CACTI: an in silico chemical analysis tool through the integration of chemogenomic data and clustering analysis DOI Creative Commons
Karla P. Godinez‐Macias, Elizabeth A. Winzeler

Journal of Cheminformatics, Год журнала: 2024, Номер 16(1)

Опубликована: Июль 24, 2024

Abstract It is well-accepted that knowledge of a small molecule’s target can accelerate optimization. Although chemogenomic databases are helpful resources for predicting or finding compound interaction partners, they tend to be limited and poorly annotated. Furthermore, unlike genes, identifiers often not standardized, many synonyms may exist, especially in the biological literature, making batch analysis compounds difficult. Here, we constructed an open-source annotation hypothesis prediction tool explores some largest chemical databases, mining these both common name, synonyms, structurally similar molecules. We used this Chemical Analysis Clustering Target Identification (CACTI) analyze Pathogen Box collection, set 400 drug-like active against variety microbial pathogens. Our resulted 4,315 new 35,963 pieces information hints 58 members. Scientific contributions With employment tool, comprehensive report with known evidence, close analogs drug-target obtained large-scale libraries will facilitate their evaluation future validation optimization efforts.

Язык: Английский

Unveiling Prospective Therapeutic Potential of Conserved Hypothetical Plasmodium falciparum Proteins by Using Integrated Proteo Genomic Annotation and In-Silico Therapeutic Discovery Approach DOI
Mamta Panda,

Varshita Srivastava,

Satyendra Singh

и другие.

The Protein Journal, Год журнала: 2025, Номер unknown

Опубликована: Апрель 11, 2025

Язык: Английский

Процитировано

0
Computational analysis of zoanthamine alkaloids from Zoanthus sp. as potential DKK1 and GSK-3β inhibitors for osteoporosis therapy via Wnt signaling DOI Creative Commons

Ngoc-Thac Pham,

Huong-Giang Le,

Bo‐Rong Peng

и другие.

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Апрель 24, 2025

Marine invertebrates are a rich source of structurally diverse secondary metabolites with broad biological activities, making them valuable for drug discovery. The genus Zoanthus is particularly noteworthy, producing numerous bioactive alkaloids, including the zoanthamines, which show promise in treating osteoporosis. Osteoporosis, debilitating bone disease characterized by reduced mineral density and increased fracture risk, linked to Wnt signaling pathway dysregulation. This highly conserved maintains tissue homeostasis crucial neurogenesis, synapse formation, development. Dickkopf-1 (DKK1) glycogen synthase kinase-3β (GSK-3β), key regulators, established therapeutic targets study employed an integrated computational approach-combining molecular docking, extensive dynamics (MD) simulations, functional theory (DFT) calculations-to assess inhibitory potential 69 zoanthamine-type alkaloids against DKK1 GSK-3β. MD analyzing root mean square deviation (RMSD), fluctuation (RMSF), radius gyration, free energy landscape, provided insights into protein-ligand complex stability interactions. Binding energies were calculated using MM-PBSA method combined interaction entropy. DFT calculations further elucidated electronic structure reactivity most promising inhibitors (3α-hydroxyzoanthenamine, epioxyzoanthamine, 7α-hydroxykuroshine E, norzoanthamine), exhibited favorable binding interactions residues target proteins. integrative approach demonstrates power methods discovery, highlighting zoanthamine as lead compounds innovative osteoporosis therapies.

Язык: Английский

Процитировано

0
Sesamol as a potent anticancer compound: from chemistry to cellular interactions DOI
Ajay Kumar, Payal Bajaj,

Brahmjot Singh

и другие.

Naunyn-Schmiedeberg s Archives of Pharmacology, Год журнала: 2024, Номер 397(7), С. 4961 - 4979

Опубликована: Янв. 5, 2024

Язык: Английский

Процитировано

3
Protein target similarity is positive predictor of in vitro antipathogenic activity: a drug repurposing strategy for Plasmodium falciparum DOI Creative Commons
Reagan M. Mogire, Silviane A. Miruka,

Dennis W. Juma

и другие.

Journal of Cheminformatics, Год журнала: 2024, Номер 16(1)

Опубликована: Май 30, 2024

Abstract Drug discovery is an intricate and costly process. Repurposing existing drugs active compounds offers a viable pathway to develop new therapies for various diseases. By leveraging publicly available biomedical information, it possible predict compounds’ activity identify their potential targets across diverse organisms. In this study, we aimed assess the antiplasmodial of from Repurposing, Focused Rescue, Accelerated Medchem (ReFRAME) library using in vitro bioinformatics approaches. We assessed blood-stage liver-stage drug susceptibility assays. used protein sequences known ReFRAME with high (EC 50 < 10 uM) conduct protein-pairwise search similar Plasmodium falciparum 3D7 proteins (from PlasmoDB) NCBI BLAST. further association between compounds' level similarity predicted P. target simple linear regression analyses. BLAST analyses revealed 735 that were 226 associated compounds. Antiplasmodial was positively degree (percentage identity, E value, bit score), number targets, respective mutagenesis index fitness scores (R 2 0.066 0.92, P 0.05). Compounds essential or those druggability 1 showed highest activity.

Язык: Английский

Процитировано

3
An experimental and computational approach to evaluate the antidiabetic activity of Commiphora wightii gum extract DOI Creative Commons
Shalini Jain, Mukesh Kumar Sharma, Nidhi Gupta

и другие.

Journal of Ayurveda and Integrative Medicine, Год журнала: 2024, Номер 16(1), С. 101038 - 101038

Опубликована: Дек. 19, 2024

Язык: Английский

Процитировано

1
CACTI: an in silico chemical analysis tool through the integration of chemogenomic data and clustering analysis DOI Creative Commons
Karla P. Godinez‐Macias, Elizabeth A. Winzeler

Journal of Cheminformatics, Год журнала: 2024, Номер 16(1)

Опубликована: Июль 24, 2024

Abstract It is well-accepted that knowledge of a small molecule’s target can accelerate optimization. Although chemogenomic databases are helpful resources for predicting or finding compound interaction partners, they tend to be limited and poorly annotated. Furthermore, unlike genes, identifiers often not standardized, many synonyms may exist, especially in the biological literature, making batch analysis compounds difficult. Here, we constructed an open-source annotation hypothesis prediction tool explores some largest chemical databases, mining these both common name, synonyms, structurally similar molecules. We used this Chemical Analysis Clustering Target Identification (CACTI) analyze Pathogen Box collection, set 400 drug-like active against variety microbial pathogens. Our resulted 4,315 new 35,963 pieces information hints 58 members. Scientific contributions With employment tool, comprehensive report with known evidence, close analogs drug-target obtained large-scale libraries will facilitate their evaluation future validation optimization efforts.

Язык: Английский

Процитировано

0