Article
Chemistry, Physical
V. S. S. L. Prasad Talluri, Botagoz Mutaliyeva, Altynay Sharipova, Vamseekrishna Ulaganathan, Sri Santhi Lanka, Saule Aidarova, Aliya Suigenbayeva, Aiym Tleuova
Summary: L-asparaginase is an important enzyme used in therapeutic applications, and immobilization can minimize its side effects and improve its performance.
ADVANCES IN COLLOID AND INTERFACE SCIENCE
(2023)
Article
Biochemical Research Methods
Raziyeh Masumshah, Rosa Aghdam, Changiz Eslahchi
Summary: This study presents a neural network-based method for predicting polypharmacy side effects, which outperforms five well-established methods in terms of accuracy, complexity, and running time speed. The proposed method utilizes novel feature vectors and drug-protein interaction information to improve prediction efficiency.
BMC BIOINFORMATICS
(2021)
Review
Chemistry, Multidisciplinary
Piermichele Kobauri, Frank J. Dekker, Wiktor Szymanski, Ben L. Feringa
Summary: Photopharmacology is an attractive approach for targeted drug action using light, where molecular photoswitches are introduced into biologically active small molecules for optical control. This review categorizes photopharmacological efforts based on medicinal chemistry strategies, focusing on diffusible photochromic ligands modified with E-Z bond isomerization photoswitches. Photoswitchable ligands are often designed as analogs of existing compounds using various approaches. Through analyzing instructive examples, the state of the art and future opportunities for rational design in photopharmacology are discussed.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Engineering, Environmental
Yijie Li, Mingyang Zhang, Haijie Han, Baohong Zhang, John B. Matson, Defu Chen, Wei Li, Yin Wang
Summary: Peptide-based supramolecular photodynamic therapy (PDT) is a new modality for cancer treatments that utilizes the biological activities and self-assembling potential of peptides to enhance the delivery selectivity of photosensitizers. This review surveys the recent advancements in the rational design and preparation of peptide-based PDT systems for targeted delivery and anti-tumor treatments, analyzing different synthetic approaches and discussing future outlooks and challenges in the field.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Medicine, General & Internal
Seyma Handan Akyon, Fatih Cagatay Akyon, Tarik Eren Yilmaz
Summary: This study aims to reduce the complications of polypharmacy by evaluating age, drugs, and chronic diseases to prepare an auxiliary tool. A comprehensive tool was developed, and an AI-supported web application was designed and developed. The results showed that using this tool significantly reduced the time required to detect drug interactions and had a high coverage rate.
FRONTIERS IN MEDICINE
(2023)
Article
Computer Science, Interdisciplinary Applications
Liyi Yu, Meiling Cheng, Wangren Qiu, Xuan Xiao, Weizhong Lin
Summary: Unexpected side effects are a major factor leading to the failure of drug trials, so discovering potential side effects in a computational manner can improve the success rate of drug screening. However, previous methods have mainly focused on a single perspective, neglecting the need to consider multiple types of information about drugs. In this study, a hybrid embedding graph neural network model is proposed to integrate various drug features and predict potential side effects, outperforming other advanced methods.
JOURNAL OF BIOMEDICAL INFORMATICS
(2022)
Review
Pharmacology & Pharmacy
Ryan K. Tan, Yang Liu, Lei Xie
Summary: This survey reviews the state-of-the-art reinforcement learning methods and their applications in drug design. The challenges of applying reinforcement learning in systems pharmacology and personalized medicine are discussed, along with potential solutions.
EXPERT OPINION ON DRUG DISCOVERY
(2022)
Review
Biochemistry & Molecular Biology
Myunggyo Lee, Hyejin Shin, Musun Park, Aeyung Kim, Seongwon Cha, Haeseung Lee
Summary: Herbal medicine is a multi-component treatment, but its molecular mechanism of action on the human body is unknown. Systems pharmacology, which interprets pharmacological effects of drugs from interaction networks, is increasingly used to study herbal medicine. Recent studies combine network-based approaches and high-throughput omics technology to explore the complex mechanisms and direct associations between herbs and genes.
Review
Pharmacology & Pharmacy
Yang Chen, Naiying Chen, Xun Feng
Summary: This review discusses the development of skin-specific drug delivery systems and the impact of important stimuli on pharmaceutical formulation design, as well as introducing the characteristics of nanoscale drug carriers and the advantages of dual stimuli responsive drug delivery systems.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Multidisciplinary Sciences
Yuanzhi Huang, Xupeng Jin, Jiayi Liu, Wei Wu, Huiping Wang
Summary: This study used network pharmacology to explore the molecular mechanism of Artemisia argyi as a potential therapy for rheumatism. Results showed that Artemisia argyi may affect multiple targets and pathways to exert its therapeutic effects on rheumatism, reflecting the characteristics of traditional Chinese medicine.
SCIENTIFIC REPORTS
(2022)
Article
Mathematical & Computational Biology
Meng Jiang, Bo Zhou, Lei Chen
Summary: The study of drug side effects is important in drug discovery. Traditional experimental methods for determining side effects are time-consuming and expensive, making computational methods increasingly popular. This study proposes a new path-based method for identifying drug side effects using a heterogeneous network, which shows good performance and outperforms other network-based methods.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2022)
Review
Pharmacology & Pharmacy
Cong-Fei Xu, Guo-Jun Chen, Ying-Li Luo, Yue Zhang, Gui Zhao, Zi-Dong Lu, Anna Czarna, Zhen Gu, Jun Wang
Summary: The CRISPR-Cas system has revolutionized genome editing, but efficient delivery to target tissues/cells remains a challenge. This review summarizes the characteristics of different CRISPR-Cas therapeutic tools and investigates current in vivo delivery systems, emphasizing the requirements for efficient delivery in clinical settings and the safety of different tools.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Review
Engineering, Biomedical
Dong Liu, Ting Wang, Yuan Lu
Summary: The article discusses the potential applications of untethered microrobots in medical treatment, particularly focusing on the advantages of active drug delivery systems compared to traditional passive systems. It introduces an integrated 5D radar chart analysis model and addresses the various factors that need to be considered before clinical application of microrobots.
ADVANCED HEALTHCARE MATERIALS
(2022)
Article
Food Science & Technology
Xue-song Wang, Mi-jun Peng, Chun-tao He
Summary: The antihypertensive effects of Eucommia ulmoides extract were tested using leaf extracts, bark extract, chlorogenic acid (CGA), and captopril in normal and hypertensive rats. CGA was found to be the main active component in the extract, and it showed antihypertensive effects through multiple biological processes. However, CGA had lower bioavailability compared to captopril, which limited its antihypertensive effects.
JOURNAL OF FUNCTIONAL FOODS
(2022)
Article
Computer Science, Artificial Intelligence
Shuangjia Zheng, Youhai Tan, Zhenyu Wang, Chengtao Li, Zhiqing Zhang, Xu Sang, Hongming Chen, Yuedong Yang
Summary: Proteolysis-targeting chimeras (PROTACs) are effective tools for degrading disease-related proteins, but their design and optimization is challenging. This study proposes a novel approach using deep learning and molecular simulations to accelerate rational PROTAC design, leading to the discovery of a novel BRD4-degrading PROTAC.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Urology & Nephrology
Rany M. Salem, Jennifer N. Todd, Niina Sandholm, Joanne B. Cole, Wei-Min Chen, Darrell Andrews, Marcus G. Pezzolesi, Paul M. McKeigue, Linda T. Hiraki, Chengxiang Qiu, Viji Nair, Chen Di Liao, Jing Jing Cao, Erkka Valo, Suna Onengut-Gumuscu, Adam M. Smiles, Stuart J. McGurnaghan, Jani K. Haukka, Valma Harjutsalo, Eoin P. Brennan, Natalie van Zuydam, Emma Ahlqvist, Ross Doyle, Tarunveer S. Ahluwalia, Maria Lajer, Maria F. Hughes, Jihwan Park, Jan Skupien, Athina Spiliopoulou, Andrew Liu, Rajasree Menon, Carine M. Boustany-Kari, Hyun M. Kang, Robert G. Nelson, Ronald Klein, Barbara E. Klein, Kristine E. Lee, Xiaoyu Gao, Michael Mauer, Silvia Maestroni, Maria Luiza Caramori, Ian H. de Boer, Rachel G. Miller, Jingchuan Guo, Andrew P. Boright, David Tregouet, Beata Gyorgy, Janet K. Snell-Bergeon, David M. Maahs, Shelley B. Bull, Angelo J. Canty, Colin N. A. Palmer, Lars Stechemesser, Bernhard Paulweber, Raimund Weitgasser, Jelizaveta Sokolovska, Vita Rovite, Valdis Pirags, Edita Prakapiene, Lina Radzeviciene, Rasa Verkauskiene, Nicolae Mircea Panduru, Leif C. Groop, Mark McCarthy, Harvest F. Gu, Anna Mollsten, Henrik Falhammar, Kerstin Brismar, Finian Martin, Peter Rossing, Tina Costacou, Gianpaolo Zerbini, Michel Marre, Samy Hadjadj, Amy J. McKnight, Carol Forsblom, Gareth McKay, Catherine Godson, A. Peter Maxwell, Matthias Kretzler, Katalin Susztak, Helen M. Colhoun, Andrzej Krolewski, Andrew D. Paterson, Per-Henrik Groop, Stephen S. Rich, Joel N. Hirschhorn, Jose C. Florez
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2019)
Article
Cell Biology
Ki Wung Chung, Poonam Dhillon, Shizheng Huang, Xin Sheng, Rojesh Shrestha, Chengxiang Qiu, Brett A. Kaufman, Jihwan Park, Liming Pei, Joseph Baur, Matthew Palmer, Katalin Susztak
Article
Genetics & Heredity
Adrienne Tin, Jonathan Marten, Victoria L. Halperin Kuhns, Yong Li, Matthias Wuttke, Holger Kirsten, Karsten B. Sieber, Chengxiang Qiu, Mathias Gorski, Zhi Yu, Ayush Giri, Gardar Sveinbjornsson, Man Li, Audrey Y. Chu, Anselm Hoppmann, Luke J. O'Connor, Bram Prins, Teresa Nutile, Damia Noce, Masato Akiyama, Massimiliano Cocca, Sahar Ghasemi, Peter J. van Der Most, Katrin Horn, Yizhe Xu, Christian Fuchsberger, Sanaz Sedaghat, Saima Afaq, Najaf Amin, Johan Arnlov, Stephan J. L. Bakker, Nisha Bansal, Daniela Baptista, Sven Bergmann, Mary L. Biggs, Ginevra Biino, Eric Boerwinkle, Erwin P. Bottinger, Thibaud S. Boutin, Marco Brumat, Ralph Burkhardt, Eric Campana, Archie Campbell, Harry Campbell, Robert J. Carroll, Eulalia Catamo, John C. Chambers, Marina Ciullo, Maria Pina Concas, Josef Coresh, Tanguy Corre, Daniele Cusi, Sala Cinzia Felicita, Martin H. de Borst, Alessandro De Grandi, Rene de Mutsert, Aiko P. J. de Vries, Graciela Delgado, Ayse Demirkan, Olivier Devuyst, Katalin Dittrich, Kai-Uwe Eckardt, Georg Ehret, Karlhans Endlich, Michele K. Evans, Ron T. Gansevoort, Paolo Gasparini, Vilmantas Giedraitis, Christian Gieger, Giorgia Girotto, Martin Ggele, Scott D. Gordon, Daniel F. Gudbjartsson, Vilmundur Gudnason, Toomas Haller, Pavel Hamet, Tamara B. Harris, Caroline Hayward, Andrew A. Hicks, Edith Hofer, Hilma Holm, Wei Huang, Nina Hutri-Kahonen, Shih-Jen Hwang, M. Arfan Ikram, Raychel M. Lewis, Erik Ingelsson, Johanna Jakobsdottir, Ingileif Jonsdottir, Helgi Jonsson, Peter K. Joshi, Navya Shilpa Josyula, Bettina Jung, Mika Kahonen, Yoichiro Kamatani, Masahiro Kanai, Shona M. Kerr, Wieland Kiess, Marcus E. Kleber, Wolfgang Koenig, Jaspal S. Kooner, Antje Korner, Peter Kovacs, Bernhard K. Kramer, Florian Kronenberg, Michiaki Kubo, Brigitte Kuhnel, Martina La Bianca, Leslie A. Lange, Benjamin Lehne, Terho Lehtimaki, Jun Liu, Markus Loeffler, Ruth J. F. Loos, Leo-Pekka Lyytikainen, Reedik Magi, Anubha Mahajan, Nicholas G. Martin, Winfried Marz, Deborah Mascalzoni, Koichi Matsuda, Christa Meisinger, Thomas Meitinger, Andres Metspalu, Yuri Milaneschi, Christopher J. ODonnell, Otis D. Wilson, J. Michael Gaziano, Pashupati P. Mishra, Karen L. Mohlke, Nina Mononen, Grant W. Montgomery, Dennis O. Mook-Kanamori, Martina Mueller-Nurasyid, Girish N. Nadkarni, Mike A. Nalls, Matthias Nauck, Kjell Nikus, Boting Ning, Ilja M. Nolte, Raymond Noordam, Jeffrey R. O'Connell, Isleifur Olafsson, Sandosh Padmanabhan, Brenda W. J. H. Penninx, Thomas Perls, Annette Peters, Mario Pirastu, Nicola Pirastu, Giorgio Pistis, Ozren Polasek, Belen Ponte, David J. Porteous, Tanja Poulain, Michael H. Preuss, Ton J. Rabelink, Laura M. Raffield, Olli T. Raitakari, Rainer Rettig, Myriam Rheinberger, Kenneth M. Rice, Federica Rizzi, Antonietta Robino, Igor Rudan, Alena Krajcoviechova, Renata Cifkova, Rico Rueedi, Daniela Ruggiero, Kathleen A. Ryan, Yasaman Saba, Erika Salvi, Helena Schmidt, Reinhold Schmidt, Christian M. Shaffer, Albert Smith, Blair H. Smith, Cassandra N. Spracklen, Konstantin Strauch, Michael Stumvoll, Patrick Sulem, Salman M. Tajuddin, Andrej Teren, Joachim Thiery, Chris H. L. Thio, Unnur Thorsteinsdottir, Daniela Toniolo, Anke Tonjes, Johanne Tremblay, Andre G. Uitterlinden, Simona Vaccargiu, Pim van der Harst, Cornelia M. van Duijn, Niek Verweij, Uwe Voelker, Peter Vollenweider, Gerard Waeber, Melanie Waldenberger, John B. Whitfield, Sarah H. Wild, James F. Wilson, Qiong Yang, Weihua Zhang, Alan B. Zonderman, Murielle Bochud, James G. Wilson, Sarah A. Pendergrass, Kevin Ho, Afshin Parsa, Peter P. Pramstaller, Bruce M. Psaty, Carsten A. Boeger, Harold Snieder, Adam S. Butterworth, Yukinori Okada, Todd L. Edwards, Kari Stefansson, Katalin Susztak, Markus Scholz, Iris M. Heid, Adriana M. Hung, Alexander Teumer, Cristian Pattaro, Owen M. Woodward, Veronique Vitart, Anna Koettgen
Article
Immunology
Gaia M. Coppock, Lillian R. Aronson, Jihwan Park, Chengxiang Qiu, Jeongho Park, Jonathan H. DeLong, Enrico Radaelli, Katalin Susztak, Christopher A. Hunter
JOURNAL OF IMMUNOLOGY
(2020)
Article
Cell Biology
Xiangchen Gu, Hongliu Yang, Xin Sheng, Yi-An Ko, Chengxiang Qiu, Jihwan Park, Shizheng Huang, Rachel Kember, Renae L. Judy, Joseph Park, Scott M. Damrauer, Girish Nadkarni, Ruth J. F. Loos, Vy Thi Ha My, Kumardeep Chaudhary, Erwin P. Bottinger, Ishan Paranjpe, Aparna Saha, Christopher Brown, Shreeram Akilesh, Adriana M. Hung, Matthew Palmer, Aris Baras, John D. Overton, Jeffrey Reid, Marylyn Ritchie, Daniel J. Rader, Katalin Susztak
Summary: The study identified a potential correlation between low expression of MANBA in the kidneys of individuals with CKD risk genotype and an increased incidence of renal failure in individuals with rare loss-of-function coding variants in MANBA. The findings highlight the importance of the MANBA gene in kidney health, as it is highly expressed in human kidney tubule cells and appears to play a role in kidney disease development.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Editorial Material
Multidisciplinary Sciences
Chengxiang Qiu, Jay Shendure
Summary: Previous studies on gastrulation process have been limited to snapshots at different time points. Now, a mouse model can continuously map the transitions between cell types in time, providing a more dynamic understanding of embryonic development.
Article
Genetics & Heredity
Xin Sheng, Yuting Guan, Ziyuan Ma, Junnan Wu, Hongbo Liu, Chengxiang Qiu, Steven Vitale, Zhen Miao, Matthew J. Seasock, Matthew Palmer, Myung K. Shin, Kevin L. Duffin, Steven S. Pullen, Todd L. Edwards, Jacklyn N. Hellwege, Adriana M. Hung, Mingyao Li, Benjamin F. Voight, Thomas M. Coffman, Christopher D. Brown, Katalin Susztak
Summary: This study generated cell-type-specific eQTL maps in the human kidney using over 600 microdissected kidney samples, highlighting the cell types influencing kidney function, hypertension, and other traits.
Article
Multidisciplinary Sciences
Tomohito Doke, Shizheng Huang, Chengxiang Qiu, Xin Sheng, Matthew Seasock, Hongbo Liu, Ziyuan Ma, Matthew Palmer, Katalin Susztak
Summary: The study identified CASP9 as a key gene associated with eGFR and demonstrated its causal role in kidney disease development by improving mitophagy and reducing inflammation and apoptosis.
Article
Genetics & Heredity
Chengxiang Qiu, Junyue Cao, Beth K. Martin, Tony Li, Ian C. Welsh, Sanjay Srivatsan, Xingfan Huang, Diego Calderon, William Stafford Noble, Christine M. Disteche, Stephen A. Murray, Malte Spielmann, Cecilia B. Moens, Cole Trapnell, Jay Shendure
Summary: This article comprehensively describes the cellular trajectories of mammalian development by integrating multiple single-cell RNA sequencing datasets. It also identifies transcription factors as candidate regulators of each cell type's specification and finds cell-type homologs across vertebrate evolution.
Article
Multidisciplinary Sciences
Gianluca Amadei, Charlotte E. Handford, Chengxiang Qiu, Joachim De Jonghe, Hannah Greenfeld, Martin Tran, Beth K. Martin, Dong-Yuan Chen, Alejandro Aguilera-Castrejon, Jacob H. Hanna, Michael B. Elowitz, Florian Hollfelder, Jay Shendure, David M. Glover, Magdalena Zernicka-Goetz
Summary: Researchers have successfully assembled stem cell-derived embryo models composed of embryonic stem cells, trophoblast stem cells, and extraembryonic endoderm stem cells, and demonstrated their ability to recapitulate the development of mouse embryos. This study provides a powerful tool for studying the roles of different cell lineages and genes in development.
Article
Biochemical Research Methods
Beth K. Martin, Chengxiang Qiu, Eva Nichols, Melissa Phung, Rula Green-Gladden, Sanjay Srivatsan, Ronnie Blecher-Gonen, Brian J. Beliveau, Cole Trapnell, Junyue Cao, Jay Shendure
Summary: Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for gene expression analysis at the single-cell level. In this study, a simplified and optimized sci-RNA-seq protocol is presented, which offers improved speed, robustness, sensitivity, and cost-effectiveness compared to the original method. The protocol allows for RNA profiling of various tissue types and challenging samples, such as older mouse embryos or adult tissues. The optimized protocol is demonstrated by analyzing a large number of nuclei from an E16.5 mouse embryo in a single experiment, and a low-input protocol called 'Tiny-Sci' is introduced for experiments with limited materials.
Article
Medicine, Research & Experimental
Tomohito Doke, Shizheng Huang, Chengxiang Qiu, Hongbo Liu, Yuting Guan, Hailong Hu, Ziyuan Ma, Junnan Wu, Zhen Miao, Xin Sheng, Jianfu Zhou, Aili Cao, Jianhua Li, Lewis Kaufman, Adriana Hung, Christopher D. Brown, Richard Pestell, Katalin Susztak
Summary: The study integrated various methods to identify Dachshund homolog 1 (DACH1) as a kidney disease risk gene, revealing its crucial role in regulating the development of renal fibrosis.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Multidisciplinary Sciences
Xin Sheng, Chengxiang Qiu, Hongbo Liu, Caroline Gluck, Jesse Y. Hsu, Jiang He, Chi-yuan Hsu, Daohang Sha, Matthew R. Weir, Tamara Isakova, Dominic Raj, Hernan Rincon-Choles, Harold I. Feldman, Raymond Townsend, Hongzhe Li, Katalin Susztak
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Urology & Nephrology
Archna Bajaj, Andrea Ihegword, Chengxiang Qiu, Aeron M. Small, Wei-Qi Wei, Lisa Bastarache, QiPing Feng, Rachel L. Kember, Marjorie Risman, Roy D. Bloom, David L. Birtwell, Heather Williams, Christian M. Shaffer, Jinbo Chen, Joshua C. Denny, Daniel J. Rader, C. Michael Stein, Scott M. Damrauer, Katalin Susztak
KIDNEY INTERNATIONAL
(2020)
Article
Medicine, Research & Experimental
Jihwan Park, Yuting Guan, Xin Sheng, Caroline Gluck, Matthew J. Seasock, A. Ari Hakimi, Chengxiang Qiu, James Pullman, Amit Verma, Hongzhe Li, Matthew Palmer, Katalin Susztak