フロアプラン指向高位合成手法とイジング計算機応用に関する研究

早大学位記番号:新7790早稲田大

In silico panning for a non-competitive peptide inhibitor

BACKGROUND: Peptide ligands have tremendous therapeutic potential as efficacious drugs. Currently, more than 40 peptides are available in the market for a drug. However, since costly and time-consuming synthesis procedures represent a problem for high-throughput screening, novel procedures to reduce the time and labor involved in screening peptide ligands are required. We propose the novel approach of 'in silico panning' which consists of a two-stage screening, involving affinity selection by docking simulation and evolution of the peptide ligand using genetic algorithms (GAs). In silico panning was successfully applied to the selection of peptide inhibitor for water-soluble quinoprotein glucose dehydrogenase (PQQGDH). RESULTS: The evolution of peptide ligands for a target enzyme was achieved by combining a docking simulation with evolution of the peptide ligand using genetic algorithms (GAs), which mimic Darwinian evolution. Designation of the target area as next to the substrate-binding site of the enzyme in the docking simulation enabled the selection of a non-competitive inhibitor. In all, four rounds of selection were carried out on the computer; the distribution of the docking energy decreased gradually for each generation and improvements in the docking energy were observed over the four rounds of selection. One of the top three selected peptides with the lowest docking energy, 'SERG' showed an inhibitory effect with K(i )value of 20 μM. PQQGDH activity, in terms of the V(max )value, was 3-fold lower than that of the wild-type enzyme in the presence of this peptide. The mechanism of the SERG blockage of the enzyme was identified as non-competitive inhibition. We confirmed the specific binding of the peptide, and its equilibrium dissociation constant (K(D)) value was calculated as 60 μM by surface plasmon resonance (SPR) analysis. CONCLUSION: We demonstrate an effective methodology of in silico panning for the selection of a non-competitive peptide inhibitor from small virtual peptide library. This study is the first to demonstrate the usefulness of in silico evolution using experimental data. Our study highlights the usefulness of this strategy for structure-based screening of enzyme inhibitors

Population pharmacokinetic modeling of GS‐441524, the active metabolite of remdesivir, in Japanese COVID‐19 patients with renal dysfunction

腎障害患者におけるレムデシビルの薬物動態モデルを構築 --新型コロナウイルス感染症治療薬の適正使用に向けて--. 京都大学プレスリリース. 2021-11-25.Remdesivir, a prodrug of the nucleoside analog GS-441524, plays a key role in the treatment of coronavirus disease 2019 (COVID-19). However, owing to limited information on clinical trials and inexperienced clinical use, there is a lack of pharmacokinetic (PK) data in patients with COVID-19 with special characteristics. In this study, we aimed to measure serum GS-441524 concentrations and develop a population PK (PopPK) model. Remdesivir was administered at a 200 mg loading dose on the first day followed by 100 mg from day 2, based on the package insert, in patients with an estimated glomerular filtration rate (eGFR) greater than or equal to 30 ml/min. In total, 190 concentrations from 37 Japanese patients were used in the analysis. The GS-441524 trough concentrations were significantly higher in the eGFR less than 60 ml/min group than in the eGFR greater than or equal to 60 ml/min group. Extracorporeal membrane oxygenation in four patients hardly affected the total body clearance (CL) and volume of distribution (Vd) of GS-441524. A one-compartment model described serum GS-441524 concentration data. The CL and Vd of GS-441524 were significantly affected by eGFR readjusted by individual body surface area and age, respectively. Simulations proposed a dose regimen of 200 mg on day 1 followed by 100 mg once every 2 days from day 2 in patients with an eGFR of 30 ml/min or less. In conclusion, we successfully established a PopPK model of GS-441524 using retrospectively obtained serum GS-441524 concentrations in Japanese patients with COVID-19, which would be helpful for optimal individualized therapy of remdesivir

Measuring the Shock Stage of Asteroid Regolith Grains by Electron Back-Scattered Diffraction

We have been analyzing Itokawa samples in order to definitively establish the degree of shock experienced by the regolith of asteroid Itokawa, and to devise a bridge between shock determinations by standard light optical petrography, crystal structures as determined by electron and X-ray diffraction. These techniques would then be available for samples returned from other asteroid regoliths

Measuring Shock Stage of ltokawa Regolith Grains by Electron Back-Scattered Diffraction and Synchrotron X-Ray Diffraction

We have been analyzing Itokawa samples in order to definitively establish the degree of shock experienced by the regolith of asteroid Itokawa, and to devise a bridge between shock determinations by standard light optical petrography, crystal structures as determined by electron and X-ray diffraction techniques. We are making measurements of olivine crystal structures and using these to elucidate critical regolith impact processes. We use electron back-scattered diffraction (EBSD) and synchrotron X-ray diffraction (SXRD). We are comparing the Itokawa samples to L and LL chondrite meteorites chosen to span the shock scale experienced by Itokawa, specifically Chainpur (LL3.4, Shock Stage 1), Semarkona (LL3.00, S2), Kilabo (LL6, S3), NWA100 (L6, S4) and Chelyabinsk (LL5, S4). In SXRD we measure the line broadening of olivine reflections as a measure of shock stage. In this presentation we concentrate on the EBSD work. We employed JSC's Supra 55 variable pressure FEG-SEM and Bruker EBSD system. We are not seeking actual strain values, but rather indirect strain-related measurements such as extent of intra-grain lattice rotation, and determining whether shock state "standards" (meteorite samples of accepted shock state, and appropriate small grain size) show strain measurements that may be statistically differentiated, using a sampling of particles (number and size range) typical of asteroid regoliths. Using our system we determined that a column pressure of 9 Pa and no C-coating on the sample was optimal. We varied camera exposure time and gain to optimize mapping performance, concluding that 320x240 pattern pixilation, frame averaging of 3, 15 kV, and low extractor voltage yielded an acceptable balance of hit rate (>90%), speed (11 fps) and map quality using an exposure time of 30 ms (gain 650). We found that there was no strong effect of step size on Grain Orientation Spread (GOS) and Grain Reference Orientation Deviation angle (GROD-a) distribution; there was some effect on grain average Kernel Average Misorientation (KAM) (reduced with smaller step size for the same grain), as expected. We monitored GOS, Maximum Orientation Spread (MOS) and GROD-a differences between whole olivine grains and sub-sampled areas, and found that there were significant differences between the whole grain dataset and subsets, as well as between subsets, likely due to sampling-related "noise". Also, in general (and logically) whole grains exhibit greater degrees of cumulative lattice rotation. Sampling size affects the apparent strain character of the grain, at least as measured by GOS, MOS and GROD-a. There were differences in the distribution frequencies of GOS and MOS between shock stages, and in plots of MOS and GOS vs. grain diameter. These results are generally consistent with those reported this year. However, it is unknown whether the differences between samples of different shock states exceeds the clustering of these values to the extent that shock stage determinations can still be made with confidence. We are investigating this by examination of meteorites with higher shock stage 4 to 5. Our research will improve our understanding of how small, primitive solar system bodies formed and evolved, and improve understanding of the processes that determine the history and future of habitability of environments on other solar system bodies. The results will directly enrich the ongoing asteroid and comet exploration missions by NASA and JAXA, and broaden our understanding of the origin and evolution of small bodies in the early solar system, and elucidate the nature of asteroid and comet regolith

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements