Review
Oncology
Enrique Hernandez-Lemus, Mireya Martinez-Garcia
Summary: Cancer is a complex pathology recognized as a major public health problem worldwide. Various therapeutic strategies are available, with a shift towards pathway-based dysfunctions in treatment approaches due to the heterogeneous nature of tumors. Collaboration among multidisciplinary teams is essential for analyzing high-throughput experiments and improving clinical outcomes for oncological patients.
FRONTIERS IN ONCOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Lin-hui Zhai, Kai-feng Chen, Bing-bing Hao, Min-jia Tan
Summary: Protein post-translational modifications (PTMs) are crucial for protein activity regulation and are involved in diseases. PTM regulatory enzymes are important drug targets. Mass spectrometry-based proteomics enables systematic characterization of PTMs for drug target identification, mechanism elucidation and biomarker discovery in personalized therapy.
ACTA PHARMACOLOGICA SINICA
(2022)
Article
Chemistry, Multidisciplinary
Jessica K. Holien, Lachlan Coff, Andrew J. Guy, Jennifer C. Boer
Summary: During the COVID-19 lockdowns, online learning activities were developed for undergraduate and master's students. An integrative, industry-based research assignment was designed to guide students through a drug discovery project. This assignment allowed students to apply diverse bioinformatic principles to analyze biological and chemical data and make meaningful predictions. It served as the final assessment of the students' knowledge.
JOURNAL OF CHEMICAL EDUCATION
(2023)
Article
Biochemistry & Molecular Biology
Patrizio di Micco, Albert A. Antolin, Costas Mitsopoulos, Eloy Villasclaras-Fernandez, Domenico Sanfelice, Daniela Dolciami, Pradeep Ramagiri, Ioan L. Mica, Joseph E. Tym, Philip W. Gingrich, Huabin Hu, Paul Workman, Bissan Al-Lazikani
Summary: canSAR is the largest public cancer drug discovery and translational research knowledgebase, integrating billions of experimental measurements from various fields and applying unique machine learning algorithms for drug discovery.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Pharmacology & Pharmacy
Hongli Liu, Haoran Zhang, Adriaan P. Ijzerman, Dong Guo
Summary: Research on residence time contributes to the translation of in vitro potency to in vivo efficacy and safety, serving as a method to predict drug pharmacological activity and side effects. Integrating residence time into the early stages of drug discovery and development aids in obtaining promising clinical candidates. Further research and optimization of residence time measurement will facilitate the development of safer and more effective drugs.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Biochemical Research Methods
Isadora Leitzke Guidotti, Alessandra Neis, Daniela Peres Martinez, Fabiana Kommling Seixas, Karina Machado, Frederico Schmitt Kremer
Summary: In this study, a computational tool called Bambu was developed to generate QSAR models from high-throughput screening bioassays datasets. The tool was able to identify a wide variety of molecules with potential melanoma cell growth inhibitors and outperformed another QSAR model generation tool, QSAR-Co, in terms of accuracy, recall, F1, and ROC AUC.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Review
Medicine, Research & Experimental
Nicholas J. Coltman, Ruth A. Roberts, James E. Sidaway
Summary: Early de-risking of drug targets and chemistry is crucial for the success of drug projects. Target safety assessments use data science to identify and mitigate potential safety risks, taking advantage of the latest developments in the field.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2023)
Review
Chemistry, Multidisciplinary
Gina Porras, Francois Chassagne, James T. Lyles, Lewis Marquez, Micah Dettweiler, Akram M. Salam, Tharanga Samarakoon, Sarah Shabih, Darya Raschid Farrokhi, Cassandra L. Quave
Summary: The crisis of antibiotic resistance highlights the importance of exploring plant natural products as a potential source of antibacterial compounds. This review systematically examines the antibacterial activity of 459 plant-derived compounds, with a focus on 183 compounds that show promising potential as antibiotics. The rich chemodiversity and clinical effectiveness of plant NPs make them a valuable resource for future antibiotic discovery and development efforts.
Review
Biochemistry & Molecular Biology
Dafei Xie, Qi Huang, Pingkun Zhou
Summary: DNA damage caused by cosmic radiation is a major obstacle to human space exploration. This review focuses on the proteins involved in DNA damage response (DDR), including ATM, DNA-PKcs, CtIP, MDM2, and ubiquitin ligases, which are modulated by post-translational modifications such as phosphorylation and ubiquitylation. The involvement and function of acetylation, methylation, PARylation, and their associated proteins were also investigated. Additionally, the lack of radioprotectors despite the consideration of radiosensitizers is addressed, and new perspectives for the research and development of future agents against space radiation are proposed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Medicinal
Masilamani Elizabeth Sobhia, Ketan Ghosh, Gajjala Siva Kumar, Srikanth Sivangula, Kapil Laddha, Sonia Kumari, Harish Kumar
Summary: This review highlights the significance of water molecules in protein environments and the bottleneck created by the lack of well-resolved crystal structures in developing molecules for critical therapeutic targets. It also provides a common platform for researchers to consider various aspects related to water molecules.
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2022)
Article
Pharmacology & Pharmacy
Gilda Padalino, Avril Coghlan, Giampaolo Pagliuca, Josephine E. Forde-Thomas, Matthew Berriman, Karl F. Hoffmann
Summary: Schistosomiasis is an important neglected tropical disease, and chemotherapy is currently the main strategy. However, the sustainability of this strategy is at risk. This study demonstrates how schistosome-specific resources, together with the open-access drug discovery database ChEMBL, can be used to accelerate the discovery and development of schistosome drugs.
Review
Chemistry, Multidisciplinary
Duan Ni, Zongtao Chai, Ying Wang, Mingyu Li, Zhengtian Yu, Yaqin Liu, Shaoyong Lu, Jian Zhang
Summary: Allostery is a biological phenomenon where orthosteric sites are regulated by distal allosteric sites, triggering responses to perturbations such as ligand binding or mutations. Recent advances in biophysics, particularly in structural bioinformatics, have improved understanding of allosteric effects, leading to more rational structure-based drug discovery methods.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Clinical Neurology
Rachel Barenie, Jonathan Darrow, Jerry Avorn, Aaron S. Kesselheim
Summary: Pregabalin was discovered with significant public funding at Northwestern University and further developed by Parke-Davis until its FDA approval in 2004. Research indicates that the development of pregabalin relied on both public sector and industry contributions to its discovery.
Review
Chemistry, Medicinal
Ravinder Sharma, Gunpreet Kaur, Parveen Bansal, Viney Chawla, Vikas Gupta
Summary: Despite challenges in drug development, bioinformatics analysis using integrated genomics, proteomics, and bioinformatics can accelerate drug discovery and characterization while also predicting adverse effects and drug resistance. Combinatorial techniques such as proteomics, genomics, bioinformatics, molecular docking, and mass spectrometry have been crucial in understanding the drug-creation process. This article provides an overview of these techniques and their importance in drug development.
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Uttpal Anand, Anustup Bandyopadhyay, Niraj Kumar Jha, Jose M. Perez de la Lastra, Abhijit Dey
Summary: Protein-protein interactions play a crucial role in drug development, but disrupting PPIs with small molecules is challenging. Peptides with both conformational rigidity and flexibility are able to target difficult binding interfaces. Over 80 peptide drugs have been approved for various diseases, including cancer and HIV infection. New strategies, such as peptide display libraries and integrated genomics, are being developed for peptide drug discovery.
Article
Health Care Sciences & Services
Fagen Xie, Chengyi Zheng, Albert Yuh-Jer Shen, Wansu Chen
HEALTH INFORMATICS JOURNAL
(2017)
Article
Ophthalmology
Chengyi Zheng, Yi Luo, Cheryl Mercado, Lina Sy, Steven J. Jacobsen, Brad Ackerson, Bruno Lewin, Hung Fu Tseng
CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY
(2019)
Article
Computer Science, Information Systems
Chengyi Zheng, Wei Yu, Fagen Xie, Wansu Chen, Cheryl Mercado, Lina S. Sy, Lei Qian, Sungching Glenn, Gina Lee, Hung Fu Tseng, Jonathan Duffy, Lisa A. Jackson, Matthew F. Daley, Brad Crane, Huong Q. McLean, Steven J. Jacobsen
INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS
(2019)
Article
Cardiac & Cardiovascular Systems
Chengyi Zheng, Benjamin C. Sun, Yi-Lin Wu, Ming-Sum Lee, Ernest Shen, Rita F. Redberg, Maros Ferencik, Shaw Natsui, Aniket A. Kawatkar, Visanee V. Musigdilok, Adam L. Sharp
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2020)
Article
Cardiac & Cardiovascular Systems
Shaw Natsui, Benjamin C. Sun, Ernest Shen, Rita F. Redberg, Maros Ferencik, Ming-Sum Lee, Visanee Musigdilok, Yi-Lin Wu, Chengyi Zheng, Aniket A. Kawatkar, Adam L. Sharp
Summary: There is wide variation in physician-level admission rates for evaluation of emergency department chest pain, even within a well-integrated health system. Patients evaluated by high-admitting physicians did not have a clear benefit in terms of 30-day death or acute myocardial infarction.
CIRCULATION-CARDIOVASCULAR QUALITY AND OUTCOMES
(2021)
Article
Immunology
Chengyi Zheng, Lina S. Sy, Hilary Tanenbaum, Yun Tian, Yi Luo, Bradley Ackerson, Hung Fu Tseng
Summary: The study found that an automated natural language processing algorithm showed high sensitivity and specificity in identifying herpes zoster ophthalmicus (HZO) cases, suitable for large-scale population studies. Results indicated that age, sex, and race were strongly associated with the risk of herpes zoster ophthalmicus among patients with herpes zoster.
OPEN FORUM INFECTIOUS DISEASES
(2021)
Article
Cardiac & Cardiovascular Systems
Derek Q. Phan, Chengyi Zheng, Tydus Thai, Bryant Hammershaimb, Karo Gyurjian, Sej Patel, Aiyu Chen, Ming-Sum Lee
Summary: Cardiorespiratory fitness is associated with better survival. Patients over 80 years old with high fitness levels have comparable or even better survival rates than their younger counterparts with lower fitness levels. Chronological age alone should not be the only factor when considering prognosis.
AMERICAN JOURNAL OF CARDIOLOGY
(2022)
Article
Medicine, General & Internal
Chengyi Zheng, Jonathan Duffy, In-Lu Amy Liu, Lina S. Sy, Wansu Chen, Lei Qian, Ronald A. Navarro, Denison S. Ryan, Sunhea S. Kim, Cheryl Mercado, Steven J. Jacobsen
Summary: This retrospective cohort study estimated the risk for shoulder conditions after vaccination and identified possible risk factors. The results suggest a small absolute risk for shoulder conditions after vaccination, with factors such as age, sex, outpatient visits, comorbidity index, and vaccine type associated with an increased risk of shoulder conditions.
ANNALS OF INTERNAL MEDICINE
(2022)
Article
Public, Environmental & Occupational Health
Chengyi Zheng, Jonathan Duffy, In-Lu Amy Liu, Lina S. Sy, Ronald A. Navarro, Sunhea S. Kim, Denison S. Ryan, Wansu Chen, Lei Qian, Cheryl Mercado, Steven J. Jacobsen
Summary: A natural language processing (NLP) method was developed to identify cases of shoulder injury related to vaccine administration (SIRVA) from clinical notes. The algorithm showed high sensitivity and reasonable specificity in identifying positive SIRVA cases, which can potentially be used in future population-based studies to identify this rare adverse event, avoiding labor-intensive chart review validation.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2022)
Article
Clinical Neurology
David M. Kent, Lester Y. Leung, Eric J. Puttock, Andy Y. Wang, Patrick H. Luetmer, David F. Kallmes, Jason Nelson, Sunyang Fu, Chengyi Zheng, Ellen M. Vickery, Hongfang Liu, Alastair J. Noyce, Wansu Chen
Summary: This study found that incidentally discovered white matter disease was associated with subsequent Parkinson disease, especially in younger age groups and with increased severity of white matter disease. However, covert brain infarction did not appear to be associated with subsequent Parkinson disease.
ANNALS OF NEUROLOGY
(2022)
Article
Cardiac & Cardiovascular Systems
David M. M. Kent, Lester Y. Y. Leung, Yichen Zhou, Patrick H. H. Luetmer, David F. F. Kallmes, Jason Nelson, Sunyang Fu, Eric J. J. Puttock, Chengyi Zheng, Hongfang Liu, Wansu Chen
Summary: Covert cerebrovascular disease (CCD) is associated with dementia, but the risk of dementia associated with incidentally discovered CCD is unknown.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2023)
Article
Infectious Diseases
Ana Florea, Lina S. Sy, Bradley K. Ackerson, Lei Qian, Yi Luo, Tracy Becerra-Culqui, Gina S. Lee, Yun Tian, Chengyi Zheng, Radha Bathala, Sara Y. Tartof, Laura Campora, Maria Angeles Ceregido, Anastasia Kuznetsova, Jean-Etienne Poirrier, Dominique Rosillon, Laura Valdes, Brigitte Cheuvart, Narcisa Mesaros, Nadia Meyer, Adrienne Guignard, Hung-Fu Tseng
Summary: This study evaluated the risk of congenital anomalies in infants following prenatal vaccination with the Tdap vaccine. The results showed a significantly increased risk of congenital anomalies in certain body systems among vaccinated women. However, these findings may be attributed to improved diagnosis rather than a direct association with the vaccine.
INFECTIOUS DISEASES AND THERAPY
(2023)
Article
Cardiac & Cardiovascular Systems
Chengyi Zheng, Ming-sum Lee, Nisha Bansal, Alan S. Go, Cheng Chen, Teresa N. Harrison, Dongjie Fan, Amanda Allen, Elisha Garcia, Ben Lidgard, Daniel Singer, Jaejin An
Summary: This study developed and applied natural language processing (NLP) algorithms to identify recurrent atrial fibrillation (AF) episodes following rhythm control therapy initiation using electronic health records (EHRs). The NLP algorithms showed high performance in identifying AF recurrences and were more effective than a code-based approach alone. The findings demonstrate the potential of NLP algorithms in evaluating treatment effectiveness and developing tailored interventions for AF.
EUROPEAN HEART JOURNAL-QUALITY OF CARE AND CLINICAL OUTCOMES
(2023)
Article
Urology & Nephrology
Gary W. Chien, Jeff M. Slezak, Teresa N. Harrison, Howard Jung, Joy S. Gelfond, Chengyi Zheng, Edward Wu, Richard Contreras, Ronald K. Loo, Steven J. Jacobsen
Article
Health Care Sciences & Services
Joan J. Ryoo, Michael Batech, Chengyi Zheng, Raymond W. Kim, Michael K. Gould, A. Robert Kagan, Winston W. Lien
ANNALS OF PALLIATIVE MEDICINE
(2017)
Review
Pharmacology & Pharmacy
Karlie R. Sharma, Christine M. Colvis, Griffih P. Rodgers, Douglas M. Sheeley
Summary: There are many genes within the druggable genome that have not been studied, and the US National Institutes of Health's program provides resources to explore these genes, with the potential for rapid impact on human health.
DRUG DISCOVERY TODAY
(2024)
Review
Pharmacology & Pharmacy
Mohammad Sameer Khan, B. H. Jaswanth Gowda, Waleed H. Almalki, Tanuja Singh, Amirhossein Sahebkar, Prashant Kesharwani
Summary: Mitochondria-specific functional liposomes hold great potential for cancer therapy. This review discusses the association between mitochondria and tumor formation, as well as the advantages of liposomes in delivering drugs to mitochondria.
DRUG DISCOVERY TODAY
(2024)
Review
Pharmacology & Pharmacy
Choong Yong Ung, Cristina Correia, Hu Li, Christopher M. Adams, Jennifer J. Westendorf, Shizhen Zhu
Summary: With increasing human life expectancy, the global medical burden of chronic diseases is growing. Chronic diseases often involve malfunctioning of multiple organs, and understanding the interorgan crosstalk is crucial to understanding the etiology of chronic diseases. Researchers have proposed the locked-state model (LoSM) and cutting-edge systems biology and artificial intelligence strategies to decipher chronic multiorgan locked states. The findings have important clinical implications for improving treatments for chronic diseases.
DRUG DISCOVERY TODAY
(2024)