Jirundon Yuvaniyama, Ph.D.

Research Project in JY Laboratory

Research Interests

Research interests in Yuvaniyama Laboratory focus around three-dimensional structures of proteins. These include elucidation of protein structures and related applications such as rational drug design and protein engineering. Equipped with an in-house X-ray imaging plate system mounted on a 5 kW-rotating-copper-anode X-ray generator and an X-Stream cryo-system, X-ray diffraction from protein crystals can be routinely collected at cryo-temperature (around –180°C). The system is used for optimization of crystallization conditions or cryo-protectants for synchrotron data collection as well as full in-house data collection, allowing for structure determination of both novel proteins and various complexes of proteins with known structures.

In collaboration with Prof. Yongyuth Yuthavong at the National Center for Genetic Engineering and Biotechnology (BIOTEC), we determined the first structure of Plasmodium falciparum dihydrofolate reductase–thymidylate synthase (PfDHFR–TS), a bifunctional enzyme target for antimalarial chemotherapy (Yuvaniyama, 2003; Chitnumsub, 2004; Yuthavong, 2005). Determination of Trypanosoma brucei and Trypanosoma cruzi DHFR–TS structures are in progress. We also helped solving structures of Vibrio carchariae chitinase A (Songsiriritthigul, 2005), Anopheles dirus glutathione transferase mutant (Wongsantichon, 2006), as well as rice BGlu1 ?-Glucosidase (Chuenchor, 2006; Chuenchor, 2008). In addition, through collaboration with Assoc. Prof. Pimchai Chaiyen, elucidation of structures of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) from Pseudomonas sp. MA-1 (Oonanant, 2005) and the reductase component (C₁) of p-hydroxyphenyl¬acetate hydroxylase (HPAH) from Acinetobacter baumannii is ongoing.

With availability of a three-dimensional structure of a protein, its structure-based properties may be revealed: catalytic mechanism as well as involvement of active-site residues and a prosthetic group may be deduced; ligand-interacting amino acids may be identified; and surface electrostatic potential may be estimated, for examples. In rational drug design, a protein important to the treatment of a disease is identified as a drug target. Structures of the target protein in various complexes are elucidated and compared in order to learn about ligand recognition. Then, chemical compounds may be modeled in the active site of the target protein to tightly bind to and specifically inhibit it. The designed compounds are subsequently synthesized, tested against the target in vitro and in vivo, and subjected to pharmacokinetic/pharmacodynamic studies. Lead compounds with desired properties would be further tested in animals and the successful candidates would enter clinical trials prior to drug registration. Working with Prof. Yuthavong’s team at BIOTEC as well as researchers from Chulalongkorn University, Thailand; Monash University, Australia; and London School of Hygiene and Tropical Medicine, United Kingdom, we have been developing antimalarial inhibitors against PfDHFR–TS with support from Medicine for Malaria Venture (MMV) (Kamchonwongpaisan, 2005). We also focus on another antimalarial target Plasmodium falciparum plasmepsins I and II (PfPM-I and PfPM-II), key aspartic proteinases responsible for host hemoglobin degradation in the plasmodial parasites.

In addition to drug design research, we have been using the knowledge of protein three-dimensional structures to guide mutageneses of the protein in order to change their properties. Before we could crystallize the full-length PfDHFR–TS, we had worked on a recombinant, monofunctional PfDHFR, of which the C-terminal TS domain had been removed. The single-domain PfDHFR protein, although catalytically active, had very limited solubility. We attempted to probe the PfDHFR domain boundary at its N-terminus by truncation experiments (Wattanarangsan, 2003) and to generate mutants with improved solubility (Japrung, 2005) based on a homology model. Besides the PfDHFR mutations, we have also been attempting to generate mutants of PfPM-I and PfPM-II that would allow for crystallization and structure determination of PfPM-I, for aforementioned drug design research (Siripurkpong, 2002).