HTS by NMR of Combinatorial Libraries: A Fragment-Based Approach to Ligand Discovery

Wu, Bainan; Zhang, Ziming; Noberini, Roberta; Barile, Elisa; Giulianotti, Marc A.; Pinilla, Clemencia; Houghten, Richard A.; Pasquale, Elena B.; Pellecchia, Maurizio

doi:10.1016/j.chembiol.2012.10.015

Cited by 73 publications

(110 citation statements)

References 65 publications

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“…Therefore, we have recently proposed to test mixture based libraries with protein–NMR screening methods, [14] as these approaches present a number of unique advantages over any other assay. First, protein-NMR assays enable the unambiguous identification of hit compounds even in complex mixtures, nearly void of possible false positive or false negatives.…”

Section: Hts By Nmr: a Powerful Approach For The Identification Ofmentioning

confidence: 99%

“…We have recently proposed a novel approach, termed HTS by NMR,[14] in which the principles of positional scanning combinatorial chemistry [15] and fragment-based drug design are combined with protein-NMR spectroscopy [5] to iteratively identify and optimize PPIs antagonists from collections of >100,000 peptide mimetics. The approach seems also particularly effective in the fragment-hit to lead optimization stages of PPIs, when a positional scanning library is generated from an initial weak binder previously identified from a FBDD campaign, and tested by protein NMR spectroscopy.…”

Section: Introductionmentioning

confidence: 99%

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High-Throughput Screening by Nuclear Magnetic Resonance (HTS by NMR) for the Identification of PPIs Antagonists

Wu¹,

Barile²,

De³

et al. 2015

CTMC

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In recent years the ever so complex field of drug discovery has embraced novel design strategies based on biophysical fragment screening (fragment-based drug design; FBDD) using nuclear magnetic resonance spectroscopy (NMR) and/or structure-guided approaches, most often using X-ray crystallography and computer modeling. Experience from recent years unveiled that these methods are more effective and less prone to artifacts compared to biochemical high-throughput screening (HTS) of large collection of compounds in designing protein inhibitors. Hence these strategies are increasingly becoming the most utilized in the modern pharmaceutical industry. Nonetheless, there is still an impending need to develop innovative and effective strategies to tackle other more challenging targets such as those involving protein-protein interactions (PPIs). While HTS strategies notoriously fail to identify viable hits against such targets, few successful examples of PPIs antagonists derived by FBDD strategies exist. Recently, we reported on a new strategy that combines some of the basic principles of fragment-based screening with combinatorial chemistry and NMR-based screening. The approach, termed HTS by NMR, combines the advantages of combinatorial chemistry and NMR-based screening to rapidly and unambiguously identify bona fide inhibitors of PPIs. This review will reiterate the critical aspects of the approach with examples of possible applications.

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Section: Hts By Nmr: a Powerful Approach For The Identification Ofmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

High-Throughput Screening by Nuclear Magnetic Resonance (HTS by NMR) for the Identification of PPIs Antagonists

Wu¹,

Barile²,

De³

et al. 2015

CTMC

Self Cite

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“…ephrin-binding pocket of Eph receptors with potencies approaching the nanomolar range [10], or smaller synthetic peptides with micromolar potency [11,12]. Most of these peptides suffer from a significant proteolytic degradation in vivo, albeit chemical modifications allowed to improve their metabolic stability in rat plasma [13].…”

Section: Introductionmentioning

confidence: 99%

Δ5-Cholenoyl-amino acids as selective and orally available antagonists of the Eph–ephrin system

Castelli

Tognolini

Vacondio

et al. 2015

European Journal of Medicinal Chemistry

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The Eph receptor-ephrin system is an emerging target for the development of novel anti-angiogenic therapies. Research programs aimed at developing small-molecule antagonists of the Eph receptors are still in their initial stage as available compounds suffer from pharmacological drawbacks, limiting their application in vitro and in vivo. In the present work, we report the design, synthesis and evaluation of structure-activity relationships of a class of Δ(5)-cholenoyl-amino acid conjugates as Eph-ephrin antagonists. As a major achievement of our exploration, we identified N-(3β-hydroxy-Δ(5)-cholen-24-oyl)-L-tryptophan (UniPR1331) as the first small molecule antagonist of the Eph-ephrin system effective as an anti-angiogenic agent in endothelial cells, bioavailable in mice by the oral route and devoid of biological activity on G protein-coupled and nuclear receptors targeted by bile acid derivatives.

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“…The mechanistic investigations into this miR17 /PTP-oc/EphA4 regulatory axis have identified two novel potential drug targets for anti-resorptive therapy: 1) EphA4, and 2) miR17 . In this regard, EphA4 is an attractive drug target for an anti-resorptive therapy for the following reasons: a) mature osteoclasts express primarily the EphA4 (27,83,85); b) the forward signaling of EphA4 can effectively be activated by soluble EphA4-binding Efn-fc chimeric proteins (27); c) several Efn fragment-based EphA4 ligands (103) and EphA4-interacting small-molecules (104) have been identified; and d) direct injection of EfnA5-fc (an EphA4 ligand) into the spinal cord of mice with spinal cord injury promoted EphA4-induced axonal regeneration and functional recovery (105,106). The miR17 is also an appealing drug target, as miR17 modulators or mimics could be used to develop novel and effective anti-resorptive therapies.…”

Section: Discussionmentioning

confidence: 99%

A novel miR17 /protein tyrosine phosphatase-oc/EphA4 regulatory axis of osteoclast activity

Lau

Sheng

2018

Archives of Biochemistry and Biophysics

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Information about the molecular mechanisms leading to the activation of the osteoclast is relatively limited. While there is compelling evidence that the signaling mechanisms of Src and integrin β3 are essential for osteoclast activation, the regulation of these two signaling mechanisms is not fully understood. In this review, evidence supporting a novel regulatory axis of osteoclast activation that plays an upstream regulatory role in both the Src and integrin β3 signaling during osteoclast activation is discussed. This regulatory axis contains three unique components: a structurally unique transmembrane protein-tyrosine phosphatase, PTP-oc, EphA4, and miR17. In the first component, PTP-oc activates the Src signaling through dephosphorylation of the inhibitory tyr-527 of Src. This in turn activates the integrin β3 signaling, enhances the JNK2/NFκB signaling, promotes the ITAM/Syk signaling, and suppresses the ITIM/Shp1 signaling; the consequence of which is activation of the osteoclast. In the second component, EphA4 inhibits osteoclast activity by suppressing the integrin β3 signaling. PTP-oc relieves the suppressive actions of EphA4 by directly dephosphorylating EphA4. In the third component, PTP-oc expression is negatively regulated by miR17. Accordingly, suppression of miR17 during osteoclast activation upregulates the PTP-oc signaling and suppresses the EphA4 signaling, resulting in the activation of the osteoclast. This regulatory axis is unique, in that each of the three components acts to exert suppressive action on their respective immediate downstream inhibitory step. Because the final downstream event is the EphA4-mediated inhibition of osteoclast activation, the overall effect of this mechanism is the stimulation of osteoclast activity.

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HTS by NMR of Combinatorial Libraries: A Fragment-Based Approach to Ligand Discovery

Cited by 73 publications

References 65 publications

High-Throughput Screening by Nuclear Magnetic Resonance (HTS by NMR) for the Identification of PPIs Antagonists

High-Throughput Screening by Nuclear Magnetic Resonance (HTS by NMR) for the Identification of PPIs Antagonists

Δ5-Cholenoyl-amino acids as selective and orally available antagonists of the Eph–ephrin system

A novel miR17 /protein tyrosine phosphatase-oc/EphA4 regulatory axis of osteoclast activity

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