Article
Biochemistry & Molecular Biology
Yan Guo, Yulong Jin, Bingfeng Wang, Boping Liu
Summary: The study systematically evaluated the inhibitory mechanism of BMS-200-related small-molecule inhibitors in PD-L1 dimer using molecular dynamics simulations and binding free energy analysis. The results show that these inhibitors can promote the dimerization of PD-L1 and mainly bind with specific regions of the PD-L1 dimer. Additionally, compared to (S)-BMS-200, (R)-BMS-200 is more likely to form hydrogen bonds with charged residues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Xiaowen Zhou, Jiangfeng Du, Xiuman Zhou, Xiaoshuang Niu, Wanqiong Li, Chunxia Chen, Sifan Lv, Aijun Wu, Shanshan Gou, Yixuan Sun, Wenjie Zhai, Lu Qiu, Yuanming Qi, Wenshan Zhao, Yanfeng Gao
Summary: The study utilized molecular dynamics simulations and in silico mutagenesis to analyze the interaction between the immune checkpoint molecule TIGIT and its ligand PVR. It identified potential residues for interaction and predicted high affinity PVR mutants that showed enhanced inhibitory effects compared to wild type PVR in cancer immunotherapy.
CELL COMMUNICATION AND SIGNALING
(2021)
Article
Chemistry, Multidisciplinary
Carlos A. Ramos-Guzman, Milorad Andjelkovic, Kirill Zinovjev, J. Javier Ruiz-Pernia, Inaki Tunon
Summary: In this study, the by-residue decomposition of noncovalent interactions and analysis of naturally occurring mutations were used to detect potential mutations in the 3CL protease of SARS-CoV-2 that confer resistance to nirmatrelvir. It was found that the E166V mutation reduces the binding affinity of the protease to nirmatrelvir and increases the activation free energy for the formation of the covalent enzyme-inhibitor complex, resulting in resistance to the treatment with this drug. The conclusions of this study can be useful for predicting the consequences of introducing nirmatrelvir in the virus fitness landscape and designing new inhibitors targeting possible resistance mechanisms.
Article
Biochemistry & Molecular Biology
Xuehui Guo, Yiming Jiang, Daiqian Xie, Yanzi Zhou
Summary: Poly(ethylene terephthalate) (PET) is widely used in daily life, but its non-degradability causes environmental and health problems. PETase from Ideonella sakaiensis has shown the highest PET degradation activity, but the crystal structure of the PET-PETase complex remains unknown. Molecular docking and dynamics simulations were used to study the binding and interactions between PET and PETase. The PET oligomers adopt stable conformations in a shallow cleft on PETase, with only four moieties fitting in the binding cleft. This study provides insights into PET binding and can aid the design of more efficient PETase variants for plastic degradation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Nisha Amarnath Jonniya, Sayan Poddar, Subhasmita Mahapatra, Parimal Kar
Summary: Dengue virus is the most important emerging viral disease, causing nearly 400 million infections yearly, with no approved therapies. Lifelong immunity against the same serotype but severe disease in heterotypic infections. Understanding antibody neutralization mechanism crucial for vaccine design.
CELL BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Chemistry, Medicinal
Bharath Raghavan, Mirko Paulikat, Katya Ahmad, Lara Callea, Andrea Rizzi, Emiliano Ippoliti, Davide Mandelli, Laura Bonati, Marco De Vivo, Paolo Carloni
Summary: Currently, in silico drug design in the initial stages of drug discovery can benefit from first-principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, but many applications are limited by the short time scales that this approach can cover. The development of scalable first principle QM/MM MD interfaces that fully exploit current exascale machines is crucial in overcoming this problem and allowing for the study of ligand binding to protein with first principle accuracy. This study showcases the use of the Multiscale Modeling in Computational Chemistry (MiMiC) QM/MM framework, which demonstrates strong scaling and parallel efficiency of >70% up to >80,000 cores, making it a promising candidate for exascale applications.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Lea El Khoury, David L. Mobley, Dongmei Ye, Susan B. Rempe
Summary: The study predicted the binding mode of organophosphorus hydrolase with paraoxon using docking and molecular dynamics, identifying three hot-spot residues involved in the stability of the active site. Experimental results showed specific mutants exhibited enhanced substrate binding affinity for paraoxon.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yinli Gao, Hanxun Wang, Lanlan Shen, Hanqing Xu, Minghui Deng, Maosheng Cheng, Jian Wang
Summary: The inhibition of PD-1/PD-L1 interaction through small molecule inhibitors has shown potential in cancer immunotherapy.
BIOORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yu Wang, Baozhu Dong, Dong Wang, Xinyu Jia, Qian Zhang, Wanyou Liu, Hongyou Zhou
Summary: This study investigated the target sites of (-)-Spirobrassinin using molecular docking, molecular dynamics simulations, and biological experiments. It found that (-)-Spirobrassinin inhibits crucial enzymes involved in plant metabolic pathways and disrupts the metabolism of abscisic acid and gibberellin. Molecular dynamics simulations revealed stable interactions between (-)-Spirobrassinin and specific residues of photosystem II D1. This study provides valuable insights into the mode of action of (-)-Spirobrassinin and highlights its potential as a natural herbicide from Brassicaceae plants.
APPLIED SCIENCES-BASEL
(2023)
Article
Biotechnology & Applied Microbiology
Michael Kenn, Rudolf Karch, Lisa Tomasiak, Michael Cibena, Georg Pfeiler, Heinz Koelbl, Wolfgang Schreiner
Summary: This research examines the molecular motion of PD-1 with its binding partner PD-L1 and proposes a method of quantifying minute differences in molecular motion using semi-rigid domains as reference frames. Several reliable reference frames are established for future investigations based on molecular motion.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yanjun Zhang, Lu Chen, Zhonghua Wang, Yiren Zhu, Huifang Jiang, Jie Xu, Fei Xiong
Summary: This study investigated the relationship between the structure and activity of DABO derivatives as HIV-1 reverse transcriptase inhibitors. The results showed that the designed molecules had higher predictive activity and their stability was verified through MD simulation and binding free energy. Furthermore, the pharmacokinetic properties of the designed molecule were confirmed using ADMET.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Lea El Khoury, Zhifeng Jing, Alberto Cuzzolin, Alessandro Deplano, Daniele Loco, Boris Sattarov, Florent Hedin, Sebastian Wendeborn, Chris Ho, Dina El Ahdab, Theo Jaffrelot Inizan, Mattia Sturlese, Alice Sosic, Martina Volpiana, Angela Lugato, Marco Barone, Barbara Gatto, Maria Ludovica Macchia, Massimo Bellanda, Roberto Battistutta, Cristiano Salata, Ivan Kondratov, Rustam Iminov, Andrii Khairulin, Yaroslav Mykhalonok, Anton Pochepko, Volodymyr Chashka-Ratushnyi, Iaroslava Kos, Stefano Moro, Matthieu Montes, Pengyu Ren, Jay W. Ponder, Louis Lagardere, Jean-Philip Piquemal, Davide Sabbadin
Summary: We report a computationally driven discovery of new SARS-CoV-2 main protease (M-pro) inhibitors, whose potency has been significantly improved from initial non-covalent ligands to final covalent compound. The study highlights the power of structure-based computational strategies for drug design and provides insights for further optimization of M-pro inhibitors.
Article
Biochemistry & Molecular Biology
Erich Michel, Stefano Cucuzza, Peer R. E. Mittl, Oliver Zerbe, Andreas Plueckthun
Summary: The study aims to improve the stability of proteins for applications in therapeutics, diagnostics, and basic research. By designing a novel N-cap protein, the stability of proteins was successfully enhanced, addressing the issue of partial unfolding and making the proteins more resistant to proteolysis and aggregation.
Article
Biochemistry & Molecular Biology
Laxman Durgam, Jishu Pagag, Y. Indra Neela, Lalitha Guruprasad
Summary: The Zika virus NS3-helicase is a promising drug target for inhibiting viral replication. Through amino acid mutational analyses, two crucial binding sites of NS3-helicase were identified. Potential inhibitors were discovered through virtual screening, molecular docking, and molecular dynamics simulations, with their drug-like properties analyzed. These findings are significant for the development of new inhibitors to treat Zika virus infection.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Jinying Cheng, Xue Yin, Lulu Wang, Xianxian Liu, Fang Yang, Liguo Zhang, Tonggang Liu
Summary: This study investigates the molecular mechanism of species-selective targeting of fungal versus human HSP90 triggered by the compound A11. The results provide insights into the conformational changes and binding affinities of compound A11 to fungal and human HSP90 and identify key residues for favorable binding. This study has important implications for the development of selective inhibitors targeting fungal HSP90.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biology
Ranran Shi, Yubing Li, Ling Ran, Yu Dong, Xiuman Zhou, Jingwen Tang, Lu Han, Mingshuang Wang, Liwei Pang, Yuanming Qi, Yahong Wu, Yanfeng Gao
Summary: Researchers identified three HLA-A2-restricted neoepitopes that could induce specific antitumor T cell responses in non-MSI-H colorectal cancer, showing promise for potential immunotherapy. The combination of adoptive T cell therapy based on these neoepitopes with immune checkpoint inhibitors, such as anti-PD-1, could provide a promising treatment strategy for non-MSI-H colorectal cancer.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Chemistry, Organic
Xiyuan Zhang, Cong Zhang, Bo Jiang, Yanfeng Gao, Xiufang Xu, Zhiwei Miao
Summary: We report regiodivergent ligand-controlled palladium-catalyzed asymmetric cycloaddition reactions. By using different chiral ligands, the reactions can be controlled to give different reaction pathways and stereoselectivities.
Article
Automation & Control Systems
Jianbo Yu, Chaoang Xiao, Tianzhong Hu, Yanfeng Gao
Summary: This paper introduces a new multi-scale morphological filtering method called selective weighted multi-scale morphological filter (SWMMF). This method combines filtering results of different scales based on an adaptive weighting strategy to enhance the extraction of faulty components. The effectiveness of this approach is proven by comparing it with single-scale and average weighting filters on simulation and real-world cases (bearing vibration signals with different defects).
Article
Materials Science, Multidisciplinary
Wenhu Xu, Jin Yang, Mingjian Peng, Yixuan Zhao, Hongbin Liu, Peiran Deng, Yanfeng Gao, Hua Zhang
Summary: This study proposed a torch-offset CMT-CS welding method for joining different aluminum alloys and copper. The experiments showed that the offset distance had a significant influence on the weld heat input and the wettability of the filler material. Moreover, changing the joint configuration led to variations in the mechanical properties and fracture modes of the weld.
JOURNAL OF MATERIALS ENGINEERING AND PERFORMANCE
(2023)
Article
Chemistry, Physical
Jiadong Zhou, Chao Zhu, Yao Zhou, Jichen Dong, Peiling Li, Zhaowei Zhang, Zhen Wang, Yung-Chang Lin, Jia Shi, Runwu Zhang, Yanzhen Zheng, Huimei Yu, Bijun Tang, Fucai Liu, Lin Wang, Liwei Liu, Gui-Bin Liu, Weida Hu, Yanfeng Gao, Haitao Yang, Weibo Gao, Li Lu, Yeliang Wang, Kazu Suenaga, Guangtong Liu, Feng Ding, Yugui Yao, Zheng Liu
Summary: This study reveals a competitive-chemical-reaction-based growth mechanism that allows for the growth of transition metal chalcogenides and transition metal phosphorous chalcogenides with different compositions and phases. It provides an interesting platform for the exploration of 2D TMPCs and TMCs.
Article
Oncology
Ranran Shi, Xiuman Zhou, Liwei Pang, Mingshuang Wang, Yubing Li, Chunxia Chen, Haoming Ning, Lihan Zhang, Guangxing Yue, Lu Qiu, Wenshan Zhao, Yuanming Qi, Yahong Wu, Yanfeng Gao
Summary: The majority of non-microsatellite instability-high colorectal cancers are immunologically cold due to poor CD8(+) T cell infiltration. The discovered cancer-testis antigen (CTA) ODF2 is negatively correlated with CD8(+) T cell infiltration and can improve CTA infiltration through upregulating interleukin-15.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2023)
Correction
Medicine, Research & Experimental
Zhenzhen Chen, Pingping Zhu, Yushun Zhang, Yating Liu, Yuling He, Lifen Zhang, Yanfeng Gao
MOLECULAR PHARMACEUTICS
(2022)
Article
Nanoscience & Nanotechnology
Yanfeng Gao, Dongtao Zhou, Qin Xu, Jingjing Li, Wen Luo, Jingjing Yang, Yongchun Pan, Ting Huang, Yanping Wang, Bangshun He, Yujun Song, Yuzhen Wang
Summary: In this study, a fluorescent bacteria counting immunoassay (FBCIA) strategy was developed for ultrasensitive quantification of protein biomarkers. The strategy involved a cascade signal conversion and amplification strategy, which enabled the conversion of target protein concentration to countable bacterial number. The developed platform demonstrated highly sensitive detection of CEA and PSA with low detection limits, and a smartphone device was also developed for point-of-care counting. The good consistency between FBCIA and clinical ELISA validated the high reliability and promising potential of the platform in clinical applications.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Applied
Xiyuan Zhang, Yanfeng Gao, Zhiwei Miao
Summary: Palladium-catalyzed asymmetric [4+3] cycloadditions of indene-2-carbaldehydes and 4-vinyl benzoxazinanones proceeded smoothly in the presence of chiral phosphine ligands to give the corresponding functionalized 5H-benzo[b]azepines (26 examples, 60% to 89% yield, 88:12 to 95.5:4.5 er) under mild conditions.
ADVANCED SYNTHESIS & CATALYSIS
(2023)
Article
Chemistry, Analytical
Yanfeng Gao, Yanping Wang, Xinli Liu, Zhenxing Zhu, Zhun Li, Zhibin Zhang, Yi Yin, William Chi Shing Cho, Yujun Song, Yuzhen Wang
Summary: We developed a signal amplification method based on streamlined click reactions to immobilize large amounts of hemin on graphene oxide nanosheets, allowing for highly sensitive detection of various biological targets. The designed platform shows great promise for graphene-based nanozymes and sensitive biosensing in a wider range of applications.
ANALYTICA CHIMICA ACTA
(2023)
Article
Chemistry, Multidisciplinary
Wen Su, Mixiao Tan, Zhihang Wang, Jie Zhang, Wenping Huang, Haohao Song, Xinye Wang, Haitao Ran, Yanfeng Gao, Guangjun Nie, Hai Wang
Summary: Proteolysis targeting chimeras (PROTACs) technology is a promising method for degrading disease-associated proteins. In this study, carbon-dot (CD)-based PROTACs (CDTACs) were developed to degrade membrane proteins via the ubiquitin-proteasome system. CDTACs demonstrated efficient degradation of programmed cell death ligand 1 (PD-L1) and activation of the stimulator of interferon genes (STING) pathway, leading to the inhibition of tumor growth. CDTACs offer advantages such as targeted tumor accumulation, immune system activation, and in vivo detection compared to small-molecule-based PROTACs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Fisheries
Shiyong Yang, Weikai Sui, Xiaoyu Ren, Xiaoyu Wang, Guixian Bu, Fengyan Meng, Xiaohan Cao, Guozhi Yu, Xingfa Han, Anqi Huang, Qiuxia Liang, Jiayun Wu, Yanfeng Gao, Xiuhong Wang, Xianyin Zeng, Xiaogang Du, Yunkun Li
Summary: In this study, the TLR18 and UNC93B1 genes were cloned from Schizothorax prenanti. It was found that TLR18 can activate immune response through NF-kappa B and type I IFN pathways in teleost fishes, and UNC93B1 positively regulates TLR18-mediated NF-kappa B signal.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Engineering, Industrial
Jianbo Yu, Shijin Li, Xing Liu, Yanfeng Gao, Shijin Wang, Changhui Liu
Summary: This paper proposes a new method, DCGRUA-AE, for fault detection in dynamic industrial processes. The method integrates CGRU, attention mechanism, and auto-encoder to learn both global and local features of dynamic process data. The feasibility and superiority of the method have been verified through experiments on four industrial processes.
INTERNATIONAL JOURNAL OF PRODUCTION RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Yongchun Pan, Xiaowei Luan, Yanfeng Gao, Fei Zeng, Xuyuan Wang, Dongtao Zhou, Wanqi Li, Yuzhen Wang, Bangshun He, Yujun Song
Summary: Researchers have designed a cancer-activated nanomachine based on porous upconversion nanoparticles for precise phototherapy. The nanosystem contains a telomerase substrate primer and encapsulates 5-aminolevulinic acid and D-arginine. After coating with hyaluronic acid, the nanomachine can easily enter tumor cells and induce efficient accumulation of protoporphyrin IX via biosynthetic pathway. The nanomachine can respond to near-infrared light and generate active singlet oxygen through Förster resonance energy transfer. Moreover, it can relieve tumor hypoxia by converting D-arginine into nitric oxide, thereby improving the phototherapy effect.
Article
Oncology
Xinghua Sui, Chunxia Chen, Xiuman Zhou, Xueyan Wen, Chao Shi, Guanyu Chen, Juan Liu, Zhuoying He, Yongjie Yao, Yin Li, Yanfeng Gao
Summary: This study integrated single-cell transcriptomic sequencing and large microarray sequencing to investigate key cell subtypes and therapeutic targets in esophageal squamous cell carcinoma (ESCC). The researchers discovered that the chemokine CCL18 secreted by tumor associated macrophages promotes tumor cell proliferation through the JAK2/STAT3 signaling pathway and leads to poor prognosis of ESCC. CCL18 blockade was found to significantly prevent the progression of ESCC, providing novel therapeutic targets and strategies for ESCC treatment.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)