Review
Chemistry, Medicinal
Victor T. Sabe, Thandokuhle Ntombela, Lindiwe A. Jhamba, Glenn E. M. Maguire, Thavendran Govender, Tricia Naicker, Hendrik G. Kruger
Summary: Computer-aided drug design (CADD) is a pivotal approach in contemporary pre-clinical drug discovery, utilizing various computational techniques and software programs to achieve desired outcomes. Research evaluated the techniques and software programs used in CADD, along with experimental validations. The application of CADD has led to the discovery of numerous approved drugs, with a growing trend in the field.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Ge Wang, Yuhao Bai, Jiarui Cui, Zirui Zong, Yuan Gao, Zhen Zheng
Summary: This review provides an overview of the importance of the RAS gene family and its relevance to cancer development, as well as the challenges in designing drugs targeting RAS. Computer-aided drug design (CADD) offers new approaches for finding RAS-targeted drugs.
Article
Health Care Sciences & Services
Paolo Scolozzi, Francesco Michelini, Claude Crottaz, Alexandre Perez
Summary: Computer-aided design and computer-aided manufacturing (CAD/CAM) techniques have proven to be valuable in dental implant surgery, improving the success rate and patient satisfaction while ensuring implant parallelism. This study analyzed the clinical and radiological data of thirteen edentulous patients treated using CAD/CAM techniques, showing successful outcomes.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Chemistry, Medicinal
Isadora Silva Luna, Thalisson Amorim de Souza, Marcelo Sobral da Silva, Klinger Antonio da Franca Rodrigues, Luciana Scotti, Marcus Tullius Scotti, Francisco Jaime Bezerra Mendonca-Junior
Summary: In this study, a series of 2-amino-thiophene (2-AT) derivatives were virtually screened and evaluated using cheminformatics tools. Eleven potential anti-leishmanial 2-AT derivatives were identified, which exhibited good activity against the parasite and low cytotoxicity. Ligand-based virtual screening proved to be effective in selecting candidates for the development of new anti-leishmanial agents, and 2-AT derivatives showed promise as hit compounds.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Review
Chemistry, Medicinal
Yijie Liu, Jie Yang, Meilun Chen, Xiaoling Lu, Zheng Wei, Chunhua Tang, Peng Yu
Summary: This study summarizes the docking characteristics of four mainstream molecular docking software programs (Auto dock, Auto dock Vina, MOE, and hex Dock) in recent years, and evaluates the accuracy and prediction performance of these software programs for aptamer docking based on experimental data, providing guidance for researchers in selecting molecular docking software. Additionally, this review provides a detailed overview of the application of computer-aided virtual screening in aptamer screening, thus providing a direction for future development in this field.
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Laura Llorach-Pares, Alfons Nonell-Canals, Conxita Avila, Melchor Sanchez-Martinez
Summary: Computer-aided drug design techniques can be applied to the study of marine natural products, unlocking their therapeutic potential, reducing the amount of natural products required, and simplifying the research process.
Review
Biochemistry & Molecular Biology
Beatriz Suay-Garcia, Jose I. Bueso-Bordils, Antonio Falco, Gerardo M. Anton-Fos, Pedro A. Aleman-Lopez
Summary: Traditionally, drug development involved time-consuming and costly processes, but the application of virtual combinatorial chemistry and virtual screening can greatly accelerate the search and development of drugs, while saving costs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Medicinal
Deborah Giordano, Carmen Biancaniello, Maria Antonia Argenio, Angelo Facchiano
Summary: Computer-aided drug discovery techniques have reduced the time and costs involved in developing new drugs. Pharmacophore approaches, which define the molecular features required for the binding of a molecule to a specific receptor, have proven to be one of the most interesting tools in this field. The use of computational tools for pharmacophore modeling and virtual screening has resulted in successful studies and applications.
Review
Biochemistry & Molecular Biology
Sebastjan Kralj, Marko Jukic, Urban Bren
Summary: This study reviewed commercially available and marketed SARS-CoV-2-targeted libraries and evaluated their design methods. The lack of information on library design and primary literature references, as well as the absence of detailed details on molecular docking software, pharmacophore or filter design, hinder the use of these libraries in drug design. Commercial drug companies need to focus on and improve these issues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Haoyi Yang, Hengyu Wang, Jia Feng, Jianmin Liao, Yuanyuan Lu
Summary: A molecular docking-based virtual screening approach was used to identify inhibitors of TrxR1 with a new binding site from the SPECS database. Compound 22 was found to be a reversible inhibitor of TrxR1 U498C mutant, with its interaction centered on the inactive site Trp114. Amino acid mutations centered on Trp114 were shown to regulate the activity of TrxR1. This discovery provides insights for the discovery of new TrxR1 inhibitors.
ARABIAN JOURNAL OF CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Yelena Guttman, Zohar Kerem
Summary: This article reviews the existing computational tools and databases relevant to predicting CYP-mediated food-drug interactions (FDIs). Computer-aided approaches and structure-based methods are used to narrow down potential targets and explore the structural nature of the interaction between compounds and CYP enzymes. However, ligand-based machine-learning approaches for virtual screening are still underutilized in this field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Georgia Dorahy, Jake Zheng Chen, Thomas Balle
Summary: Central nervous system (CNS) disorders lack sufficient treatment options, leading to a demand for new therapies. Computer-aided drug design (CADD) techniques offer a solution by minimizing time and cost burdens associated with drug research and development. CADD encompasses ligand-based and structure-based methods, including deep learning techniques, which have shown promise in CNS drug discovery. This review investigates various CADD techniques and their applications in CNS drug discovery from 2018 to November 2022.
Review
Biochemistry & Molecular Biology
Murtala A. Ejalonibu, Segun A. Ogundare, Ahmed A. Elrashedy, Morufat A. Ejalonibu, Monsurat M. Lawal, Ndumiso N. Mhlongo, Hezekiel M. Kumalo
Summary: Developing new antibiotics targeting resistant Mycobacterium tuberculosis is an appealing strategy to combat the global tuberculosis epidemic, with computational techniques playing a key role in drug design and discovery. Recent advancements in technology have enhanced the chances of drug development, offering hope in the fight against tuberculosis resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Jian-hong Gan, Ji-xiang Liu, Yang Liu, Shu-wen Chen, Wen-tao Dai, Zhi-Xiong Xiao, Yang Cao
Summary: Computational identification of new targets for existing drugs is advantageous for drug repurposing, and a parameter-free virtual screening server called DrugRep has been developed to facilitate this process.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Chemistry, Multidisciplinary
Yu-Min Fang, Tzu-Lin Kao
Summary: This study compares the emotional response, flow experience, and operational performance of design novices using VR free-form modeling and conventional parametric CAD modeling. The findings show that VR free-form modeling elicits more positive and intense emotional responses, but its overall flow experience does not exceed expectations. There were no significant differences in concentration, time distortion sense, or control between the two techniques.
APPLIED SCIENCES-BASEL
(2023)
Article
Biotechnology & Applied Microbiology
Tin Wee Tan, Chao Xie, Mark De Silva, Kuan Siong Lim, C. Pawan K. Patro, Shen Jean Lim, Kunde Ramamoorthy Govindarajan, Joo Chuan Tong, Khar Heng Choo, Shoba Ranganathan, Asif M. Khan
Article
Ecology
Shen Jean Lim, Brenton G. Davis, Danielle E. Gill, Jillian Walton, Erika Nachman, Annette Summers Engel, Laurie C. Anderson, Barbara J. Campbell
Article
Microbiology
Shen Jean Lim, Louie Alexander, Annette Summers Engel, Audrey T. Paterson, Laurie C. Anderson, Barbara J. Campbell
Article
Oncology
Velda J. Gonzalez-Mercado, Jean Lim, Lawrence Berk, Mary Esele, Carmen S. Rodriguez, Gerardo Colon-Otero
CURRENT PROBLEMS IN CANCER
(2020)
Correction
Ecology
Shen Jean Lim, Brenton G. Davis, Danielle E. Gill, Jillian Walton, Erika Nachman, Annette Summers Engel, Laurie C. Anderson, Barbara J. Campbell
Review
Biology
Shen Jean Lim, Seth R. Bordenstein
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Nursing
Velda J. Gonzalez-Mercado, Wendy A. Henderson, Anujit Sarkar, Jean Lim, Leorey N. Saligan, Lawrence Berk, Larry Dishaw, Susan McMillan, Maureen Groer, Farrah Sepehri, Gail D'Eramo Melkus
Summary: This study aimed to investigate the differences in severity of fatigue, sleep disturbance, and depression symptoms between rectal cancer patients before and after chemotherapy and radiation therapy, as well as the relationship between gut microbial diversity and symptom occurrence. Results indicated that participants with co-occurring symptoms reported greater fatigue severity and showed differences in specific microbial abundances, with a prediction accuracy of 74% using microbiome data. This suggests a potential association between gut microbiota and co-occurring symptoms, laying the groundwork for a microbiota-based classifier.
BIOLOGICAL RESEARCH FOR NURSING
(2021)
Article
Oncology
Velda J. Gonzalez-Mercado, Jean Lim, Sara Marrero, Elsa Pedro, Leorey N. Saligan
Summary: This study aimed to compare the differences in gut microbial diversity and abundances between fatigued and non-fatigued rectal cancer patients at the end of CRT, as well as predicted functional pathways of the gut microbiome.
SUPPORTIVE CARE IN CANCER
(2021)
Article
Microbiology
Shen Jean Lim, Andreas Seyfang, Samia Dutra, Bradley Kane, Maureen Groer
Article
Nursing
Velda J. Gonzalez-Mercado, Jean Lim, Gary Yu, Frank Penedo, Elsa Pedro, Raul Bernabe, Maribel Tirado-Gomez, Bradley Aouizerat
Summary: The study aimed to compare gut microbial diversity and predicted functional pathways between rectal cancer patients with high versus low co-occurring symptoms before neoadjuvant chemotherapy and radiation therapy. Results showed significant differences in bacterial taxa and pathways between participants with high and low co-occurring symptoms, warranting detailed examination of bacteria and pathways mediating these symptoms.
BIOLOGICAL RESEARCH FOR NURSING
(2021)
Article
Microbiology
Shen Jean Lim, Brenton Davis, Danielle Gill, John Swetenburg, Laurie C. Anderson, Annette Summers Engel, Barbara J. Campbell
Summary: Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Our analysis of the microbiome content of Stewartia floridana collected from Florida revealed a monospecific gammaproteobacterial endosymbiont and a low-abundance Spirochaeta-like species, indicating possible facultative association with scavenging and nutrient cycling roles. The expressed genes of the symbionts and host suggest species-species communications and the need for further study of interactions in the lucinid hosts, their microbiomes, and the environment.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Microbiology
Shen Jean Lim, Miriam Aguilar-Lopez, Christine Wetzel, Samia V. O. Dutra, Vanessa Bray, Maureen W. Groer, Sharon M. Donovan, Thao Ho
Summary: The gut microbiota of preterm infants is influenced by various factors, including genetic relatedness. Siblings share similar gut microbial composition, particularly at <= 3 weeks postnatal age, suggesting genetic or shared maternal and environmental effects on the preterm infant gut microbiota. Additionally, weeks on bovine milk-based fortifier and weight gain velocity were significant predictors of alpha diversity in preterm infants.
Article
Biotechnology & Applied Microbiology
Shen Jean Lim, Luke R. Thompson, Craig M. Young, Terry Gaasterland, Kelly D. Goodwin
Summary: Methane hydrates are significant natural gas reserves with implications for global carbon cycling and climate change. This study provides the first analysis of metagenomes associated with the methane ice worm, a polychaete species that colonizes methane hydrates. The study reveals the metabolic capabilities and microbial community composition of this elusive marine polychaete.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Helen Park, Shen Jean Lim, Jonathan Cosme, Kyle O'Connell, Jilla Sandeep, Felimon Gayanilo, George R. Cutter Jr, Enrique Montes, Chotinan Nitikitpaiboon, Sam Fisher, Hassan Moustahfid, Luke R. Thompson
Summary: Microbial communities in the ocean play critical roles in regulating biogeochemical processes and have important implications for marine ecosystems. Understanding their diversity and function is key to comprehending spatiotemporal variations. Recent advancements in DNA sequencing and computational analysis have opened up new possibilities for studying marine microbial communities. In this study, the utility of deep learning tools for taxonomic classification is explored, showing promising results and highlighting the importance of considering genomic diversity and class imbalance in future machine learning work.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biology
Luke R. Thompson, Sean R. Anderson, Paul A. Den Uyl, Nastassia Patin, Shen Jean Lim, Grant Sanderson, Kelly D. Goodwin
Summary: This article introduces Tourmaline, a Python-based workflow that implements QIIME 2 and allows for automated analysis of environmental amplicon data. The workflow improves efficiency and decreases the time required for data analysis, from data generation to actionable results.