reporter gene expression directed by enhancer/promoter of various genes, such as cdc2, IL-2 and SV40 early genes. All GEX1 compounds showed cytotoxic activities in the same order of the up-regulating activities on gene expression, suggesting that these two activities are related. Despite the up-regulating activities on the reporter gene expression, GEX1A/herboxidiene did not enhance the expression of any endogenous genes involved in the cell cycle, proliferation and apoptosis. Although the unique effects of GEX1 compounds on cell cycle and the reporter gene expression were similar to those of trichostatin A (TSA), an inhibitor of histone deacetylase (HDAC), GEX1A/herboxidiene did not affect histone acetylation in cells. In addition, GEX1A/herboxidiene treatment gave rise to the shorter sized transcripts of the cdc25A and cdc2 genes as well as the normal sized ones. These results suggest that GEX1 compounds modulate gene expression by an unknown mechanism.

https://www.jstage.jst.go.jp/article/antibiotics1968/55/10/55_10_863/_pdf

GEX1 compounds, novel antitumor antibiotics related to herboxidiene, produced by Streptomyces sp. II. The effects on cell cycle progression and gene expression.

The structure-activity relationship for FR901464, a potent cell-cycle inhibitor, was examined by synthesizing its analogs. A versatile method for converting FR901464 was devised. This method made it possible to synthesize biologically active FR901464-biotin conjugates which could be used to isolate the binding proteins.

https://www.tandfonline.com/doi/pdf/10.1271/bbb.68.2178

Structure-activity Relationship for FR901464: A Versatile Method for the Conversion and Preparation of Biologically Active Biotinylated Probes

GEX1 Compounds, Novel Antitumor Antibiotics Related to Herboxidiene, Produced by Streptomyces sp. Part 2. The Effects on Cell Cycle Progression and Gene Expression.

Tatsuhiko Yoshida

Papers

Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA.

GEX1 compounds, novel antitumor antibiotics related to herboxidiene, produced by Streptomyces sp. II. The effects on cell cycle progression and gene expression.

Structure-activity Relationship for FR901464: A Versatile Method for the Conversion and Preparation of Biologically Active Biotinylated Probes

GEX1 Compounds, Novel Antitumor Antibiotics Related to Herboxidiene, Produced by Streptomyces sp. Part 2. The Effects on Cell Cycle Progression and Gene Expression.