Selective Targeting of the TPX2 Site of Importin‐α Using Fragment‐Based Ligand Design

Holvey, Rhian S.; Valkov, Eugene; Neal, David; Stewart, Murray; Abell, Chris

doi:10.1002/cmdc.201500014

Cited by 11 publications

(11 citation statements)

References 39 publications

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“…Recently, Holvey et al published small-molecule compounds that bind specifically but weakly ( K D = ~ 1–10 mM) to the minor NLS-binding site of importin-α 43 . Among the minor-site specific compounds developed by Holvey et al , the “compound 17” has the highest affinity ( K D = 0.9 mM) 43 . In the crystal structure of importin-α bound to this compound, two molecules of the compound bound to the minor NLS-binding site 43 .…”

Section: Resultsmentioning

confidence: 99%

“…Among the minor-site specific compounds developed by Holvey et al , the “compound 17” has the highest affinity ( K D = 0.9 mM) 43 . In the crystal structure of importin-α bound to this compound, two molecules of the compound bound to the minor NLS-binding site 43 . Strikingly, the compound bound to the binding pockets for the three critical residues (K7, R8, and M13) of NP ncNLS: one molecule of the compound bound to the binding pockets P1′ and P2′ (the binding pockets for K7 and R8 of NP; marked by dashed ellipses in the lower panel of Fig.…”

Section: Resultsmentioning

confidence: 99%

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Structure of importin-α bound to a non-classical nuclear localization signal of the influenza A virus nucleoprotein

Nakada

Hirano

Matsuura

2015

Sci Rep

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A non-classical nuclear localization signal (ncNLS) of influenza A virus nucleoprotein (NP) is critical for nuclear import of viral genomic RNAs that transcribe and replicate in the nucleus of infected cells. Here we report a 2.3 Å resolution crystal structure of mouse importin-α1 in complex with NP ncNLS. The structure reveals that NP ncNLS binds specifically and exclusively to the minor NLS-binding site of importin-α. Structural and functional analyses identify key binding pockets on importin-α as potential targets for antiviral drug development. Unlike many other NLSs, NP ncNLS binds to the NLS-binding domain of importin-α weakly with micromolar affinity. These results suggest that a modest inhibitor with low affinity to importin-α could have anti-influenza activity with minimal cytotoxicity.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Structure of importin-α bound to a non-classical nuclear localization signal of the influenza A virus nucleoprotein

Nakada

Hirano

Matsuura

2015

Sci Rep

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“…One of the key advantages of this approach is the more efficient coverage of chemical space by compounds of lower molecular weight, requiring smaller screening libraries compared with HTS. In the context of PPIs, numerous examples of inhibitors have been identified using this approach ( Abdel-Rahman et al., 2011; Douse et al., 2015; Gao et al., 2014; Holvey et al., 2015; Jose et al., 2012; Lund et al., 2015; Molzan et al., 2012; Moore et al., 2009; Patrone et al., 2013; Van Molle et al., 2012; Yin et al., 2014 ). Prominent examples include the Bcl-2 inhibitor ABT-737 ( Oltersdorf et al., 2005 ), inhibitors of the RAS oncogene ( Maurer et al., 2012 ), and inhibitors of the BET bromodomains ( Chung et al., 2012 ).…”

Section: Main Textmentioning

confidence: 99%

Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions

Laraia

McKenzie

Spring

et al. 2015

Chemistry & Biology

139

107

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Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling, and disease. Approaches to modulate PPIs with small molecules have therefore attracted increasing interest over the past decade. However, there are a number of challenges inherent in developing small-molecule PPI inhibitors that have prevented these approaches from reaching their full potential. From target validation to small-molecule screening and lead optimization, identifying therapeutically relevant PPIs that can be successfully modulated by small molecules is not a simple task. Following the recent review by Arkin et al., which summarized the lessons learnt from prior successes, we focus in this article on the specific challenges of developing PPI inhibitors and detail the recent advances in chemistry, biology, and computation that facilitate overcoming them. We conclude by providing a perspective on the field and outlining four innovations that we see as key enabling steps for successful development of small-molecule inhibitors targeting PPIs.

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“…More than 120 crystal structures of Impα have been solved since 1998 (S. cerevisiae Impα, PDB ID 1BK5 37 ) followed by the first mammalian Impα (M. musculus, PDB ID 1IAL 22 ) and cocrystallized Impα with NLS peptides 7,36 . Most of the Impα structures deposited in the Protein Data Bank are MmImpα complexed to NLS peptides from several organisms 10 but also synthetic NLS peptides 8 and small molecules 57 . In addition, H. sapiens Impα variants [12][13][14]16,48,57 , O. sativa 33,39 , A. thaliana 40 and N. crassa 41 structures were also solved.…”

Section: Discussionmentioning

confidence: 99%

“…Most of the Impα structures deposited in the Protein Data Bank are MmImpα complexed to NLS peptides from several organisms 10 but also synthetic NLS peptides 8 and small molecules 57 . In addition, H. sapiens Impα variants [12][13][14]16,48,57 , O. sativa 33,39 , A. thaliana 40 and N. crassa 41 structures were also solved. The analysis of these structures clearly demonstrates that the overall Impα structures are highly conserved among them 8,41 , and only their solenoid curvatures may vary, particularly between proteins from different phylogenetic families 58 .…”

Section: Discussionmentioning

confidence: 99%

Comparative study of the interactions between fungal transcription factor nuclear localization sequences with mammalian and fungal importin-alpha

Bernardes

Fukuda

Silva

et al. 2020

Sci Rep

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importin-α (impα) is an adaptor protein that binds to cargo proteins (containing nuclear Localization Sequences-NLSs), for their translocation to the nucleus. The specificities of the Impα/nLS interactions have been studied, since these features could be used as important tools to find potential NLSs in nuclear proteins or even for the development of targets to inhibit nuclear import or to design peptides for drug delivery. Few structural studies have compared different Impα variants from the same organism or impα of different organisms. Previously, we investigated nuclear transport of transcription factors with Neurospora crassa impα (ncimpα). Herein, NIT-2 and PAC-3 transcription factors NLSs were studied in complex with Mus musculus impα (MmImpα). calorimetric assays demonstrated that the PAC-3 NLS peptide interacts with both Impα proteins with approximately the same affinity. The NIT-2 NLS sequence binds with high affinity to the Impα major binding site from both organisms, but its binding to minor binding sites reveals interesting differences due to the presence of additional interactions of NIT-2-NLS with MmImpα. These findings, together with previous results with Impα from other organisms, indicate that the differential affinity of NLSs to minor binding sites may be also responsible for the selectivity of some cargo proteins recognition and transport. Nucleocytoplasmic protein trafficking regulation between cell compartments is a fundamental biological process for eukaryotic organisms. The translocation of proteins across the nuclear envelope occurs through nuclear pore complexes (NPC) which, in most cases, it is an active carrier-mediated transport process 1,2. This mechanism requires additional carrier proteins or transport factors that generally belong to the β-karyopherin superfamily and specific nuclear targeting signals. The best-characterized signals are known as nuclear localization sequences (NLS), which are recognized by the importin-α protein (Impα). Impα is an adaptor protein that links the cargo protein to a carrier protein (importin-β; Impβ) that, through transient interactions between Impβ and NPC proteins, translocates the Impα/Impβ/cargo protein complex to the cell nucleus. This process is known as the classical nuclear import pathway and is probably the most extensively used and heavily researched nuclear import mechanism 3-5. The classical NLS (cNLS) is characterized by one or two amino acid basic clusters and is defined as monopartite or bipartite. Consensus sequences for these two cNLS were proposed and correspond to K(K/R)X(K/R) and KRX 10-12 K(K/R)X(K/R) (where X corresponds to any residue, but positively charged amino acids are preferred at this position and hydrophobic ones are also acceptable), respectively 4,6-9. These sequences bind to Impα through

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Selective Targeting of the TPX2 Site of Importin‐α Using Fragment‐Based Ligand Design

Cited by 11 publications

References 39 publications

Structure of importin-α bound to a non-classical nuclear localization signal of the influenza A virus nucleoprotein

Structure of importin-α bound to a non-classical nuclear localization signal of the influenza A virus nucleoprotein

Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions

Comparative study of the interactions between fungal transcription factor nuclear localization sequences with mammalian and fungal importin-alpha

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