1. Development of methodology to efficiently synthesize biologically active compounds
The coming of the post-genome era has induced the need to develop biologically active compounds that can selectively control chiral target molecules such as proteins. We are involved in the development of catalytic asymmetric reactions in order to efficiently synthesize biologically active asymmetric molecules.
1) Development of catalytic asymmetric reactions
In order to develop catalytic systems that can be applied to various asymmetric reactions, the development of catalytic reactions based on new concepts is significant. Our group has focused on the use of soft transition metals, such as palladium and nickel, towards the development of new catalytic complexes and reactions. These transition metal catalysts induce the formation of chiral enolates from carbonyl compounds in water or alcoholic solvents, enabling various asymmetric reactions under mild conditions. Based on this concept, we succeeded in the development of asymmetric carbon-carbon bond formation reactions, asymmetric fluorination reactions and asymmetric cascade reactions, leading to the generation of various asymmetric molecules.
2) Catalytic asymmetric synthesis of biologically active compounds
Through the development of new asymmetric reactions, biologically active compounds, such as pharmaceutical drug molecules can be efficiently synthesized. We have devised methods to synthesize the following biologically active compounds (e.g. anticoagulant, drug for stroke therapy and glutamine receptor agonist).
3) Development of new trifluoromethylation reactions
Ongoing efforts continue in various areas of research on the utilization of fluorine to improve or modify the functions of organic molecules. However, the direct incorporation of fluorine through fluorination of the organic framework or incorporation of the CF3 moiety by the trifluoromethylation reaction remains to be challenging. Our research group has worked on the development of asymmetric fluorination reactions using palladium or nickel catalysts. We are currently involved in the development of new reactions using an electrophilic trifluoromethylation reagent (Togni’s reagent), which has led to success in the development of trifluoromethylation reactions of indole derivatives and alkenes.
- RIKEN RESEARCH Research Highlights (November 24, 2006)
- RIKEN RESEARCH Research Highlights (September 7, 2007)
- RIKEN RESEARCH Research Highlights (September 19, 2008)
- RIKEN RESEARCH Research Highlights (June 4, 2010)
- RIKEN RESEARCH Research Highlights (September 28, 2012)
- RIKEN RESEARCH Research Highlights (October 5, 2012)
- RIKEN RESEARCH Research Highlights (September 27, 2013)
- RIKEN RESEARCH Research Highlights (June 19, 2015)
- Chem-Station (June 29, 2016)
- RIKEN RESEARCH Research Highlights (August 19, 2016)
2. Synthetic organic chemistry orientated towards biological research – the design, synthesis and biological activity evaluation of new molecules based on natural products and biomolecules
Our research group is focused on the synthesis of molecules that possess unique biological activity, useful for biological and chemical biology research. Although natural products and biomolecules themselves have characteristic biological activity, we are considering the design of molecules that overcome the disadvantages of these precedents along with incorporation of new functionalities. In particular, our interest lies in controlling post-translational protein modifications and elucidating the relationship between biological activity and the structures and/or the conformations of compounds. We are also looking into the behavior of molecules within the cell and their selectivity to the binding of proteins. Our purpose is to apply the developed molecules towards drug discovery and structural biological research.
1) Creation of activity regulating molecules for protein phosphorylation related enzymes
Phosphorylation of proteins is one of the most important post-translational protein modifications substantially related to cell signalling. Although many protein phosphorylation regulating molecules have been developed, activity regulating molecules that can specifically target either the phosphorylation enzymes (> 500 types) or the dephosphorylation enzymes (> 100 types) remain scarce. We are currently involved in the development of activity regulating molecules that target protein kinase C or dual-specific protein phosphotases, which is a protein phosphorylation enzyme or are a family of protein dephosphorylation enzymes, respectively. As target molecules for protein kinase C, we have synthesized IB derivatives based on the physiological ligand diacylglycerol. As inhibitors for dual-specific phosphotases, we have developed RE derivatives based on the natural product RK-682, with improved cell permeability and enzyme selectivity.
2) Creation of ganglioside analogues to elucidate the function and state of lipid microdomains
Gangliosides are glycolipids containing sialic acids, which are related to various biological phenomena occurring in the microdomain on cell membranes. We have focused on the lability of the ganglioside structure and are aiming to contribute to “microdomain” research through the development of metabolically stable analogues. By replacing the labile glycoside (O–sialoside) linkage of sialic acid with a C–sialoside bond, we are directed towards the development of analogues with retention of the characteristics related to the natural occurring form. We have succeeded in synthesizing the CF2-linked ganglioside GM4 analogue, which has led to clarification of some of its biological functions.
3) Natural product synthesis orientated towards structure-activity relationships: synthesis of new libraries
We are currently undergoing total synthesis of unique compounds possessing biological activity, such as the natural product, physalin and spectomycin B1. In particular, we are developing synthetic methods of these molecules that can be used to construct libraries for structure-activity relationship studies. The complex DEFGH ring section for physalin has been synthesized up to now.
4) Chemical biology research based on the natural product chaetocin
4-1) Histone methyltransferase inhibitor
Chaetocin is a natural alkaloid reported to inhibit histone methyltransferase, which is an enzyme that plays an important role in epigenetic regulation. This natural product exhibits a complex structure where the 4-ring skeletal framework containing an epithiadiketopiperazine unit is dimerized through a quaternary carbon centre. Total synthesis of this molecule has been achieved in our laboratory. We have also investigated the structure-activity relationship based on chaetocin, to find that the sulfur functionality plays a significant role in methyltransferase inhibition activity. Our current research focuses on the synthesis of methyltransferase inhibitors with higher activity through further structural elaboration.
4-2) Apoptosis inducer
During the evaluation of chaetocin’s activity in cells, we found that the enantiomer of chaetocin exhibited higher apoptosis-inducing activity than the natural product, by a different activity from histone methyltransferase inhibitory activity. Through investigation of the action mechanism, it was found that apoptosis was induced via a different mechanism from current anti-cancer agents. We are currently carrying out further structural development of chaetocin in order to separate histone methyltransferase inhibitory activity and find application as a new type of anti-cancer agent.
- RIKEN RESEARCH Research Highlights (April 18, 2008)
- RIKEN RESEARCH Research Highlights (July 3, 2009)
- RIKEN RESEARCH Research Highlights (May 7, 2010)
3. Development of new cell death inhibitors and elucidation of the action mechanism
Cells constituting our body maintain homeostasis in living organisms through differentiation and proliferation. Cell death, once considered as a passive phenomenon, is recently being understood as being strictly controlled and to be crucial for the maintenance of life. In particular, apoptosis has attracted attention as being an active cell death (programmed cell death). Its characteristic morphological changes (cell shrinkage, blebbing, condensation/fragmentation of the nucleus) and molecular mechanism has been studied and elucidated in great detail. In contrast, necrosis has been considered as a passive and nonphysiological cell death, induced by physical injury from external causes. Nevertheless, the involvement of necrosis in neurodegenerative diseases (e.g. Alzheimer’s disease) and ischemic heart diseases (e.g. myocardial and cerebral infraction) suggests the existence of an induction mechanism in some types of necrosis. Although the detailed mechanism is still unclear, we anticipated that compounds that inhibit necrosis would be the key to elucidation of the mechanism.
We have succeeded in developing IM-54, a compound that selectively inhibits necrosis triggered by oxidative stress, and does not inhibit apoptosis induced by physiological death ligands or anti-cancer agents. Using IM-54, we are aiming to clarify the molecular mechanism of necrosis.
4. Development of new methodology to identify the binding protein and the binding site of biologically active compounds
Identification of the binding protein and the binding site of biologically active compounds for elucidation of its action mechanism remain to be a challenging topic in chemical biology research. This is because it is necessary to incorporate tag molecules that do not interfere with the activity of the compound. Subsequently, an efficient purification method to release the desired target molecule is also essential. In order to overcome this challenge, we have developed a methodology utilizing an alkyne as a small tag molecule and a cobalt complex immobilized on an affinity resin for direct purification.
5. Development of imaging technology for small molecules using Raman spectroscopy
In order to study the localization of small molecules in cells, incorporation of fluorescent groups and imaging using fluorescent microscopy is a commonly used method. Unfortunately, there are many cases where the activity of the molecule is impaired due to the relatively large size of the incorporated fluorescent group. Hence, we decided to address this disadvantage by developing a new methodology.
Raman microscopy is capable of directly analyzing molecules by observing their Raman scattering, reflecting the vibration frequency of specific functionalities. Small alkyne tags exhibit characteristic and strong Raman scattering that are not originally present in cellular molecules. Accordingly, we decided to use alkynes as tags for imaging by Raman microscopy.
As a molecule possessing an alkyne moiety, we examined the potential of EdU (5-ethynyl-2’-deoxyuridine). EdU is known to be taken up by DNA within the nucleus as it is a mimic of dT (deoxythymidine), which is a constituent of DNA. Observation of the EdU-treated cell under a Raman microscope led to detection of the Raman scattering originating from the alkyne vibration frequency of EdU. We were also able to monitor the progressive incorporation of EdU into the nucleus of the cell. Currently we are aiming to establish of this methodology as a new imaging technique for small molecules.
- JST press release (March 22, 2011)
- RIKEN RESEARCH Research Highlights (May 27, 2011)
- RIKEN NEWS (June, 2011)
- RIKEN RESEARCH Research Highlights (April 12, 2013)
- RIKEN RESEARCH Research Highlights (July 17, 2015)