Article
Chemistry, Medicinal
Koon Mook Kang, Ingoo Lee, Hojung Nam, Yong-Chul Kim
Summary: This study combines AI deep learning model and experimental screening to successfully identify 16 new hit compounds and discover a novel putative binding site for P2X3R. These results may accelerate the development of novel chemical-class drugs for P2X3R antagonists.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jin-ping Pang, Chao Shen, Wen-fang Zhou, Yun-xia Wang, Lu-hu Shan, Xin Chai, Ying Shao, Xue-ping Hu, Feng Zhu, Dan-yan Zhu, Li Xiao, Lei Xu, Xiao-hong Xu, Dan Li, Ting-jun Hou
Summary: The androgen receptor (AR) is a crucial transcription factor in prostate cancer development, and finding novel anti-AR therapeutics to combat mutation-induced resistance is challenging. In this study, a virtual screening strategy based on the crystal structure of the DNA binding domain (DBD) of AR identified a potential hit, Cpd39, that could block the binding of AR DBD to DNA and inhibit AR transcriptional activity effectively. Cpd39 also demonstrated safety and potency in inhibiting the proliferation of various prostate cancer cell lines, suggesting it could be a promising starting point for new therapeutics for castration-resistant PCa.
ACTA PHARMACOLOGICA SINICA
(2022)
Article
Chemistry, Multidisciplinary
Ammar Ammar, Rachel Cavill, Chris Evelo, Egon Willighagen
Summary: A large database of 0.6 million mutated binding site protein-ligand complexes, called PSnpBind, has been constructed to provide a reference dataset for studying the effects of natural variants on drug targets. This database is important for developing machine learning algorithms and studying protein-ligand affinity.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Biology
Leonardo Bruno Federico, Guilherme Martins Silva, Suzane Quintana Gomes, Isaque Antonio Galindo Francischini, Mariana Pegrucci Barcelos, Cleydson Breno Rodrigues dos Santos, Luciano T. Costa, Joaquin Maria Campos Rosa, Carlos Henrique Tomich de Paula da Silva
Summary: Microtubules play a crucial role in cancer treatment, especially due to their unique structure and the colchicine binding site (CBS). Through virtual screening and molecular dynamics simulations, four promising CBS inhibitors were identified, offering potential for the development of safer drugs.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Wei Liu, Hairui Jia, Minghao Guan, Minxuan Cui, Zhuxuan Lan, Youyou He, Zhongjie Guo, Ru Jiang, Guoqiang Dong, Shengzheng Wang
Summary: In this study, a novel tubulin inhibitor E27 was discovered through structural optimization. E27 demonstrated significant antitumor activity, inhibition of cancer cell migration, induction of apoptosis, and cell cycle arrest.
BIOORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Samo Guzelj, Tihomir Tomasic, Ziga Jakopin
Summary: A hybrid docking and pharmacophore modeling approach was used to identify key interactions between NOD2 ligands and residues in the putative ligand-binding site. Two NOD2 antagonist compounds were identified as hits and represent valuable starting points for future optimization.
Article
Pharmacology & Pharmacy
Gaia Pasqualetto, Marika Zuanon, Andrea Brancale, Mark T. Young
Summary: The ATP-gated ion channels P2X4 and P2X7 receptors are drug targets for inflammatory pain. Through virtual screening, a compound (GP-25) was found to display antagonist activity at human P2X7 but not at human P2X4. Further screening led to the discovery of five additional compounds with antagonist activity at human P2X7. Docking experiments revealed the structural basis for the lack of activity of GP-25 at human P2X4.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xiaoyu Ding, Zijie Zhao, Yue Wu, Hao Zhang, Kaixian Chen, Cheng Luo, Xiaomin Luo, Heng Xu
Summary: The study evaluated binding sites of Nur77 with small molecules and discovered compound 13e with the strongest binding affinity, predicting its binding mode. This compound showed significant anti-inflammatory activity in TNF-α-induced HepG2 cell model.
BIOORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Yunshuo Zhao, Xiaotong Chen, Sifan Lyu, Zhe Ding, Yahong Wu, Yanfeng Gao, Jiangfeng Du
Summary: Overactivation of P2X7 receptors promotes tumor growth and invasion, and inhibiting its activation may be a potentially effective anti-tumor therapy strategy. This study identified several novel P2X7R antagonists through a combination of homology modeling and other methods, which effectively prevented P2X7R pore opening and could be further explored for their anti-cancer activity.
CHEMICAL BIOLOGY & DRUG DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Mukuo Wang, Shujing Hou, Ye Liu, Dongmei Li, Jianping Lin
Summary: The study identified CB2 antagonists using a virtual screening approach and Compound 8 showed the best binding affinity and antagonistic activity, serving as a lead for further development of CB2 drugs. The developed approach could also be utilized to design potent ligands for other therapeutic targets.
Article
Automation & Control Systems
Xiaoqi Liang, Hu Mei, Minyao Qiu, Siyao Deng, Yufang Li, Yanlan Ke, Pingqing Wang, Yingwu Yang
Summary: In this study, a molecular generation model of OX1R antagonists was successfully built using a GRU-based deep neural network combined with transfer learning. The model accurately grasp the SMILES grammar of drug-like molecules and tends to generate potential OX1R antagonists. Using GCN and traditional screening methods, the study obtained potential OX1R antagonists with good drug-like and druggability properties. This research integrates the advantages of traditional and data-driven drug design methods and provides important references for lead compound discovery of OX1R antagonists.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2022)
Article
Multidisciplinary Sciences
Sebastian Guenther, Patrick Y. A. Reinke, Yaiza Fernandez-Garcia, Julia Lieske, Thomas J. Lane, Helen M. Ginn, Faisal H. M. Koua, Christiane Ehrt, Wiebke Ewert, Dominik Oberthuer, Oleksandr Yefanov, Susanne Meier, Kristina Lorenzen, Boris Krichel, Janine-Denise Kopicki, Luca Gelisio, Wolfgang Brehm, Ilona Dunkel, Brandon Seychell, Henry Gieseler, Brenna Norton-Baker, Beatriz Escudero-Perez, Martin Domaracky, Sofiane Saouane, Alexandra Tolstikova, Thomas A. White, Anna Haenle, Michael Groessler, Holger Fleckenstein, Fabian Trost, Marina Galchenkova, Yaroslav Gevorkov, Chufeng Li, Salah Awel, Ariana Peck, Miriam Barthelmess, Frank Schluenzen, P. Lourdu Xavier, Nadine Werner, Hina Andaleeb, Najeeb Ullah, Sven Falke, Vasundara Srinivasan, Bruno Alves Franca, Martin Schwinzer, Hevila Brognaro, Cromarte Rogers, Diogo Melo, Joanna J. Zaitseva-Doyle, Juraj Knoska, Gisel E. Pena-Murillo, Aida Rahmani Mashhour, Vincent Hennicke, Pontus Fischer, Johanna Hakanpaa, Jan Meyer, Philip Gribbon, Bernhard Ellinger, Maria Kuzikov, Markus Wolf, Andrea R. Beccari, Gleb Bourenkov, David von Stetten, Guillaume Pompidor, Isabel Bento, Saravanan Panneerselvam, Ivars Karpics, Thomas R. Schneider, Maria Marta Garcia-Alai, Stephan Niebling, Christian Guenther, Christina Schmidt, Robin Schubert, Huijong Han, Juliane Boger, Diana C. F. Monteiro, Linlin Zhang, Xinyuanyuan Sun, Jonathan Pletzer-Zelgert, Jan Wollenhaupt, Christian G. Feiler, Manfred S. Weiss, Eike-Christian Schulz, Pedram Mehrabi, Katarina Karnicar, Aleksandra Usenik, Jure Loboda, Henning Tidow, Ashwin Chari, Rolf Hilgenfeld, Charlotte Uetrecht, Russell Cox, Andrea Zaliani, Tobias Beck, Matthias Rarey, Stephan Guenther, Dusan Turk, Winfried Hinrichs, Henry N. Chapman, Arwen R. Pearson, Christian Betzel, Alke Meents
Summary: The study identified 37 compounds that bind to the SARS-CoV-2 main protease through a high-throughput x-ray crystallographic screen of two repurposing drug libraries. Among these compounds, one peptidomimetic and six nonpeptidic compounds showed antiviral activity in cell-based viral reduction assays at nontoxic concentrations. The identification of two allosteric binding sites presents potential targets for drug development against SARS-CoV-2.
Article
Oncology
Zahra Rezaei, Mehdi Asadi, Mohammad Nazari Montazer, Elnaz Rezaeiamiri, Saeed Bahadorikhalili, Mohsen Amini, Massoud Amanlou
Summary: This study developed a pharmacophore model and used molecular docking to synthesize and evaluate a series of new tubulin inhibitors, finding that compounds with certain structural features exhibited the highest activity.
ANTI-CANCER AGENTS IN MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Binjie Li, Tianji Zhang, Hui Cao, Vito Ferro, Jinping Li, Mingjia Yu
Summary: The spike protein on the surface of the SARS-CoV-2 virus is crucial for its fusion with host cells, and heparan sulfate facilitates this fusion process. Researchers have developed a pentasaccharide library to disrupt the interaction between heparan sulfate and the receptor binding domain (RBD) of the spike protein. Molecular modeling and drug-likeness calculations were performed to assess the antiviral properties of the most promising pentasaccharide. The findings provide valuable insights for the development of HS-mimetics as potential anti-SARS-CoV-2 agents.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Qingtong Zhou, Wanjing Guo, Antao Dai, Xiaoqing Cai, Marton Vass, Chris de Graaf, Wenqing Shui, Suwen Zhao, Dehua Yang, Ming-Wei Wang
Summary: Allosteric modulators offer pharmacological advantages by affecting downstream signaling without competing for orthosteric sites. Computational approaches were used to identify allosteric modulators targeting GLP-1R, resulting in the discovery of negative and positive modulators through structure-based and ligand-based virtual screening methods, respectively. This computational approach may be applicable for discovering allosteric modulators of other GPCRs.