Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari; Kimura, Kaname*; Matsumura, Hiroyoshi*; et al.

Proceedings of the National Academy of Sciences of the United States of America, 106(12), p.4641 - 4646, 2009/03

https://doi.org/10.1073/pnas.0809400106

To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in the catalytic aspartates Asp25 and Asp125. The structure of HIV-1 protease in complex with transition-state analog KNI-272 was determined by combined neutron crystallography at 1.9 resolution and X-ray crystallography at 1.4 resolution. The resulting structural data shows that the catalytic residue Asp25 is protonated and that Asp125 is deprotonated. The proton on Asp25 makes a hydrogen bond with the carbonyl group of the allophenylnorstatine group in KNI-272. The deprotonated Asp125 bonds to the hydroxyl proton of Apns. The results provide direct experimental evidence for proposed aspects of the catalytic mechanism of HIV-1 protease; and can therefore contribute substantially to the development of specific inhibitors for therapeutic application.

Recent activities of Pb-Bi technology for ADS at JAERI

Kikuchi, Kenji; Saito, Shigeru; Kurata, Yuji; Futakawa, Masatoshi; Sasa, Toshinobu; Oigawa, Hiroyuki; Umeno, Makoto*; Mori, Keijiro*; Takano, Hideki; Wakai, Eiichi

Proceedings of 11th International Conference on Nuclear Engineering (ICONE-11) (CD-ROM), 7 Pages, 2003/04

In order to construct ADS Target Test facility in J-PARC project the research and development on Pb-Bi technology have been carried, which cover target design with computer simulation, flowing loop test, stagnant corrosion test, oxygen sensor and cleaning techniques. Obtained results are as follows: Corrosion rate of SUS316 under flowing Pb-Bi at 1m/s at 450C is 0.1 mm / 3000 hrs. Fe and Cr were melted into lead bismuth from SS316 in the high temperature part and deposited in the low-temperature part according to the difference of solubility. The corrosion thickness decreases with increasing Cr content in the stagnant corrosion test at saturated oxygen concentration. Reliable oxygen sensors are to be developed by using suitable reference electrodes. As a result of cleaning tests, blushing process was needed to remove Pb-Bi effectively after immersion in the silicon oil. The mixed acid easily dissolved Pb-Bi and removed almost perfectly. But specimens themselves were affected by coloring.

After-service inspection of HENDEL in-core structure test section T; 1, Inspection results at dismantlement

Fujisaki, Katsuo; Inagaki, Yoshiyuki; ; ; ; ; Sekita, Kenji; Morisaki, Norihiro; *; Iwatsuki, Jin*; et al.

JAERI-Tech 97-053, 57 Pages, 1997/10

JAERI-Tech-97-053.pdf:3.26MB

no abstracts in English

Neutron crystal structure analysis of HIV-1 protease complexed with KNI-272

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari; Matsumura, Hiroyoshi*; Sugiyama, Shigeru*; et al.

no journal, , 

We have determined a crystal structure of HIV-1 protease by neutron crystallography. The development of HIV-1 protease inhibitors is regarded as a major success of structure-based drug design and contributes to establish highly active anti-retroviral therapy for AIDS. To further understand the catalytic mechanism of HIV-1 protease and interaction between HIV-1 protease and its inhibitor, we have determined the crystal structure of HIV-1 protease in complex with a inhibitor, KNI-272 to 2.3 resolution by neutron crystallography. Our results indicates that the carbonyl group of allophenylnorstatine (Apns) in KNI-272 forms a significant hydrogen bond with protonated Asp 25, and the hydrogen atom from the hydroxyl group of Apns forms a remarkable hydrogen bond with the deprotonated Asp125. These results show direct evidence that Asp25 provides a proton to carbonyl group of substrate and Asp125 contributes to activate the attacking water molecule as a nucleophile.

Structure analysis of HIV-1 protease by neutron diffraction

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari; Matsumura, Hiroyoshi*; Sugiyama, Shigeru*; et al.

no journal, , 

no abstracts in English

Crystal structure analysis of HIV-1 protease by complementary use of synchrotron radiation and neutron

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro*; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari*; Matsumura, Hiroyoshi*; Sugiyama, Shigeru*; et al.

no journal, , 

In this study, we determined crystal structures of HIV-1 protease complexed with inhibitor by neutron and X-ray crystallography. Finally, we refined the structures to R-factor of 17.3% and free R-factor 20.3% by neutron crystallography and to R-factor of 10.4 % and free R-factor 12.4% by X-ray crystallography. The result shows that Asp 25 residue is protonated and Asp 125 is deprotonated. These information is important to resolve catalytic mechanism and design of new potent inhibitor.