Article
Multidisciplinary Sciences
Thamir A. Alandijany, Mai M. El-Daly, Ahmed M. Tolah, Leena H. Bajrai, Aiah M. Khateb, Geethu S. Kumar, Amit Dubey, Vivek Dhar Dwivedi, Esam I. Azhar
Summary: This study demonstrates the repurposing of tetracycline-derived drugs as a therapeutic solution for monkeypox viral infection.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Himansu Kumar, Lin-Ya Tang, Chengyuan Yang, Pora Kim
Summary: Fusion genes play a crucial role in cancer therapeutics, but many fusion proteins have not been thoroughly studied. To address this, we have developed a computational pipeline and a resource that provides sequence and structural information of human fusion proteins, which can be used for developing new therapeutic strategies.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Computer Science, Artificial Intelligence
Jeff Guo, Vendy Fialkova, Juan Diego Arango, Christian Margreitter, Jon Paul Janet, Kostas Papadopoulos, Ola Engkvist, Atanas Patronov
Summary: Guo and colleagues introduce curriculum learning extension to REINVENT, a de novo molecular design framework, which improves training efficiency by providing increasingly difficult problems over epochs.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Biochemistry & Molecular Biology
Faisal A. Almalki, Ahmed M. Shawky, Ashraf N. Abdalla, Ahmed M. Gouda
Summary: A 2D similarity/docking study was conducted to predict the potential binding modes of icotinib, almonertinib, and olmutinib into EGFR. The three drugs showed high similarity with erlotinib, osimertinib, and WZ4003, and exhibited higher binding free energies compared to co-crystallized ligands. Analysis of the top-scoring poses revealed potential binding modes of the drugs.
Article
Chemistry, Medicinal
Tania Jimenez, Juliana Botero, Dorleta Otaegui, Javier Calvo, Frank J. Hernandez, Eider San Sebastian
Summary: The study identified and described the interaction mode and cleavage process of an undecamer oligonucleotide probe based on a pair of deoxythymidines flanked by modified nucleotides for micrococcal nuclease biosensing. Truncated pentamer probes were designed to improve specificity and efficiency of biosensing. Computational and experimental techniques were used to reveal a novel two-step phosphodiester bond hydrolysis mechanism, crucial for rational oligonucleotide design process.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Yuta Tsukamoto, Takahiro Hiono, Shintaro Yamada, Keita Matsuno, Aileen Faist, Tobias Claff, Jianyu Hou, Vigneshwaran Namasivayam, Anja vom Hemdt, Satoko Sugimoto, Jin Ying Ng, Maria H. Christensen, Yonas M. Tesfamariam, Steven Wolter, Stefan Juranek, Thomas Zillinger, Stefan Bauer, Takatsugu Hirokawa, Florian I. Schmidt, Georg Kochs, Masayuki Shimojima, Yi-Shuian Huang, Andreas Pichlmair, Beate M. Kuemmerer, Yoshihiro Sakoda, Martin Schlee, Linda Brunotte, Christa E. Mueller, Manabu Igarashi, Hiroki Kato
Summary: Scientists have discovered the importance of host RNA modification in the initiation of influenza virus replication. They found that a derivative of a natural product called TFMT can inhibit this modification and restrict influenza virus replication. TFMT acts synergistically with approved anti-influenza drugs.
Article
Chemistry, Multidisciplinary
Lan Phuong Nguyen, Rasel Ahmed Khan, Soomin Kang, Hobin Lee, Jong-Ik Hwang, Hong-Rae Kim
Summary: In this study, potential new structures of LPAR1 antagonists were discovered through high-throughput virtual screening. Five structures were identified and validated using an LPAR1-dependent calcium flux assay. The crystal structures showed superior performance in structure-based virtual screening compared to a predictive model. Furthermore, improving precision in the screening process did not necessarily enhance the enrichment of hits. The analysis of protein-ligand interactions laid the groundwork for the discovery of novel LPAR1 antagonists.
Article
Chemistry, Multidisciplinary
Rajendra R. Kshirsagar, Pradip K. Gadekar, Vijay M. Khedkar, Vijayaparthasarathi Vijayakumar
Summary: Acetyl octadecynoic acid exerts its anti-diabetic activity by activating the PI3K pathway to increase insulin-stimulated glucose uptake in myotubes. Site-specific modification and structure-activity relationship studies provide potential for generating promising derivatives. Compounds 5, 6, 27, 28, 31, 32, and 33 from the series show the best activity with EC50 values ranging from 7.00 to 16.14 mu M.
Article
Engineering, Biomedical
Limei Ma, Yang Nie, Qian Feng, Jianshu Cao, Shaoya Guan
Summary: This paper explores the application of deep learning methods in vascular image registration, compares the performance of different CNN models, and discusses the optimization of network structures. The experiments demonstrate that these networks are suitable for vascular image registration, with Alex-reg achieving the best performance.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2024)
Article
Chemistry, Physical
Yuejiang Yu, Chun Cai, Jiayue Wang, Zonghua Bo, Zhengdan Zhu, Hang Zheng
Summary: Uni-Dock is a GPU-accelerated molecular docking program that supports various scoring functions and excels in speed and efficiency compared to other GPU-accelerated programs. It achieves significant speedup by optimizing data flow and implementing parallel processing, outperforming previous docking programs like AutoDock Vina. Uni-Dock has demonstrated improved performance in docking experiments, and it has been proven to be the fastest GPU-accelerated docking program to date, especially in screening ultralarge molecular libraries.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Medicinal
Adrian Krzyzanowski, Lea Marie Esser, Anthony Willaume, Renaud Prudent, Christoph Peter, Peter't Hart, Herbert Waldmann
Summary: The PRMT5-MEP50 methyltransferase is a major target for the development of anticancer drugs. Researchers have designed and synthesized a new peptide compound that specifically inhibits the interaction between PRMT5 and adaptor proteins RioK1 and pICln. This new inhibitor has great potential for further biological investigations.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Yuto Unoh, Shota Uehara, Kenji Nakahara, Haruaki Nobori, Yukiko Yamatsu, Shiho Yamamoto, Yuki Maruyama, Yoshiyuki Taoda, Koji Kasamatsu, Takahiro Suto, Kensuke Kouki, Atsufumi Nakahashi, Sho Kawashima, Takao Sanaki, Shinsuke Toba, Kentaro Uemura, Tohru Mizutare, Shigeru Ando, Michihito Sasaki, Yasuko Orba, Hirofumi Sawa, Akihiko Sato, Takafumi Sato, Teruhisa Kato, Yuki Tachibana
Summary: S-217622 is the first oral noncovalent, nonpeptidic SARS-CoV-2 3CL protease inhibitor clinical candidate, which could be a potential oral agent for treating COVID-19.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Sarah Huff, Indrasena Reddy Kummetha, Shashi Kant Tiwari, Matthew B. Huante, Alex E. Clark, Shaobo Wang, William Bray, Davey Smith, Aaron F. Carlin, Mark Endsley, Tariq M. Rana
Summary: This study identifies a class of compounds targeting the SARS-CoV-2 main protease that can inhibit viral replication. The compounds were found through medicinal chemistry and rational drug design strategies and offer a potential framework for the development of future COVID-19 treatments.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Riccardo Guareschi, Iva Lukac, Ian H. Gilbert, Fabio Zuccotto
Summary: The optimization of compounds' binding affinity for a biological target is crucial for drug development. The paper introduces SophosQM, a quantum mechanics-based approach that accurately predicts binding affinities of compounds to proteins. The method combines accuracy, reliability, and speed, and exhibits satisfactory performance in predicting the binding affinities of 70 compounds.
Article
Plant Sciences
Nicole E. Avalon, Jordan Nafie, Carolina De Marco Verissimo, Luke C. Warrensford, Sarah G. Dietrick, Amanda R. Pittman, Ryan M. Young, Fiona L. Kearns, Tracess Smalley, Jennifer M. Binning, John P. Dalton, Mark P. Johnson, H. Lee Woodcock, A. Louise Allcock, Bill J. Baker
Summary: A new molecule, Tuaimenal A, was discovered in the previously unexplored soft coral Duva florida from cold water benthic environments. It has a highly substituted chromene core and a new carbon scaffold. Functional assays and in silico docking experiments confirmed that Tuaimenal A selectively inhibits the viral main protease (3CLpro) of SARS-CoV-2.
JOURNAL OF NATURAL PRODUCTS
(2022)