NATPRO Journal

Transcriptomic Profiling of Aging Reveals Coordinated Pathway Decline and a Candidate Reversal Compound 

Received: July 11, 2025; Revised: September 22, 2025; Accepted: September 27, 2025; Published: September 29, 2025

NATPRO J (2025) 2: 25-33

Authors: Kyungmin Kim1, Bumho Yoo1, and Seong-Eui Hong2*

1HuGeX, Co., Ltd., 20, Songdogukje-daero 286beon-gil, Yeonsu-gu, Incheon, 22013, Republic of Korea. 2 4th Floor, Dream Hall, Korea Polytechnic Colleage– Seongnam Campus 398, Sujeong-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13122 Republic of Korea.

https://doi.org/10.23177/NJ025.701

Abstract: Aging is a complex biological process marked by widespread and coordinated transcriptional changes across multiple functional pathways. To investigate these changes, we analyzed RNA-seq data from human breast primary skin fibroblast cultured over extended passages, comparing early (P6) and late (P36) stages to model replicative aging. Differential expression analysis revealed 1,378 genes significantly altered with aging. Among these, five major pathways were consistently affected: G2-M Checkpoint, Myc Targets V1, Cholesterol Homeostasis, Interferon Alpha Response, and Inflammatory Response. To explore therapeutic implications, we integrated these gene signatures with the LINCS L1000 Chem Pert up dataset. Bosutinib, a Src/Abl kinase inhibitor, emerged as a top candidate predicted to reverse aging-associated transcriptional decline across all five functional categories. These findings highlight the utility of transcriptomic profiling combined with perturbation-based analysis to uncover biological changes linked to aging and nominate pharmacological candidates with geroprotective potential.

Keywords: aging, transcriptome, pathway

Structure and Bioactivity of Acidic Polysaccharides from Natural Resources 

Received: June 11, 2025; Revised: July 21, 2025; Accepted: July 22, 2025; Published: July 26, 2025

NATPRO J (2025) 2: 13-24

Author: Toshihiko Toida*

Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuoh-ku, Chiba 263-8675, Japan

https://doi.org/10.23177/NJ025.601

Abstract: Interest in naturally occurring polysaccharides has steadily increased over the past two decades. These compounds have found applications in a variety of fields, including nutraceuticals, cosmetics, pharmaceuticals, and biomedicine. As studies of the structure-activity relationships (SAR) of glycans have progressed, the biological significance and functions of natural polysaccharides have become clearer. This progress has been fueled by significant advancements in enabling technologies, including various isolation and purification methods, chemical reactions that elucidate structures, and analytical tools such as nuclear magnetic resonance (NMR) and mass spectrometry (MS). Recent technological advances have revealed that some polysaccharides have irregular functional group patterns or branched sugar units within regular structures. This review will focus on the SAR of some acidic polysaccharides in the context of pharmaceuticals and nutraceuticals, and new concepts regarding the biological functions of polysaccharides as matrikines, with a particular focus on chondroitin sulfate.

Keywords: acidic polysaccharides, glycosaminoglycans, structure-activity relationship (SAR), nutraceutical; pharmaceutical

Substrate Specificity Determinant of C-Deglycosidase from Human Gut Bacterium Dorea sp. MRG-IFC3

Received: May 19, 2025; Revised: July 14, 2025; Accepted: July 16, 2025; Published: July 21, 2025

NATPRO J (2025) 2: 9-12

Authors: Heji Kim1, Huynh Thi Ngoc Mi1, Joong-Hoon Ahn2, and Jaehong Han1*

1Metalloenzyme Research Group and Department of Plant Science and Technology, Chung-Ang University, 4726 Seodong-daero, Anseong 17546, Republic of Korea. 2Department of Integrative Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 05029, Republic of Korea

https://doi.org/10.23177/NJ025.501

Abstract: The C-deglycosidase from the human gut bacterium Dorea sp. MRG-IFC3 shows high substrate specificity and only cleaves the C-glycosidic bond of puerarin. To elucidate the origin of the peculiar substrate specificity of the C-deglycosidase from the MRG-IFC3 strain, the genes of the C-deglycosidase d3dgpBC were cloned from the MRG-IFC3 strain, and the amino acid sequence was compared with those from the closely related PUE strain. The primary protein structure comparison revealed that four amino acid differences at the positions of 105 and 118 in D3dgpB and at the positions of 196 and 200 in D3dgpC. Except the residue Q118B, all three were found at the surface of the X-ray protein structure of the closely related DgpBC, PDB:7BVR. The residue Q118B was found near the catalytic Mn(II) site at the substrate binding pocket. The modified C-deglycosidase, D3dgpBC with the Q118BP mutation, was prepared to investigate the substrate specificity. The modified enzyme catalyzed the cleavage of the glycosidic C-C bond of various C-glycoside including vitexin, orientin, and puerarin. Thus, Q118B was identified as a key residue preventing flavone C-glycosides from binding to the active site. This work emphasizes the genomics study of gut metabolism through high-throughput sequencing cannot fully reflect the health-promoting effects of the human gut microbiota.

Keywords: gut metabolism, C-deglycosidase, Dorea sp. MRG-IFC3, puerarin, substrate specificity

Identification of Bioactive Polyphenols from Wild-Type Phellinus linteus Using LC-MS and NMR

Received: February 19, 2025; Revised: April 1, 2025; Accepted: April 7, 2025; Published: April 14, 2025

NATPRO J (2025) 2: 1-7

Authors: Papawee Saiki1, Leo J. L. D. Van Griensven2, and Toshihiko Toida3*

1Cellular and Molecular Biotechnology Research Institute, National Institute of Advance Industrial Science and Technology, Tsukuba 305-8566, Japan

2Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands. 3Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, Japan

https://doi.org/10.23177/NJ025.201

Abstract: Phellinus linteus (L.) Quel. has been used in traditional Asian medicine for over two centuries against a variety of diseases. Many researchers have focused on the antioxidant properties of polyphenols from Phellinus linteus (P. linteus), however, this mushroom lacks identification of its polyphenols. We demonstrated the presence of nine polyphenol compounds i.e. 3,4-dihydroxybenzaldehyde, 4-(3,4-dihydroxyphenyl)-3-buten-2-one, interfungin A, inonoblin C, phelligridin D, interfungin B, inoscavin E, inoscavin C and methylinoscavin D in the ethanol extract of P. linteus fruiting bodies by LC-MS. The chromatographic separation was performed on a common reversed-phase C18 column using a water–acetonitrile with formic acid gradient program and the detection was achieved by ESI source operated in negative ion mode. Further characterization of P. linteus polyphenols was done by proton nuclear magnetic resonance spectroscopy (1H NMR) which showed strong proton resonances of 3,4-dihydroxybenzaldehyde, interfungin A, inonoblin C, phelligridin D, inoscavin E and inoscavin C.

Keywords: LC-MS, NMR, Phellinus linteus, polyphenol