Fragment-based drug design began more than ten years ago and has been steadily gaining in popularity. This review discusses how fragments have been used to choose druggable targets, and what parameters need to be evaluated if a fragment hit is to be considered a suitable ligand for development. Examples of fragment-based screening from the recent literature are reviewed to highlight the various approaches used, along with the possible application of additional techniques to fragment screening against immobilized targets. Finally, mention is made of two different areas, multi-target drug discovery and selective tumor cell targeting, where fragment-based approaches may play an important role in the future.
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IUCrJ
March 2025
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China.
Heat-shock protein 90 (HSP90) is a highly active molecular chaperone that plays a crucial role in cellular function. It facilitates the folding, assembly and stability of various oncogenic proteins, particularly kinases and transcription factors involved in regulating tumor growth and maintenance signaling pathways. Consequently, HSP90 inhibitors are being explored as drugs for cancer therapy.
View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale) 06120, Germany.
Reliable in silico prediction of fragment binding modes remains a challenge in current drug design research. Due to their small size and generally low binding affinity, fragments can potentially interact with their target proteins in different ways. In the current study, we propose a workflow aimed at predicting favorable fragment binding sites and binding poses through multiple short molecular dynamics simulations.
View Article and Find Full Text PDFCurr Drug Discov Technol
December 2024
Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, PushpViharSector-3, M-B Road, New Delhi, 110017, India.
Background: Computer-Aided Drug Design (CADD) approaches are essential in the drug discovery and development process. Both academic institutions and pharmaceutical and biotechnology corporations utilize them to enhance the efficacy of bioactive compounds.
Objective: This study aims to entice researchers by investigating the benefits of Computer-Aided Drug and Design (CADD) and its fundamental principles.
J Cheminform
January 2025
Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK.
Current strategies centred on either merging or linking initial hits from fragment-based drug design (FBDD) crystallographic screens generally do not fully leaverage 3D structural information. We show that an algorithmic approach (Fragmenstein) that 'stitches' the ligand atoms from this structural information together can provide more accurate and reliable predictions for protein-ligand complex conformation than general methods such as pharmacophore-constrained docking. This approach works under the assumption of conserved binding: when a larger molecule is designed containing the initial fragment hit, the common substructure between the two will adopt the same binding mode.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
Triple-negative breast cancer (TNBC) is one of the most fatal malignancies in the world, accounting for 42% of all deaths due to metastasis. The significant development is hindered by the multi-drug resistance and poor patient compliance. PIK3CA gene mutation is one of the important causes of TNBC, which causes dysregulation of the cell cycle and cell proliferation.
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