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Article

Comprehensive Similarity Algorithm and Molecular Dynamics Simulation-Assisted Terahertz Spectroscopy for Intelligent Matching Identification of Quorum Signal Molecules (N-Acyl-Homoserine Lactones)

by
Lintong Zhang
1,
Xiangzeng Kong
1,*,
Fangfang Qu
1,*,
Linjie Chen
1,
Jinglin Li
2,
Yilun Jiang
1,
Chuxin Wang
1,
Wenqing Zhang
1,
Qiuhua Yang
3 and
Dapeng Ye
1
1
Center for Artificial Intelligence in Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
Fujian Provincial Key Laboratory of Terahertz Functional Devices and Intelligent Sensing, Fuzhou University, Fuzhou 350108, China
3
Fisheries Research Institute of Fujian, Fuzhou 350025, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(3), 1901; https://doi.org/10.3390/ijms25031901
Submission received: 16 December 2023 / Revised: 25 January 2024 / Accepted: 30 January 2024 / Published: 5 February 2024
(This article belongs to the Section Molecular Informatics)
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Abstract

To investigate the mechanism of aquatic pathogens in quorum sensing (QS) and decode the signal transmission of aquatic Gram-negative pathogens, this paper proposes a novel method for the intelligent matching identification of eight quorum signaling molecules (N-acyl-homoserine lactones, AHLs) with similar molecular structures, using terahertz (THz) spectroscopy combined with molecular dynamics simulation and spectral similarity calculation. The THz fingerprint absorption spectral peaks of the eight AHLs were identified, attributed, and resolved using the density functional theory (DFT) for molecular dynamics simulation. To reduce the computational complexity of matching recognition, spectra with high peak matching values with the target were preliminarily selected, based on the peak position features of AHL samples. A comprehensive similarity calculation (CSC) method using a weighted improved Jaccard similarity algorithm (IJS) and discrete Fréchet distance algorithm (DFD) is proposed to calculate the similarity between the selected spectra and the targets, as well as to return the matching result with the highest accuracy. The results show that all AHL molecular types can be correctly identified, and the average quantization accuracy of CSC is 98.48%. This study provides a theoretical and data-supported foundation for the identification of AHLs, based on THz spectroscopy, and offers a new method for the high-throughput and automatic identification of AHLs.
Keywords: Gram-negative pathogens; quorum signaling molecules; terahertz spectroscopy; molecular dynamics simulation; spectral similarity calculation Gram-negative pathogens; quorum signaling molecules; terahertz spectroscopy; molecular dynamics simulation; spectral similarity calculation

Share and Cite

MDPI and ACS Style

Zhang, L.; Kong, X.; Qu, F.; Chen, L.; Li, J.; Jiang, Y.; Wang, C.; Zhang, W.; Yang, Q.; Ye, D. Comprehensive Similarity Algorithm and Molecular Dynamics Simulation-Assisted Terahertz Spectroscopy for Intelligent Matching Identification of Quorum Signal Molecules (N-Acyl-Homoserine Lactones). Int. J. Mol. Sci. 2024, 25, 1901. https://doi.org/10.3390/ijms25031901

AMA Style

Zhang L, Kong X, Qu F, Chen L, Li J, Jiang Y, Wang C, Zhang W, Yang Q, Ye D. Comprehensive Similarity Algorithm and Molecular Dynamics Simulation-Assisted Terahertz Spectroscopy for Intelligent Matching Identification of Quorum Signal Molecules (N-Acyl-Homoserine Lactones). International Journal of Molecular Sciences. 2024; 25(3):1901. https://doi.org/10.3390/ijms25031901

Chicago/Turabian Style

Zhang, Lintong, Xiangzeng Kong, Fangfang Qu, Linjie Chen, Jinglin Li, Yilun Jiang, Chuxin Wang, Wenqing Zhang, Qiuhua Yang, and Dapeng Ye. 2024. "Comprehensive Similarity Algorithm and Molecular Dynamics Simulation-Assisted Terahertz Spectroscopy for Intelligent Matching Identification of Quorum Signal Molecules (N-Acyl-Homoserine Lactones)" International Journal of Molecular Sciences 25, no. 3: 1901. https://doi.org/10.3390/ijms25031901

APA Style

Zhang, L., Kong, X., Qu, F., Chen, L., Li, J., Jiang, Y., Wang, C., Zhang, W., Yang, Q., & Ye, D. (2024). Comprehensive Similarity Algorithm and Molecular Dynamics Simulation-Assisted Terahertz Spectroscopy for Intelligent Matching Identification of Quorum Signal Molecules (N-Acyl-Homoserine Lactones). International Journal of Molecular Sciences, 25(3), 1901. https://doi.org/10.3390/ijms25031901

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