15 research outputs found
AI is a viable alternative to high throughput screening: a 318-target study
: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery
Characterization of the Prion Protein Binding Properties of Antisense Oligonucleotides
Antisense oligonucleotides (ASOs) designed to lower prion protein (PrP) expression in the brain through RNase H1-mediated degradation of PrP RNA are in development as prion disease therapeutics. ASOs were previously reported to sequence-independently interact with PrP and inhibit prion accumulation in cell culture, yet in vivo studies using a new generation of ASOs found that only PrP-lowering sequences were effective at extending survival. Cerebrospinal fluid (CSF) PrP has been proposed as a pharmacodynamic biomarker for trials of such ASOs, but is only interpretable if PrP lowering is indeed the relevant mechanism of action in vivo and if measurement of PrP is unconfounded by any PrP–ASO interaction. Here, we examine the PrP-binding and antiprion properties of ASOs in vitro and in cell culture. Binding parameters determined by isothermal titration calorimetry were similar across all ASOs tested, indicating that ASOs of various chemistries bind full-length recombinant PrP with low- to mid-nanomolar affinity in a sequence-independent manner. Nuclear magnetic resonance, dynamic light scattering, and visual inspection of ASO–PrP mixtures suggested, however, that this interaction is characterized by the formation of large aggregates, a conclusion further supported by the salt dependence of the affinity measured by isothermal titration calorimetry. Sequence-independent inhibition of prion accumulation in cell culture was observed. The inefficacy of non-PrP-lowering ASOs against prion disease in vivo may be because their apparent activity in vitro is an artifact of aggregation, or because the concentration of ASOs in relevant compartments within the central nervous system (CNS) quickly drops below the effective concentration for sequence-independent antiprion activity after bolus dosing into CSF. Measurements of PrP concentration in human CSF were not impacted by the addition of ASO. These findings support the further development of PrP-lowering ASOs and of CSF PrP as a pharmacodynamic biomarker
Evaluation of a Cyclopentane-Based γ‑Amino Acid for the Ability to Promote α/γ-Peptide Secondary Structure
We report the asymmetric synthesis
of the γ-amino acid (1<i>R</i>,2<i>R</i>)-2-aminomethyl-1-cyclopentane carboxylic
acid (AMCP) and an evaluation of this residue’s potential to
promote secondary structure in α/γ-peptides. Simulated
annealing calculations using NMR-derived distance restraints obtained
for α/γ-peptides in chloroform reveal that AMCP-containing
oligomers are conformationally flexible. However, additional evidence
suggests that an internally hydrogen-bonded helical conformation is
partially populated in solution. From these data, we propose characteristic
NOE patterns for the formation of the α/γ-peptide 12/10-helix
and discuss the apparent conformational frustration of AMCP-containing
oligomers
Evaluation of a Cyclopentane-Based γ‑Amino Acid for the Ability to Promote α/γ-Peptide Secondary Structure
We report the asymmetric synthesis
of the γ-amino acid (1<i>R</i>,2<i>R</i>)-2-aminomethyl-1-cyclopentane carboxylic
acid (AMCP) and an evaluation of this residue’s potential to
promote secondary structure in α/γ-peptides. Simulated
annealing calculations using NMR-derived distance restraints obtained
for α/γ-peptides in chloroform reveal that AMCP-containing
oligomers are conformationally flexible. However, additional evidence
suggests that an internally hydrogen-bonded helical conformation is
partially populated in solution. From these data, we propose characteristic
NOE patterns for the formation of the α/γ-peptide 12/10-helix
and discuss the apparent conformational frustration of AMCP-containing
oligomers
Diversity-oriented synthesis encoded by deoxyoligonucleotides
Abstract Diversity-oriented synthesis (DOS) is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors and derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We also show screening results for three diverse protein targets. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery