Article
Chemistry, Medicinal
Yuan Zhang, Juan Liu, Xin Wu, Suming Yang, Yao Li, Songbin Liu, Saifei Zhu, Xuan Cao, Zhizhong Xie, Xiaoyong Lei, Honglin Huang, Junmei Peng
Summary: The anti-chronic myeloid leukemia activity of thiazole aminobenzamide derivatives was tested in vitro using a viability assay method and was found to exhibit good inhibitory activities. Analysis using CoMFA and CoMSIA showed a relationship between the structure of these derivatives and their inhibition of leukemia cell activity, with specific substitutions improving the anti-CML activity.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Jin-Hee Kim, Jin-Hyun Jeong
Summary: In this study, a series of thieno-pyrimidine derivatives were analyzed using three-dimensional quantitative structure-activity relationship (3D-QSAR) to identify key structural features for inhibitory biological activities. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were established, showing reliable and robust performance. The predictive capabilities of these models were confirmed through external validation and progressive scrambling stability test. This research provides valuable information for the further optimization and design of novel inhibitors against metastatic breast cancer.
Article
Chemistry, Multidisciplinary
Yunmei Liu, Zejie Tian, Hui Li, Zhenhua Liu, Lei Shi, Lingyan Yang
Summary: In this study, 3D-QSAR models were constructed to investigate the structure-activity relationship of chrysin. The structures of 54 chrysin derivatives were constructed using SYBYL-X 2.0 software, and the models were built using CoMFA and CoMSIA methods. The results showed that certain groups attached to the 7-O-alkane chain of chrysin, such as amino acids, enhance its activity, while excessively long chains or bulky hydrophobic groups reduce the activity. On the other hand, the introduction of bulky hydrophobic groups on the side chains of amino acids increases the activity of the molecule.
JOURNAL OF MATHEMATICAL CHEMISTRY
(2023)
Article
Agriculture, Multidisciplinary
Lihui Shao, Su Zhao, Song Yang, Xiang Zhou, Yan Li, Chengpeng Li, Danping Chen, Zhuirui Li, Guiping Ouyang, Zhenchao Wang
Summary: To discover novel antibacterial agents, two series of quinazolinone derivatives with novel structures were synthesized and their bioactivity against plant bacteria was tested. Compound D32 was identified as a potent antibacterial inhibitor against Xanthomonas oryzae pv. Oryzae (Xoo), with better inhibitory capacity compared to the commercial drugs. Further investigation revealed the mechanism of action of D32, which provides clues for the development of new therapeutic strategies.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Physical
Ankitkumar Patel, Hardik Bhatt, Bhumika Patel
Summary: This study carried out 3D-QSAR research on Tankyrase inhibitors using various techniques, providing significant insights for the design of novel quinazolinone derivatives as potent inhibitors.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Chemistry, Organic
Praveen M. Parkali, A. Shyam Kumar, Pohamba K. Johanna, Shilomboleni T. Prodensia, Sruthi Turaga, Vinod Shaiva, Gurubasavaraj Pujar, Shrinivas D. Joshi, Tejraj M. Aminabhavi, Sheshagiri R. Dixit
Summary: Molecular docking and 3D-QSAR studies were conducted on a series of pyrimidine derivatives to develop inhibitors for Enoyl ACP Reductase, a key enzyme in fatty acid biosynthesis and antitubercular drug development. Results from the models and structural features analysis provided insights into predicting better inhibitory potency and the importance of specific amino acid residue interactions. This study contributes to the development of novel Enoyl ACP reductase inhibitors by understanding the specific activity of compounds.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Biochemistry & Molecular Biology
Amina Goudzal, Abdellah El Aissouq, Hicham El Hamdani, El Ghalia Hadaji, Abdelkrim Ouammou, Mohammed Bouachrine
Summary: In this study, a 3D-QSAR analysis was performed on a series of 2, 4, 5-trisubstituted imidazole derivatives to design potent kinase II alpha subunit (CK2) inhibitors. The COMFA and COMSIA models showed excellent performance with high Q(2) and R-2 values. The validity of the models was confirmed through various validation tests. The study's findings provide useful theoretical references for future experimental studies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Pharmacology & Pharmacy
Yuwei Wang, Yifan Guo, Shaojia Qiang, Ruyi Jin, Zhi Li, Yuping Tang, Elaine Lai Han Leung, Hui Guo, Xiaojun Yao
Summary: In this study, the structure-activity relationships and binding modes of a series of anthraquinone derivatives targeting PGAM1 were investigated using 3D-QSAR, molecular docking, and molecular dynamics simulations, which showed satisfactory predictive ability. Molecular dynamics simulations revealed key residues and dominant interactions, as well as stable hydrogen bond formations during the ligand binding process. Overall, the study provided theoretical guidance for the design of new anthraquinone derivatives as PGAM1 inhibitors.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Bhumi M. Shah, Sneha R. Sagar, Priti Trivedi
Summary: Researchers have identified DPP IV as a target for diabetes treatment, and 3D QSAR studies have helped to determine important structural features of triazole derivatives, leading to the design of novel compounds that may serve as promising DPP IV inhibitors for the treatment of diabetes.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Medicinal
Han Lv, Yongli Du, Xiehuang Sheng, Zhipei Gao, Jingkang Shen
Summary: The study focused on exploring the structure-activity relationship of CDK4 inhibitor analogs and designing potent CDK4 inhibitors for breast cancer therapy. By establishing a 3D quantitative structure-activity relationship model and conducting molecular dynamics simulation studies, valuable insights were gained for developing novel CDK4 inhibitors. Four novel inhibitors with satisfactory predicted binding affinity to CDK4 were successfully designed based on the findings.
FUTURE MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Agata Zieba, Tuomo Laitinen, Jayendra Z. Patel, Antti Poso, Agnieszka A. Kaczor
Summary: The study successfully constructed 3D-QSAR CoMFA and CoMSIA models for a series of 31 FAAH inhibitors with 1,3,4-oxadiazol-2-one moiety, which showed good statistical parameters and were validated using various techniques. The field contributions in the CoMFA and CoMSIA models varied, influencing the ligand-enzyme interactions in different ways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Organic
Chao Ma, Wen-guang Liu, Wen-ding Liu, Chang-cheng Xi, Fei Xiong, Shu-ping Zhang
Summary: This paper presents a study on the structure-activity relationship of a series of HBV capsid assembly inhibitors using 3D-QSAR methods. The models show high predictive ability and the binding mode between compounds and receptor protein was explored through molecular docking, confirming the relationship revealed by the QSAR models.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Multidisciplinary Sciences
Suparna Ghosh, Seketoulie Keretsu, Seung Joo Cho
Summary: The study utilized molecular modeling techniques to analyze ROCK1 inhibitors, and identified compounds with higher predictive activity, which may aid in designing more effective ROCK1 inhibitors.
Article
Chemistry, Multidisciplinary
Fangfang Wang, Wei Yang, Ran Li, Zhihai Sui, Guijuan Cheng, Bo Zhou
Summary: Through 3D-QSAR and molecular dynamics simulations, the structure-activity relationships and mechanism of actions of FAK inhibitors were investigated, predicting the inhibitory activities of novel inhibitors and guiding the optimization of FAK inhibitors with higher inhibitory activities.
ARABIAN JOURNAL OF CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Keerti Vishwakarma, Hardik Bhatt
Summary: This study focuses on the design of novel telomerase inhibitors using various methods, including ligand-based and structure-based approaches. In-depth experimental research was conducted using 3D-QSAR, molecular docking, and molecular dynamics simulation, with results suggesting the potential for developing potent telomerase inhibitors.
JOURNAL OF MOLECULAR MODELING
(2021)
Article
Environmental Sciences
Fei Ding, Ling-Xu Li, Wei Peng, Yu-Kui Peng, Bing-Qi Liu
Article
Chemistry, Multidisciplinary
Peng Wu, Fangfang Fang, Jinshuai Song, Wei Peng, Jia Liu, Chunsen Li, Zexing Cao, Binju Wang
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Chemistry, Multidisciplinary
Jian-bo Wang, Qun Huang, Wei Peng, Peng Wu, Da Yu, Bo Chen, Binju Wang, Manfred T. Reetz
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Pharmacology & Pharmacy
Fei Ding, Wei Peng, Yu-Kui Peng, Bing-Qi Liu
Article
Biochemistry & Molecular Biology
Chun-Chi Chen, Jing Xue, Wei Peng, Binju Wang, Lilan Zhang, Weidong Liu, Tzu-Ping Ko, Jian-Wen Huang, Shuyu Zhou, Jian Min, Lixin Ma, Longhai Dai, Rey-Ting Guo, Xuejing Yu
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2020)
Article
Environmental Sciences
Huiyu Zhao, Barbara Bojko, Fengmao Liu, Janusz Pawliszyn, Wei Peng, Xinquan Wang
Review
Agronomy
Liu Xu, Yong Xie, Risong Na, Qing X. Li
PEST MANAGEMENT SCIENCE
(2020)
Article
Environmental Sciences
Fei Ding, Wei Peng, Yu-Kui Peng, Bing-Qi Liu
Article
Chemistry, Multidisciplinary
Xiaodong Zhang, Yun Hu, Wei Peng, Chenghua Gao, Qiong Xing, Binju Wang, Aitao Li
Summary: In this study, the oxidizing activity of CYP109B1 was reconstituted by coupling redox pairs or fusing it to the reductase domain of two self-sufficient P450 enzymes. The best redox pair for CYP109B1 was found to be Fdr_0978/Fdx_1499 from Synechococcus elongatus, showing over 99% conversion with 73% 15 beta selectivity for testosterone. The enzyme displayed good activity and selectivity toward testosterone derivatives, with a shift in selectivity for specific substrates.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Applied
Zhanfeng Wang, Wenhan Fang, Wei Peng, Peng Wu, Binju Wang
Summary: Activation of dioxygen allows metalloenzymes to mediate various oxidative transformations crucial for biosynthesis and metabolism processes. Recent computational insights into oxygen activation by copper-dependent enzymes are essential for understanding their structure-function relationships and engineering these metalloenzymes for novel functions.
TOPICS IN CATALYSIS
(2022)
Article
Chemistry, Physical
Wei Peng, Xiaoyang Qu, Sason Shaik, Binju Wang
Summary: This study deciphers the catalytic cycle of pMMO in the presence of the physiological reductant duroquinol (DQH(2)), revealing that O-2 activation is initiated by the Cu-C(ii)-DQH(-) species. The research also uncovers the important roles of the phenol co-substrate for O-2 activation.
Article
Chemistry, Multidisciplinary
Yuanyuan Jiang, Wei Peng, Zhong Li, Cai You, Yue Zhao, Dandan Tang, Binju Wang, Shengying Li
Summary: This study analyzed the activities of three CYP152 peroxygenases towards fatty acids, revealing unique selectivity mechanisms and unexpected product formation. Insights into the Compound I-mediated aldehyde formation mechanism provide new understanding of the unusual mechanisms of CYP152 peroxygenases.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Fei Ding, Wei Peng