Fragment-Based Lead Discovery Using X-ray Crystallography

Hartshorn, Michael J.; Murray, Christopher W.; Cleasby, Anne; Frederickson, Martyn; Tickle, Ian J.; Jhoti, Harren

doi:10.1021/jm0495778

Cited by 394 publications

(347 citation statements)

References 62 publications

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“…We would emphasize that this is not nonspecific binding that is occurring, but because the fragment has low molecular complexity it is able to bind to complementary protein motifs in several locations. This is consistent with the fact that the electron densities of the fragments are typically very well defined and that, although they exhibit very low binding affinity, with K d often in the millimolar range, the interactions they make are highly efficient (27). Indeed, these crystal structures of protein-fragment complexes are a good basis to develop novel chemical tools that would probe the function of these secondary binding sites and experimentally confirm their role, if any, in biological processes.…”

Section: Discussionsupporting

confidence: 76%

“…This resulted in 5,590 holo X-ray crystal structures, comprising 4,950 distinct compounds and 24 protein targets. The exact protocols and screening cascades that led to the data presented here will have varied according to the target, but in broad lines our approach has been described by Hartshorn et al (27,28). In some cases we had collected data for different mutant forms of a protein, and in these cases data from all forms was used.…”

Section: Resultsmentioning

confidence: 99%

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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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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: Discussionsupporting

confidence: 76%

Section: Resultsmentioning

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

106

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“…Broad spectrum tyrosine kinase inhibitors exist, but FGFR is never the most potently inhibited kinase and such mixed inhibitors fail to inhibit FGFR completely because of intervening kinase activities and their associated toxicities. Starting with fragment-derived hits, we used a structure-based design (25)(26)(27) to optimize lead molecules to potent FGFR inhibitors with selectivity against VEGFR2, which shares 57% sequence identity with the kinase domain of FGFR1-3 and 54% with that of FGFR4. Further optimization of pharmacokinetic properties resulted in a series of imidazopyridine leads, the properties of which are described here.…”

Section: Introductionmentioning

confidence: 99%

Potent, Selective Inhibitors of Fibroblast Growth Factor Receptor Define Fibroblast Growth Factor Dependence in Preclinical Cancer Models

Squires

Ward²,

Saxty³

et al. 2011

Molecular Cancer Therapeutics

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We describe here the identification and characterization of 2 novel inhibitors of the fibroblast growth factor receptor (FGFR) family of receptor tyrosine kinases. The compounds exhibit selective inhibition of FGFR over the closely related VEGFR2 receptor in cell lines and in vivo. The pharmacologic profile of these inhibitors was defined using a panel of human tumor cell lines characterized for specific mutations, amplifications, or translocations known to activate one of the four FGFR receptor isoforms. This pharmacology defines a profile for inhibitors that are likely to be of use in clinical settings in disease types where FGFR is shown to play an important role. Mol Cancer Ther; 10(9); 1542-52. Ó2011 AACR.

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“…Indeed, MCSS molecular probe maps can be used to derive active site pharmacophore models [29]. Somewhat analogous experimental molecular probe mapping and fragment-based ligand discovery approaches have shown success [30][31][32][33][34][35][36].…”

Section: Introductionmentioning

confidence: 99%

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

Evensen

Joseph‐McCarthy

Weiss

et al. 2007

J Comput Aided Mol Des

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Combinatorial synthesis and large scale screening methods are being used increasingly in drug discovery, particularly for finding novel lead compounds. Although these ''random'' methods sample larger areas of chemical space than traditional synthetic approaches, only a relatively small percentage of all possible compounds are practically accessible. It is therefore helpful to select regions of chemical space that have greater likelihood of yielding useful leads. When three-dimensional structural data are available for the target molecule this can be achieved by applying structure-based computational design methods to focus the combinatorial library. This is advantageous over the standard usage of computational methods to design a small number of specific novel ligands, because here computation is employed as part of the combinatorial design process and so is required only to determine a propensity for binding of certain chemical moieties in regions of the target molecule. This paper describes the application of the Multiple Copy Simultaneous Search (MCSS) method, an active site mapping and de novo structure-based design tool, to design a focused combinatorial library for the class II MHC protein HLA-DR4. Methods for the synthesizing and screening the computationally designed library are presented; evidence is provided to show that binding was achieved. Although the structure of the protein-ligand complex could not be determined, experimental results including cross-exclusion of a known HLA-DR4 peptide ligand (HA) by a compound from the library. Computational model building suggest that at least one of the ligands designed and identified by the methods described binds in a mode similar to that of native peptides.

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Fragment-Based Lead Discovery Using X-ray Crystallography

Cited by 394 publications

References 62 publications

Detection of secondary binding sites in proteins using fragment screening

Detection of secondary binding sites in proteins using fragment screening

Potent, Selective Inhibitors of Fibroblast Growth Factor Receptor Define Fibroblast Growth Factor Dependence in Preclinical Cancer Models

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

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