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Free energy calculation device, method, program, and recording medium with said program recorded thereon

A computing device and computing method technology, applied in computing, complex mathematical operations, design optimization/simulation, etc., can solve problems such as inability to calculate combined free energy, not a practical computing method, long computing time, etc.

Active Publication Date: 2017-08-01
OSAKA UNIV +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, there are the following problems: it requires a long calculation time and is not a practical calculation method
However, when calculating the free energy of binding, in the calculation process, as in the particle intercalation method, there is a process of repeating the sampling process to generate a plurality of final states consisting of ligand-protein-bound complexes and solvents, so The sampling process mentioned above refers to randomly selecting the position coordinates in the initial state composed of solvents and proteins without ligands, and adding ligands to the position coordinates, so this method cannot calculate the binding free energy

Method used

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  • Free energy calculation device, method, program, and recording medium with said program recorded thereon
  • Free energy calculation device, method, program, and recording medium with said program recorded thereon
  • Free energy calculation device, method, program, and recording medium with said program recorded thereon

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0379] (1) Calculation of ΔG4a

[0380] Regarding the change represented by reaction formula (7), the complex L 0 R and constitute the complex L present in the 0 The atomic assembly before the change of the water molecules around R is called "atom assembly A", and the complex L 1 R and constitute the complex L present in the 1 The changed atomic aggregate of the water molecules around R is regarded as "atomic aggregate AB", and the sum of the free energy of the atomic aggregate A before the change and the free energy of the fragment B, and the value after the change are calculated according to the mathematical formula (1). The free energy difference ΔG4a' of the atomic aggregate AB.

[0381] [chemical formula 5]

[0382]

[0383] It should be noted that since ΔG4a is the amount of free energy change related to the change represented by the reaction formula (8), the value obtained by multiplying the ΔG4a' calculated according to the mathematical formula (1) with a minus ...

Embodiment 2

[0588] Using Ligand L 3 to replace ligand L 2 , performed the same operation as in Example 1, and calculated ΔΔG.

[0589] Ligand L 3 The chemical structure of is as follows.

[0590] [chemical formula 20]

[0591]

[0592] Ligand L 3 The partial charge of each atom of is as follows.

[0593] [chemical formula 21]

[0594]

[0595] The structure of Fragment B is as follows.

[0596] [chemical formula 22]

[0597]

[0598] Here, as described below, ΔΔG was calculated in the same manner as in Example 1 by treating point charges (partial charges; 0.000) as atoms of Fragment B for convenience.

[0599] [chemical formula 23]

[0600]

[0601] The same values ​​as in Example 1 were used for ΔG4a and ΔG3a.

[0602] The calculated ΔG4b was -8.12 (kcal / mol).

[0603] The calculated ΔG3b was -5.45 (kcal / mol).

[0604] The calculated ΔΔG was -0.08 (kcal / mol).

[0605] The ΔΔG recorded in the known literature (Journal of Chemical Theory and Computation, 8, 3686-36...

Embodiment 3

[0607] Using Ligand L 4 Ligand L 2 , performed the same operation as in Example 1, and calculated ΔΔG.

[0608] Ligand L 4 The chemical structure of is as follows.

[0609] [chemical formula 24]

[0610]

[0611] Ligand L 4 The partial charge of each atom of is as follows.

[0612] [chemical formula 25]

[0613]

[0614] The structure of Fragment B is as follows.

[0615] [chemical formula 26]

[0616]

[0617] The same values ​​as in Example 1 were used for ΔG4a and ΔG3a.

[0618] The calculated ΔG4b was -23.00 (kcal / mol).

[0619] The calculated ΔG3b was -19.88 (kcal / mol).

[0620] The calculated ΔΔG was -0.53 (kcal / mol).

[0621] The ΔΔG recorded in the known literature (Journal of Chemical Theory and Computation, 8, 3686-3695 (2012) and Journal of the American Chemical Society, 99, 2331-2336 (1977)) obtained by experiment is -0.40 (kcal / mol), the difference between the ΔΔG calculated by the calculation method of the present invention and the ΔΔG obtai...

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PUM

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Abstract

The purpose of the present invention is to provide a device, a method, a program, and a recording medium with the program recorded thereon, for calculating, quickly and with high precision, differences in free energy between different molecules. To achieve this purpose, in this device, method, program, and recording medium with the program recorded thereon, Delta G is calculated on the basis of mathematical formula (1).

Description

technical field [0001] The present invention relates to a device, method, program and recording medium recording the program for calculating the free energy difference between different molecules at high speed and with high precision. Background technique [0002] Due to the development of three-dimensional structure analysis techniques such as X-ray crystal structure analysis and nuclear magnetic resonance (NMR) and genetic engineering technology, the three-dimensional structure of proteins targeted for drug development has gradually become clear. Accordingly, based on the three-dimensional structure of the protein, the molecular structure of a ligand that activates or inhibits the biological function (biological function) of the protein is actively being developed. [0003] As one of the particularly important techniques for developing the molecular structure of a ligand based on the three-dimensional structure of a protein, molecular dynamics or Monte Carlo can be cited, ...

Claims

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Application Information

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IPC IPC(8): G06F19/12G16B5/20G16B5/30
CPCG16B5/00G16B5/30G16B5/20G06F30/20G06F2111/10G06F17/18
Inventor 松林伸幸增田友秀谷村隆次
Owner OSAKA UNIV
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