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Machine learning and proteochemometric models for Cereblon glue activity predictions
No full textTargeted protein degradation (TPD) is a rapidly developing drug discovery methodology with unique efficacy and target scope stemming from its degradation-based activity. Molecular glue degraders are a promising arm of TPD, as evidenced by the FDA-approved therapeutics within this class, the increasing number of degraders in clinical development, and their predisposition to drug-likeness. Cereblon (CRBN) glue degraders mediate target degradation by generating a neomorphic interface between CRBN and a protein of interest. While promising, the complicated nature of this CRBN-glue-target ternary complex makes the rational design of molecular glue degraders challenging. For other drug modalities, predictive modeling has been established to help leverage existing activity data and generate quantitative structure-activity relationships (QSAR). However, the applicability of machine learning-based QSAR strategies for glues remains unclear. Herein, machine learning methodologies have been benchmarked for CRBN glue activity predictions with promising performance. Generated models include single-task and multi-task classifiers which leverage more than a hundred internal screening campaigns across thousands of CRBN glues to predict glue-mediated recruitment of targets to CRBN. Our results show that the activity of CRBN glue degraders can be modeled well by both classical single-task and multi-task approaches, with 89% of models producing an area under the receiver operating characteristic curve (ROC AUC) > 0.8 and 70% of models producing a Matthew’s Correlation Coefficient (MCC) > 0.2 for these primary screening data. Importantly, our findings also indicated that the combination of compound information and simple protein descriptors in the so-called proteochemometric models improves performance, with >80% of the models exhibiting higher ROC AUC and MCC scores over their single-task counterparts. Taken together, our investigations show that PCM modeling is a successful approach for molecular glue degraders. The proposed machine learning approaches can aid compound prioritization based on recruitment efficacy and target selectivity, thus have the potential to facilitate the design and discovery of CRBN molecular glues with therapeutic potential
Buchwald-Hartwig Aminations of Aryl Halides Using Nitroaromatics as Coupling Partners: Overcoming Hydrodehalogenation Pathway in Water
No full text: A novel catalytic aqueous micellar technology has been developed for the C-N cross-coupling of nitroarenes with aryl halides. The catalytic cycle involves in-situ reduction of nitroaromatics and subsequent coupling of resulting amine with aryl halide, while avoiding undesired hydrodehalogenation of aryl halide. The bimetallic palladium-copper (Pd-Cu) nanocatalyst configuration in aqueous micelles facilitates the amination pathway selectively, possibly through in-situ formation of Cu-hydride species. These species prevent Pd-hydride-mediated hydrodehalogenation. The nanocata-lyst has been thoroughly characterized using various spectroscopic and imaging tools, including 31P and 1H nuclear magnetic resonance, X-ray absorption spectroscopy (XAS), and high-resolution transmission electron microscopy. The oxidation states of Cu and Pd have been verified using X-ray photoelectron spectroscopy, while metal-metal and metal-ligand contact has been confirmed by XAS. Control experiments have been performed to determine the significance of aqueous micelles and each constituent of the nanocatalyst on the desired reaction pathway. As revealed by control mass spectrometry, the reaction pathway does not involve azo- or nitroso-type intermediates. The catalytic methodol-ogy can be applied to numerous substrates with excellent functional and protecting group tolerance. The scalability of this method has been demonstrated in a gram-scale reaction
A small molecule VHL molecular glue degrader for cysteine dioxygenase 1
No full textThe Von Hippel-Lindau Tumor Suppressor gene product (pVHL) is an E3 ligase substrate receptor that binds proline-hydroxylated HIF1-α, leading to its ubiquitin-dependent degradation. By using protein arrays, we identified a small molecule that binds the HIF1-α binding pocket on pVHL and functions as a molecular glue degrader of the neosubstrate cysteine dioxygenase (CDO1) by recruiting it into the VHL-cullin-ring E3 ligase complex and leading to its selective degradation. The CDO1 binding region involved in VHL recruitment was characterized through a combination of mutagenesis and protein-protein docking coupled with molecular dynamics-based solvation analysis. The X-ray structure of the ternary complexes of VHL, CDO1, and degrader molecules confirms the binding region prediction and provides atomic insights into key molecular glue interactions
A high throughput cell stretch device for investigating mechanobiology in vitro
No full textMechanobiology is a rapidly advancing field, with growing evidence that mechanical signaling plays key roles in health and disease. To accelerate mechanobiology-based drug discovery, novel in vitro systems are needed that enable mechanical perturbation of cells in a format amenable to high throughput screening. Here, both a mechanical stretch device and 192-well silicone flexible linear stretch plate were designed and fabricated to meet high throughput technology needs for cell stretch-based applications. To demonstrate the utility of the stretch plate in automation and screening, cell dispensing, liquid handling, high content imaging, and high throughput sequencing platforms were employed. Using this system, an assay was developed as a biological validation and proof-of-concept readout for screening. A mechano-transcriptional stretch response was characterized using focused gene expression profiling measured by RNA-mediated oligonucleotide Annealing, Selection, and Ligation with Next-Gen sequencing (RASL-seq). Using articular chondrocytes, a gene expression signature containing stretch responsive genes relevant to cartilage homeostasis and disease was identified. The possibility for integration of other stretch sensitive cell types (e.g. cardiovascular, airway, bladder, gut, musculoskeletal), in combination with alternative phenotypic readouts (e.g. protein expression, proliferation or spatial alignment), broadens the scope of high throughput stretch and allows for wider adoption by the research community. This high throughput mechanical stress device fills an unmet need in phenotypic screening technology to support drug discovery in mechanobiology-based disease areas
Micelle Enabled Buchwald-Hartwig Amination in Water with the Bening by Design Surfactant TPGS-750-M for the Synthesis of the JAK Inhibitor 4-((2-Chlorophenyl)amino)-6-((6-methylpyridin-2-yl)amino)nicotinamide
No full textAn efficient and scalable Buchwald-Hartwig amination towards the synthesis of the API candidate 4-((2-
Chlorophenyl)amino)-6-((6-methylpyridin-2-yl)amino)nicotinamide as a JAK inhibitor was described. The process
was developed using water and a water-miscible co-solvent. It was facilitated by the benign by design surfactant
TPGS-750-M, that promoted the robust and reliable preparation of our target compound in high yields, with
improved reaction profile and via an operationally simple protocol
Random Effects Meta-Analysis of Contingency Tables with Complete and Partially Complete Data, with Application to COVID-19 Research
No full textWe present a random effects meta-analytic approach for analyzing exchangeable 2 × 2 × 2 tables of COVID-19 deaths classified by two comorbidities, for example, diabetes and hypertension. We take the marginal tables of comorbidities as multinomial with table-specific cell probabilities drawn from a Dirichlet distribution. Conditionally hereon, we model the death counts for cell in the 2 × 2 table of possible comorbidity combinations as independent binomial random variables. We allow for a randomly drawn normally distributed frailty to model the correlation of the death counts within the same study. For complete tables, this model can be fitted by standard statistical software. We propose an approximate ML imputation procedure by which tables with missing entries can be completed enabling the use of the same standard procedures and giving a better estimate of model parameters than one would get by leaving partial tables out. The properties of the method are illustrated by simulations
C3 Selective Hydroxylation of Pyridines via Photochemical Valence Isomerization of Pyridine N-Oxides.
No full textThe C-H hydroxylation of the pyridine C3 position is a highly desirable transformation but remains a great challenge due to the inherent electronic properties of this heterocycle core which bring difficulties in chemical reactivity and regioselectivity. Herein we present an efficient method for formal C3 selective hydroxylation of pyridines via photochemical valence isomerization of pyridine N-oxides. This metal-free transformation features operational simplicity and compatibility with a diverse array of functional groups, and the resulting hydroxylated products are amenable to further elaboration to synthetically useful building blocks. The synthetic utility of this strategy is further demonstrated in the effective late-stage functionalization of pyridine-containing medicinally relevant molecules and versatile derivatizations of 3-pyridinols
Complement factor B inhibition or deletion is not sufficient to prevent neurodegeneration in a murine model of glaucoma.
No full textPurpose: Activation of the classical complement pathway is thought to contribute to the development and progression of glaucoma. The role of alternative complement or amplification of common complement pathways in glaucoma is not well understood. We evaluated complement factor B expression in post-mortem human ocular tissues with or without glaucoma, and the effect of FB inhibition and deletion in a mouse ocular hypertensive model of glaucoma induced by photopolymerized hyaluronic acid glycidyl methacrylate (HAGM).
Methods: Human CFB mRNA in postmortem human eyes was assessed by RNAscope and TaqMan. The HAGM model was performed on C57BL6/J mice. The effect of FB in the HAGM model was evaluated with an oral FB small molecule inhibitor and Cfb-/- mice. Complement mRNA and proteins in mouse eyes were assessed by TaqMan and Western blot, respectively.
Results: CFB mRNA in human glaucomatous macular neural retina and optic nerve head was upregulated. Cfb mRNA is also upregulated in the HAGM model. Oral FB inhibitor, ED-79-GX17, dosed daily at 200 mg/kg for 3 days post IOP induction in WT mice showed complement inhibition in ocular tissues and significantly inhibited systemic complement levels. Daily dosing of ED-79-GX17 for 30 days or Cfb deletion was also unable to prevent RGC or axon loss 30 days post IOP induction in mice.
Conclusion: The essential alternative complement component FB may not substantially contribute to RGC loss in glaucoma in the mouse model of ocular hypertension despite upregulation of Cfb expression and activation of the alternative pathway. The relevance of these findings to human glaucoma remains to be determined
Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans.
No full textDysfunctional extracellular matrices (ECM) contribute to aging and disease. Repairing dysfunctional ECM could potentially prevent age-related pathologies. Interventions promoting longevity also impact ECM gene expression. However, the role of ECM composition changes in healthy aging remains unclear. Here we perform proteomics and in-vivo monitoring to systematically investigate ECM composition (matreotype) during aging in C. elegans revealing three distinct collagen dynamics. Longevity interventions slow age-related collagen stiffening and prolong the expression of collagens that are turned over. These prolonged collagen dynamics are mediated by a mechanical feedback loop of hemidesmosome-containing structures that span from the exoskeletal ECM through the hypodermis, basement membrane ECM, to the muscles, coupling mechanical forces to adjust ECM gene expression and longevity via the transcriptional co-activator YAP-1 across tissues. Our results provide in-vivo evidence that coordinated ECM remodeling through mechanotransduction is required and sufficient to promote longevity, offering potential avenues for interventions targeting ECM dynamics
Clearance of extracellular human amyloid-β aggregates in by nutraceutical and pharmaceutical interventions.
No full textNumerous anti-amyloid therapies have seen recent clinical development and approval, such as the monoclonal antibodies aducanumab and lecanemab. However, in Alzheimer's disease patients, amyloid-β (Aβ) plaques are found embedded in the extracellular matrix and surrounded by collagens, which might hinder these antibodies from targeting the plaques. We reasoned that various different nutraceutical and pharmaceutical agents might induce collagen and extracellular matrix turnover and removal of these collagen-embedded amyloid-β (Aβ) plaques. To address this idea, here, we used a transgenic strain, LSD2104 , expressing fluorescent human Aβ as an model for secreted amyloid aggregation in the extracellular matrix. We performed a screen of various nutraceuticals and pharmaceuticals along with different combinations, and we found that quercetin 350 µM and rifampicin 75 µM successfully cleared the extracellular amyloid plaque burden compared to the 0.2% DMSO control group, with a combination of the two agents producing the maximum effect compared to either drug alone. These results may implicate the exploration of combination therapeutics of nutraceuticals and pharmaceuticals in the clearance of amyloid-β (Aβ) plaques in Alzheimer's disease