Article
Food Science & Technology
Wen Li, Wanchao Chen, Jinbin Wang, Zhengpeng Li, Zhong Zhang, Di Wu, Mengqiu Yan, Haile Ma, Yan Yang
Summary: This study revealed the binding conformations between undecapeptides from Stropharia rugosoannulata and ACE receptor through molecule docking. GQEDYDRLRPL, a screened undecapeptide, showed better receptor binding capacity and higher secondary mass spectral abundance. The interaction of GQEDYDRLRPL with the ACE receptor affected the overall structure of the receptor and exhibited strong binding. In vitro and in vivo experiments demonstrated its superior antihypertensive effects.
Article
Biochemistry & Molecular Biology
Linan Zhao, Le Fu, Guangping Li, Yongxin Yu, Juan Wang, Haoran Liang, Mao Shu, Zhihua Lin, Yuanqiang Wang
Summary: In this study, 3D-QSAR models were established to investigate the relationship between molecular structure and inhibitory activity for multivariate-substituted 4-oxyquinazoline HDAC6 inhibitors. The models showed good predictive ability and passed internal verification, external verification, and AD testing. Molecular docking and dynamics simulation were used to explore the interaction between compounds and HDAC6. The study provided theoretical references for designing compounds with higher activity and offered a new idea for the development of novel HDAC6 inhibitors.
MOLECULAR DIVERSITY
(2023)
Article
Biochemistry & Molecular Biology
Khandekar Mangala, Walhekar Vinayak, Choudhary Aasiya, Bagul Chandrakant, Muthal Amol, Dilip Kumar, Ravindra Kulkarni
Summary: This study used ligand-based and structure-based methods to develop new inhibitors of PIM-1 kinase as anticancer agents. 3D-QSAR analysis revealed the correlation between compound structures and biological activities. Molecular docking and dynamics simulations showed that compound 26 had the highest activity and interacted with the active site of PIM-1 kinase through hydrogen bonds. The results demonstrated the successful application of ligand and structure-based strategies in drug development.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Yingqi Qiu, Yuanmeng Wang, Jiahao Lu, Qinghua Zhu, Li Jia, Fuhou Lei, Liqun Shen, Lihe Jiang, Aiqun Wu
Summary: This study involved the chemical modification of curcumin to obtain tetrahydrocurcumin and demonstrated its enhanced physiological and antioxidant activities compared to curcumin. The computational pharmacology techniques provided a theoretical basis for the development and modification of high-efficiency, low-toxicity drugs that interact with various targets of curcumin in the future.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Review
Multidisciplinary Sciences
Jiashun Mao, Javed Akhtar, Xiao Zhang, Liang Sun, Shenghui Guan, Xinyu Li, Guangming Chen, Jiaxin Liu, Hyeon-Nae Jeon, Min Sung Kim, Kyoung Tai No, Guanyu Wang
Summary: The paper discusses the integration of wet experiments, molecular dynamics simulation, and machine learning techniques to improve QSAR models, proposing a new iterative framework. It also explores the application of QSAR and machine learning in drug development and clinical trials.
Article
Biotechnology & Applied Microbiology
Yilin Hou, Qing Li, Wei He, Mingyue Li, Jiaqi Xue, Xinao Li, Yu Li
Summary: Molecular docking was used to study the biodegradation of fluoroquinolones under different conditions and design derivatives suitable for aerobic, facultative, and anaerobic biodegradation. These derivatives exhibited improved environmental friendliness and biodegradation performance.
BIOCHEMICAL ENGINEERING JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Chuanbo Li, Xiaoyu Yang, Yajun Lang, Chunying Liu, Shaohua Dou
Summary: This study investigated the effects of charged short peptides on the activity and structure of glucose oxidase (GOx). The results showed that negatively charged peptides increased enzyme activity, while positively charged peptides decreased it. The peptides altered the microenvironment and charge arrangement of GOx, resulting in conformational changes and altered enzymatic activity.
PROCESS BIOCHEMISTRY
(2023)
Article
Chemistry, Physical
Tetsuro Nagai, Akira Yoshimori, Susumu Okazaki
Summary: This study investigates a series of new Monte Carlo transition probabilities that can simulate molecular trajectories satisfying the diffusion equation. The results show good agreement with the numerical solution. The method is useful for studying long-distance transport of molecules in heterogeneous systems and many-particle dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Agronomy
Wei Zhang, Shengxin Guo, Ya Wang, Yikun Wu, Lijiao Yu, Jian Wu
Summary: Novel compounds S1-S28 were synthesized and evaluated for their curative effects against CMV. Compound S8 showed a strong binding affinity to CMV-coat protein and impacted the self-assemble of CMV particles, making it a potential lead compound for discovering a new anti-plant virus candidate.
PEST MANAGEMENT SCIENCE
(2023)
Review
Food Science & Technology
Zhiyun Peng, Guangcheng Wang, Qiao-Hui Zeng, Yufeng Li, Haiquan Liu, Jing Jing Wang, Yong Zhao
Summary: Tyrosinase is a copper-containing oxidation enzyme responsible for melanin production and plays a key role in browning, antibiotic resistance, pigment formation, etc. Synthetic tyrosinase inhibitors have great potential applications and have been widely reported in recent years.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Chemistry, Medicinal
Young-Hwan Jung, Veronica Salmaso, Zhiwei Wen, John M. Bennett, Ngan B. Phung, David Lieberman, Varun Gopinatth, John C. R. Randle, Zhoumou Chen, Daniela Salvemini, Tadeusz P. Karcz, Donald N. Cook, Kenneth A. Jacobson
Summary: Through substituting diverse groups on the central phenyl and terminal piperidine moieties, the study aimed to optimize the activity of P2Y(14)R antagonists. It was found that the introduction of an uncharged piperidine bioisostere significantly impacted receptor affinity during the experimental process.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Prangya Rath, Anuj Ranjan, Arabinda Ghosh, Abhishek Chauhan, Manisha Gurnani, Hardeep Singh Tuli, Hamza Habeeballah, Mustfa F. Alkhanani, Shafiul Haque, Kuldeep Dhama, Naval Kumar Verma, Tanu Jindal
Summary: The increase in the number of cases of type 2 diabetes mellitus (T2DM) and the complications associated with the side effects of chemical/synthetic drugs have raised concerns about the safety of the drugs. Hence, there is an urgent need to explore and identify natural bioactive compounds as alternative drugs. This article focuses on the screening of a database of polyphenols against PTP1B activity to identify a potential inhibitor. The results show that silydianin, a flavonolignan, has drug-like properties and can act as a promising natural PTP1B inhibitor to modulate insulin resistance.
Article
Chemistry, Analytical
Deepak Kumar, Rajasri Bhattacharyya, Dibyajyoti Banerjee
Summary: In this study, Fast Blue BB was identified to specifically stain the pseudoesterase activity of HSA in gel, with 2-NA as the ester substrate. The addition of neostigmine did not inhibit this activity, providing specificity to the method. A simple and novel method for HSA detection on gel was devised, allowing for accurate detection without interference from other esterases.
Article
Biochemistry & Molecular Biology
N. L. vonRanke, M. M. J. Ribeiro, L. A. Miceli, N. P. de Souza, B. A. Abrahim-Vieira, H. C. Castro, V. L. Teixeira, C. R. Rodrigues, A. M. T. Souza
Summary: In this study, molecular modeling techniques were used to investigate marine natural products with anti-HIV activity. The results suggest that dolabelladienetriol may have the potential to be developed as an effective antiretroviral drug, based on its interaction with the allosteric site of HIV-1 reverse transcriptase and its ability to induce conformational changes in the enzyme. The in silico ADMET simulations also support the promising prospects of dolabelladienetriol as a drug candidate.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Multidisciplinary
Morteza Sadeghi, Mehdi Shakouri Khomartash, Sattar Gorgani-Firuzjaee, Mahmoud Vahidi, Farhad Motevalli Khiavi, Parham Taslimi
Summary: This study found that the flower extract of D.sophia contains abundant phenolic compounds and exhibits antioxidant capacity and inhibitory activity against α-glucosidase. In vivo experiments confirmed that the consumption of flower extract can lower blood glucose levels. Molecular docking and molecular dynamics simulations suggested that one of the compounds has a stronger binding affinity with α-glucosidase. Therefore, the flower extract of D.sophia can be used as a natural additive with anti-diabetic properties.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Yoshifumi Fukunishi, Tadaaki Mashimo, Takashi Kurosawa, Yoshinori Wakabayashi, Hironori K. Nakamura, Koh Takeuchi
MOLECULAR INFORMATICS
(2020)
Article
Chemistry, Medicinal
Atsushi Tokuhisa, Ryo Kanada, Shuntaro Chiba, Kei Terayama, Yuta Isaka, Biao Ma, Narutoshi Kamiya, Yasushi Okuno
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Chemistry, Multidisciplinary
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2020)
Article
Chemistry, Medicinal
Junichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Biochemistry & Molecular Biology
Miho Emori, Nobutaka Numoto, Akane Senga, Gert-Jan Bekker, Narutoshi Kamiya, Yuma Kobayashi, Nobutoshi Ito, Fusako Kawai, Masayuki Oda
Summary: The study demonstrated that Cut190*SS increased thermal stability while maintaining enzymatic function, attributed to the formation of a disulfide bond by Cys250 and Cys296. Results indicated that although the metal-binding properties of Cut190*SS series differed, the enzyme retained its ability to utilize Ca2+ to accelerate conformational change, thereby preserving its functionality.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Gert-Jan Bekker, Ikuo Fukuda, Junichi Higo, Yoshifumi Fukunishi, Narutoshi Kamiya
Summary: The study utilized McMD technique to investigate the binding mechanism of two inhibitors (ABT-737 and WEHI-539) to the cryptic site of Bcl-xL, showing that stable binding configurations were formed via predominantly hydrophobic interactions, and the ligands modulated the conformational preference of Bcl-xL's sub-pockets.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Medicinal
Kei Moritsugu, Koh Takeuchi, Narutoshi Kamiya, Junichi Higo, Isao Yasumatsu, Yoshifumi Fukunishi, Ikuo Fukuda
Summary: This study reveals the molecular mechanism underlying the change in cell permeability of cyclic peptides, which is attributed to the loss of flexibility in modified residues leading to conformational changes that decrease cell permeability.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Mitsugu Araki, Shigeyuki Matsumoto, Gert-Jan Bekker, Yuta Isaka, Yukari Sagae, Narutoshi Kamiya, Yasushi Okuno
Summary: Capturing the dynamic processes of biomolecular systems in atomistic detail remains difficult, but researchers have developed a method using high-frequency ultrasound perturbation to accelerate MD simulations and detect binding events between proteins and inhibitors. This innovative approach has successfully accelerated slow binding rates and revealed microscopic kinetic features, offering deeper insights into the interactions controlling biomolecular processes.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Tomonori Hayami, Narutoshi Kamiya, Kota Kasahara, Takeshi Kawabata, Jun-ichi Kurita, Yoshifumi Fukunishi, Yoshifumi Nishimura, Haruki Nakamura, Junichi Higo
Summary: A study using a genetic algorithm-guided multi-dimensional virtual-system-coupled canonical molecular dynamics method analyzed the interactions between sertraline, YN3, acitretin and the mSin3B protein. The results showed that only sertraline and YN3 exhibited high affinity for binding to the cleft of mSin3B, forming a hydrophobic core, while acitretin did not. This study proposes a new approach to design compounds that competitively inhibit ligand-receptor binding.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Medicinal
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Summary: This study utilized the McMD method for structure-based dynamic docking experiments to investigate the structure and ligand interactions of G-protein-coupled receptor systems. Through simulation and analysis, the stability of different ligand binding states and intermediates were revealed, providing valuable insights for the rational design of drugs targeting GPCRs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Gert-Jan Bekker, Narutoshi Kamiya
Summary: The study utilized the McMD-based dynamic docking method to investigate the binding mechanism of an HIV-1 Nef protein epitope to HLA-A*2402, successfully reproducing the native complex structure and elucidating details of the peptide binding process, providing insights for the development of new vaccines.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Junichi Higo, Kota Kasahara, Gert-Jan Bekker, Benson Ma, Shun Sakuraba, Shinji Iida, Narutoshi Kamiya, Ikuo Fukuda, Hidetoshi Kono, Yoshifumi Fukunishi, Haruki Nakamura
Summary: In this study, a GA-mD-VcMD simulation method was used to investigate the binding mechanism of bosentan to hETB protein. The results showed that bosentan was initially captured by the tip region of hETB and then slid to the root region of the N-terminal tail. During this sliding, bosentan passed the gate of the binding pocket and formed attractive native contacts with the receptor. The study provides insights into the binding mechanism of bosentan to hETB protein.
SCIENTIFIC REPORTS
(2022)
Review
Biophysics
Gert-Jan Bekker, Narutoshi Kamiya
Summary: Multicanonical molecular dynamics-based dynamic docking is a powerful tool that accurately predicts the binding configuration between flexible molecules, provides insights into binding pathways, and can identify alternative binding sites through exhaustive sampling.
BIOPHYSICAL REVIEWS
(2022)
Article
Biology
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Summary: Dynamic docking simulations reveal the interactions and conformational changes of the intrinsically disordered region of Bim and its cryptic binding site in Bcl-xL, a pro-survival protein involved in cancer progression.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Gert-Jan Bekker, Nobutaka Numoto, Maki Kawasaki, Takahiro Hayashi, Saaya Yabuno, Yuko Kozono, Takeyuki Shimizu, Haruo Kozono, Nobutoshi Ito, Masayuki Oda, Narutoshi Kamiya
Summary: This study investigates the complex structure and binding mechanism of a modified Wilms' Tumor 1 (mWT1) protein epitope to the Asian-dominant allele HLA-A*24:02 (HLA-A24) in aqueous solution. The research reveals that an encounter complex is formed between the N-terminal's positive charge of the mWT1 peptide and a negative residue cluster on the surface of HLA-A24, followed by the binding of the peptide to form the native complex structure. Furthermore, the study suggests that the binding depends on the intrinsic affinity between the MHC molecule and the antigen peptide.