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The research on antibiotics requires the integration of broad areas, such as microbiology, organic chemistry, biochemistry and pharmacology. It is similar to the field of chemical biology

that is recently popular as an approach for drug discovery. When we isolate a new compound from a microorganism, we can pursue the interesting research on chemistry and biology. In this

review, I would like to introduce our achievements in relation to reveromycin A.

Currently, antibiotics are widely used in medicine and agriculture as antimicrobial compounds. Selman A Waksman (1888–1973)1 originally defined an antibiotic as a substance produced by one

microorganism that interferes with the growth or function of other microorganisms. Since the mid-1950s, several antitumor compounds and molecules with other bioactivities have been isolated

from microorganisms, broadening the definition of antibiotics to include antitumor compounds, enzyme inhibitors and other compounds. Despite this broadening of the recognized biological

activities of microbial metabolites, the term ‘antibiotic’ should be used to refer to an antimicrobial substance to eliminate confusion. From a different perspective, ‘antibiotics’ can be

understood as the name of an academic field in the same sense that economics, physics, and mathematics are academic fields. Thus, we recognize ‘antibiotics’ as an academic area that

integrates broader areas, such as microbiology, organic chemistry, biochemistry, and pharmacology. Recently, the field of chemical biology, which integrates chemistry and biology, has

provided a productive approach to drug discovery. The concept of ‘antibiotics’ is similar to the concept of ‘chemical biology.’

In this review, I would like to introduce our achievements in relation to reveromycin A that was isolated from a soil microbial strain. The starting point of our research is always the

isolation of new compounds. Once such a compound is identified, we can pursue unique lines of research, including studies of its mode of action and biosynthesis. Our chemical biology

research thus originates in antibiotics research.

I would first like to describe RIKEN, the abbreviation for the Japanese name for the Institute of Physical and Chemical Research. RIKEN was modeled on the Kaiser Wilhelm Society and was

formally founded in 1917. In 2003, Nobel laureate Dr Ryoji Noyori assumed the presidency of RIKEN. In 2015, RIKEN became one of the national research and development institutions and Dr

Hiroshi Matsumoto succeeded Dr Noyori as the president. RIKEN is the largest comprehensive research institution in Japan, with a diverse range of scientific disciplines.

When we trace the history of chemical biology in RIKEN, we recall two pioneers of ‘Nogei Kagaku’, a discipline that is similar to agricultural chemistry and that aims to explain unsolved

biological phenomena by understanding chemical compounds.2, 3 Umetaro Suzuki (1874–1943) aimed to cure beriberi and he isolated oryzanin from rice bran; this compound is now known as

thiamine (vitamin B1). This was the first vitamin to be identified and its discovery initiated the field of vitaminology. Teijiro Yabuta (1888–1977) revealed the cause of bakanae (or

‘foolish seedling’) disease in rice plants. Bakanae disease is caused by a fungal infection by Gibberella fujikuroi. Yabuta isolated gibberellin from the fungus, a molecule that was

subsequently detected ubiquitously in plants and was ultimately recognized as a plant hormone. Our chemical biology research at RIKEN has developed from the foundations established by these

scientists. Kin-ichiro Sakaguchi (1897–1994) was an applied microbiologist who proposed the establishment of a culture collection to provide a central microorganism stock for Japan. This

collection has ensured that important microorganisms are safely stored and can be readily accessed by researchers who want to use them for their investigations or inventions. Storage and

distribution of these microorganisms support the work of both basic and industrial research. This pioneering work encouraged me to establish the chemical bank, a natural product depository

(NPDepo) at RIKEN. Saburo Suzuki and Kiyoshi Isono were former directors of the RIKEN Antibiotics Laboratory that I currently direct. In the 1960s, they discovered polyoxin, an antifungal

compound that was marketed worldwide.4 Moreover, the studies that resulted in the discovery of polyoxin initiated various lines of basic research, such as mode of action and total synthesis

studies.5, 6

When I became the director of the Antibiotics Laboratory at RIKEN, I focused on microbial metabolites that were active against cancer cells. We isolated novel compounds from microorganisms,

and tested these using chemical and biological approaches.7

We have been investigating and controlling protein activities using small molecules. In molecular biology, gene mutation, gene knockout and RNA interference are the major strategies used to

analyze protein function.8 Although these methods are reliable and specific to the gene of interest, they can take a long time to produce results. Chemical biology or chemical genetic

approaches use small molecules that alter protein function rapidly and conditionally, just by their addition or removal. We named these ‘bioprobes’ and they provide useful tools to

investigate the biological functions of proteins.8, 9 Some of these compounds are commercially available (Figure 1).

During an antitumor compound screening study, reveromycin A was isolated from a soil bacteria, Streptomyces reveromyceticus SN-593, and found to inhibit mitogenic activity induced by

epidermal growth factor.10 We subsequently examined the antitumor activity of reveromycin A in vivo and revealed its mode of action.11, 12, 13, 14

Reveromycin A showed potent in vivo antitumor activity against hormone-dependent tumors, such as ovarian cancer and prostate cancer, but was not as active against other types of tumors.14

However, even in mice where reveromycin A did not cure the tumors, it did protect from terminal-stage cachexia and hypercalcemia. This observation indicated that reveromycin A might be

involved in calcium homeostasis. Bone provides a calcium reservoir and its remodeling is regulated by osteoblasts and osteoclasts. We evaluated the effects of reveromycin A on osteoclasts

and osteoblasts. As shown in Table 1, reveromycin A was not strongly cytotoxic to tumor cells, but it did have potent and selective effects on osteoclasts. When reveromycin A was added to a

coculture of osteoclasts and osteoblasts, the osteoclasts were killed and the osteoblasts survived. The data clearly demonstrated this selective toxicity of reveromycin A toward osteoclasts

(Figure 2).15

The effect of reveromycin A on osteoblast and osteoclast cocultures prepared from rodent bone marrow. Osteoclasts and osteoblasts were cocultured in the absence (upper panel) or presence

(lower panel) of reveromycin A.

Next, we wanted to know why reveromycin A selectively killed osteoclasts. We assumed that reveromycin A did not penetrate the cell membrane because of the acidity derived from three

carboxylic acid residues (Figure 3). In general, acidic compounds show poor membrane permeability under normal conditions because the plasma membrane consists of negatively charged

phospholipids. However, mature osteoclasts form an acidic environment to resorb bones. Under these acidic conditions, the protonation of carboxylic acid in reveromycin A is suppressed and

reveromycin A can enter osteoclasts.

The mode of action of reveromycin A that is selectively incorporated into osteoclasts.

To test this hypothesis, we synthesized [3H]-labeled reveromycin A and demonstrated its selective incorporation into osteoclasts. As shown in Figure 4, reveromycin A was incorporated into

the mature osteoclasts in their acidic environment, but not into the macrophages; these are the osteoclast precursor cells and they do not produce acid. Reveromycin A also failed to enter

other cell lines. These observations suggested that the selective toxicity of reveromycin A related to its membrane permeability. The low membrane permeability of osteoblasts and osteoclast

precursor cells rendered them resistant to reveromycin A, but the acidic environment formed by mature osteoclasts made them highly sensitive to reveromycin A.

Incorporation of [3H]reveromycin A into cells. BG-1, human ovarian carcinoma cells; Colon26, mouse rectal carcinoma cells; HeLa, human cervical carcinoma cells; Mφ, mouse macrophages;

MC3T3-E1, mouse osteoblastic cells; MDCK, canine kidney epithelial cells; OCs, mouse osteoclasts; RAW264, mouse macrophages; UAMS, mouse osteoblastic cells.

To reveal the molecular target of reveromycin A, we collaborated with Dr Miyakawa’s group in Hiroshima University.16, 17 The target was identified as isoleucyl-transfer RNA (tRNA) synthetase

using a genetic approach in Saccharomyces cerevisiae.17 One amino acid substitution, from asparagine to aspartic acid at position 660 in the yeast isoleucyl-tRNA synthetase gene (ILS1p),

produced a reveromycin-resistant enzyme (Figure 5). Later, we carried out biochemical analyses that revealed that isoleucyl-tRNA synthetase is also the target of reveromycin A in

osteoclasts. Isoleucyl-tRNA synthetase is an essential enzyme for protein synthesis in prokaryotes and eukaryotes. Analyses of one point mutation in this enzyme indicated that the

reveromycin A-binding site was located at the editing domain of isoleucyl-tRNA synthetase. The amino acid sequence of this domain is conserved in eukaryotic organisms, but differs in

prokaryotes. Therefore, reveromycin A inhibited the enzyme activity of eukaryotic isoleucyl-tRNA synthetase, but not of bacterial isoleucyl-tRNA synthetase. Moreover, the survival of

osteoclasts is more dependent on isoleucine and glutamine than on proline and alanine. When isoleucine or glutamine is removed from the cell culture medium, osteoclasts rapidly enter

apoptosis.

Amino acid sequences of human, yeast and bacterial isoleucyl-transfer RNA (tRNA) synthetase. The yeast enzyme may be resistant to reveromycin A because of the lack of a potential binding

sequence of amino acids.

Taken together, we could propose two mechanisms underlying the specific effects of reveromycin A on mature osteoclasts. The first relates to the membrane permeability of reveromycin A that

does not enter normal cells but can penetrate osteoclasts because of their acidic environment. The second relates to the greater dependency of osteoclasts on isoleucine for survival, as

compared with other cell types.

Osteoporosis is caused by augmented osteoclast activity. Metastatic bone disease is also mediated by osteoclast function.18 Therefore, osteoclasts are the ideal therapeutic target to treat

both osteoporosis and bone metastasis.

We first examined the antiosteoporotic activity of reveromycin A using an ovary-removed mouse model. The removal of the ovaries from female mice causes similar symptoms as those seen in

postmenopausal human osteoporosis. Figure 6 shows the bone density of the trabecular bone area15 that was markedly reduced in the ovary-removed mice. However, this bone density loss was

suppressed in mice treated with reveromycin A. Similar protective effects were observed in mice receiving a low-calcium diet.15, 19

Reveromycin A prevented osteoporosis in ovariectomized mice. The mouse trabecular bones are shown in the upper panel (soft X-ray). (a) Bone prepared from a mouse without intact ovaries. (b)

Bone prepared from an ovariectomized mouse. (c) Bone from an ovariectomized mouse treated with reveromycin A. Reveromycin A was injected intravenously at the indicated dose twice daily.

Quantification of trabecular density by peripheral quantitative computed tomography (pQCT) is shown in the lower panel. *P