-
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 10689 -
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 10496 -
KAIST Welcomes Freshmen at the 2015 Convocation Ceremony
Around 1,600 freshmen and their parents gathered on March 12, 2015 at the main auditorium on campus for the KAIST convocation ceremony. A total of 796 freshmen joined the convocation ceremony.
The ceremony proceeded with the freshmen oath, administered by freshmen representatives Ja-Young Ryu (a graduate of the Korea Science Academy) and Yun-Min Song (a graduate of Changwon Science High School). Vice Minister Jae-Yoo Choi of Science, ICT and Future Planning, the Republic of Korea, and President Steve Kang of KAIST delivered congratulatory messages, respectively. Members of KAIST student clubs performed a music concert to celebrate the event.
In his message, Vice Minister Choi said, “Scientists should not be afraid of failure but have a challenging spirit. As always, the Korean government will provide students with generous support by creating an environment for education and research, in which students can reach their potential and realize imagination into reality.”
President Kang urged students to be respectful and thankful to others, to master their expertise in depth, to take social responsibilities, and to improve on global communication skills. He continued, “With all the best intellectuals you will meet at KAIST, you will face a much more challenging environment compared to high school. Even if it gets too difficult and you fail, do not be discouraged but please have the heart to get back up and try again.”
Freshmen representatives, Ja-Young Ryu (a female student) and Yun-Min Song (a male student), are administering the student oath in front of President Sung-Mo Kang in the picture below.
2015.03.02 View 6273 -
The Real Time Observation of the Birth of a Molecule
From right to left: Dr. Kyung-Hwan Kim, Professor Hyotcherl Lhee, and Jong-Gu Kim, a Ph.D. candidate
Professor Hyotcherl Lhee of the Department of Chemistry at KAIST and Japanese research teams jointly published their research results showing that they have succeeded in the direct observation of how atoms form a molecule in the online issue of Nature on February 19, 2015.
The researchers used water in which gold atoms ([Au(CN) 2- ]) are dissolved and fired X-ray pulses over the specimen in femtosecond timescales to study chemical reactions taking place among the gold atoms. They were able to examine in real time the instant process of how gold atoms bond together to become a molecule, to a trimer or tetramer state.
This direct viewing of the formation of a gold trimer complex ([Au(CN) 2- ] 3 ) will provide an opportunity to understand complex chemical and biological systems.
For details, please see the following press release that was distributed by the High Energy Accelerator Research Organization, KEK, in Japan:
Direct Observation of Bond Formations
February 18, 2015
A collaboration between researchers from KEK, the Institute for Basic Science (IBS), the Korea Advanced Institute of Science and Technology (KAIST), RIKEN, and the Japan Synchrotron Radiation Research Institute (JASRI) used the SACLA X-ray free electron laser (XFEL) facility for a real time visualization of the birth of a molecular that occurs via photoinduced formation of a chemical bonds. This achievement was published in the online version of the scientific journal “Nature” (published on 19 February 2015).
Direct “observation” of the bond making, through a chemical reaction, has been longstanding dream for chemists. However, the distance between atoms is very small, at about 100 picometer, and the bonding is completed very quickly, taking less than one picosecond (ps). Hence, previously, one could only imagine the bond formation between atoms while looking at the chemical reaction progressing in the test-tube.
In this study, the research group focused on the process of photoinduced bond formation between gold (Au) ions dissolved in water. In the ground state (S 0 state in Fig. 1) Au ions that are weakly bound to each other by an electron affinity and aligned in a bent geometry. Upon a photoexcitation, the S 0 state rapidly converts into an excited (S 1 state in Fig. 1) state where Au-Au covalent bonds are formed among Au ions aligned in a linear geometry. Subsequently, the S 1 state transforms to a triplet state (T 1 state in Fig. 1) in 1.6 ps while accompanying further contraction of Au-Au bonds by 0.1 Å. Later, the T 1 state of the trimer converts to a tetramer (tetramer state in Fig. 1) on nanosecond time scale. Finally, the Au ions returned to their original loosely interacting bent structure.
In this research, the direct observation of a very fast chemical reaction, induced by the photo-excitation, was succeeded (Fig. 2, 3). Therefore, this method is expected to be a fundamental technology for understanding the light energy conversion reaction. The research group is actively working to apply this method to the development of viable renewable energy resources, such as a photocatalysts for artificial photosynthesis using sunlight.
This research was supported by the X-ray Free Electron Laser Priority Strategy Program of the MEXT, PRESTO of the JST, and the the Innovative Areas "Artificial Photosynthesis (AnApple)" grant from the Japan Society for the Promotion of Science (JSPS).
Publication: Nature , 518 (19 February 2015)
Title: Direct observation of bond formation in solution with femtosecond X-ray scattering
Authors: K. H. Kim 1 , J. G. Kim 1 , S. Nozawa 1 , T. Sato 1 , K. Y. Oang, T. W. Kim, H. Ki, J. Jo, S. Park, C. Song, T. Sato, K. Ogawa, T. Togashi, K. Tono, M. Yabashi, T. Ishikawa, J. Kim, R. Ryoo, J. Kim, H. Ihee, S. Adachi. ※ 1: These authors contributed equally to the work.
DOI: 10.1038/nature14163
Figure 1. Structure of a gold cyano trimer complex (Au(CN) 2 - ) 3 .
Figure 2. Observed changes in the molecular structure of the gold complex
Figure 3. Schematic view of the research of photo-chemical reactions by the molecular movie
2015.02.27 View 12694 -
KAIST Develops Subminiature, Power-Efficient Air Pollution Sensing Probe
Professor Inkyu Park and his research team from the Department of Mechanical Engineering at KAIST have developed a subminiature, power-efficient air-pollution sensing probe that can be applied to mobile devices. Their research findings were published online in the January 30th issue of Scientific Reports.
As air pollution has increased, people have taken greater interest in health care. The developed technology could allow people to measure independently the air pollution level of their surrounding environments.
Previous instruments used to measure air pollution levels were bulky and consumed a lot of power. They also often produced inaccurate results when measuring air pollution in which different toxic gases were mixed. These problems could not be resolved with existing semiconductor manufacturing process.
Using local temperature field control technology, Professor Park’s team succeeded in integrating multiple heterogeneous nanomaterials and fitting them onto a small, low-power electronic chip. This microheating sensor can heat microscale regions through local hydrothermal synthesis. Because it requires a miniscale amount of nanomaterials to manufacture, the sensor is most suitable for mobile devices.
Professor Park said, “Our research will contribute to the development of convergence technology in such field as air pollution sensing probes, biosensors, electronic devices, and displays.”
The team's research was supported by the Ministry of Education and the Ministry of Science, ICT and Future Planning, Republic of Korea.
Figure 1 – The Concept of Multiple Nanomaterial Device and Numerical Simulation Results of Precursor Solutions
Figure 2 - Multiple Nanomaterial Manufactured in a Microscale Region
2015.02.27 View 10938 -
Dr. Dong-Hee Chung Honored with OYRA by Korean Physicists in America
Dr. Dong-Hee Chung, a KAIST alumnus (class of 2002) who is currently a professor of the Physics Department at the Pennsylvania State University (Penn State), received the 2015 Outstanding Young Researcher Award (OYRA) by the Association of Korean Physicists in America (AKPA).
The award ceremony was held on March 3, 2015 at AKPA’s annual conference. According to AKPA, Dr. Chung was recognized for his research achievements in the fields of the early universe, dark energy, and galaxy formation.
Dr. Chung finished both his undergraduate and graduate degrees at KAIST and received his doctorate in 2004 from the University of Texas at Austin. He was appointed a professor at Penn State in 2014.
2015.02.27 View 7339 -
Ethiopian Minister of Education Visits KAIST
An Ethiopian delegation headed by the Minister of Education visited the KAIST campus on February 26, 2015. The delegation consisted of Mr. Demitu Hambisa, Minister of Education, Mr. Dibaba Abdetta, Ethiopian Ambassador to Korea, Dr. Jang-Kyu Lee, President of Adama Science and Technology University (ASTU), and Mr. Nurelegne Tefera, President of Addis Ababa Science and Technology University (AASTU).
Minister Hambisa explained the purpose of his visit, “We would like to learn about what KAIST has achieved over the years for Korea and its people and increase exchanges and cooperation between our universities and KAIST.”
KAIST and the two Ethiopian universities, ASTU and AASTU, signed memoranda of understanding for cooperative programs in science and engineering education.
Established in 1993, ASTU appointed Dr. Jang-Kyu Lee, a former professor from Seoul National University, Korea, to become its president since 2011. President Lee is the first Korean ever to have served the institution.
2015.02.26 View 8140 -
KAIST Signs MOU with Jeonju City
KAIST signed a memorandum of understanding for the development of new industries based on convergence technology with the government of Jeonju City on February 26, 2015. Located in the south west portion of the Korean peninsula, Jeonju City is home to a rich historical and cultural heritage.
Taking advantage of its proximity to the university's campus, the city will cooperate with KAIST to develop the local economy through creating new industries and jobs. To that end, KAIST and Jeonju will foster carbon-based industry, 3D printing technology, the Internet of Things, and emerging technologies. The two organizations also hope this cooperation will produce highly educated manpower for research and development in the city and offer the city to conduct national research projects.
President Sung-Mo Kang and Mayor Seung-Soo Kim pose after signing in the picture below.
2015.02.26 View 7912 -
KAIST Team Wins International Hacking Competition, "SECCON CTF 2014"
KAIST’s white hacker team, “TOFEL Beginner,” secured the first place in an international hacking competition, SECCON CTF 2014. SECCON is an international hacking competition which has operated for more than 20 years. It uses the Capture the Flag (CTF) method. Last year’s competition was held in Tokyo on December 7, 2014.
The TOFEL Beginner team consisted of two KAIST graduate students and two researchers from a private security company based in Korea: In-Soo Yoon of Computer Science, Eun-Soo Kim of the Graduate School of Information Security (GSIS), and Jong-Ho Lee and Jung-Hoon Lee of Raon Secure.
Of 4,186 competitors, 24 teams made it to the finals. The TOFEL Beginner took the lead with 4,506 points compared with HITCON (3,112 points) of Taiwan and PPP (2,858 points) of the USA.
With this victory, the KAIST team qualified to participate in the most renowned international hacking competition, the DEF CON Hacking Conference in 2015.
Professor Yongdae Kim of the Electrical Engineering Department at KAIST, who advised the TOEFL Beginner team, said, “Our members have achieved an outstanding result. By taking advantage of this opportunity, KAIST will continue to offer the best programs in information security in Korea and hopefully beyond.”
2015.02.24 View 10256 -
The Number of KAIST Doctoral Graduates to Reach Over Ten Thousands
The ten-thousandth doctoral graduate received her degree in the commencement ceremony on February 13, 2015.
KAIST has contributed to the development of science, technology, and industry in Korea by fostering talents in advanced science and engineering.
Since its establishment forty-four years ago, more than ten-thousand KAIST alumni have received their doctorates. This year’s graduation ceremony took place on February 13, 2015, at the Sports Complex on campus, awarding the ten-thousandth doctoral degree.
Dr. Sun-Mi Cho of the Department of Biological Sciences received the ten-thousandth doctoral degree. A graduate of Jeon-Nam Science High School, Dr. Cho also received her Bachelor of Science degree from KAIST.
Dr. Cho wrote a dissertation entitled “GABA from reactive astrocytes impairs learning and memory in Alzheimer disease.” Her dissertation adviser was Professor Daesoo Kim of the Department of Biological Sciences.
Dr. Cho, who will be a post-doctorate researcher at the Biological Sciences Department, said, “It was my childhood dream to receive a doctorate from KAIST. I cannot believe that I’m the ten-thousandth doctoral graduate, for which I’m very grateful.” She continued, “I hope to become a neuroscientist where I can be of help to the sick.”
In 1978, KAIST only had two doctoral graduates, but since 1987 there have been more than one hundred graduates each year, two hundred since 1994, and four hundred since 2000. In 2015, 522 doctoral students graduated.
One of the first doctoral graduates, Dong-Yol Yang (class of 1978 in the Mechanical Engineering Department), became a professor at the same department of KAIST. Professor Yang expressed his thoughts on the news, “There was a trend in Korea to go overseas for Ph.D. degrees in the early 1970s, but it changed when KAIST began to select candidates for Master’s degrees in 1973 and Doctoral degrees in 1975. Talented Korean students came to KAIST laboratories, and its graduates were known for their knowledge and skills. Now, we see that the talent is coming from overseas.”
At the 2015 Commencement, KAIST conferred 522 Doctoral, 1,241 Master’s, and 915 Bachelor of Science (B.S.) degrees.
Since its inception in 1971, KAIST has granted 10,403 doctor's, 26,402 master's, and 51,412 bachelor's degrees.
In the picture below, Professor Dong-Yol Yang (left) seats next to Dr. Sun-Mi Cho (right), the recipient of 10,000th doctoral degree.
2015.02.16 View 10352 -
The 2015 KAIST Commencement
A total of 2,678 students (522 for Doctor's, 1,241 for Master’s, and 915 for Bachelor's) graduated.
Twin brothers received their Ph.D. degrees together.
KAIST held its commencement ceremony on February 13, 2015. Approximately 8,000 people including the graduating class, their families, faculty, staff, and friends attended the ceremony and celebrated this milestone.
President Steve Kang of KAIST congratulated the graduating students and stressed the importance of their “contribution to social growth with a compassionate heart and expertise” in his commencement address. He also mentioned that all graduates would be recognized as a “Very Important Person (VIP)” and laid out the essential characteristics of what constitutes a “true VIP”: vision, innovation, and perseverance.
Among the graduates were twin brothers, Dae-Ok Kim of the Energy, Environment, Water, and Sustainability (EEWS) Graduate School and Dae-Woo Kim of the Department of Chemical and Biomolecular Engineering, who received their doctorates on the same day.
The older brother, Dr. Dae-Ok Kim received both his Bachelor of Science (B.S.) and Master’s degrees from KAIST’s Department of Chemical and Biomolecular Engineering and later was admitted to the EEWS Graduate School for his doctorate. His dissertation was an “Investigation on the behaviors of gas molecules in water-filled nanopores: Applications to energy and environmental technology.” Professor Huen Lee of Chemical and Biomolecular Engineering was his faculty adviser.
Dr. Dae-Ok Kim said, “It was a great advantage to conduct cooperative research with my brother by sharing information and discussing each other’s fields.” After graduating, Dr. Kim plans to research gas hydrates and porous materials at KAIST’s Energy and Environmental Systems Lab for a year and to continue his research on applications in the United States.
The younger brother, Dr. Dae-Woo Kim received his B.S. from KAIST’s Department of Chemical and Biomolecular Engineering and was admitted to the Master of Science-Ph.D. Integrated Degree Program in the same department. His doctoral thesis was on “Direct visualization of large-area domains of two dimensional materials by using optical birefringency.” His faculty adviser was Professor Hee Tae Jung of Chemical and Biomolecular Engineering.
Dr. Dae-Woo Kim said, “During my time at the graduate school, I could overcome my difficulties by talking frankly to my brother. Our relationship deepened as we reached our academic goals together at KAIST.”
Dr. Dae-Woo Kim, who published more than 25 papers in international journals such as Nature and Nanotechnology, received the Silver Prize in the Human Tech Paper Awards sponsored by Samsung Electronics Corp. in 2011. After graduating, Dr. Kim will research graphene and 2D material structure control at KAIST’s Organic Opto-Electronic Materials Lab for a year and take up further research on their applications in the United States.
KAIST Commencement 2015
In the picture below, the twins pose together at the 2015 commencement. At the left is Dae-Ok Kim (elder brother) and the right is Dae-Woo Kim.
2015.02.16 View 9024 -
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 9745