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System Approach Using Metabolite Structural Similarity Toward TOM Suggested
A Korean research team at KAIST suggests that a system approach using metabolite structural similarity helps to elucidate the mechanisms of action of traditional oriental medicine.
Traditional oriental medicine (TOM) has been practiced in Asian countries for centuries, and is gaining increasing popularity around the world. Despite its efficacy in various symptoms, TOM has been practiced without precise knowledge of its mechanisms of action. Use of TOM largely comes from empirical knowledge practiced over a long period of time. The fact that some of the compounds found in TOM have led to successful modern drugs such as artemisinin for malaria and taxol (Paclitaxel) for cancer has spurred modernization of TOM.
A research team led by Sang-Yup Lee at KAIST has focused on structural similarities between compounds in TOM and human metabolites to help explain TOM’s mechanisms of action. This systems approach using structural similarities assumes that compounds which are structurally similar to metabolites could affect relevant metabolic pathways and reactions by biosynthesizing structurally similar metabolites.
Structural similarity analysis has helped to identify mechanisms of action of TOM. This is described in a recent study entitled “A systems approach to traditional oriental medicine,” published online in Nature Biotechnology on March 6, 2015. In this study, the research team conducted structural comparisons of all the structurally known compounds in TOM and human metabolites on a large-scale. As a control, structures of all available approved drugs were also compared against human metabolites. This structural analysis provides two important results. First, the identification of metabolites structurally similar to TOM compounds helped to narrow down the candidate target pathways and reactions for the effects from TOM compounds. Second, it suggested that a greater fraction of all the structurally known TOM compounds appeared to be more similar to human metabolites than the approved drugs. This second finding indicates that TOM has a great potential to interact with diverse metabolic pathways with strong efficacy. This finding, in fact, shows that TOM compounds might be advantageous for the multitargeting required to cure complex diseases. “Once we have narrowed down candidate target pathways and reactions using this structural similarity approach, additional in silico tools will be necessary to characterize the mechanisms of action of many TOM compounds at a molecular level,” said Hyun Uk Kim, a research professor at KAIST.
TOM’s multicomponent, multitarget approach wherein multiple components show synergistic effects to treat symptoms is highly distinctive. The researchers investigated previously observed effects recorded since 2000 of a set of TOM compounds with known mechanisms of action. TOM compounds’ synergistic combinations largely consist of a major compound providing the intended efficacy to the target site and supporting compounds which maximize the efficacy of the major compound. In fact, such combination designs appear to mirror the Kun-Shin-Choa-Sa design principle of TOM.
That principle, Kun-Shin-Choa-Sa (君臣佐使 or Jun-Chen-Zuo-Shi in Chinese) literally means “king-minister-assistant-ambassador.” In ancient East Asian medicine, treating human diseases and taking good care of the human body are analogous to the politics of governing a nation. Just as good governance requires that a king be supported by ministers, assistants and/or ambassadors, treating diseases or good care of the body required the combined use of herbal medicines designed based on the concept of Kun-Shin-Choa-Sa. Here, the Kun (king or the major component) indicates the major medicine (or herb) conveying the major drug efficacy, and is supported by three different types of medicines: the Shin (minister or the complementary component) for enhancing and/or complementing the efficacy of the Kun, Choa (assistant or the neutralizing component) for reducing any side effects caused by the Kun and reducing the minor symptoms accompanying major symptom, and Sa (ambassador or the delivery/retaining component) which facilitated the delivery of the Kun to the target site, and retaining the Kun for prolonged availability in the cells.
The synergistic combinations of TOM compounds reported in the literature showed four different types of synergisms: complementary action (similar to Kun-Shin), neutralizing action (similar to Kun-Choa), facilitating action or pharmacokinetic potentiation (both similar to Kun-Choa or Kun-Sa). Additional structural analyses for these compounds with synergism show that they appeared to affect metabolism of amino acids, co-factors and vitamins as major targets.
Professor Sang Yup Lee remarks, “This study lays a foundation for the integration of traditional oriental medicine with modern drug discovery and development. The systems approach taken in this analysis will be used to elucidate mechanisms of action of unknown TOM compounds which will then be subjected to rigorous validation through clinical and in silico experiments.”
Sources: Kim, H.U. et al. “A systems approach to traditional oriental medicine.” Nature Biotechnology. 33: 264-268 (2015).
This work was supported by the Bio-Synergy Research Project (2012M3A9C4048759) of the Ministry of Science, ICT and Future Planning through the National Research Foundation. This work was also supported by the Novo Nordisk Foundation.
The picture below presents the structural similarity analysis of comparing compounds in traditional oriental medicine and those in all available approved drugs against the structures of human metabolites.
2015.03.09 View 9469 -
Interactions Features KAIST's Human-Computer Interaction Lab
Interactions, a bi-monthly magazine published by the Association for Computing Machinery (ACM), the largest educational and scientific computing society in the world, featured an article introducing Human-Computer Interaction (HCI) Lab at KAIST in the March/April 2015 issue (http://interactions.acm.org/archive/toc/march-april-2015).
Established in 2002, the HCI Lab (http://hcil.kaist.ac.kr/) is run by Professor Geehyuk Lee of the Computer Science Department at KAIST. The lab conducts various research projects to improve the design and operation of physical user interfaces and develops new interaction techniques for new types of computers. For the article, see the link below:
ACM Interactions, March and April 2015
Day in the Lab: Human-Computer Interaction Lab @ KAIST
http://interactions.acm.org/archive/view/march-april-2015/human-computer-interaction-lab-kaist
2015.03.02 View 8989 -
Professor Sang Yup Lee Appointed Founding Board Member of Cell Systems
Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering at KAIST has been appointed a member of the founding editorial board of the newly established journal Cell Systems.
Cell Systems will be a sister journal of Cell, one of the three most prestigious scientific journals along with Nature and Science, that publishes a wide range of papers on biological engineering. The first issue of Cell Systems will be published this July.
Cell Systems plans to publish innovative discoveries, reviews of various research instruments, and research findings on integrated and quantified systems in the field of biology.
Professor Lee is a pioneer in metabolic engineering of microorganism with a focus on biopolymers and metabolites production. He is the editor-in-chief of Biotechnology Journal and serves on the editorial board of numerous international journals. He is also a member of the Global Agenda Council of the World Economic Forum and the Presidential Advisory Committee on Science and Technology in Korea.
Professor Lee said, “Cell Systems will present research findings that discuss whole biological systems methodically.” He continued, “I hope many research findings of Korean scholars will be published in Cell Systems, which will become a representative journal of systems biology and systems biological engineering.”
2015.02.13 View 8565 -
KAIST's Thermoelectric Generator on Glass Fabric Receives the Grand Prize at the Netexplo Forum 2015
The forum announced top ten IT innovations expected to change the world and selected the grand prize on February 4, 2014.
Established in 2007 by Martine Bidegain and Thierry Happe in partnership with the French Senate and the French Ministry for the Digital Economy, the Netexplo Observatory is an independent global organization that studies the impact of digital technology and innovation on society and business.
Every year, the Netexplo Observatory hosts an international conference, the Netexplo Forum, in Paris, France, which surveys digital innovation worldwide. The 8th forum was held in partnership with the United Nations Educational, Scientific and Cultural Organization (UNESCO) on February 4-5, 2015, at the UNESCO House in Paris.
Prior to the conference, the Netexplo Forum 2015 named the top ten most promising digital technologies that will greatly impact the world.
Among them was Professor Byung Jin Cho’s research on a wearable thermoelectric generator (http://www.eurekalert.org/pub_releases/2014-04/tkai-tgo041014.php). The generator was selected as the most innovative technology this year.
Professor Cho of KAIST’s Electrical Engineering Department developed a glass fabric-based thermoelectric generator that is extremely light and flexible and that produces electricity from the heat of the human body. This technology can be applied widely to wearable computers and mobile devices.
The full list of innovations follows below:
Wearable Thermo-Element, South Korea: The human body becomes a source of energy for mobile devices.
W.Afate 3D-printer, Togo: An environmentally friendly fablab that makes a low-cost 3D-printer from recycling electronic components.
Slack, USA: By combining email, Skype, and file-sharing and social networks, internal communication becomes much easier and simpler.
PhotoMath, Croatia: A free app that enables smartphone users to solve mathematical problems simply by scanning the mathematical texts.
Kappo, Chile: Connected cyclists produce and transmit useful data for urban planning to make the city more bike-friendly.
Branching Minds, USA: An improved learning process for students in difficulty through a personalized approach.
Baidu Kuai Sou, China: Smart chopsticks that can check food hazards.
SCio, Israel: A pocket molecular sensor with various applications and data
Rainforest Connection, USA: Fighting deforestation with recycled smartphones
Sense Ebola Followup, Nigeria: A mobile tool to help contain Ebola
For more details on the wearable thermos-element which received the 2015 Netexplo Award, please go to https://www.netexplo.org/en/intelligence/innovation/wearable-thermo-element.
Pictures 1 and 2: A high-performance wearable thermoelectric generator that is extremely flexible and light.
Picture 3: Senator Catherine Morin-Desailly (left) of the French Parliament presents the 2015 Netexplo Award to Professor Byung Jin Cho (right) on February 4, 2015 at the UNESCO House in Paris.
Credit of Loran Dhérines
Picture 4: Professor Byung Jin Cho (left) poses with Dr. Joël de Rosnay (right).
Credit of Loran Dhérines
2015.02.06 View 12855 -
"Software Welcomes Girls" Camp at KAIST
KAIST’s Department of Computer Science organized a software (SW) training camp from January 25-29, 2015 in the Creative Learning Building on campus to promote talented women for the field of information technology (IT).
Hosted by the National Information Society Agency in Korea and the Korea Foundation for the Advancement of Science and Creativity, the training camp was comprised of a junior program to educate primary and secondary school students along with teachers and parents, while university students, software developers, and female professionals who had interrupted their careers participated in a senior camp.
In the junior camp, participants learned how to employ Scratch and App Inventor as well as microprocessors by using Arduino and Raspberry Pi. During the camp, students including those from multicultural families attended lectures from professors and software designers and received a career consulting session from them. The conference organizers will provide long-term mentoring for the primary and secondary school students by graduate student participants and other volunteer experts.
The senior camp consisted of a program entitled “More Women, Better SW!” and a special lecture on “Women in SOS (Software Optimization Services)” took place at Google Korea. University students, teachers, and SW developers had an opportunity to design applications intended to improve daily living. At the “Women in SOS” program, Professor Alice Oh of KAIST and other industry experts gave talks about successful women IT personnel and digital literacy.
One of the organizers, Professor Yoon-Joon Lee from the Computer Science Department said, “Software-centered societies in the future will demand delicate intuition and cooperative leadership, which are characteristics of women.” He added that “I hope more women become interested in this field through this event.”
2015.02.02 View 7079 -
Danish Minister for Higher Education and Science Visits KAIST
Sofie Carsten Nielsen, the Minister for Higher Education and Science of Denmark, accompanied by her delegation, visited KAIST on January 21, 2015 to study outstanding cases of creative economy and to discuss methods of cooperation.
Her delegation included other distinguished members including Thomas Lehmann, the Danish ambassador to Korea, Peter Olesen, Chairman of Innovation Foundation Denmark Governing Board, and Martin Bendsøe, Senior Vice President and Dean of Technical University of Denmark.
After attending the "Electronic Communication Double Degree Agreement" signing ceremony between KAIST’s Department of Electrical Engineering and the Technical University of Denmark, Minister Nielsen visited KAIST’s Institute of Entrepreneurship to observe bilateral industry-university collaborations between KAIST and Denmark and discussed future development plans.
Also, the Grundfos Student Innovation Camp, sponsored by Grundfos, the world's largest pump manufacturer based in Denmark, took place at KAIST from October 26-31, 2014 where Grundfos professionals as well as students from Seoul National University, KAIST, and Technical University of Denmark (DTU) exchanged ideas and opinions on energy efficiency.
KAIST is currently conducting 19 collaborative projects including seven joint researches and seven joint degrees with DTU.
Minister Sofie Carsten Nielsen stands fifth from the left in the front row in the first picture below.
2015.01.27 View 8488 -
Light Driven Drug-Enzyme Reaction Catalytic Platform Developed
Low Cost Dye Used, Hope for Future Development of High Value Medicinal Products to Treat Cardiovascular Disease and Gastric Ulcers
A KAIST research team from the Departments of Materials Science and Engineering and of Chemical and Biomolecular Engineering, led respectively by Professors Chan Beum Park and Ki Jun Jeong, has developed a new reaction platform to induce drug-enzyme reaction using light.
The research results were published in the journal Angewandte Chemie, International Edition, as the back cover on 12 January 2015.
Applications of this technology may enable production of high value products such as medicine for cardiovascular disease and gastric ulcers, for example Omeprazole, using an inexpensive dye.
Cytochrome P450 is an enzyme involved in oxidative response which has an important role in drug and hormone metabolism in organisms. It is known to be responsible for metabolism of 75% of drugs in humans and is considered a fundamental factor in new drug development.
To activate cytochrome P450, the enzyme must receive an electron by reducing the enzyme. In addition, NADPH (a coenzyme) needs to be present. However, since NADPH is expensive, the use of cytochrome P450 was limited to the laboratory and has not yet been commercialized.
The research team used photosensitizer eosin Y instead of NADPH to develop “Whole Cell Photo-Biocatalysis” in bacteria E. coli. By exposing inexpensive eosin Y to light, cytochrome P450 reaction was catalyzed to produce the expensive metabolic material.
Professor Park said, “This research enabled industrial application of cytochrome P450 enzyme, which was previous limited.” He continued, “This technology will help greatly in producing high value medical products using cytochrome P450 enzyme.”
The research was funded by the National Research Foundation of Korea and KAIST's High Risk High Return Project (HRHRP).
Figure 1: Mimetic Diagram of Electron Transfer from Light to Cytochrome P450 Enzyme via Eosin Y, EY
Figure 2: The back cover of Angewandte Chemie published on 12 January 2015, showing the research results
2015.01.26 View 9581 -
President Kang to Present at the World Economic Forum
President Sung-Mo Kang of KAIST will attend the World Economic Forum (WEF) as a member of the Global University Leaders Forum (GULF) to represent KAIST. GULF is attended by the world leaders of education and research. Its members represent 26 universities drawn from around the world including Harvard University. KAIST is the only Korean university to be invited.
WEF will be held in Davos, Switzerland, for four days, starting on 21 January 2015. He will discuss the future of higher education, the issues and solutions of science and society at GULF.
By attending GULF, KAIST expects to strengthen its network with top universities around the world and raise KAIST’s profile on an international basis. President Kang said, “The invitation for KAIST to attend the GULF is an evidence of its raised global status.” He continued, “I will show the innovative and challenging achievements KAIST has made to the leaders of the world.”
The theme of the 2015 World Economic Forum Annual Meeting 2015 is “The New Global Context” to discuss the integration of economic growth and society, employment and work force, environment and resource scarcity, the future of the Internet, and international crime and anti-corruption.
The World Economic Forum was established in 1971 by Klaus Schwab who is also its Executive Chairman. More than 2,500 people including German Chancellor Angela Merkel, French President François Hollande, Chinese Premier Li Keqiang, Google President Eric Schmidt, and Microsoft CEO Satya Nadella will attend this year's forum.
2015.01.22 View 8064 -
KAIST Announces the Recipients of Distinguished Alumni Awards
The KAIST Alumni Association (KAA) announced four “Proud KAIST Alumni” awards recipients for the year 2014: Sung-Wook Park, the Chief Executive Officer and President of SK Hynix; Seung Ho Shin, the President of Kangwon National University; Kew-Ho Lee, the President of the Korea Research Institute of Chemical Technology; and Mun-Kee Choi, the former Minister of Science, ICT and Future Planning of the Republic of Korea. The award ceremony took place during the 2015 KAA’s New Year's ceremony on January 17, 2015 at the Palace Hotel in Seoul.
Sung-Wook Park (M.S. ’82 and Ph.D. ’88, Department of Materials Science and Engineering), the Chief Executive Officer and President of SK Hynix, has worked as an expert in the field of memory semi-conductors for the past 30 years. He developed innovative technology and improved production efficiency, enabling the Korean semi-conductor industry to become a global leader.
Seung Ho Shin (M.S. ’79 and Ph.D. ’87, Department of Physics), the President of Kangwon National University (KNU), worked in the field of optical information processing, producing excellent research achievements and teaching the next generation of scientists. As the president of KNU, he has set an exemplary leadership in higher education.
Kew-Ho Lee (M.S. ’75, Department of Chemistry), the President of the Korea Research Institute of Chemical Technology, pioneered the field of separation film production which contributed greatly to Korean technological developments. He led several domestic and international societies to facilitate dynamic exchanges between industry and academia and with the international community.
Mun-Kee Choi (M.S. ’76, Department of Industrial and Systems Engineering), the former Minister of Science, ICT and Future Planning, the Republic of Korea, is a great contributor to the information and communications technology in Korea, working as a leader in the field of broadband integrated service digital network. He is also an educator for gifted students in science and technology, and a manager of the Electronics and Telecommunications Research Institute.
The Alumni Association established the “Proud KAIST Alumni Awards” in 1992 to recognize its alumni’s outstanding contributions to Korea and KAIST.
Pictured from left to right, Sung-Wook Park (the Chief Executive Officer and President of SK Hynix), Seung Ho Shin (the President of Kangwon National University), Kew-Ho Lee (the President of the Korea Research Institute of Chemical Technology), and Mun-Kee Choi (the former Minister of Science, ICT and Future Planning)
2015.01.19 View 12717 -
Professor Eunjoon Kim Is KAIST's Person of the Year 2014
KAIST announced that it has named Chair Professor Eunjoon Kim of the Department of Biological Sciences as its “Person of the Year 2014.” The award ceremony took place at the auditorium on campus on January 5, 2014.
Established in 2001, the award has been presented to a KAIST faculty member who has made great achievements in research and education, thereby contributing to the advancement of KAIST.
Professor Kim was the first to identify the mechanism of synapse formation between neurons during his post-doctoral program at Harvard Medical School in 1995. The research was published in Nature.
In 2011, Professor Kim discovered that the lack of protein GIT1, a neuronal synapse in the brain, caused ADHD (Attention Deficit Hyperactivity Disorder). He is widely recognized for his work concerning synapse proteins and brain disease related research that set the foundation for future medical developments.
In his award speech, Professor Kim said, “Whenever a research finding concerning a new drug therapy or research is published, I receive many inquiries from the parents of children with ADHD or autism. As a scientist, I would like to focus my research ultimately to help those in pain, rather than just pursuing research excellence or reputation.”
2015.01.06 View 9750 -
Professor Mikyoung Lim Receives the MediaV Young Researcher Award
Professor Mikyoung Lim of the Department of Mathematical Sciences at KAIST received the MediaV Young Researchers Award at the International Conference on Inverse Problems and Related Topics that took place at the National Taiwan University, Taiwan, on December 15-19, 2014.
The Conference established the MediaV Young Researcher Award in 2010 to recognize distinguished scholars who are age 40 or younger and have made important contributions to the field of inverse problems. This year, two recipients were chosen for the award.
Professor Lim has focused her research on the incremental reading of incomprehensible materials’ imaging and the effect of invisibility cloaking.
The other awardee was Kui Ren, a professor at the University of Texas at Austin.
2014.12.27 View 9819 -
KAIST Establishes a Center for Human Rights and Ethics
KAIST hosted an opening ceremony on November 27, 2014 for its Center for Human Rights and Ethics (CHRE) located in the Education Support Building on campus.
President Steve Kang and other senior administrators participated in the ceremony, pledging to eliminate violence, corruption, and prejudice on the campus.
The CHRE was created to provide members of the KAIST community with one-stop service to report and process human rights violation cases and issues related to corruption and illegalities such as verbal abuse, physical assault, sexual harassment, and bribes. The center will also launch campaigns to promote and strengthen awareness of human rights and ethics within the university.
The Director of CHRE, Professor Young-hee Kim of the Department of Humanities and Social Sciences at KAIST said, “The center will serve an important role in the improvement of human rights and in the reestablishment of moral standards in KAIST. I hope KAIST members make the most of the center wherever they face injustice and unequal treatment during their study and work at the campus.”
2014.12.08 View 6640