Predicting/validating the effect of activators on the binding effect of sirtuin to nicotinamide adenine

An activator and complex technology, applied in the fields of dietary supplements and biomedicine, can solve the problems of insufficient optimization of the system configuration, and the system does not jump out of the local energy minimum point, etc. The effect of accurate data

Active Publication Date: 2022-08-05
HANGZHOU NUOSHEN TECH CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

For example, consider how the combination of activator and Sirtuin affects NAD + Combination with Sirtuin, the conventional method exists for Sirtuin / activator / NAD + The system configuration is not fully optimized so that the system does not jump out of the local energy minimum point

Method used

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  • Predicting/validating the effect of activators on the binding effect of sirtuin to nicotinamide adenine
  • Predicting/validating the effect of activators on the binding effect of sirtuin to nicotinamide adenine
  • Predicting/validating the effect of activators on the binding effect of sirtuin to nicotinamide adenine

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0062] According to the above method and process, by predicting the effect of pterostilbene on NAD + The effect of binding with SIRT1 verifies that pterostilbene can be used as an activator of SIRT1. The specific steps are as follows:

[0063] The SIRT1 protein structure file was obtained from the PDB library as 5BTR.pdb. This structure contains resveratrol, which needs to be removed from the resveratrol molecule, NAD + The pdb structure file can be obtained from 4IF6.pdb; the charge and spatial structure information of pterostilbene molecule were calculated by Gaussian and the structure file was obtained by VMD.

[0064] Complete NAD with GOLD + Docking and scoring with Pterostilbene and SIRT1 to obtain SIRT1 / NAD + Complex structure and SIRT1 / Pterostilbene / NAD + composite structure.

[0065] The complex, SIRT1, pterostilbene and NAD in the above two systems were obtained by AmberTools + The topology file, prmtop file and inpcrd file are converted into Gromacs format thr...

Embodiment 2

[0070] According to the above method flow, by predicting the effect of pyrroloquinoline quinone (PQQ) on NAD + The effect of binding to SIRT3 verifies that PQQ can act as an activator of SIRT3. The specific steps are as follows:

[0071] The SIRT3 protein structure file was obtained from the PDB library as 4FVT.pdb. This structure contains NAD + analog carba-NAD + and Ac-CS2, both need to be removed, NAD + The pdb structure file of PQQ can be obtained from 4IF6.pdb; the charge and spatial structure information of PQQ molecule are calculated by Gaussian and the structure file is obtained by VMD.

[0072] Complete NAD with GOLD + Docking and scoring with PQQ and SIRT3 to obtain SIRT3 / NAD + Complex structure and SIRT3 / PQQ / NAD + composite structure.

[0073] The complex, SIRT3, PQQ and NAD in the above two systems were obtained by AmberTools, respectively + The topology file, prmtop file and inpcrd file are converted into Gromacs format through Acpype.py, and molecular dyn...

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Abstract

The invention discloses a prediction / verification polyphenolic compound activator for Sirtuin and nicotinamide adenine (NAD + ) combined effect-influence method, using a series of computational treatments and replica exchange molecular dynamics simulations of complex systems, Sirtuin / NAD + Complex structure and Sirtuin / Activator / NAD + The complex structure can be globally optimized and a steady-state configuration can be obtained. On this basis, the structural stability comparison, residue stability comparison and NAD of the two complex systems were carried out. + Binding energy comparison with Sirtuin, prediction / validation of activator to NAD + Effects of binding effects with Sirtuin. Compared with the experimental method, this method has lower time and labor cost, and can help the pre-screening of the experiment. Compared with traditional calculation methods, this method provides a more accurate protein mono- / bi-molecular steady-state configuration, thereby making the judgment of stability and binding energy more accurate, improving the accuracy of activator prediction / verification as a whole, and improving efficiency.

Description

technical field [0001] The invention relates to the technical field of dietary supplements and biomedicine, in particular to a prediction / verification of the effect of a polyphenolic compound activator on Sirtuin and nicotinamide adenine (NAD) + ) combined with the method of effect influence. Background technique [0002] Mammalian Sirtuins are nicotinamide adenine (NAD) + )-dependent class III deacetylase family, which mediates important physiological functions such as apoptosis, mitochondrial production, cellular stress, and cellular aging through histone deacetylation. There are seven kinds of Sirtuins (SIRT1-7) in the human body, which have different positions and functions. SIRT1, SIRT6 and SIRT7 are mainly located in the nucleus, SIRT2 is mainly located in the cytoplasm, and SIRT3, SIRT4 and SIRT5 are mainly located in the mitochondria, and they have roles in mediating inflammation, tumor, and aging. During aging, NAD in the body + The decline in levels affects the...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B15/00G16C20/20
CPCG16C20/10G16C20/30G16B15/30G16C20/40
Inventor 李骏黄易寒汤小苏
Owner HANGZHOU NUOSHEN TECH CO LTD
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