US20160083712A1

US20160083712A1 - Csn5 polypeptides and uses thereof for screening therapeutic agents

Info

Publication number: US20160083712A1
Application number: US14/435,375
Authority: US
Inventors: Aude ECHALIER; Christian Dumas; Melissa BIROL
Original assignee: Centre National de la Recherche Scientifique CNRS; Institut National de la Sante et de la Recherche Medicale INSERM; Universite de Montpellier
Current assignee: Centre National de la Recherche Scientifique CNRS; Institut National de la Sante et de la Recherche Medicale INSERM; Universite de Montpellier
Priority date: 2012-10-12
Filing date: 2013-10-14
Publication date: 2016-03-24
Also published as: EP2906590B1; AU2013328550A1; AU2013328550B2; WO2014057134A1; US20170242009A1; EP2906590A1; US10203328B2; CN105263956A

Abstract

The present invention relates to mutated CSN5 polypeptides and their use in a method of screening modulators of CSN5 activity that could be used as therapeutic agents.

Description

FIELD OF THE INVENTION

The present invention relates to CSN5 polypeptides and uses thereof for screening therapeutic agents.

BACKGROUND OF THE INVENTION

Cell-signaling processes mediated by ubiquitinylation, the post-translational covalent conjugation of ubiquitin molecules, are of prime importance for cellular activity and particularly for protein turnover. Ubiquitin-ligase enzymes, E3s, are responsible for the last step of the ubiquitinylation reaction. The E3 cullin-RING ubiquitin ligases (CRLs) represent the main ubiquitin ligase family. Among several factors that regulate CRL activity, cullin neddylation/deneddylation cycles are central (1).
The COP9 signalosome (CSN), a large multiprotein complex that resembles the 19S lid of the 26S proteasome, plays a central role in the regulation of the E3-cullin RING ubiquitin ligases (CRLs). Due to the fact that a large number of proteins are ubiquitinylated by CRLs, the COP9 signalosome (CSN) is implicated in the control of a significant proportion of the proteome, including pro-oncogenes (for example Myc), tumor suppressors (for example p53) and other important cellular protagonists. Different biological and biochemical functions of the CSN complex have been studied over the years, but by far the most studied is its role as a CRL deneddylase. The catalytic activity of the CSN complex, carried by subunit 5 (CSN5/Jab1), resides in the deneddylation of the CRLs, that is the hydrolysis of the cullin-Nedd8 isopeptide bond. Structurally, the CSN is an eight-subunit complex of about 320 kDa (six PCI (proteasome COP9 eIF3)-based subunits and two Mpr1-Pad1-N-terminal [MPN]-containing subunits). Subunit 5 (CSN5), one of the MPN-containing subunits, carries a zinc-dependent isopeptidase catalytic centre that contains a JAMM (Jab1/MPN/Mov34) motif (also known as MPN+ motif; (2)). Recent detailed studies suggested that the organization of the CSN complex resembles that of the 26S proteasome lid (3), with the deubiquitinase enzyme Rpn11 being the equivalent of the deneddylating subunit CSN5 (2, 4).
The CSN, implicated in various cellular functions, ranging from cell cycles, to circadian rhythm, to immunity, is a very well conserved multi-protein complex in eukaryotes, from plants to mammalian cells. Its importance in cellular functions has been highlighted by genetic studies (5). The physiology of the CSN in normal cells has been well researched, and many studies have found a strong link between the CSN and cancers (6). Intriguingly, the CSN cancer implication is attributable to mainly CSN5, which is located on human chromosome 8q—itself often amplified in cancers.
Smaller forms of the holo-CSN complex, with variable compositions, have been found in vivo (7-11). Although important in cell cycle progression, these sub-CSN complexes have not yet been fully functionally characterized (12). It is interesting that, as alluded to for Rpn11 in the context of the proteasome lid (4), CSN5 is found in two forms, a holo-CSN-associated form that is catalytically active and a holo-CSN-independent state void of isopeptidase activity (2, 3). The modularity and topology of the CSN complex have been explored in vitro by non-denaturing mass spectrometry (MS), which revealed that CSN5 is a peripheral subunit that can homo-dimerize outside of the CSN complex and interacts mostly with the other MPN-containing subunit, CSN6, in the context of the CSN complex (3). The potential interactions of CSN5 with other CSN subunits, namely CSN1, CSN2, CSN4 and CSN7, have been highlighted in earlier reports (1, 8, 13, 14).
Whereas CSN-dependent CSN5 displays isopeptidase activity, it is intrinsically inactive in other physiologically relevant forms. To elucidate the molecular regulation of CSN5 activity, the inventors structurally and functionally characterized it in its CSN-independent form by X-ray crystallography, molecular dynamics (MD) simulations, and in vitro studies. Furthermore, the invention provides a preliminary glimpse into the rational screening of small molecules, antibodies, peptides, pseudopeptide, and polypeptides inhibitors of CSN5 isopeptidase activity.

SUMMARY OF THE INVENTION

DETAILED DESCRIPTION OF THE INVENTION

The inventors analyzed the crystal structure of human CSN5 in its catalytically inactive form to illuminate the molecular basis for its activation state. The inventors demonstrate that CSN5 presents a catalytic domain that brings essential elements to understand its activity control. Although the CSN5 active site is catalytically competent and compatible with di-isopeptide binding, the Ins-1 segment obstructs access to its substrate binding-site and structural rearrangements are necessary for the substrate pocket formation. Detailed study of CSN5 by MD unveils signs of flexibility and plasticity of the Ins-1 segment. These analyses led to the identification of a molecular trigger implicated in the active/inactive switch that is sufficient to impose on CSN5 an active isopeptidase state. The inventors demonstrate that a single mutation in the Ins-1 segment restores a deneddylase activity. This invention presents the first detailed insights into CSN5 regulation. These experiments contributed to the design of a constitutively active form of CSN5, shedding lights on its activation control mechanism at a molecular level.
The inventors demonstrated that the substitution of the Arg106 amino acid residue by another amino acid residue excepting proline restores a constitutive isopeptidase activity and the ability for CSN5 to recruit Nedd8.
The inventors also demonstrated that the two subunits of the COP9 signalosome CSN5 and CSN6 associate to form a stable heterodimer. The inventors demonstrated that CSN6 is able to significantly enhance CSN5 isopeptidase and deneddylase activity, this effect is consistently more marked in the context of the activatory mutant form of CSN5, CSN5 R106T than of the WT form.

DEFINITIONS

As used herein, the term “CSN5” has its general meaning in the art (1-5) and refers to COP9 signalosome complex subunit 5. The term CSN5 is also known as Jab1. Exemplary amino acid sequences of CSN5 are depicted in table A (SEQ ID NO: 1-16). The term also includes the function conservative variants of SEQ ID NO: 1-16.

TABLE A

CSN5 polypeptides.

		GI		Position of the
Protein		accession	Sequence	critical amino	Fragment
name	Species	number	number	acid residue	of interest

CSN5	Homo sapiens	119607334	SEQ ID NO: 1	106	53-252
CSN5	Homo sapiens	119607336	SEQ ID NO: 2	151	98-297
CSN5	Taeniopygia guttata	197129932	SEQ ID NO: 3	111	58-257
CSN5	Gallus gallus	86129524	SEQ ID NO: 4	110	57-256
CSN5	Cricetulus griseus	354501019	SEQ ID NO: 5	108	55-254
CSN5	Crotalus adamanteus	387015268	SEQ ID NO: 6	109	56-255
CSN5	Mustela putorius furo	355680616	SEQ ID NO: 7	114	61-260
CSN5	Xenopus laevis	148233750	SEQ ID NO: 8	104	51-250
CSN5	Tetraodon nigroviridis	47213973	SEQ ID NO: 9	105	52-251
CSN5	Amblyomma maculatum	346471157	SEQ ID NO: 10	103	50-249
CSN5	Crassostrea gigas	405954518	SEQ ID NO: 11	103	50-249
CSN5	Papilio xuthus	389609837	SEQ ID NO: 12	110	57-256
CSN5	Bombyx mori	223890174	SEQ ID NO: 13	110	57-256
CSN5	Anopheles gambiae	347968735	SEQ ID NO: 14	101	48-247
CSN5	Bombus impatiens	350403594	SEQ ID NO: 15	109	56-255
CSN5	Schistosoma mansoni	353231618	SEQ ID NO: 16	127	75-273

As used herein, the term “Function-conservative variants” denotes polypeptides derived from a polypeptide of the invention in which a given amino acid residue in a protein or enzyme has been changed without altering the overall conformation and function of the polypeptide, including, but not limited to, replacement of an amino acid with one having similar properties (such as, for example, polarity, hydrogen bonding potential, acidic, basic, hydrophobic, aromatic, and the like). Amino acids other than those indicated as conserved may differ in a protein so that the percent of protein or amino acid sequence similarity between any two proteins of similar function may vary and may be, for example, from 70% to 99% as determined according to an alignment method such as by the Cluster Method, wherein similarity is based on the MEGALIGN algorithm. A “function-conservative variant” also includes a polypeptide which has at least 20% amino acid identity as determined by BLAST or FASTA algorithms, preferably 40% more preferably 60%, preferably at least 75%, most preferably at least 85%, and even more preferably at least 90%, and which has the same or substantially similar properties or functions as the native or parent protein to which it is compared, and which has the critical amino acid at a position equivalent to the arginine at position 106 in SEQ ID NO: 1.
The amino acid residue critical for the active/inactive switch of the polypeptide of the invention refers to amino acid residue at position equivalent to the conserved arginine at position 106 in SEQ ID NO: 1 which is important in keeping the polypeptide of the invention in a conformation not competent for Nedd8 binding and which is critical for the active/inactive switch of the polypeptide of the invention to allow an active isopeptidase state.
As used herein, the term “CSN6” has its general meaning in the art (1) and refers to COP9 signalosome complex subunit 6. Exemplary amino acid sequences of CSN6 are depicted in table B (SEQ ID NO: 17-25). The term also includes the function conservative variants of SEQ ID NO: 17-25

TABLE B

CSN6 polypeptides.

Protein		GI accession	Sequence	Fragment
name	Species	number	number	of interest

CSN6	Homo sapiens	Q7L5N1	SEQ ID NO: 17	31-193
CSN6	Bos taurus	A6QQ21	SEQ ID NO: 18	28-190
CSN6	Cricetulus	G3I5F0	SEQ ID NO: 19	25-187
	griseus
CSN6	Salmo salar	B9EPB6	SEQ ID NO: 20	20-182
CSN6	Xenopus laevis	Q6NUC2	SEQ ID NO: 21	22-184
CSN6	Tetraodon	H3DE60	SEQ ID NO: 22	20-182
	nigroviridis
CSN6	Anoplopoma	C3KHN7	SEQ ID NO: 23	20-182
	fimbria
CSN6	Crassostrea	K1QRE1	SEQ ID NO: 24	22-178
	gigas
CSN6	Drosophila	Q9VCY3	SEQ ID NO: 25	38-200
	melanogaster

Polypeptides of the Invention

The present invention relates to a fragment of a CSN5 polypeptide wherein the amino acid residue critical for the active/inactive switch of the polypeptide was substituted to allow an active isopeptidase state.
In some embodiments the present invention relates to a polypeptide comprising

- an amino acid sequence ranging from amino acid at position 53 to amino acid at position 252 in SEQ ID NO: 1 wherein the amino acid at position 106 in SEQ ID NO: 1 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 98 to amino acid at position 297 in SEQ ID NO: 2 wherein the amino acid at position 151 in SEQ ID NO: 2 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 58 to amino acid at position 257 in SEQ ID NO: 3 wherein the amino acid at position 111 in SEQ ID NO: 3 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 57 to amino acid at position 256 in SEQ ID NO: 4 wherein the amino acid at position 110 in SEQ ID NO: 4 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 55 to amino acid at position 254 in SEQ ID NO: 5 wherein the amino acid at position 108 in SEQ ID NO: 5 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 56 to amino acid at position 255 in SEQ ID NO: 6 wherein the amino acid at position 109 in SEQ ID NO: 6 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 61 to amino acid at position 260 in SEQ ID NO: 7 wherein the amino acid at position 114 in SEQ ID NO: 7 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 51 to amino acid at position 250 in SEQ ID NO: 8 wherein the amino acid at position 104 in SEQ ID NO: 8 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 52 to amino acid at position 251 in SEQ ID NO: 9 wherein the amino acid at position 105 in SEQ ID NO: 9 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 50 to amino acid at position 249 in SEQ ID NO: 10 wherein the amino acid at position 103 in SEQ ID NO: 10 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 50 to amino acid at position 249 in SEQ ID NO: 11 wherein the amino acid at position 103 in SEQ ID NO: 11 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 57 to amino acid at position 256 in SEQ ID NO: 12 wherein the amino acid at position 110 in SEQ ID NO: 12 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 57 to amino acid at position 256 in SEQ ID NO: 13 wherein the amino acid at position 110 in SEQ ID NO: 13 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 48 to amino acid at position 247 in SEQ ID NO: 14 wherein the amino acid at position 101 in SEQ ID NO: 14 is substituted by another amino acid,
- an amino acid sequence ranging from amino acid at position 56 to amino acid at position 255 in SEQ ID NO: 15 wherein the amino acid at position 109 in SEQ ID NO: 15 is substituted by another amino acid,
- or an amino acid sequence ranging from amino acid at position 75 to amino acid at position 273 in SEQ ID NO: 16 wherein the amino acid at position 127 in SEQ ID NO: 16 is substituted by another amino acid, and function-conservative variants thereof.

The present invention relates to a CSN5 polypeptide wherein the amino acid residue critical for the active/inactive switch of the polypeptide was substituted to allow an active isopeptidase state.
In some embodiments, the present invention relates to a polypeptide comprising

- an amino acid sequence SEQ ID NO: 1 wherein the amino acid at position 106 in SEQ ID NO: 1 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 2 wherein the amino acid at position 151 in SEQ ID NO: 2 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 3 wherein the amino acid at position 111 in SEQ ID NO: 3 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 4 wherein the amino acid at position 110 in SEQ ID NO: 4 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 5 wherein the amino acid at position 108 in SEQ ID NO: 5 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 6 wherein the amino acid at position 109 in SEQ ID NO: 6 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 7 wherein the amino acid at position 114 in SEQ ID NO: 7 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 8 wherein the amino acid at position 104 in SEQ ID NO: 8 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 9 wherein the amino acid at position 105 in SEQ ID NO: 9 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 10 wherein the amino acid at position 103 in SEQ ID NO: 10 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 11 wherein the amino acid at position 103 in SEQ ID NO: 11 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 12 wherein the amino acid at position 110 in SEQ ID NO: 12 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 13 wherein the amino acid at position 110 in SEQ ID NO: 13 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 14 wherein the amino acid at position 101 in SEQ ID NO: 14 is substituted by another amino acid,
- an amino acid sequence SEQ ID NO: 15 wherein the amino acid at position 109 in SEQ ID NO: 15 is substituted by another amino acid,
- or an amino acid sequence SEQ ID NO: 16 wherein the amino acid at position 127 in SEQ ID NO: 16 is substituted by another amino acid, and function-conservative variants thereof.

Typically, the amino acid residue critical for the active/inactive switch of the CSN5 polypeptide or of the fragment of the CSN5 polypeptide is substituted by any amino acid residue excepting proline to allow an active isopeptidase state.
The present invention also relates a kit of parts comprising at least one CSN5 polypeptide according to the invention or a fragment thereof and at least one CSN6 polypeptide or a fragment thereof.
The polypeptides of the invention may be produced by any technique known per se in the art, such as, without limitation, any chemical, biological, genetic or enzymatic technique, either alone or in combination.
Knowing the amino acid sequence of the desired sequence, one skilled in the art can readily produce said polypeptides, by standard techniques for production of polypeptides. For instance, they can be synthesized using well-known solid phase method, preferably using a commercially available peptide synthesis apparatus (such as that made by Applied Biosystems, Foster City, Calif.) and following the manufacturer's instructions.
Alternatively, the polypeptides of the invention can be synthesized by recombinant DNA techniques as is now well-known in the art. For example, these fragments can be obtained as DNA expression products after incorporation of DNA sequences encoding the desired polypeptide into expression vectors and introduction of such vectors into suitable eukaryotic or prokaryotic hosts that will express the desired polypeptide, from which they can be later isolated using well-known techniques or corresponding cell-free systems (such as E coli, wheat germ systems).

Nucleic Acids, Vectors and Recombinant Host Cells of the Invention

The present invention also relates to a nucleic acid molecule encoding polypeptides according to the invention.
A “coding sequence” or a sequence “encoding” an expression product, such as a RNA, peptide, protein, or enzyme, is a nucleotide sequence that, when expressed, results in the production of that RNA, peptide, protein, or enzyme, i.e., the nucleotide sequence encodes an amino acid sequence for that peptide, protein or enzyme. A coding sequence for a protein may include a start codon (usually ATG) and a stop codon.
These nucleic acid molecules may be obtained by conventional methods well known to those skilled in the art, in particular by site-directed mutagenesis of the gene encoding the native protein. Typically, said nucleic acid is a DNA or RNA molecule, which may be included in a suitable vector, such as a plasmid, cosmid, episome, artificial chromosome, phage or viral vector.
So, a further object of the present invention relates to a vector and an expression cassette in which a nucleic acid molecule of the invention is associated with suitable elements for controlling transcription (in particular promoter, enhancer and, optionally, terminator) and, optionally translation, and also the recombinant vectors into which a nucleic acid molecule in accordance with the invention is inserted. These recombinant vectors may, for example, be cloning vectors, or expression vectors.
The terms “vector”, “cloning vector” and “expression vector” mean the vehicle by which a DNA or RNA sequence (e.g. a foreign gene) may be introduced into a host cell, so as to transform the host and promote expression (e.g. transcription and translation) of the introduced sequence.
Any expression vector for animal cell may be used, as long as a gene encoding a polypeptide or chimeric derivative of the invention can be inserted and expressed. Examples of suitable vectors include pAGE107, pAGE103, pHSG274, pKCR, pSG1 beta d2-4 and the like.
Other examples of plasmids include replicating plasmids comprising an origin of replication, or integrative plasmids, such as for instance pUC, pcDNA, pBR, and the like.
Other examples of viral vector include adenoviral, retroviral, herpes virus and AAV vectors. Such recombinant viruses may be produced by techniques known in the art, such as by transfecting packaging cells or by transient transfection with helper plasmids or viruses. Typical examples of virus packaging cells include PA317 cells, PsiCRIP cells, GPenv+ cells, 293 cells, etc. Detailed protocols for producing such replication-defective recombinant viruses may be found for instance in WO 95/14785, WO 96/22378, U.S. Pat. No. 5,882,877, U.S. Pat. No. 6,013,516, U.S. Pat. No. 4,861,719, U.S. Pat. No. 5,278,056 and WO 94/19478.
Examples of promoters and enhancers used in the expression vector for animal cell include early promoter and enhancer of SV40 (Mizukami T. et al. 1987), LTR promoter and enhancer of Moloney mouse leukemia virus (Kuwana Y et al. 1987), promoter (Mason J O et al. 1985) and enhancer (Gillies S D et al. 1983) of immunoglobulin H chain and the like.
The invention also includes gene delivery systems comprising a nucleic acid molecule of the invention. This includes for instance viral transfer vectors such as those derived from retrovirus, adenovirus, adeno associated virus, lentivirus, which are conventionally used in gene therapy. This also includes gene delivery systems comprising a nucleic acid molecule of the invention and a non-viral gene delivery vehicle. Examples of non viral gene delivery vehicles include liposomes and polymers such as polyethylenimines, cyclodextrins, histidine/lysine (HK) polymers, etc.
Another object of the invention is also a prokaryotic or eukaryotic host cell genetically transformed with at least one nucleic acid molecule according to the invention.
The term “transformation” means the introduction of a “foreign” (i.e. extrinsic or extracellular) gene, DNA or RNA sequence to a host cell, so that the host cell will express the introduced gene or sequence to produce a desired substance, typically a protein or enzyme coded by the introduced gene or sequence. A host cell that receives and expresses introduced DNA or RNA bas been “transformed”.
Preferably, for expressing and producing the polypeptides, and in particular the polypeptide according to the invention, eukaryotic cells, in particular mammalian cells, and more particularly human cells, will be chosen.
The construction of expression vectors in accordance with the invention, the transformation of the host cells can be carried out using conventional molecular biology techniques. The polypeptide of the invention, can, for example, be obtained by culturing genetically transformed cells in accordance with the invention and recovering the derivative expressed by said cell, from the culture. They may then, if necessary, be purified by conventional procedures, known in themselves to those skilled in the art, for example by fractionated precipitation, in particular ammonium sulphate precipitation, electrophoresis, gel filtration, affinity chromatography, etc.
In particular, conventional methods for preparing and purifying recombinant proteins may be used for producing the proteins in accordance with the invention.
In some embodiments, the invention relates to a non human transgenic animal transforming with an acid nucleic according to the invention. Typically, said animal is a mouse.

Screening Methods of the Invention

The present invention also relates to polypeptide of the invention for use in a method of screening modulators of CSN5 activity that could be used as therapeutic agents.
The present invention also relates to a method of screening therapeutic agents comprising the steps of:
i) providing a CSN5 polypeptide according to the invention or a fragment thereof,
ii) providing at least one CSN5 isopeptidase substrate,
iii) providing a candidate agent,
iv) measuring the binding of the substrate using appropriate biophysical techniques and/or measuring the activity of the CSN5 polypeptide,
v) and positively selecting candidate agents that modulates CSN5 activity.
The inventors demonstrated that CSN6 is able to significantly enhance CSN5 isopeptidase and deneddylase activity.
Accordingly, the present invention also relates to a method of screening therapeutic agents comprising the steps of:
i) providing a CSN5 polypeptide such as a CSN5 polypeptide selected from the group consisting of SEQ ID NO: 1-16, or a CSN5 polypeptide according to the invention or a fragment thereof,
ii) providing a CSN6 polypeptide or a fragment thereof,
iii) providing at least one CSN5 isopeptidase substrate (synthetic or natural),
iv) providing a candidate agent,
v) measuring the binding of the substrate using appropriate biophysical techniques and/or measuring the activity of the CSN5 polypeptide,
vi) and positively selecting candidate agents that modulates CSN5 activity.
Typically, the CSN5 isopeptidase substrates include but are not limited to a C-terminal-Nedd8-peptide (the LRGG tetrapeptide) or Nedd8 peptide linked to a detectable agent i.e. any reporter chemical group such as a fluorescent label (AMC) or a radioactive label (radio-labeled amino acid), or from neddylated proteins such as cullins or cullin fragments.
Typically, the screening method of the invention use standard or high throughput (HTP) assays.
Typically, the candidate agents include but are not limited to small organic molecules, antibodies, peptides or polypeptides.
Methods for measuring the activity of the CSN5 polypeptide are well known in the art. For example, measuring the CSN5 activity involves measuring a constitutive isopeptidase activity, measuring the ability for CSN5 to recruit Nedd8, measuring the CRLs deneddylase activity or determining a Ki on the CSN5 cloned and transfected in a stable manner into a CHO cell line in the presence or absence of the candidate agent. In vitro, ex vivo assays (e.g. cell lysates) and in vivo assays may be used to assess the potency and selectivity of the candidate agents to reduce CSN5 activity. Biophysical techniques such as crystallography may also be used.
Activities of the candidate agents, their ability to bind CSN5 and their ability to inhibit CSN5 activity may be tested using isolated cells, human embryonic kidney cells (HEK), or Escherichia coli expressing constitutively active CSN5, CHO cell line cloned and transfected in a stable manner by the constitutively active CSN5.
Cells and Escherichia coli expressing wild-type (WT) CSN5 may be used to assess selectivity of the candidate agents.
In one embodiment, the present invention relates to a method of screening therapeutic agents comprising the steps of:
i) providing a CSN5 polypeptide according to the invention or a fragment thereof,
ii) providing a candidate agent,
iii) measuring the binding of the candidate agent to the CSN5 polypeptide using appropriate biophysical techniques,
iv) and positively selecting candidate agents that bind to the CSN5 polypeptide.
In one embodiment, the present invention relates to a method of screening therapeutic agents comprising the steps of:
i) providing a CSN5 polypeptide such as a CSN5 polypeptide selected from the group consisting of SEQ ID NO: 1-16, or a CSN5 polypeptide according to the invention or a fragment thereof,
ii) providing a CSN6 polypeptide or a fragment thereof,
iii) providing a candidate agent,
iv) measuring the binding of the candidate agent to the CSN5 polypeptide using appropriate biophysical techniques,
v) and positively selecting candidate agents that bind to the CSN5 polypeptide.
Methods for measuring the binding of the candidate agent to the CSN5 polypeptide are well known in the art. For example, measuring the binding of the candidate agent to the CSN5 polypeptide may be performed by biophysical techniques such as binding tests (for example and not restricted to: Isothermal calorimetry (ITC), fluorescence anisotropy, Surface Plasmon Resonance (SPR), NMR) and crystallography.
Typically, the candidate agent may be an agent that dissociates the CSN5/CSN6 complex. Measuring CSN5/CSN6 complex dissociation may be performed by biophysical techniques such as Isothermal calorimetry (ITC) and Surface Plasmon Resonance (SPR).
Typically the therapeutic agent screened by the screening method of the invention will be suitable for the treatment of disease or perturbation related to CSN5 inhibition such as cancer.

Kits of the Invention

The invention also relates to a kit for performing the methods as above described, wherein said kit comprises a fragment of a CSN5 polypeptide or a CSN5 polypeptide according to the invention. The kit may also include a fragment of a CSN6 polypeptide or a CSN6 polypeptide. The kit may also include a CSN5 substrate. The kit may also comprise means for measuring the isopeptidase activity level of the CSN5 polypeptide. The kit may also contain other suitably packaged reagents and materials needed for the particular analysis protocol, and standards.
The invention will be further illustrated by the following examples. However, these examples should not be interpreted in any way as limiting the scope of the present invention.

EXAMPLES

Example 1

Material & Methods

Construct Design, Cloning, Expression and Purification.

The human wild-type (WT) and CSN5 mutant proteins were obtained by heterologous expression in Escherichia coli (E. coli). cDNA coding for full-length (1-334) CSN5 was cloned into the pGEX-6P1 vector (GE Healthcare). Expression trials under standard conditions revealed that the majority of recombinant CSN5 in Escherichia coli was expressed in truncated forms ranging from 29 to 31 kDa. The corresponding purified CSN5 fragments were identified using N-terminal sequencing and electrospray-mass spectrometry. The lowest-molecular-weight fragment was assigned the sequence 1-257. Subcloning of the corresponding DNA fragment was performed using the pGEX-6P1 vector. Site directed mutagenesis was performed using the QuikChange Lightning Site-Directed mutagenesis kit (Stratagene) and point mutation oligonucleotides (Eurogentec). All constructs and mutations were checked by DNA sequencing (Beckman Coulter Genomics).
Expression of CSN5_1-257wild type (WT) and mutant forms in Rosetta or BL21pLysS E. coli cells (Novagen) and purification were performed using standard conditions. Induced bacterial cells were resuspended in the purification buffer (20 mM Na-2-(N-morpholino)ethanesulfonic acid (Na-MES), pH 6.5, 100 mM NaCl, 0.002% monothioglycerol (MTG)) supplemented with EDTA-free protease inhibitor cocktail (Roche) and were lysed by sonication. Cell lysate was clarified by centrifugation and applied onto a gravity-flow Glutathione Sepharose 4B column (GE Healthcare). Glutathione S-transferase (GST)-tagged CSN5_1-257was eluted by 20 mM reduced glutathione in the purification buffer and was cleaved overnight at 4° C. by GST-3C protease. The sample was concentrated and loaded onto a Superdex 75 gel filtration column (GE Healthcare). A final polishing step was used to separate CSN5_1-257from contaminating GST. The resulting pure CSN5_1-257was concentrated to 10 mg mL-1 and stored at −80° C. until further use. Protein concentrations were measured with a Nanodrop (ThermoScientific) at 280 nm using their theoretical extinction coefficient.
Selenomethionine (SeMet)-labeled CSN5_1-257was expressed in methionine-auxotrophic E. coli strain B834 in minimum medium supplemented with SeMet following the manufacturer's instructions (Molecular Dimensions). Although the production yield was smaller, the rest of the 2 purification procedure was unchanged.
Preparation of Rbx1/Nedd8-Cul1-CTP/Cul1-NTD
420 μg of Rbx1/Cul1-CTP/Cul1-NTD were subjected to neddylation using the Enzo Life Sciences neddylation kit. Neddylation reaction mixture was loaded on a Superdex 75 10/300 GL gel filtration column, equilibrated in 20 mM NaMES pH6.5, 200 mM NaCl, 5 mM DTT, to isolate Rbx1/Nedd8-Cul1-CTP/Cul1-NTD. Rbx1/Nedd8-Cul1-CTP/Cul1-NTD containing fractions were pooled and concentrated to 7 mg·mL⁻¹and stored at −80° C. until further use.
Crystallization, Data Collection and Structure Determination
Purified CSN5_1-257samples were centrifuged through a 0.2-μm filtration unit and subjected to nanolitre crystallization trials using commercial screening kits. Crystals were grown using the sitting drop vapor diffusion method, mixing equal volumes of the protein and the crystallization well solution (0.1 M Na-HEPES, pH 7.5, 27% PEG3350, 0.7 M KSCN). Diffraction data sets were collected on crystals directly frozen in liquid nitrogen. SeMet-labeled CSN5_1-257crystals diffracted to 2.6 Å and belonged to the C-centered monoclinic space group with two molecules in the asymmetric unit. A dataset was collected at 2.6-Å resolution from a SeMet-labeled CSN5_1-257crystal at the ID14-EH4 beamline (ESRF, France) and used to solve the structure using the single-wavelength anomalous dispersion (SAD) method. The dataset was reduced and processed (Table S1) using MOSFLM, SCALA and TRUNCATE from the CCP4 software package (12). The completeness in the last resolution shell fell gradually beyond 2.7 Å due to anisotropic diffraction and radiation-induced damage.
The initial substructure determination and phasing at 2.6-Å resolution performed using AutoSol Wizard of the Phenix package (13) were not successful. Twenty-two heavy-atom sites were localized from anomalous differences data using the charge flipping algorithm (14) as implemented in the SUPERFLIP program (15). All selenium sites except two from SeMet alternate conformations and one zinc site were localized using the SUPERFLIP program (root mean square [r.m.s.] deviation of 0.55 Å with the final refined coordinates). This substructure was used for SAD phasing using the PHASER program (16).
Density modification and automatic tracing in the Resolve program of the Phenix package produced a starting model that assigned 67% of total residues and 48% of side chains. There were two molecules per asymmetric unit as related by a local two-fold axis perpendicular to the crystallographic dyad axis. The structure was completed by iterative model building in Coot (17) and refinement in REFMAC (18) using individual restrained thermal factor refinements and weak non-crystallographic symmetry restraints. The final rounds of refinement were performed using Phenix (13) incorporating six Translation/Libration/Screw (TLS) groups per chain, which produced a model with good statistics and geometry (Table S1) as examined with Molprobity (19). The final model consisted of two chains with residues 2-197 and 219-257, two zinc ions, 52 water molecules, and three thiocyanate ions and was refined to an R_freevalue of 27.4% and an R value of 21.6%. All non-Gly residues fell within the allowed regions of the Ramachandran plot.
Molecular Dynamics Simulations
The A chain from the CSN5_1-257crystal structure was used as the initial structure for MD simulations on the WT protein and the R106 (T, G and P) variants. The missing loop (residues 198-218) was built using the MODELLER program (20, 21). The models of the variants were prepared by mutating the appropriate R106 residue before the solvation step using the Coot software. The atoms within 10 Å of the mutated residue were minimized. All the water molecules from the initial model were removed except the one bound to the catalytic zinc. Rather than using covalent bonds or harmonic restraints to maintain the zinc environment, the inventors employed the cationic dummy atom approach (21), which imposes orientational constraints for the four zinc ligands (His138, His140, Glu151 and water) in the tetrahedral configuration. The protonation state of the other ionisable side chains was set to their normal values at pH 7. The resulting structure was surrounded by a periodic octahedral box of TIP3P water. This procedure resulted in a total of 4,029 protein atoms, including the zinc ion and the catalytic water molecule, solvated by 17,000-18,500 water molecules. All MD simulations were performed with the AMBER11 program (22) with the ff03 force field parameters (23) and the additional force field for the zinc atom environment (21). Optimization and relaxation of solvent were initially performed by means of energy minimizations and MD simulations while keeping the solute atoms constrained to their initial positions with weak force constants.
After equilibration was established by gradually increasing the temperature from 100 to 300 K for 50 ps, the system was subjected to short (100-ps) MD simulations with decreasing constraints at a constant temperature of 300 K and a constant pressure of 1 bar. The 40-ns production run was conducted with constrained bond lengths involving hydrogen atoms and using the Shake algorithm (24), the Verlet integrator with a 2-fs time step for seven the calculation of forces and Langevin dynamics for temperature control. A cut-off radius of 9 Å was used to compute the non-bonded steric interactions. The electrostatic interactions were calculated with the particle-mesh Ewald method (25). The missing counterions were substituted with a net-neutralizing plasma over the periodic box. The ptraj module in the AmberTools package (26) was used to extract data from trajectories and to analyze structural and dynamic properties. All computations including the minimizations and the MD simulations were performed on a HP Z800 workstation equipped with two GPU Tesla C1060 and quad-core Xeon 2.4 GHz processors.
Rotamerically Induced Perturbations.
Large conformational changes, as those frequently coupled to catalytic function, are occurring in the order of 10^thof picoseconds to millisecond timescale. Such long computationally demanding MD calculations are thus difficult to simulate. The Rotamerically Induced Perturbation (RIP) method was designed by Ho and Agard (27) to induce large conformational rearrangements of structural segments at the surface of a protein in short simulation times. This new MD approach is particularly useful to identify potentially mobile structural elements or loops. The RIP local thermal excitation of rotameric rotations was applied on each isolated residue in CSN5_1-257. The kinetic energy transfer to residues in spatial proximity was analyzed to explore the strength of contacts anchoring local segments and reveal their conformational flexibility (28). For each perturbed residue, a 10 ps simulation is produced using the same starting CSN5 monomeric model, equilibrated at 300 K. A RIP perturbation pulse is applied every 100 fs. The MD simulations were performed using the Amber11 package (26) with an GB/SA implicit solvent model and Python scripts implementing the RIP protocol (http://boscoh.com/rip/). The deformability map (average Ca r.m.s. deviation values) generated from the analysis of the various trajectories provides an excellent indicator of conformational flexibility and reveals buried tertiary couplings.
Isopeptidase Assays Using AMC Derived Substrates.
For the isopeptidase assay using LRGG-AMC substrate, GST-tagged CSN5_1-257protein and different mutants were diluted to 0.2 μg μL⁻¹in reaction buffer (40 mM Tris-HCl pH8.5, 5% glycerol, 1 mM DTT), in the presence of 250 μM LRGG-AMC. The isopeptidase activity of the ubiquitin specific protease 2 catalytic domain (USP2CD; purchased from Boston Biochem.) was used as a control in the same conditions but at a concentration of 0.02 μg μL⁻¹. The effect of zinc chelation was carried out by pre-incubation of CSN5 in the presence of 10 mM ethylene diamine tetraacetic acid (EDTA). The effect of temperature on the isopeptidase activity was evaluated by pre-incubation of the enzymes at 60° C. water bath for 20 min. For the isopeptidase assay using Nedd8-AMC substrate, CSN5_1-257protein and different mutants (R106T, R106A, R106G, R106P, E76A, E76A/R106T) prepared in the same conditions were diluted to 0.2 μg μL⁻¹immediately before in the reaction buffer (40 mM Tris-HCl pH8.5, 1 mM DTT). The CSN complex purified from erythrocytes and purchased from Enzo Life Sciences was used at 0.01 μg μL⁻¹. The reactions setup on ice were started by the addition of the substrate (2 μM Nedd8-AMC) to the reaction mixture and followed at 28° C. Isopeptidase assays were monitored in duplicate in a 96-well fluorescence plate on a Tecan Saphire, by following the increase of fluorescence intensity (λ_excitation=380 nm; λ_emission=460 nm), i.e. the hydrolysis of the isopeptide bond between LRGG/Nedd8 and AMC.
Deneddylation of Rbx1/Nedd8-Cul1-CTP/Cul1-NTD.
The CSN complex at 4.8 ng μL⁻¹, CSN5_1-257protein and R106T variant diluted to 0.33 μg μL⁻¹in 20 mM Tris-HCl pH7.5, 50 mM NaCl were incubated in the presence of 38 μM Rbx1/Nedd8-Cul1-CTP/Cul1-NTD 3 hours at 32° C. Proteins separated on a 10% Tris-tricine gel were transferred on a PVDF membrane and a standard Western blotting protocol was carried out using antibodies specific of Nedd8 (Epitomics) at a dilution of 1:500. Both neddylated cullin 1 and Nedd8 released from the hydrolysis of Nedd8-cullin 1 isopeptide bond were visualized upon chemiluminescence revelation by the SuperSignal West Pico Chemiluminescent Substrate kit (Pierce).
Accession code: Coordinates and structure factor amplitudes have been deposited in the Protein Data Bank with the accession code 4F70.
Results
Overall Structure and Oligomeric Arrangement
A stable form of CSN5 comprising residues 1-257 (CSN5_1-257), identified by MS and N-terminal sequencing, was isolated and crystallized. The crystals belong to the monoclinic C-centered space group and diffracted up to 2.6-Å resolution. The crystal structure was therefore solved by selenium-SAD using diffraction data to 2.6 Å. CSN5, which is the fifth CSN subunit and consists of 334 residues, is a c-Jun-activation domain-binding protein 1 (Jab1)/MPN superfamily member with a conserved core MPN domain (51-230) and a JAMM motif (Glu76, His138, His140, Asp151). In addition to the MPN catalytic domain, CSN5 possesses N- and C-terminal regions that tightly pack against the MPN fold and form an extended catalytic domain. The asymmetric unit of CSN5_1-257crystal contains a dimer, related by a local two-fold axis perpendicular to the crystallographic two-fold axis, generating also a second dimeric arrangement. The characteristics of each plausible oligomeric arrangement were evaluated by PISA (20), which highlights two types of dimers (A-B and A-A′) and a D2 tetramer that bury a total surface area of 2,112, 1,950 and 8,970 A2, respectively.
CSN5 can Form Homo-Dimers In Vitro
Several lines of evidences in the literature suggest the propensity of CSN5 to form oligomers. Indeed, non-denaturing MS and proteomic evaluations revealed the presence of oligomers in vitro (3, 21). In eukaryotic cells, CSN5 is present in not only the CSN complex, but also in smaller complexes (between 70 and 150 kDa, while the monomer is 29 kDa) that might correspond to CSN5 oligomeric forms (10-12, 22). Together with these evidences described in the literature but not further experimentally probed, the crystal dimer properties led inventors to explore the functional relevance of CSN5 oligomerisation in vitro. To investigate the presence of the oligomeric species, inventor's experimental approach was based on chemical cross-linking, on dynamic light scattering (DLS) and on analytical ultracentrifugation (AUC). The results showed that monomers and dimers were the major species of CSN5 detected in solution. Supported by both in vitro data, these observations suggest that a dimeric CSN5 assembly could be present in solution, in equilibrium with monomeric species. It is noteworthy that other MPN-containing proteins were found to assemble in dimers in the crystals and that each of the described dimers, for which the question of the physiological relevance has not yet been addressed in vivo, proceeds via totally different interfaces (23, 24). As the biological relevance of these assemblies has not been shown, it therefore prevents further comparison in the context of the present findings. Further to these experiments and on the basis of the A-B and A-A′ dimer interface analysis, mutations or deletions were designed to selectively weaken these two inter-subunit interactions. Evaluation of the dimer disruption extent was carried out in vitro by DLS. Two leucine residues (Leu237 and Leu240) placed on one side of the helix α4, facing α6, as well as the Arg129 residue were consequently selected. DLS measurements on these interfacial mutants clearly showed a drop in particle diameter as compared to those on the WT protein. This drop, particularly marked between WT and the double mutant L237Q/L240K, is compatible with the transition from A-B dimer to mostly monomeric species. In contrast, the deletion of the C-terminal tail that mediates the A-A′ dimer does not affect as much the assembly, further supporting the idea that the A-B dimer is the preponderant assembly in solution. Taken together, these results demonstrate that CSN5 mainly forms biologically relevant dimers of the A-B type, unveiling a new level of regulation in the biology of CSN5. More that 70% of the CSN5 residues involved in this protein-protein interface are highly conserved among the 170 available sequences, further demonstrating that this assembly may be physiologically relevant.
Conserved Rigid MPN Domain is Decorated by CSN5-Specific N- and C-Terminal Extensions
The CSN5_1-257structure reveals a fold typical to the Jab1/MPN superfamily (23-28). The core of the MPN fold that consists of the central β-sheet and three α-helices (residues 51-224) is largely conserved in the MPN domain-containing structures solved to date, with a mean r.m.s. deviation of 3.2 Å over an average of 124 residues (as calculated by the DALI server (29)) and a mean r.m.s. deviation of 1 Å for the 54 most central residues (as calculated by Chimera (30)), including the recently reported CSN6 structure from Drosophila (24). Structural comparison between MPN members revealed that the region spanning from residues 97 to 129 (referred to as Ins-1) displays different conformations in the various MPN members and is sometimes partially unstructured or disordered. It is noteworthy that the lack of electron density for the CSN5 portion consisting of residues 197-219 (corresponding to Ins-2 in the structure of AMSH-LP (27)) prevented accurate modeling and analysis of this segment.
The ensemble of the CSN5-specific N- and C-terminal segments wrap around and make extensive contacts with the conserved MPN domain core. Most MPN proteins structure solved to date display reduced or no N- and C-terminal additions; with the exception of Prp8p structure that has N- and C-terminal extensions of similar size to that of CSN5 (26). However these regions adopt in CSN5, an MPN+/JAMM enzyme and in Prp8p, a scaffolding protein, very different positions and conformations with respect to the core MPN domain.
To complement and extend the structural insights obtained from crystallography, the inventors carried out a series of MD simulations. The CSN5 crystal structure suggests that the central core domain is stable and that some flanking α-helices and loops displaying higher B-factors could be locked into the structure due to the crystal packing. MD simulations of the solvated CSN5 monomer at 300 K for 40 ns confirmed that the core domain is stable and that the residues forming the Ins-2 segment, the loops and the N- and C-terminal ends display the maximum fluctuation compared with the central core domain.
CSN5 Zinc-Binding Site is Catalytically Competent, Similar to Other JAMM-Containing Motifs
As the inventors anticipated from other MPN+/JAMM proteases, the CSN5 structure contains one zinc atom. The strictly conserved zinc coordination site is composed of residues from helix α5 and a subset of the central β-sheet (β5, β5-α5, β6 and β7). The zinc is tetrahedrally coordinated to two histidine residues (His138 and His140), one Asp residue (Asp151), and a catalytic water molecule hydrogen bonded to Glu76 and Ser148. The importance of the active site zinc coordinating residues in catalysis had previously been tested by mutagenesis (2). AMSH-LP is the only structural example of an active MPN+/JAMM isopeptidase enzyme that can exist in its unbound form or in complex with its K63-Ub2 substrate (27). Therefore it provides for this enzyme family a model for a catalytically competent active site and for substrate interactions. Comparison of the zinc-binding sites of CSN5 and AMSH-LP revealed that the overall topology of their active sites is conserved. In addition, the position and environment of the Gly76-Lys63 isopeptide, straightforwardly placed in the CSN5 active site, inferred from the AMSH-LP/K63-Ub2 complex, confirmed that CSN5 adopts a catalytically competent geometry. As described similarly for the AMSH-LP/K63-Ub2 structure, the Gly76-Lys63 isopeptide bond, placed in the CSN5 zinc-binding site, is maintained via a hydrogen bond between the Gly76 carbonyl group and the Ser148 side chain hydroxyl group and between the Lys side chain amine and the Glu76 carboxylate. The inventors also investigated the role played by the catalytic zinc ion on the structure and stability of the active site. The side-chain motions of amino acids in the zinc catalytic site were analyzed. Their positions were stable over the course of the MD simulations, and their averaged inter-atomic distances from Zn2+ were in good agreement with those measured from the CSN5_1-257and AMSH-LP crystal structures. Taken together, these observations demonstrate that, as in AMSH-LP, the zinc-binding site catalytic residues of CSN5 are in a position and geometry compatible with isopeptidase activity and therefore that the zinc active site conformation of this enzyme in its isolated form is catalytically competent.
Although the CSN5 zinc-binding site and its catalytic residues are very similar to those of AMSH-LP, their active site properties and spatial accessibility have several differentiating features. In particular, the CSN5 Ins-1 region (loop β4-α4 and α4 helix) adopts a radically different topology in CSN5 and in AMSH-LP i.e. two anti-parallel β-strands and a short α-helix (residues 314-339). An additional distinguishing feature of the CSN5 zinc-binding site is the presence in its surroundings of one arginine residue, Arg106, which forms a salt bridge with Asp151. The substitution of Gln352 and Phe355 residues in AMSH-LP with a tyrosine (Tyr143) and a tryptophan (Trp146) residues in CSN5, respectively, reinforces the hydrophobic character of the CSN5 pocket). Tyr143 in CSN5 hydrogen bonds with Glu76, whereas Gln352 in AMSH-LP is orientated towards the solvent. The importance of the interaction between Glu76 and Tyr143 should be further explored because of the role played in substrate positioning by the equivalent of Glu76 in AMSH-LP, Glu292, and the fact that in MD simulations, this hydrogen bond is not maintained during the simulations.
Surroundings of the CSN5 Zinc Catalytic Site is not Competent for Nedd8 Recruitment, without Conformational Rearrangements
Two different activation states of CSN5 are described in the literature (2, 3): an active deneddylase in the context of the holo-CSN complex and an inactive form in the isolated subunit. As suggested by the inventor's data the CSN5 active site is poised for catalysis, it thus seemed logical to explore substrate binding and recruitment by this enzyme.
In the crystal structure of the AMSH-LP/K63-Ub2 complex, the two ubiquitin molecules, referred to as proximal and distal, interact with AMSH-LP via numerous electrostatic and hydrophobic interactions (27). The directionality of the isopeptide bond implies that Nedd8 would occupy the site corresponding to the distal ubiquitin in the AMSH-LP/K63-Ub2 structure. The distal ubiquitin molecule mediates the largest interaction surface area and contributes the most to the binding affinity of K63-Ub2 for AMSH-LP. Correct positioning of the K63-Ub2 isopeptide bond in the long recognition groove of AMSH-LP is ensured by interactions between AMSH-LP (in particular, the Ins-1 region, the Ins-2 loop [disordered in CSN5], and the segment between these two insertions) and the proximal and distal ubiquitins. The C-terminal portion of the distal ubiquitin adopts an extended conformation that fits in the substrate binding groove delimitated by two α-helices and a β-hairpin. Ubiquitin and Nedd8 molecules are 58% identical over 76 residues and adopt the same fold (31, 32). The interactions with the last four residues of ubiquitin/Nedd8, preceding the isopeptide bond are likely to be preserved in CSN5. Only one residue, position 72 (arginine and alanine, respectively in ubiquitin and Nedd8) differentiates ubiquitin from Nedd8 in the last 10 residues. Analysis of the AMSH-LP residues implicated in the distal ubiquitin recognition site revealed that more than 50% are conserved or semi-conserved in CSN5. However, most of the residues for which no equivalent could be found in CSN5 belong to the Ins-1 region, which has a very different conformation in the CSN5 and AMSH-LP structures. Consequently, without the structure of CSN5 in its active state, detailed analysis of the substrate binding site in CSN5 is prevented.
Despite the high conservation of the interaction site in CSN5, the conformation of the Ins-1 observed here sterically precludes Nedd8 binding. Extensive structural changes of this segment, which probably confers some of the specificity for Nedd8 ligand would be required to create a fully competent binding site.
An Arginine Residue Contributes to the Control of CSN5 Isopeptidase Activation State
The major difference at the active site level between CSN5 and AMSH-LP corresponds to the conformation of the Ins-1 insertion. It is therefore most interesting to note that the Ins-1 segment of CSN5 shows signs of flexibility, as indicated by high B-factor values and the fact that it exhibits significant conformational variability within representatives of the MPN family. Moreover, MD simulations flagged two portions of the Ins-1 region as highly flexible (residues 98-108 and 122-129). The CSN5 segments 100-105 and 108-112, bracketing the residue Arg106, display ample movements opening onto the solvent in MD simulations, whereas Arg106 contributes significantly to the anchoring of the Ins-1 segment to the zinc-binding site via its salt bridge with Asp151. MD studies confirmed the potential importance of Arg106 with this salt bridge being maintained in the 40-ns trajectories. The observations that Arg106 plays a role in CSN5 plasticity were further probed and confirmed by rotamerically induced perturbation (RIP) simulations (33). These data demonstrate that the intrinsic flexibility and plasticity of the Ins-1 region allow major conformational rearrangements to accommodate Nedd8 binding and that Arg106 have here a triggering function for structural rearrangement of the Ins-1 segment.
To evaluate the role of Arg106 as a potentially important protagonist in CSN5 activation switch, the inventors have tested the effect of Arg106 substitution by a threonine (R106T) on CSN5 isopeptidase activity and Nedd8 binding. In agreement with published data in the literature (2, 3), the inventors confirmed that the CSN5_1-257WT form is void of isopeptidase activity and showed that the R106T substitution is sufficient to restore constitutive isopeptidase activity against two isopeptidase substrates, LRGG-AMC and Nedd8-AMC. These results demonstrate that the conformational relaxation of the Ins-1 region allows substrate binding and additionally corroborates inventor's analysis on the intrinsic topological competence of the zinc binding site for catalysis.
To complement these activity data, pull-down experiments, using GST-CSN5_1-257as the bait and Nedd8 as the target, showed that the WT form was unable to bind Nedd8, whereas the R106T form was. This confirms that releasing the Ins-1 segment from its anchoring point is sufficient to expose a functional binding site for Nedd8. Taken together, these data strongly demonstrate the implication of Arg106 in the active/inactive switch of CSN5.

DISCUSSION

The roles of the CSN complex span from cell cycle control to immunity. Mediated probably through its deneddylase activity, the function of the CSN complex is important for cellular homeostasis, as highlighted by its implication in proliferative diseases (reviewed in (5)). The sequence alignment of the CSN catalytic subunit, CSN5, from different organisms reveals highly conserved features throughout the sequence and the evolutionary tree, in agreement with the essentiality of the csn5 gene previously highlighted for several species (Dictostelium discoideum, Drosophila melanogaster and Mus musculus (1)) and with its catalytic function within the CSN complex. One major means of controlling CSN function is the traffic of the catalytic subunit CSN5, which shuttles between the holo-CSN, sub-CSN complexes, and CSN-independent forms, but displays isopeptidase activity only in the context of the holo-CSN complex (3).
Despite the importance of CSN regulatory mechanisms, they remain largely unknown and poorly understood. The present invention reveals that CSN5 can be found in different oligomeric states in vitro and may predominantly follow a monomer-dimer equilibrium. The interaction between CSN5 and various partners has been investigated in previous studies, but only in its monomeric form (reviewed in (6)). Its assembly in dimers reveals a largely unexplored aspect of the protein regulation and may be relevant in mediating protein-protein interactions and subcellular localization of CSN5.
A second important aspect in CSN5 biology that is addressed in this work is its activation state in the CSN-independent context. To glean insights into CSN5 isopeptidase activity regulation, the inventors used structural biology and in silico MD simulations, which together created a first detailed picture of CSN5 activity control. The crystal structure of CSN5 in a CSN-independent form displays an extended catalytic domain that revealed a number of features, contributing to our understanding of the enzyme's activation and substrate recruitment. In analogy to the structure of AMSH-LP (27), the apo form of CSN5 adopts a zinc-binding site geometry that appears compatible with isopeptidase activity and potentially with binding of the Gly76-Lys63 isopeptide, as extrapolated from the co-crystal structure of AMSH-LP/K63-Ub2 to the CSN5 zinc-binding site. Unlike AMSH-LP/K63-Ub2, however, investigation of the recruitment of Nedd8 by CSN5 revealed that the exosite is not formed in CSN5 and that the Ins-1 segment would require substantial structural rearrangement for Nedd8 to bind. These observations were confirmed by analysis of Ins-1 flexibility and plasticity by in silico simulations. The present invention also helped understanding the molecular events that trigger these conformational changes in CSN5. MD and RIP calculations pointed to a role for the conserved Arg106 in keeping this segment in a conformation not competent for Nedd8 binding. This implication of this residue, validated by in vitro experiments, led to the confirmation that Arg106 is an important protagonist in CSN5 activation switch. Indeed, substitution of this residue by a threonine restores a constitutive isopeptidase activity and the ability for CSN5 to recruit Nedd8.
Integration of CSN5 into the CSN complex and the consequent protein—protein interactions with CSN subunits such as CSN6, as highlighted by non-denaturing MS experiments (3), are likely to play a part in both CSN5 activation and substrate recruitment. Whereas CSN5 is probably the subunit most responsible for Nedd8 association, other CSN components, such as CSN2, have been shown to bind cullins (1). CSN5 incorporation into the CSN complex probably does not lead to global structural reshaping of the enzyme. Instead, the structural changes are likely to be limited to the Ins-1 segment (identified as malleable in our MD calculations), the Ins-2 region (disordered in the crystal), and possibly the C-terminal domain (residues 258-334) to prime the deneddylating molecule for catalysis. Integration of CSN5 in the CSN complex is probably providing the conformational energy necessary for the activation switch.
Taken together, our study results suggest that CSN5 in its CSN-independent form is deficient in substrate recruitment and that a single residue contributes significantly to the activation switch and that its biology might be further complicated by the presence of oligomeric forms. This discovery provides the framework for further biochemical and functional investigations to elaborate on the regulatory pathways in which CSN5 intervenes.

Example 2

Activation of CSN5 Isopeptidase Activity by CSN6

Material & Methods
Expression and purification. For the CSN5 protein (WT and variant forms), the expressions and purifications were carried out using protocols described previously. Solubly expressing CSN6 constructs were designed and CSN6 was expressed as a fusion protein with GST. The purification protocol follows that of CSN5's with a change of the buffer composition (20 mM Tris-HCl pH7.5, 150 mM NaCl).
Activity measurements. The substrates were used at different concentrations (0 to 400 μM for LRGG-AMC; 0 to 20 μM for Nedd8-AMC; 0 to 2 μM for Nedd8-cullin 1; 0 to 100 μM for pro-Nedd8). The buffer used in the activity measurements is composed of 50 mM Tris-HCl pH 7.5, 50 mM NaCl. All the measurements were done at 37° C. on a Tecan Sapphire fluorimeter (except for Nedd8-cullin 1). For the activity measurements corresponding to Nedd8-cullin 1, cullin 1 deneddylation was followed by gel shift assay and the bands were quantified after an anti-Nedd8 Western blot.
Results
Soluble constructs of CSN5 and CSN6 MPN domains were designed and the corresponding protein fragments were successfully expressed in bacteria.
Their spatial proximity in the Cop9 signalosome complex brought us to investigate a possible direct association between these two MPN domain-containing subunits. Indeed the two subunits of the Cop9 signalosome associate to form a gel filtration stable hetero-dimer. Further characterised in terms of affinity and topology, the dissociation constant of the dimer is around 1-5 μM (ITC) and that its organisation could be consistent with that of CSN5 or Mov34 homo-dimer as probed by a mutagenesis analysis.
These results subsequently brought us to evaluate the effect of CSN6 on CSN5 isopeptidase activity. To do so the inventors use three different substrates (two synthetic (LRGG-AMC; Nedd8-AMC) and one natural (Nedd8-cullin 1)) to show that CSN6 is able to significantly enhance CSN5 isopeptidase activity. Interestingly this effect is consistently more marked in the context of the activatory mutant form of CSN5, CSN5 R106T than the WT form.

REFERENCES

1. Wei N, Serino G, & Deng X W (2008) The COP9 signalosome: more than a protease. Trends Biochem Sci 33(12):592-600.
2. Cope G A, et al. (2002) Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science 298(5593):608-611.
3. Sharon M, et al. (2009) Symmetrical modularity of the COP9 signalosome complex suggests its multifunctionality. Structure 17(1):31-40.
4. Maytal-Kivity V, Reis N, Hofmann K, & Glickman M H (2002) MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function. BMC Biochem 3:28.
5. Kato J Y & Yoneda-Kato N (2009) Mammalian COP9 signalosome. Genes Cells 14(11):1209-1225.
6. Shackleford T J & Claret F X (2010) JAB1/CSN5: a new player in cell cycle control and cancer. Cell Div 5:26.
7. Freilich S, et al. (1999) The COP9 signalosome is essential for development of Drosophila melanogaster. Curr Biol 9(20):1187-1190.
8. Kwok S F, et al. (1998) Arabidopsis homologs of a c-Jun coactivator are present both in monomeric form and in the COP9 complex, and their abundance is differentially affected by the pleiotropic cop/det/fus mutations. Plant Cell 10(11):1779-1790.
9. Mundt K E, Liu C, & Carr A M (2002) Deletion mutants in COP9/signalosome subunits in fission yeast Schizosaccharomyces pombe display distinct phenotypes. Mol Biol Cell 13(2):493-502.
10. Oron E, et al. (2002) COP9 signalosome subunits 4 and 5 regulate multiple pleiotropic pathways in Drosophila melanogaster. Development 129(19):4399-4409.
11. Tomoda K, et al. (2002) The cytoplasmic shuttling and subsequent degradation of p27Kip1 mediated by Jab1/CSN5 and the COP9 signalosome complex. J Biol Chem 277(3):2302-2310. 12. Fukumoto A, Tomoda K, Kubota M, Kato J Y, & Yoneda-Kato N (2005) Small Jab1-containing subcomplex is regulated in an anchorage- and cell cycle-dependent manner, which is abrogated by ras transformation. FEBS Lett 579(5):1047-1054.
13. Kapelari B, et al. (2000) Electron microscopy and subunit-subunit interaction studies reveal a first architecture of COP9 signalosome. J Mol Biol 300(5):1169-1178.
14. Serino G, et al. (1999) Arabidopsis cop8 and fus4 mutations define the same gene that encodes subunit 4 of the COP9 signalosome. Plant Cell 11(10):1967-1980.
15. Dumas C & van der Lee A (2008) Macromolecular structure solution by charge flipping. Acta Crystallogr D Biol Crystallogr D64(Pt 8):864-873.
16. McCoy A J, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40(Pt 4):658
18. Pathogenesis of Nasopharyngeal Carcinoma. Cancer Res 72(7):1890-1900.
19. Kouvaraki M A, et al. (2006) Potential role of Jun activation domain-binding protein 1 as a negative regulator of p27kip1 in pancreatic adenocarcinoma. Cancer Res 66(17):8581-8589.
20. Krissinel E & Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372(3):774-797.
21. Fang L, et al. (2008) Characterization of the human COP9 signalosome complex using affinity purification and mass spectrometry. J Proteome Res 7(11):4914-4925.
22. Tomoda K, Yoneda-Kato N, Fukumoto A, Yamanaka S, & Kato J Y (2004) Multiple functions of Jab1 are required for early embryonic development and growth potential in mice. J Biol Chem 279(41):43013-43018.
23. Sanches M, Alves B S, Zanchin N I, & Guimaraes B G (2007) The crystal structure of the human Mov34 MPN domain reveals a metal-free dimer. J Mol Biol 370(5):846-855.
24. Zhang H, Gao, Z.-Q., Wang, W.-J., Liu, G. F., Shtykova, E. V., Xu, J.-.H., Li, L.-F., Su, X.-D., Dong, Y.-H. (2012) The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6. FEBS Letters 586(8):1147-1153.
25. Ambroggio X I, Rees D C, & Deshaies R J (2004) JAMM: a metalloprotease-like zinc site in the proteasome and signalosome. PLoS Biol 2(1):E2.
26. Pena V, Liu S, Bujnicki J M, Luhrmann R, & Wahl M C (2007) Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa. Mol Cell 25(4):615-624.
27. Sato Y, et al. (2008) Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains. Nature 455(7211):358-362.
28. Tran H J, Allen M D, Lowe J, & Bycroft M (2003) Structure of the Jab1/MPN domain and its implications for proteasome function. Biochemistry 42(39):11460-11465.
29. Holm L & Rosenstrom P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38(Web Server issue):W545-549.
30. Pettersen E F, et al. (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605-1612.
31. Whitby F G, Xia G, Pickart C M, & Hill C P (1998) Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. J Biol Chem 273(52):34983-34991.
32. Ramage R, et al. (1994) Synthetic, structural and biological studies of the ubiquitin system: the total chemical synthesis of ubiquitin. Biochem J 299 (Pt 1):151-158.
33. Ho B K & Agard D A (2009) Probing the flexibility of large conformational changes in protein structures through local perturbations. PLoS Comput Biol 5(4):e1000343.

Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present disclosure.

Claims

1. A polypeptide comprising

an amino acid sequence ranging from amino acid at position 53 to amino acid at position 252 in SEQ ID NO: 1 wherein the amino acid at position 106 in SEQ ID NO: 1 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 98 to amino acid at position 297 in SEQ ID NO: 2 wherein the amino acid at position 151 in SEQ ID NO: 2 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 58 to amino acid at position 257 in SEQ ID NO: 3 wherein the amino acid at position 111 in SEQ ID NO: 3 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 57 to amino acid at position 256 in SEQ ID NO: 4 wherein the amino acid at position 110 in SEQ ID NO: 4 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 55 to amino acid at position 254 in SEQ ID NO: 5 wherein the amino acid at position 108 in SEQ ID NO: 5 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 56 to amino acid at position 255 in SEQ ID NO: 6 wherein the amino acid at position 109 in SEQ ID NO: 6 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 61 to amino acid at position 260 in SEQ ID NO: 7 wherein the amino acid at position 114 in SEQ ID NO: 7 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 51 to amino acid at position 250 in SEQ ID NO: 8 wherein the amino acid at position 104 in SEQ ID NO: 8 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 52 to amino acid at position 251 in SEQ ID NO: 9 wherein the amino acid at position 105 in SEQ ID NO: 9 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 50 to amino acid at position 249 in SEQ ID NO: 10 wherein the amino acid at position 103 in SEQ ID NO: 10 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 50 to amino acid at position 249 in SEQ ID NO: 11 wherein the amino acid at position 103 in SEQ ID NO: 11 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 57 to amino acid at position 256 in SEQ ID NO: 12 wherein the amino acid at position 110 in SEQ ID NO: 12 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 57 to amino acid at position 256 in SEQ ID NO: 13 wherein the amino acid at position 110 in SEQ ID NO: 13 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 48 to amino acid at position 247 in SEQ ID NO: 14 wherein the amino acid at position 101 in SEQ ID NO: 14 is substituted by another amino acid,

an amino acid sequence ranging from amino acid at position 56 to amino acid at position 255 in SEQ ID NO: 15 wherein the amino acid at position 109 in SEQ ID NO: 15 is substituted by another amino acid,

or an amino acid sequence ranging from amino acid at position 75 to amino acid at position 273 in SEQ ID NO: 16 wherein the amino acid at position 127 in SEQ ID NO: 16 is substituted by another amino acid, and function-conservative variants thereof.

2. The polypeptide according to claim 1 comprising

an amino acid sequence SEQ ID NO: 1 wherein the amino acid at position 106 in SEQ ID NO: 1 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 2 wherein the amino acid at position 151 in SEQ ID NO: 2 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 3 wherein the amino acid at position 111 in SEQ ID NO: 3 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 4 wherein the amino acid at position 110 in SEQ ID NO: 4 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 5 wherein the amino acid at position 108 in SEQ ID NO: 5 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 6 wherein the amino acid at position 109 in SEQ ID NO: 6 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 7 wherein the amino acid at position 114 in SEQ ID NO: 7 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 8 wherein the amino acid at position 104 in SEQ ID NO: 8 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 9 wherein the amino acid at position 105 in SEQ ID NO: 9 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 10 wherein the amino acid at position 103 in SEQ ID NO: 10 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 11 wherein the amino acid at position 103 in SEQ ID NO: 11 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 12 wherein the amino acid at position 110 in SEQ ID NO: 12 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 13 wherein the amino acid at position 110 in SEQ ID NO: 13 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 14 wherein the amino acid at position 101 in SEQ ID NO: 14 is substituted by another amino acid,

an amino acid sequence SEQ ID NO: 15 wherein the amino acid at position 109 in SEQ ID NO: 15 is substituted by another amino acid,

or an amino acid sequence SEQ ID NO: 16 wherein the amino acid at position 127 in SEQ ID NO: 16 is substituted by another amino acid, and function-conservative variants thereof.

3. The polypeptide according to claim 1, wherein the amino acid substituted by another amino acid is substituted by any amino acid excepting proline.

4. A kit of parts comprising at least one CSN5 polypeptide according to claim 1 or a fragment thereof and at least one CSN6 polypeptide or a fragment thereof.

5. A nucleic acid encoding for a polypeptide according to claim 1.

6. A vector comprising the nucleic acid according to claim 5.

7. A host cell, which has been transformed by the nucleic acid according to claim 5.

8. A method of screening therapeutic agents comprising the steps of:

i) providing a CSN5 polypeptide according to claim 1 or a fragment thereof,

ii) providing at least one CSN5 isopeptidase substrate,

iii) providing a candidate agent,

iv) measuring the binding of the substrate using appropriate biophysical techniques and measuring the activity of the CSN5 polypeptide,

v) and positively selecting candidate agents that modulates CSN5 activity.

9. A method of screening therapeutic agents comprising the steps of:

i) providing a CSN5 polypeptide selected from the group consisting of SEQ ID NO: 1-16, or a CSN5 polypeptide according to claim 1 or a fragment thereof,

ii) providing a CSN6 polypeptide or a fragment thereof,

iii) providing at least one CSN5 isopeptidase substrate,

iv) providing a candidate agent,

v) measuring the binding of the substrate using appropriate biophysical techniques and measuring the activity of the CSN5 polypeptide,

vi) and positively selecting candidate agents that modulates CSN5 activity.

10. A method of screening therapeutic agents comprising the steps of:

i) providing a CSN5 polypeptide according to claim 1 or a fragment thereof,

ii) providing a candidate agent,

iv) measuring the binding of the candidate agent to the CSN5 polypeptide using appropriate biophysical techniques,

v) and positively selecting candidate agents that bind to the CSN5 polypeptide.