Drug discovery is stochastic. The effectiveness of candidate compounds in satisfying design objectives is unknown ahead of time, and the tools used for prioritization-predictive models and assays-are inaccurate and noisy. In a typical discovery campaign, thousands of compounds may be synthesized and tested before design objectives are achieved, with many others ideated but deprioritized. These challenges are well-documented, but assessing potential remedies has been difficult. We introduce , a framework for modeling the stochastic process of drug discovery. Emulating biochemical assays with realistic surrogate models, we simulate the progression from weak hits to sub-micromolar leads with viable ADME. We use this testbed to examine how different ideation, scoring, and decision-making strategies impact statistical measures of utility, such as the probability of program success within predefined budgets and the expected costs to achieve target candidate profile (TCP) goals. We also assess the influence of affinity model inaccuracy, chemical creativity, batch size, and multi-step reasoning. Our findings suggest that reducing affinity model inaccuracy from 2 to 0.5 pIC50 units improves budget-constrained success rates tenfold. DrugGym represents a realistic testbed for machine learning methods applied to the hit-to-lead phase. Source code is available at www.drug-gym.org.
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http://dx.doi.org/10.1101/2024.05.28.596296 | DOI Listing |
Front Biosci (Landmark Ed)
November 2024
Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 230022 Hefei, Anhui, China.
Background: Gallstone formation is a common digestive ailment, with unclear mechanisms underlying its development. Dysfunction of the gallbladder smooth muscle (GSM) may play a crucial role, particularly with a high-fat diet (HFD). This study aimed to investigate the effects of an HFD on GSM and assess how it alters contractility through changes in the extracellular matrix (ECM).
View Article and Find Full Text PDFJACS Au
December 2024
Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.
High-throughput screening (HTS) is a crucial technique for identifying potential hits to fuel drug discovery pipelines. However, this process naturally concentrates nuisance compounds that are not optimizable yet signal positively in a convincing manner. To be able to understand what types of nuisance compounds a particular assay is sensitive to, would be of great utility in being able to prioritize progressable over nonprogressable screening hits.
View Article and Find Full Text PDFJACS Au
December 2024
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No. 345 Lingling Road, Shanghai 200032, China.
Macrocyclization is a compelling strategy for conventional drug design for improving biological activity, target specificity, and metabolic stability, but it was rarely applied to the design of PROTACs possibly due to the mechanism and structural complexity. Herein, we report the rational design of the first series of "Head-to-Tail" macrocyclic PROTACs. The resulting molecule exhibited pronounced Brd4 protein degradation with low nM DC values while almost totally dismissing the "hook effect", which is a general character and common concern of a PROTAC, in multiple cancer cell lines.
View Article and Find Full Text PDFJACS Au
December 2024
Faculty of Synthetic Biology, Shenzhen University of Advanced Technology, Shenzhen 518055, China.
The origin of life on Earth remains one of the most perplexing challenges in biochemistry. While numerous bottom-up experiments under prebiotic conditions have provided valuable insights into the spontaneous chemical genesis of life, there remains a significant gap in the theoretical understanding of the complex reaction processes involved. In this study, we propose a novel approach using a roto-translationally invariant potential (RTIP) formulated with pristine Cartesian coordinates to facilitate the simulation of chemical reactions.
View Article and Find Full Text PDFOncol Res
December 2024
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
Background: Triple-negative breast cancer (TNBC), characterized by its lack of traditional hormone receptors and HER2, presents a significant challenge in oncology due to its poor response to conventional therapies. Autophagy is an important process for maintaining cellular homeostasis, and there are currently autophagy biomarkers that play an effective role in the clinical treatment of tumors. In contrast to targeting protein activity, intervention with protein-protein interaction (PPI) can avoid unrelated crosstalk and regulate the autophagy process with minimal interference pathways.
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