A three-stage biophysical screening cascade for fragment-based drug discovery

Mashalidis, Ellene H.; Śledź, P.; Lang, Steffen; Abell, Chris

doi:10.1038/nprot.2013.130

Cited by 127 publications

(123 citation statements)

References 60 publications

Supporting

Mentioning

121

Contrasting

Unclassified

Order By: Relevance

“…The latter can be attributed to the high sensitivity of 19 F NMR as a primary screen (38). Together, NMR and SPR result in a hit rate of 6.4%, which is in the expected range for fragment-based screenings and does not suggest a low likelihood to bind drug-like molecules (31, 37, 43, 86). …”

Section: Discussionmentioning

confidence: 80%

Computational and Experimental Prediction of Human C-Type Lectin Receptor Druggability

et al. 2014

View full text Add to dashboard Cite

Mammalian C-type lectin receptors (CTLRS) are involved in many aspects of immune cell regulation such as pathogen recognition, clearance of apoptotic bodies, and lymphocyte homing. Despite a great interest in modulating CTLR recognition of carbohydrates, the number of specific molecular probes is limited. To this end, we predicted the druggability of a panel of 22 CTLRs using DoGSiteScorer. The computed druggability scores of most structures were low, characterizing this family as either challenging or even undruggable. To further explore these findings, we employed a fluorine-based nuclear magnetic resonance screening of fragment mixtures against DC-SIGN, a receptor of pharmacological interest. To our surprise, we found many fragment hits associated with the carbohydrate recognition site (hit rate = 13.5%). A surface plasmon resonance-based follow-up assay confirmed 18 of these fragments (47%) and equilibrium dissociation constants were determined. Encouraged by these findings we expanded our experimental druggability prediction to Langerin and MCL and found medium to high hit rates as well, being 15.7 and 10.0%, respectively. Our results highlight limitations of current in silico approaches to druggability assessment, in particular, with regard to carbohydrate-binding proteins. In sum, our data indicate that small molecule ligands for a larger panel of CTLRs can be developed.

show abstract

Section: Discussionmentioning

confidence: 80%

Computational and Experimental Prediction of Human C-Type Lectin Receptor Druggability

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Recently, a similar three-stage biophysical screening method was reported as a general tool for screening in fragment-based drug discovery. 29 In addition, analysis of our collective X-ray data on thienopyrimidine-based inhibitor bound in the allylic subpocket and the allosteric pocket (e.g., 6a (act) vs 6a (allo) ; PDB codes 4JVJ and 4LPG, respectively) revealed very similar interactions involved in both binding sites. For example, the π-stacking interactions between the tolyl side chain of 6a and Phe99/ Gln171 in the hFPPS/6a (act) complex are analogous to those observed in the hFPPS/6a (allo) complex with Phe206/Asn59 (Figure 5b).…”

Section: ■ Conclusionmentioning

confidence: 97%

Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases

et al. 2014

View full text Add to dashboard Cite

Human farnesyl pyrophosphate synthase (hFPPS) is the gate-keeper of mammalian isoprenoids and the key target of bisphosphonate drugs. Bisphosphonates suffer from poor "drug-like" properties and are mainly effective in treating skeletal diseases. Recent investigations have implicated hFPPS in various nonskeletal diseases, including Alzheimer's disease (AD). Analysis of single nucleotide polymorphisms in the hFPPS gene and mRNA levels in autopsy-confirmed AD subjects was undertaken, and a genetic link between hFPPS and phosphorylated tau (P-Tau) levels in the human brain was identified. Elevated P-Tau levels are strongly implicated in AD progression. The development of nonbisphosphonate inhibitors can provide molecular tools for validating hFPPS as a therapeutic target for tauopathy-associated neurodegeneration. A multistage screening protocol led to the identification of a new monophosphonate chemotype that bind in an allosteric pocket of hFPPS. Optimization of these compounds could lead to human therapeutics that block tau metabolism and arrest the progression of neurodegeneration.

show abstract

“…A 1000 compound fragment library from Maybridge was screened against caspase‐7 by differential scanning fluorimetry (DSF) 8. This primary screen resulted in several validated biophysical hits exhibiting a non‐competitive mechanism of inhibition.…”

mentioning

confidence: 99%

Allosteric Tuning of Caspase‐7: A Fragment‐Based Drug Discovery Approach

2017

View full text Add to dashboard Cite

The caspase family of cysteine proteases are highly sought‐after drug targets owing to their essential roles in apoptosis, proliferation, and inflammation pathways. High‐throughput screening efforts to discover inhibitors have gained little traction. Fragment‐based screening has emerged as a powerful approach for the discovery of innovative drug leads. This method has become a central facet of drug discovery campaigns in the pharmaceutical industry and academia. A fragment‐based drug discovery campaign against human caspase‐7 resulted in the discovery of a novel series of allosteric inhibitors. An X‐ray crystal structure of caspase‐7 bound to a fragment hit and a thorough kinetic characterization of a zymogenic form of the enzyme were used to investigate the allosteric mechanism of inhibition. This work further advances our understanding of the mechanisms of allosteric control of this class of pharmaceutically relevant enzymes, and provides a new path forward for drug discovery efforts.

show abstract

A three-stage biophysical screening cascade for fragment-based drug discovery

Cited by 127 publications

References 60 publications

Computational and Experimental Prediction of Human C-Type Lectin Receptor Druggability

Computational and Experimental Prediction of Human C-Type Lectin Receptor Druggability

Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases

Allosteric Tuning of Caspase‐7: A Fragment‐Based Drug Discovery Approach

Contact Info

Product

Resources

About