Article
Biochemical Research Methods
Piyush Agrawal, Dhruv Bhagat, Manish Mahalwal, Neelam Sharma, Gajendra P. S. Raghava
Summary: The study developed a computational model for predicting and designing anticancer peptides (ACPs), revealing residue composition preference, positional preference, and motif features of ACPs. Machine learning models were utilized and trained on different datasets, with the best models implemented on the webserver AntiCP 2.0 for free access.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Louis Becquey, Eric Angel, Fariza Tahi
Summary: This paper presents the first attempt at creating a standardized and automatically generated dataset dedicated to RNA, integrating RNA sequences, homology information, and information derived from annotation of 3D structures. Statistical descriptions of the resulting dataset are provided.
Article
Biochemistry & Molecular Biology
Gaoqi Weng, Xuanyan Cai, Dongsheng Cao, Hongyan Du, Chao Shen, Yafeng Deng, Qiaojun He, Bo Yang, Dan Li, Tingjun Hou
Summary: PROTAC-DB 2.0 is an updated online database that contains structural and experimental data about PROTACs. This second version expands the number of PROTACs to 3270 and provides additional information to aid in the understanding and design of PROTACs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Wanshan Ning, Yuxiang Wei, Letian Gao, Cheng Han, Yujie Gou, Shanshan Fu, Dan Liu, Chi Zhang, Xinhe Huang, Sicheng Wu, Di Peng, Chenwei Wang, Yu Xue
Summary: This article introduces the features and advantages of Heml 2.0 software, which can be used for visualization of biomolecular expression data and enrichment analysis. Heml 2.0 offers various clustering methods and distance metrics, and provides multiple export and visualization options, offering users convenient and comprehensive analysis tools.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Vinay Ayyappan, Ricky Wat, Calvin Barber, Christina A. Vivelo, Kathryn Gauch, Pat Visanpattanasin, Garth Cook, Christos Sazeides, Anthony K. L. Leung
Summary: ADP-ribosylation is a protein modification with significant implications in various biological processes, and ADPriboDB 2.0 serves as a rich repository of data to facilitate research and uncover insights into ADP-ribosylation. The database provides detailed information on ADP-ribosylated proteins and their modification sites, while also offering interactive tools for visualizing the local context of ADP-ribosylation. This wealth of information allows for exploration of ADP-ribosylation biology and generation of new hypotheses for experimental testing.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Le Thi Phan, Hyun Woo Park, Thejkiran Pitti, Thirumurthy Madhavan, Young-Jun Jeon, Balachandran Manavalan
Summary: Anticancer peptides are a promising class of anticancer drugs that are more effective and have fewer side effects compared to chemotherapy and targeted therapy. This study proposes a new ACP prediction model, MLACP 2.0, which outperforms existing tools and exhibits excellent performance in cross-validation and independent assessment. The model is expected to facilitate the discovery of novel ACPs and is freely available for use.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Yubin Xie, Huiqin Li, Xiaotong Luo, Hongyu Li, Qiuyuan Gao, Luowanyue Zhang, Yuyan Teng, Qi Zhao, Zhixiang Zuo, Jian Ren
Summary: The visualization of biological sequences is crucial in the field of molecular and cellular biology. IBS 2.0 is a professional tool that allows concise and clear representation of protein and nucleotide sequences. It provides abundant graphical elements and database visualization module for batch visualization of biological sequences.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Aleksandr Ianevski, Ronja M. Simonsen, Vegard Myhre, Tanel Tenson, Valentyn Oksenych, Magnar Bjoras, Denis E. Kainov
Summary: Viruses can cause outbreaks in humans and have economic and health burdens. Broad-spectrum antivirals (BSAs) and BSA-containing drug combinations (BCCs) are immediate therapeutic options for virus identification and vaccine development. DrugVirus.info 2.0 provides an integrative portal for exploration and analysis of BSAs and BCCs, expanding the database and functionality for antiviral drug development.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yangjun Zhang, Xiangyang Yao, Hui Zhou, Xiaoliang Wu, Jianbo Tian, Jin Zeng, Libin Yan, Chen Duan, Haoran Liu, Heng Li, Ke Chen, Zhiquan Hu, Zhangqun Ye, Hua Xu
Summary: This study presents an updated version of the OncoSplicing database, which integrates a large number of alternative splicing events across various cancers to provide clinically relevant information on alternative splicing.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yigang Chen, Lantian Yao, Yun Tang, Jhih-Hua Jhong, Jingting Wan, Jingyue Chang, Shidong Cui, Yijun Luo, Xiaoxuan Cai, Wenshuo Li, Qi Chen, Hsi-Yuan Huang, Zhuo Wang, Weiming Chen, Tzu-Hao Chang, Fengxiang Wei, Tzong-Yi Lee, Hsien-Da Huang
Summary: circRNAs, important molecules in cancer diagnosis, act as sponges of microRNAs to regulate transcription and translation. The updated CircNet database integrates circRNAs from various sources and predicts target miRNAs to construct high-quality circRNA-miRNA-gene regulatory networks, providing strong data support in the biomedical fields.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Valerie Cognat, Gael Pawlak, David Pflieger, Laurence Drouard
Summary: PlantRNA is a comprehensive database of tRNA gene sequences retrieved from various photosynthetic organisms, covering the entire phylogenetic tree. The database includes a large number of accurately annotated tRNA genes and provides detailed biological information.
Article
Biochemistry & Molecular Biology
Anita Donlic, Emily G. Swanson, Liang-Yuan Chiu, Sarah L. Wicks, Aline Umuhire Juru, Zhengguo Cai, Kamillah Kassam, Chris Laudeman, Bilva G. Sanaba, Andrew Sugarman, Eunseong Han, Blanton S. Tolbert, Amanda E. Hargrove
Summary: Discoveries of RNA roles in cellular physiology and pathology have led to the need for new tools to modulate the structure and function of these biomolecules. Small molecules have proven to be useful in this regard. In this study, the researchers curated a database of RNA-targeting ligands and identified distinguishing physicochemical properties. They proposed the existence of an RNA-privileged chemical space. The database was updated biennially, and a website platform was established to provide insights and tools for designing small molecules based on analyzed properties. The researchers refined the curation approach and ligand classification system, and for the first time conducted analyses of RNA structure elements to identify new targeting strategies.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Chi-Nga Chow, Chien-Wen Yang, Nai-Yun Wu, Hung-Teng Wang, Kuan-Chieh Tseng, Yu-Hsuan Chiu, Tzong-Yi Lee, Wen-Chi Chang
Summary: PlantPAN 4.0 is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. It provides extensive gene annotation and promoter sequences, helping users understand evolutionary differences and similarities among species and identify conserved non-coding sequences in homologous genes. Additionally, it offers a comprehensive collection of transcription factor binding site information and improved ChIP-seq data analysis tools for reconstructing gene regulatory networks.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Zhongyan Li, Siyu Chen, Jhih-Hua Jhong, Yuxuan Pang, Kai-Yao Huang, Shangfu Li, Tzong-Yi Lee
Summary: UbiNet 2.0 is an updated database containing experimentally verified E3-substrate interactions and rich annotations. The platform offers strictly evidence-based classification of E3 ligases and provides an interactive tool for visualizing the ubiquitination network.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Biochemistry & Molecular Biology
Aurelien F. A. Moumbock, Mingjie Gao, Ammar Qaseem, Jianyu Li, Pascal A. Kirchner, Bakoh Ndingkokhar, Boris D. Bekono, Conrad Simoben, Smith B. Babiaka, Yvette Malange, Florian Sauter, Paul Zierep, Fidele Ntie-Kang, Stefan Guenther
Summary: Antimicrobial resistance poses a global health threat, necessitating the development of new antimicrobials; most current antibiotics are natural products from streptomycetes NPs, but there is still a large untapped reservoir; StreptomeDB is the only online database allowing exploration of streptomycetes NPs, providing rich data content and real-world use cases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Austin B. Schwartz, Anshika Kapur, Zhenbo Huang, Raveendra Anangi, John M. Spear, Scott Stagg, Erminia Fardone, Zolan Dekan, Jens T. Rosenberg, Samuel C. Grant, Glenn F. King, Hedi Mattoussi, Debra Ann Fadool
Summary: The olfactory system is modulated by metabolic factors to drive changes in feeding behavior and energy homeostasis. Inhibiting Kv1.3 in the olfactory bulb can enhance excitability of output neurons and lead to metabolic responses, resulting in changes in body weight and energy metabolism.
JOURNAL OF NEUROCHEMISTRY
(2021)
Article
Anesthesiology
Fernanda C. Cardoso, Joel Castro, Luke Grundy, Gudrun Schober, Sonia Garcia-Caraballo, Tianjiao Zhao, Volker Herzig, Glenn F. King, Stuart M. Brierley, Richard J. Lewis
Summary: The discovery of two novel tarantula-venom peptides, Tap1a and Tap2a, provides potential treatment for chronic visceral pain by modulating the activity of Na-v and Ca(v)3 channels. Tap1a, in particular, shows significant analgesic effects in a mouse model, suggesting a new therapeutic approach for chronic pain.
Review
Pharmacology & Pharmacy
David A. Eagles, Chun Yuen Chow, Glenn F. King
Summary: This review examines the role of Na(V)1.7 channels in nociception, their history as a therapeutic target, and the challenges in developing potent inhibitors. Despite significant progress in drug development, effective analgesia remains elusive in clinical trials.
BRITISH JOURNAL OF PHARMACOLOGY
(2022)
Article
Medicine, Research & Experimental
Junior Gonzales, Javier Hernandez-Gil, Thomas C. Wilson, Dauren Adilbay, Mike Cornejo, Paula Demetrio de Souza Franca, Navjot Guru, Christina Schroeder, Glenn F. King, Jason S. Lewis, Thomas Reiner
Summary: Due to the potential severity and persistence of chemotherapy-induced peripheral neuropathy, there is an urgent need for a tool to quantitatively measure this nerve damage. This study demonstrates a novel approach to localize peripheral nerves using in-cell heat imaging and fluorescence imaging, laying the groundwork for future clinical diagnostics and treatments.
MOLECULAR PHARMACEUTICS
(2021)
Article
Chemistry, Medicinal
Arik J. Hone, Quentin Kaas, Ireland Kearns, Fuaad Hararah, Joanna Gajewiak, Sean Christensen, David J. Craik, J. Michael McIntosh
Summary: Research indicates that there are differences in sensitivity to ligands between human and rat a6 beta 4 nAChRs, suggesting the need to consider species variations in designing therapeutic treatments for neuropathic pain. The development of PeIA-5667 provides a new approach for creating more selective therapeutic ligands for rat a6 beta 4 nAChRs.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Ferran Nadal-Bufi, Jody M. Mason, Lai Yue Chan, David J. Craik, Quentin Kaas, Sonia Troeira Henriques
Summary: Through rational and computer-based approaches, peptidic sequences with high affinity towards a beta-sheet region were identified and grafted into a cyclic cell-penetrating scaffold to inhibit LDH5 activity effectively. This approach of targeting an interface important for LDH5 function challenges the landscape of traditional small-molecule drug discovery programs.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biology
Tim Lueddecke, Volker Herzig, Bjoern M. Von Reumont, Andreas Vilcinskas
Summary: Spiders have complex venom systems containing diverse components that work synergistically to increase overall potency, enabling them to emerge as one of the most successful animal lineages. Despite being difficult to standardize, the evolution of spider venoms is driven by mechanisms that can be better understood through genome-based studies.
BIOLOGICAL REVIEWS
(2022)
Article
Multidisciplinary Sciences
Rocio K. Finol-Urdaneta, Rebekah Ziegman, Zoltan Dekan, Jeffrey R. McArthur, Stewart Heitmann, Karen Luna-Ramirez, Han-Shen Tae, Alexander Mueller, Hana Starobova, Yanni K. -Y. Chin, Joshua S. Wingerd, Eivind A. B. Undheim, Ben Cristofori-Armstrong, Adam P. Hill, Volker Herzig, Glenn F. King, Irina Vetter, Lachlan Rash, David J. Adams, Paul F. Alewood
Summary: The venom of the King Baboon spider contains a cysteine-rich peptide that can induce pain by targeting multiple ion channels, leading to hyperexcitability in pain-sensing neurons. This peptide may be an evolutionary adaptation for pain induction in defensive venoms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Yue Wu, Zhenling Cui, Yen-Hua Huang, Simon J. de Veer, Andrey V. Aralov, Zhong Guo, Shayli V. Moradi, Alexandra O. Hinton, Jennifer R. Deuis, Shaodong Guo, Kai-En Chen, Brett M. Collins, Irina Vetter, Volker Herzig, Alun Jones, Matthew A. Cooper, Glenn F. King, David J. Craik, Kirill Alexandrov, Sergey Mureev
Summary: Advances in peptide and protein therapeutics have increased the demand for rapid and cost-effective polypeptide prototyping. A modified in vitro translation system allows efficient folding of disulfide-rich peptides and proteins in an aggregation-free and thermodynamically controlled environment.
NATURE COMMUNICATIONS
(2022)
Article
Pharmacology & Pharmacy
Jennifer R. Deuis, Lotten Ragnarsson, Samuel D. Robinson, Zoltan Dekan, Lerena Chan, Ai-Hua Jin, Poanna Tran, Kirsten L. McMahon, Shengnan Li, John N. Wood, James J. Cox, Glenn F. King, Volker Herzig, Irina Vetter
Summary: A peptide named β-theraphotoxin-Eo1a was discovered from the venom of the Tanzanian black and olive baboon tarantula, which modulates the function of Na(V)1.8 channels. Eo1a increases the peak current of Na(V)1.8 and causes significant shifts in the voltage-dependence of activation and steady-state fast inactivation.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Volker Herzig, Yong-Cyuan Chen, Yanni K-Y Chin, Zoltan Dekan, Yu-Wang Chang, Hui-Ming Yu, Paul F. Alewood, Chien-Chang Chen, Glenn F. King
Summary: This study identified a tarantula venom from Avicularia spec. that can inhibit specific subtypes of T-type calcium channels, with the active toxin being omega-Avsp1a. The research suggests that omega-Avsp1a can inhibit specific subtypes of T-type calcium channels, and the domain-1 of Ca(V)3.3 is crucial for this inhibitory effect.
Article
Biochemistry & Molecular Biology
Fernanda C. Cardoso, Sandy S. Pineda, Volker Herzig, Kartik Sunagar, Naeem Yusuf Shaikh, Ai-Hua Jin, Glenn F. King, Paul F. Alewood, Richard J. Lewis, Sebastien Dutertre
Summary: Australian tree-dwelling funnel-web spiders have venom that induces deadly symptoms and exhibits different venom composition compared to ground-dwelling species. The venom of tree-dwellers strongly modulates human voltage-gated sodium and calcium channels, while also showing potent insecticidal effects. This study contributes to understanding the molecular and pharmacological basis for severe envenomation by Australian tree-dwelling funnel-web spiders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Andrew A. Walker, Lynda E. Perkins, Andrea Battisti, Myron P. Zalucki, Glenn F. King
Summary: Ochrogaster lunifer is an Australian caterpillar that has detachable urticating setae with defensive function. These setae can cause inflammation on human skin and equine foetal loss syndrome in gravid horses if accidentally ingested. Transcriptomics and proteomics analysis identified 37 putative toxins, including multiple homologues of honeybee venom peptide secapin and proteins with similarity to odorant binding proteins, arylphorins, and the insect immune modulator Diedel. This study reveals candidate molecules that may contribute to the adverse effects of processionary caterpillar setae on human and animal health.
