Journal of computer-aided molecular design
Dec 19, 2025
Hit-to-lead (H2L) optimization is a critical stage in small-molecule drug discovery, where efficient exploration of chemical space is required to identify promising lead compounds. Conventional H2L workflows rely on iterative synthesis and experiment...
Journal of chemical information and modeling
Dec 11, 2025
The prediction of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties remains a central bottleneck in small-molecule discovery. We present the third-place solution from the PolarisHub Antiviral Competition, covering five ...
Journal of chemical information and modeling
Dec 8, 2025
MiRNA serves as a key noncoding RNA regulating gene expression and is frequently targeted as a therapeutic small molecule (SM). However, relying solely on the experimental identification of SM-miRNA interactions proves costly and inefficient. To addr...
Journal of computer-aided molecular design
Dec 3, 2025
The identification of protein target classes is a key step in drug discovery, as it enables prioritization of screening campaigns and supports target-based drug repurpose. In this study, we developed a deep-learning pipeline based on a multilayer per...
Journal of computer-aided molecular design
Nov 25, 2025
The pKa, also known as the logarithmic dissociation constant, is a crucial parameter that defines the ionization level of a molecule when it is in solution. It is essential for several physicochemical properties, including lipophilicity, solubility, ...
Journal of chemical information and modeling
Nov 18, 2025
Neuroscience is the most difficult therapeutic area for pharmaceutical drug discovery. The blood-brain barrier (BBB) prevents ∼100% of large molecules and >98% of small molecules from penetrating the central nervous system (CNS). Most small molecule ...
Proceedings of the National Academy of Sciences of the United States of America
Nov 4, 2025
Modeling the conformational heterogeneity of protein-small molecule interactions is important for understanding natural systems and evaluating designed systems but remains an outstanding challenge. We reasoned that while residue-level descriptions of...
Precise subcellular localization is crucial for the design of molecular probes and targeted therapeutics, yet selectively distinguishing organelles with similar physicochemical properties, such as lipid droplets, mitochondria, and the cell membrane, ...
European journal of medicinal chemistry
Oct 16, 2025
Staphylococcus aureus (S. aureus) is one of the most concerned Gram-positive bacteria due to its resistance to the commonly used antibiotics, methicillin. To address the threat of methicillin-resistant S. aureus (MRSA), new classes of antibiotics are...
Journal of chemical information and modeling
Oct 9, 2025
In molecular studies, the accurate parametrization of small molecules stands as an essential yet growing demand. Addressing this, we introduce ParametrizANI, a tool crafted explicitly for establishing detailed protocols for dihedral parametrization u...
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