Protein Design and Drug design
1. Biophysicists read out the real information from the DNA base sequence.
A
protein molecule is a peptide chain composed of 20 different kinds of native
amino acids, following the genetic information encoded in DNA. This peptide chain
forms a particular three-dimensional (3D) conformation to accomplish its
characteristic function under certain physiological condition. The 3D
conformation has been kept overall but differentiated during the evolution
process. Biophysicists ask: "Why dose such an amino acid sequence following the
DNA information yields a particular 3D conformation?" This attitude is
rather unique, compared with other biologists, who would just accept such
phenomenon as they do for other biological molecules. The biophysicists
approach the problem using a variety of methods. For example, a typical
approach is an empirical one to learn the principle in an inductive way, from
the relationships between the amino acid sequences of proteins and their known structures,
which are summarized in the PDB database (Protein Data Bank) with nearly 60,000 protein 3D structures. Alternatively,the most stable conformation having the lowest free energy can be sought using
physicochemical principles in deductive molecular simulations. When the
relationships are completely understood, human beings can design and produce new
artificial proteins, which have particular 3D conformations, as requested.
Dr. Shinya Honda et al. at AIST has designed a short but very stable new artificial protein with 10 amino acids forming a hairpin conformation, by using both the inductive and the deductive approaches. Its amino acid sequence is Tyr-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Tyr, and it is called CLN025. This peptide is very stable in water, and it has been confirmed by X-ray crystallography that the peptide chain has the correct hairpin conformation, as shown in Fig. 1 [1]. It has also been confirmed that the 3D conformation is deformed at high temperature. Thus, just as J. F. Champollion succeeded in reading out the text on the Rosetta stone in the ancient Egyptian hieroglyph, and then in writing new hieroglyph sentences, biophysicists are now able to correctly understand the meaning of the DNA information, build protein molecules, and to construct short but original "sentences", composed of 10 amino acids, as shown by CLN025.
2. Biophysicists rationally produce a drug.
Drugs were originally extracted from herbs and special plants or animals after a long history of trial-and-errors of human beings. In modern era, most drugs are chemically identified as particular molecules, and are synthesized with the technology of organic chemistry. In some cases, people searched for particular bacteria, which produce small compounds, and related them to available drugs. Many drug molecules target particular biological macromolecules, proteins and nucleic acids, and inhibit their functions. Now, the 3D structures of the target molecules have been determined in details, and screening and design of new drugs are being tried to find the most effective drug molecule. Here, biophysicists consider the reasons why such drugs are effective enough to inhibit the functions of the target macromolecules, and analyze the inhibition mechanism.
Dr. Tsuyoshi Inoue et al. in the Graduate School of Engineering, Osaka University, determined the complex crystal structure of the prostaglandin-D synthase (H-PGDS) and its inhibitor, HQL-79, which is known to be effective as an anti-inflammatory drug (Fig. 2), in order to understand its inhibition mechanism [2].
Based on the complex structure, they introduced the longer chains than that in the propionyl group of HQL-79, and changed its diphenyl group in the pocket to the larger ones, so that the new drug could fit better to the pocket than HQL-79. Consequently, they succeeded in producing a new drug, which can bind H-PGDS much tightly.
For an actually available drug, further careful examination is necessary against mice or humans, for possible side-effects by pharmaceutical and medical researchers. However, very new drug "seeds" are often developed by biophysicists, and collaboration with the pharmaceutical and medical researchers is frequently made to develop new drugs.
3. Biophysicists struggle with the swine flu.
In spring of 2009, swine flu, mainly originating in Mexico, quickly spread world-wide, and has finally become a pandemic. However, the good news is that a drug, Oseltamivir, known as "Tamiflu", could be effective for swine flu. Tamiflu was originally developed to inhibit the catalytic function of the virus enzyme, Neuramindase (NA). As shown in Fig. 3a, Tamiflu fits well with the catalytic pocket of the NA of H5N1 avian flu [3]. Fig. 3b and c are the 3D model structures of the NA of the swine flu, built by a homology model based on the amino acid sequence from the genome of the influenza virus. The modeling method has been developed by biophysicists, and everybody can now use it over the Internet. (For example, Spanner developed at the Institute for Protein Research, Osaka University, can be accessed at: http://www.pdbj.org/spanner/ ).
In addition, biophysicists now propose and are developing completely new drugs, inhibiting the other proteins, such as the RNA polymerase of the swine influenza virus. Thus, biophysicists study what is life, reading out and interpreting the information of the DNA base sequences, and try to develop new drugs, which are directly available for many citizens.
[References]
[1] Honda, S. et al. (2008) Crystal structure of a ten-amino acid protein. J. Am. Chem. Soc. 130, 15327-15331.
[2] Aritake, K. et al. (2006) Structural and functional characterization of HQL-79, and orally selective inhibitor of human hematopoietic prostaglandin D synthase. J. Biol. Chem. 281, 15277-15286.
[3] Russel, R. J. et al. (2006) The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 443, 45-49 (PDBID: 2hu0-chain B).
Institute for Protein Research, Osaka University, Haruki Nakamura