Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function

Saalau-Bethell, S.; Woodhead, Andrew J.; Chessari, Gianni; Carr, Maria G.; Coyle, Joseph E.; Graham, Brent; Hiscock, Steven D.; Murray, Christopher W.; Pathuri, Puja; Rich, Sharna J.; Richardson, Caroline; Williams, P.; Jhoti, Harren

doi:10.1038/nchembio.1081

Cited by 102 publications

(141 citation statements)

References 40 publications

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“…The first of these studies involved the discovery of an allosteric inhibitor of the viral protease-helicase protein HCV NS3 (18). In this case, fragment screening against the full-length protein identified a previously unknown allosteric binding site at the interface of the two domains.…”

Section: Significancementioning

confidence: 99%

Detection of secondary binding sites in proteins using fragment screening

Ludlow¹,

Verdonk²,

Saini³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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103

106

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Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.protein structure | protein function | X-ray crystallography | fragment-based drug design

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Section: Significancementioning

confidence: 99%

Detection of secondary binding sites in proteins using fragment screening

Ludlow¹,

Verdonk²,

Saini³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

103

106

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“…Owing to its ability to detect low affinity binding X-ray crystallography has been shown to be a very effective technique to identify the initial fragment hit as well as to guide the fragment hit-to-lead phase given the 3D structural information provided by the protein-fragment crystal structure. These new structure-dependent approaches have yielded not only novel lead compounds but have also uncovered new allosteric pockets that can be exploited for drug development [30]. Further, the increasing number of protein structures, together with more powerful computational methods, has resulted in extensive use of in silico approaches in many drug discovery programs.…”

Section: Structure-based Drug Discoverymentioning

confidence: 99%

High-throughput screening and structure-based approaches to hit discovery: is there a clear winner?

Jhoti¹,

Rees

Solari³

2013

Expert Opinion on Drug Discovery

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“…Primary HCv NS3 iC 50 determination using FReT-based assay 20 Bromodomain primary screening using FP and FReTbased assays 71,72,74 Arf1-Arno FP assay to triage virtual screening hits 77 Notes: A typical screening cascade comprises two or more orthogonal techniques to identify binders and triage hits. "Primary screening" refers to high-throughput techniques that can be used to screen a fragment library and detect preliminary hits.…”

Section: Sprmentioning

confidence: 99%

“…Primary screening techniques include protein-and ligandobserved nuclear magnetic resonance (NMR), X-ray crystallography, surface plasmon resonance, thermal shift assay (TSA), and biochemical assays. Notably, two-dimensional heteronuclear single quantum coherence (HSQC) NMR and X-ray crystallography, employed as frontline approaches at Abbott Laboratories (Abbott Park, IL, USA) and Astex Pharmaceuticals ( Cambridge, UK), respectively, deliver detailed information about fragment-binding modes at the earliest XiAP/ciAP1 primary screening and complex structure determination [62][63][64] HCv NS3 primary screening and complex structure determination 20 Bromodomain primary screening 73 and complex structure determination [71][72][73][74] Arf1-Arno complex structure determination 77 …”

Section: Ppi Screeningmentioning

confidence: 99%

“…Recently, Astex Pharmaceuticals carried out a screening campaign against full length NS3 to identify drug leads with a different chemical and biological profile compared with the protease inhibitors. 20 An X-ray fragment screen was performed using crystals of full length NS3 in complex with the peptide cofactor NS4a. 65 The high sensitivity of X-ray crystallography facilitated the detection of very weak fragment hits with acceptable LE.…”

Section: Hcv Ns3mentioning

confidence: 99%

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Fragment-based drug discovery and protein–protein interactions

Turnbull¹,

Boyd²,

Walse³

2014

RRBC

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Protein-protein interactions (PPIs) are involved in many biological processes, with an estimated 400,000 PPIs within the human proteome. There is significant interest in exploiting the relatively unexplored potential of these interactions in drug discovery, driven by the need to find new therapeutic targets. Compared with classical drug discovery against targets with well-defined binding sites, developing small-molecule inhibitors against PPIs where the contact surfaces are frequently more extensive and comparatively flat, with most of the binding energy localized in "hot spots", has proven far more challenging. However, despite the difficulties associated with targeting PPIs, important progress has been made in recent years with fragmentbased drug discovery playing a pivotal role in improving their tractability. Computational and empirical approaches can be used to identify hot-spot regions and assess the druggability and ligandability of new targets, whilst fragment screening campaigns can detect low-affinity fragments that either directly or indirectly perturb the PPI. Once fragment hits have been identified and confirmed using biochemical and biophysical approaches, three-dimensional structural data derived from nuclear magnetic resonance or X-ray crystallography can be used to drive medicinal chemistry efforts towards the development of more potent inhibitors. A small-scale comparison presented in this review of "standard" fragments with those targeting PPIs has revealed that the latter tend to be larger, be more lipophilic, and contain more polar (acid/base) functionality, whereas three-dimensional descriptor data indicate that there is little difference in their three-dimensional character. These physiochemical properties can potentially be exploited in the rational design of PPI-specific fragment libraries and correlate well with optimized PPI inhibitors, which tend to have properties outside currently accepted guidelines for drug-likeness. Several examples of small-molecule PPI inhibitors derived from fragment-based drug discovery now exist and are described in this review, including navitoclax, a novel Bcl-2 family inhibitor which has entered Phase II clinical trials in patients with small-cell lung cancer and chronic lymphocytic leukemia.

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Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function

Cited by 102 publications

References 40 publications

Detection of secondary binding sites in proteins using fragment screening

Detection of secondary binding sites in proteins using fragment screening

High-throughput screening and structure-based approaches to hit discovery: is there a clear winner?

Fragment-based drug discovery and protein–protein interactions

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Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function

Cited by 102 publications

References 40 publications

Detection of secondary binding sites in proteins using fragment screening

Detection of secondary binding sites in proteins using fragment screening

High-throughput screening and structure-based approaches to hit discovery: is there a clear winner?

Fragment-based drug discovery and protein&ndash;protein interactions

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Product

Resources

About

Fragment-based drug discovery and protein–protein interactions