# Patent

## Title
Methods for treating pain by inhibition of the SCN9A channel

## Abstract

The present invention relates to the discovery that mutations in SCN9A are causative of Congenital Indifference to Pain (CIP) in humans. The invention also relates to methods of utilizing the SCN9A gene and expression products thereof for the screening and identification of therapeutic agents, including small organic compounds, which are selective for SCN9A, and are useful in the treatment of pain and other disorders. The invention also relates to methods of using these compounds to treat or otherwise ameliorate such disorders.

## Background
This application is a divisional of U.S. application Ser. No. 10/369,909, filed 19 Feb. 2003 now U.S. Pat. No. 7,659,082, which claims priority of U.S. Provisional Application No. 60/357,964, filed 19 Feb. 2002, and 60/429,836, filed 26 Nov. 2002, the disclosures of all of which are hereby incorporated by reference in their entirety.


FIELD OF THE INVENTION
The present invention relates to the discovery that mutations in SCN9A are causative of Congenital Indifference to Pain in humans. The invention also relates to methods of utilizing the SCN9A gene and expression products thereof for the screening and identification of therapeutic agents, including small organic compounds, which are selective only for SCN9A, and are useful in the treatment of pain. The invention also relates to methods of using these compounds to treat or otherwise ameliorate pain.
BACKGROUND OF THE INVENTION
This invention is concerned with a hereditary pain disorder known as “Congenital Indifference To Pain” (also referred to herein “C-I-P”). It is an extremely rare but interesting medical condition. It is an autosomal recessive disorder that interferes with the normal perception of pain (see, Landrieu, P. S. G., and Allaire, C. Ann. Neurology, 27 (5):574-58 (1990) and Comings D E and Amromin G D, 1974. Neurology. September; 24(9):838-48.)
The description of the condition is fascinating. Patients are essentially completely indifferent to sensations that would cause pain in most individuals; yet at the same time they are quite able to distinguish between other sensations, such as thermal (hot/cold) and tactile (sharp/dull) sensations. Tendon reflex and vibration recognition is normal. Patients do not perceive inflammatory pain or dental pain even though there is a normal flare response to intradermal histidine injection, indicating that the peripheral arc reflex is intact. (Landrieu et al, 1990) A general description of C-I-P can be found at Online Mendelian Inheritance in Man (OMIM) reference *243000.
It is highly intriguing that the genetic mutation that underlies this disorder has such a specific and selective medical consequence. The inventors recognize that identification of the mutant gene which is associated with the disorder will provide a therapeutic target against which novel therapeutic agents can act. The inventors recognize that therapeutic agents which are highly selective for this therapeutic target, if they can be designed to mimic the effect of the mutation, have the potential to induce the same kind of analgesia, in the general population, as experienced by C-I-P patients.
It thus serves to examine in detail the physiological consequences of C-I-P. One C-I-P patient (3 years old, female) had no pain sensation but had normal thermal and tactile sensation and deep sensation. She appeared normal physically, although having tissue damage presumably resulting from the disorder, such as a shorter tongue, lack of some fingertips and multiple scars on fingers due to old burns. She learned to walk at 18 months (somewhat delayed). (Guillermo A. and A. Grinspan, “Congenital indifference to pain, a propos of a case with antecedents of consanguinity”. Rev Neurol (Paris), 1970. 123(6): 434-5). In a follow up examination at age 34, patient appeared normal. Intelligence was normal. A broken bone not identified by the patient had resulted in an orthopedic deformity. Patient had a dental prosthesis. Sweating was normal. Tendon reflex and vibration recognition was normal. Position sense was normal. Patient was able to discriminate between “hot and cold” and between “sharp and dull” but discrimination between “touch” and “pinprick” was attenuated. Her maternal grandfather and her paternal grandmother were first cousins who had a common cousin who was apparently indifferent to pain. This consanguinity is in support of autosomal recessive inheritance.
Sweating, blood pressure and other autonomic responses are quite normal. No histological abnormalities are present in the peripheral nerves. (see Comings et al (1974) and Hirsch E, Moye D, Dimon J H 3rd. South Med J, 88(8):851-857 (1995)).
Still, to date, no genes or genetic loci responsible for C-I-P have been reported. Karyotype analysis of one C-I-P patient appeared normal. (Amguerra-Escobio, 2001, unpublished observations). One of the confusing aspects that has prevented identification of genes in the past is that there are other patients who have other hereditary pain disorders which have not been properly distinguished from autosomal recessive C-I-P. This makes it significantly harder to identify the common underlying genetic cause of the disorder.
For example, there are autosomal dominant and sporadic cases of congenital indifference to pain. The inventors believe that many of these cases have a different genetic basis than autosomal recessive C-I-P. Reports of these cases may be found at Becak et al, Acta Genet. Statist. Med. 14:133-142 (1964); Comings et al (1974); Landrieu et al, 1990).
Further, there is a very different from of the disease known as Hereditary Sensory and Autonomic Neuropathy (HSAN). HSAN is the classic “insensitivity” to pain. It has been classified into types I-V (Reilly, M. M. 1998. J. Neurol 245(1):6-13). Each of these conditions is linked to an inherited neuropathy of sensory nerves. Some of these conditions have been linked to genes or genetic loci, however, none of these are believed to correspond to the genetic basis underlying C-I-P.
It should be recognized that “insensitivity” and “indifference” are often used interchangeably in the art, but that they should be properly distinguished for better understanding of the pathology of the disorder. The term “insensitivity” refers to situations in which sensory pathways are altered leading to lack of painful sensation while “indifference” refers to situations wherein the sensory pathway appears normal but there is a lack of reaction to a painful stimulus. The key distinction between these groupings is that the former are inherited neuropathies in which neuropathy is the primary part of the disease and the sensory pathway is the sole or primary part of the neuropathy, whereas in the latter, the sensory pathway appears, at a microscopic and macroscopic level, to be intact and normal. (Comings et al 1974)
Because this invention is directed towards genes, proteins and other tools which are targets for analgesic agents, an additional area of relevant background relates to existing analgesic agents and their therapeutic targets, where known.
Therapeutic agents for treatment of pain fall into two main classes—the NSAIDs (non-steroidal anti-inflammatory drugs) and the opioids. NSAIDs treat pain in a way similar to the mechanism of aspirin, the most well-known and oldest member of the class. Common NSAIDs include acetaminophen, ibuprofen and naproxen. These drugs mainly inhibit the body's ability to synthesize prostaglandins. The common mechanism of action for all NSAIDs is the inhibition of the enzyme cyclooxygenase (COX). A major commercial success has been achieved with specific inhibitors of COX-2, such as CelebrexTM from Pharmacia/Pfizer, and VioxxTM from Merck & Co. The recently launched BextraTM from Pharmacia/Pfizer, which is highly selective for inhibition of COX-2 over COX-1, is also expected to become commercial success.
Opioids act through the opioid receptor family. These drugs include the weak opioids such as codeine and Tylenol 3, and strong opioids such as morphine and methadone. Some are long acting, others are of short duration. Opioid analgesics have a tendency to addiction and dependency, and so are not ideal for long-term or chronic pain management.
Outside of the NSAIDs and opiods, there are a number of other suggested analgesic agents in clinical trials (i.e. not yet approved for marketing) which are believed to have alternative targets. Some clinical trials are attempting to establish that central neuropathic pain may respond to ion channel blockers such as blockers of calcium, sodium and/or NMDA (N-methyl-D-aspartate) channels. For example, in development are low affinity NMDA channel blocking agents for the treatment of neuropathic pain. The literature provides substantial pre-clinical electrophysiological evidence in support of the use of NMDA antagonists in the treatment of neuropathic pain. Such agents also may find use in the control of pain after tolerance to opioid analgesia occurs, particularly in cancer patients.
In accordance with the present invention, the identification of the hereditary basis for Congenital Indifference To Pain will be a key step for developing novel therapeutic agents because it has the potential to be a novel therapeutic target. This therapeutic target can be used to identify and discover more effective analgesics. Discovery of the target will also provide new methods and compositions for diagnosis of C-I-P and for distinguishing between types of inherited pain disorders.
BRIEF SUMMARY OF THE INVENTION
The present invention relates to the discovery that the human gene SCN9A (also known as Nav 1.7) when mutated, results in congenital indifference to pain.
In one aspect, the invention relates to the nucleic acid sequence for SCN9A, including the genomic sequence, mRNA or cDNA, polymorphic, allelic, isoforms (adult, neo-natal, etc.) and mutant forms thereof, and nucleic acid constructs of the gene, including vectors, plasmids and recombinant cells and transgenic organisms containing SCN9A (or knock-outs thereof). Such nucleic acid sequences are set forth in SEQ. ID Nos. 1, 3, 5, 7, 9, 11, 13, 14, 15, 17, 19.
In another aspect, the invention relates to the gene product of SCN9A, including the polypeptide, protein, and amino acid sequence, and the polymorphic, allelic, isoforms (adult, neo-natal, etc.) and mutant forms thereof, and recombinant cells and transgenic organisms wherein this polypeptide is expressed. Such amino acid sequences are set forth in SEQ. ID Nos. 2, 4, 6, 8, 10, 12, 16, 18, 20.
In one aspect of the present invention, the SCN9A gene or protein is incorporated into a screening assay whereby compounds (potential therapeutic agents) are tested to determine if they modulate SCN9A gene expression or SCN9A protein activity, thereby identifying potential therapeutic agents.
Thus, in one aspect the present invention relates to a method for identifying an agent that modulates the activity of a polynucleotide whose expression contributes to pain sensation or whose non-expression contributes to lack of pain sensation, comprising:
a) contacting under physiological conditions a chemical agent with a polynucleotide corresponding to a promoter of the SCN9A gene, preferably having the sequence of SEQ. ID NO. 14, under conditions promoting such contacting; and
b) detecting a change in the expression of said polynucleotide as a result of said contacting;
thereby identifying an agent that modulates said polynucleotide activity.
Such modulation is preferably a decrease in expression. In preferred embodiments, such expression is measured by measuring the amount of an expression product encoded by said polynucleotide, most preferably an RNA or a polypeptide. In a preferred embodiment the promoter sequence is operably linked to a reporter gene, and the assay measures relative expression of the reporter gene or its gene product.
In preferred embodiments, the polynucleotide whose expression is to be measured or monitored is present in an intact cell, preferably a mammalian cell, most preferably a neuronal cell, and may include a recombinant cell. In preferred embodiments, such an intact cell is a cell that has been engineered to comprise said polynucleotide, such as by genetic engineering, most preferably wherein the cell does not express the subject gene or polynucleotide absent having been engineered to do so.
In another aspect, the present invention relates to a method for identifying an agent that modulates the activity of a polypeptide encoded by a polynucleotide as disclosed herein, comprising:
a) contacting under physiological conditions a chemical agent with a polypeptide encoded by a polynucleotide corresponding to a SCN9A gene, preferably having the sequence of SEQ. ID NO. 1, 3, 5, 15, 17, 19; and
b) detecting a change in the activity of said polypeptide as a result of said contacting;
thereby identifying an agent that modulates said polypeptide activity.
In a preferred embodiment, the observed change in activity in step (b) is a decrease in activity, most preferably wherein said change in activity is the result of binding to or interacting with said polypeptide by said chemical agent of step (b), especially where the polypeptide is an ion channel, and the ion channel is selectively blocked by said binding. In a further preferred embodiment, the polypeptide is a sodium channel, and said blocking is voltage dependent.
In additional preferred embodiments, the polypeptide is part of a lipid bilayer, such as an intact cell, preferably a mammalian cell, such as a neuronal cell, most preferably a recombinant cell. In one such embodiment, a cell that has been engineered to comprise said polypeptide, including by genetic engineering, especially where the cell does not possess the polypeptide absent said engineering.
In one preferred embodiment of such method, the polypeptide is a polypeptide that reacts with an antibody that is specific for a polypeptide having the amino acid sequence of SEQ ID NO: 2, 4, 6, 16, 18, or 20. In another preferred embodiment, the polypeptide has an amino acid sequence at least 95% identical to, more preferably at least 98% identical to, the sequence of SEQ ID NO: 2, 4, 6, 16, 18, or 20. Alternatively, in the polypeptide the difference in the amino acid sequence from SEQ ID Nos. 2, 4, 6, 16, 18, or 20 is due only to conservative amino acid substitutions. In an especially preferred embodiment, the polypeptide has the amino acid sequence of SEQ ID NO: 2, 4, 6, 16, 18, or 20.
In a further aspect, the present invention relates to a method for identifying an analgesic agent, comprising:
a) administering to an animal an agent found to have activity using a method as disclosed herein, and
b) detecting in said animal a decrease in response to a pain stimulus due to said administering,
thereby identifying an analgesic agent.
Preferably, the animal is a mammal, such as a human being. In specific embodiments, the pain stimulus is a heat stimulus and reaction or sensitivity to hot and/or cold may be measured. In another embodiment, an electrical stimulus may be used. In all cases, the stimulus may be represented as a sharp or dull sensation.
In a preferred embodiment of the invention, the compound identified which modulates SCN9A gene expression or SCN9A polypeptide activity is selective for SCN9A as opposed to other sodium channel alpha subunits (i.e. SCN1A to SCN8A, SCN10A to SCN12A). Such selectivity of modulation is preferably at least 10%, 50%, 100%, 10 times, 20 times, 100 times, 1000 times, 10,000 times or higher for SCN9A over any other sodium channel alpha subunit. Alternatively, a compound which is selective for SCN9A may not demonstrate an absolute preference for SCN9A, but the compound may show a preference for modulating SCN9A compared to any other sodium channel which preference is greater than any other known compound.
In a further aspect, the present invention relates to a method for treating a condition in an animal afflicted with a source of chronic pain comprising administering to said animal an effective amount of an analgesic agent first identified by an assay method of the invention. Preferably, said animal is a human patient, such as a patient afflicted with a chronic ailment, such as cancer or chronic back pain.
In a further aspect, the compounds identified by the assays disclosed herein, and the methods of treating patients with such compounds, are applied to alternative or additional indications beyond analgesia, including for anesthesia, treating epilepsy, stroke and any other disorder treatable by modulating sodium channel activity.
In another aspect, the present invention relates to a method for producing a product comprising identifying an agent according to the process of the invention wherein said product is the data collected with respect to said agent as a result of said process and wherein said data is sufficient to convey the chemical structure and/or properties of said agent.
In another aspect, the present invention relates to diagnostic and pharmacogenomic compositions, kits and methods which identify the presence or absence in a patient of one or more mutations in a polynucleotide or a polypeptide corresponding to SEQ ID Nos. 1-6 and 13-20, including those specific mutations identified at SEQ ID Nos 7-12.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the pedigree for a family designated CIP-10 showing family relationships and haplotypes. Squares and circles represent males and females, respectively. Filled symbols indicate individuals with CIP. Symbols with an “N” indicate individuals diagnosed as normal, and clear symbols with a question mark indicate individuals who have not been diagnosed
FIG. 2 shows the pedigree for a family designated CIP-14. Symbols as in FIG. 1.
FIG. 3 shows the pedigree for a family designated CIP-08. Symbols as in FIG. 1.
FIG. 4a. Nucleotide sequence of the 5067G>A SCN9A mutation in CIP patient CIP-10-503 (SEQ ID NO: 23). The patient is homozygous for a G>A substitution at nt 5067 (numbered relative to the initiator methionine in Genbank record NM—002977). This corresponds to a change to a stop codon at tryptophan 1689. The wild-type amino acid sequence from an unaffected patient is shown on top (SEQ ID NO: 22) and the wild-type nucleotide sequence as SEQ ID NO: 21. The amino acid sequence for the mutant is given as SEQ ID NO: 24. FIG. 4b. Nucleotide sequence of the 984C>A SCN9A mutation in CIP patient CIP-14-A005 (SEQ ID NO: 27). The patient is homozygous for a C>A substitution at nt 984. This corresponds to a change to a stop codon at tyrosine 328. The wild-type amino acid sequence from an unaffected patient is shown on top (SEQ ID NO: 26) with the wild-type nucleotide sequence above it (SEQ ID NO: 25). The mutant amino acid sequence is SEQ ID NO: 28. FIG. 4c. Nucleotide sequence of the 2488C>T SCN9A mutation in CIP patient CIP-08-11:01 (SEQ ID NO: 31). The patient is homozygous for a C>T substitution at nt 2488. This corresponds to a change to a stop codon at arginine 830. The wild-type sequence from an unaffected patient is shown on top (SEQ ID NO: 30) with the wild-type nucleotide sequence above it (SEQ ID NO: 29). The mutant amino acid sequence is SEQ ID NO: 32.
FIG. 5a. Genomic arrangement of alternatively spliced exon 5N and 5A of the human SCN9A gene. The neonatal (N) and adult (A) isoforms are generated by a mutually exclusive alternative splicing mechanism. The length in base pairs of the introns and exons are shown. FIG. 5b. Formation of SCN9A 5N (neonatal) isoform generated by splicing. FIG. 5c. Formation of SCN9A 5A (adult) isoform generated by splicing. Bent lines indicated portions of the pre-mRNA which are removed to generate the mature mRNA for translation.
FIG. 6. Comparison of the alternatively spliced exons of other sodium channels with the two variants of human SCN9A. The cDNA sequence and the predicted amino acid sequence of the alternatively spliced exon 5 of the A and N isoforms of the human (SEQ ID NO: 33 and 35, respectively) and rabbit (SEQ ID NO: 36 and 37, respectively) SCN9A, human (SEQ ID NO: 42 and 43, respectively) and rat (SEQ ID NO: 44 and 45, respectively) SCN3A, human SCN2A2 (SEQ ID NO: 38 and 39, respectively), and rat (SEQ ID NO: 40 and 41, respectively) SCN2A1 are shown. Isoform-specific differences in the amino acid sequence are indicated below the nucleotide sequence (SEQ ID NO: 34 is the human SCN9A isoform A).
FIG. 7. The proposed transmembrane topography of the first domain of a sodium channel protein. The 30 amino acids specified by these exon 5 variants encode a short extracellular portion of the S3 transmembrane helix, the short extracellular loop between S3 and S4, and most of the S4 transmembrane helix, which is thought to be involved in sensing changes in membrane potential. The + symbols refer to the repeating basic (positively charged) residues within the S4 transmembrane segment. Amino acid 206 of SCN9A is shown as an aspartate residue (A isoforms); it would be an uncharged residue in the N isoforms (i.e. asparagine in SCN9A and SCN2A; and serine in SCN3A).
FIG. 8. Illustration of nucleotide and amino acid sequence of alternative exon 11B. Alternative splice donor sites for exon 11 found in SCN9A isoform are indicated as upstream site and downstream site. Arrow indicates the approximate position of the additional amino acids in the secondary structure of the sodium channel protein.
FIG. 9. Evolutionary conservation of the additional amino acids of Exon 11 B in other members of the sodium channel gene family (SCN9A, SCN1A, SCN8A). Here, the alignment shows human SCN9A (SEQ ID NO: 114), rat SCN9A (SEQ ID NO: 115), mouse SCN9A (SEQ ID NO: 116), rabbit SCN9A (SEQ ID NO: 117), human SCN1A (SEQ ID NO: 118), rat SCN1A (SEQ ID NO: 119), human SCN8A (SEQ ID NO: 120), rat SCN8A (SEQ ID NO: 121) and mouse SCN8A (SEQ ID NO: 122).
FIG. 10. Expression of SCN9A mRNA in various tissues of the central nervous system (CNS) and other organs. A representative gel is shown. To control for difference in the amounts of RNA among samples, pixel density relative to an internal β-actin standard was calculated. The graph shows the results of 3 relative quantitative RT-PCR experiments relative to a dorsal root ganglia (DRG) positive control.



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides a novel therapeutic target related to pain response and methods of using this target to identify useful analgesic agents, as well as methods for treating pain in human patients.
Description of SCN9A
In one aspect, the present invention identifies a gene and its corresponding protein related to pain indifference, one such embodiment being the SCN9A gene. The SCN9A gene and protein may be known to those skilled in the art under a variety of names, including voltage-gated sodium channel type IX alpha polypeptide, neuroendocrine sodium channel, peripheral sodium channel 1, Schwann cell sodium channel, NENA, NE-Na, hNE-Na, hNE, PN1, hPN1, NaS, Nas, Nav1.7, hNav1.7, and Na(v)1.7. Preliminary versions of the cDNA and amino acid sequences are found at GenBank Accession No. NM—002977.1 or XM—011955; The gene is described further at OMIM (On-line Mendelian Inheritance in Man) reference *603415.
The correct wild type nucleic acid sequence of the two isoforms of SCN9A (herein called “neo-natal” and “adult”) is herein provided for the first time. The neo-natal SCN9A nucleic acid sequence is shown in SEQ ID NO: 1 with the correct neo-natal wild type amino acid sequence set forth at SEQ ID NO: 2. Table 1 identifies where the correct wild type sequence of neo-natal SCN9A set forth in SEQ ID NO: 1 diverges from the previously available public sequences of neo-natal SCN9A. The distinction between neo-natal and adult forms is a tentative description based on alternate Exon 5 (i.e. Exon 5N (for neo-natal) and Exon 5A (for adult)) further described, below. A nucleic acid sequence encoding a predicted adult splice variant of SCN9A employing exon 5A is found in SEQ ID NO: 3. The corresponding amino acid sequence of the predicted splice variant of SCN9A employing exon 5A is found in SEQ ID NO: 4. A nucleic acid sequence employing an alternate splice donor site at the end of Exon 11, herein called Exon 11B, is set forth at SEQ ID No. 5. The corresponding amino acid sequence of the predicted splice variant of SCN9A employing Exon 11B is found at SEQ ID No. 6.
The sequences listed in Table 1, shown below, represent SEQ ID NO: 46 to 111, respectively.











TABLE 1





Sequence vari-






ations (num-


Variation in


bered relative


relation to a


to initiator
Exon/
Variation in relation
protein


methionine)
Intron
to a cDNA sequence
sequence





















Differences
26
6182_6185delGATT
not applicable
Public sequence:
AAAAGTGATTGATTCAGTTTTTTG



between all



Correct sequence:
AAAAGTGATTCAGTTTTTTG


samples or ge-


nomic sequence


and Genbank


entry


NM_002977.1


 


Mutations
 8
984C > A
Y328X
More common:
CAGAGGGGTACACCTGTGTGA






Less common:
CAGAGGGGTAAACCTGTGTGA


 



15
2488C > T
R830X
More common:
CTTTTAGCTCCGAGTCTTCAA






Less common:
CTTTTAGCTCTGAGTCTTCAA


 



26
5067G> A
W1689X
More common:
CTGCTGGCTGGGATGGATTGC






Less common:
CTGCTGGCTGAGATGGATTGC


 


Polymorphisms
 1
174A > G
not applicable
More common:
CTGGCAAACAACTGCCCTTCA






Less common:
CTGGCAAACAGCTGCCCTTCA


 



 3
444G > A
not applicable
More common:
TGAATAACCCGCCGGACTGGA






Less common:
TGAATAACCCACCGGACTGGA


 



 9
1119C > T
not applicable
More common:
CGCTGCGTGCCGCTGGCAAAA






Less common:
CGCTGCGTGCTGCTGGCAAAA


 



 9
1266G > A
not applicable
More common:
AAGAATTAGAGTTTCAACAGA






Less common:
AAGAATTAGAATTTCAACAGA


 



 9
1287A > T
not applicable
More common:
TGTTAGACCGACTTAAAAAAG






Less common:
TGTTAGACCGTCTTAAAAAAG


 



18
3448C > T
R1150W
More common:
GTTGTGTACGGAGGTTCTC






Less common:
GTTGTGTATGGAGGTTCTC


 



26
4779G > T
not applicable
More common:
CGTATTTTGTGTCCCCTACCC






Less common:
CGTATTTTGTTTCCCCTACCC


 



Intron 2
377 + 93_94delTGlnsGA
not applicable
More common:
TTTGCACCTTTGAAGACTCTGG






Less common:
TTTGCACCTTGAAAGACTCTGG


 



Intron 2
378 − 90A > T
not applicable
More common:
ATTTTTTTCTAAGGAAAAGTT






Less common:
ATTTTTTTCTTAGGAAAAGTT


 



Intron 3
478 − 219T > C
not applicable
More common:
ATATTCTTAGTTATTTCAAGT






Less common:
ATATTCTTAGCTATTTCAAGT


 



Intron 4
596 + 25T > C
not applicable
More common:
CTTTTTGAAATGGCAAATTTA






Less common:
CTTTTTGAAACGGCAAATTTA


 



Intron 4
596 + 591T > G
not applicable
More common:
TCAGAAAAATTGATTTTTACA






Less common:
TCAGAAAAATGGATTTTTACA


 



Intron 6
902 − 118T > C
not applicable
More common:
GGATGCATATTGCCTGGGACC






Less common:
GGATGCATATCGCCTGGGACC


 



Intron 8
1107 + 41A > G
not applicable
More common:
TTTGAATGGCATATGTACCTG






Less common:
TTTGAATGGCGTATGTACCTG


 



Intron 8
1107 + 48T > C
not applicable
More common:
GGCATATGTATCTGGTGTATG






Less common:
GGCATATGTACCTGGTGTATG


 



Intron 9
1314 + 76C > T
not applicable
More common:
GCGGTATATGCTTGGCCTTCT






Less common:
GCGGTATATGTTTGGCCTTCT


 



Intron 9
1314 + 199C > T
not applicable
More common:
CCCATAATCACCTCACTGCAT






Less common:
CCCATAATCATCTCACTGCAT


 



Intron 10
1603 − 388T > C
not applicable
More common:
TTTGTGAAGCTTGGGGATTGA






Less common:
TTTGTGAAGCCTGGGGATTGA


 



Intron 11
c.1942 − 2_3insT
not applicable
More common:
ATTTTTTTTTTAGGGCACGACC






Less common:
ATTTTTTTTTTTAGGGCACGACC


 



Intron 12
2072 − 14T > C
not applicable
More common:
ATGTTCTCTGTTTTTTTCTCC






Less common:
ATGTTCTCTGCTTTTTTCTCC


 



Intron 19
3769 − 70T > C
not applicable
More common:
TAGTGAGTTTTAGAATTGACT






Less common:
TAGTGAGTTTCAGAATTGACT


 



Intron 19
3769 − 4A > G
not applicable
More common:
TGTTATTTTTATAGGTTTCTT






Less common:
TGTTATTTTTGTAGGTTTCTT


 



Intron 21
4173 + 58_59delAA
not applicable
More common:
CGAAGGATATAAGTTATTCTTT






Less common:
CGAAGGATATGTTATTCTTT


 



Intron 21
4173 + 77C > A
not applicable
More common:
TTTAAATAGTCTATTAATTAT






Less common:
TTTAAATAGTATATTAATTAT


 



Intron 21
4174 − 146insA
not applicable
More common:
TTTAAAAAAATCTTTACATT






Less common:
TTTAAAAAAAATCTTTACATT


 



Intron 21
4174 − 196A > G
not applicable
More common:
ATAATTAACTAGGACTAAGAT






Less common:
ATAATTAACTGGGACTAAGAT


 



Intron 23
4365 + 99A > G
not applicable
More common:
TTCATGATTAATTTTATTAGA






Less common:
TTCATGATTAGTTTTATTAGA


 



Intron 23
4366 − 13_14insGTTT
not applicable
More common:
TTTTTTGTTTCTTTACCTTG






Less common:
TTTTTTGTTTGTTTCTTTACCTTG


 



Intron 25
4741 + 16A > T
not applicable
More common:
AATATTTATTATTCAGATTTT






Less common:
AATATTTATTTTTCAGATTTT









The present invention further provides at SEQ ID No. 7, a first mutation in the gene encoding this protein found in a first family (CIP-10) at G5067A (herein shown in the 5N/11 isoform, although 5A and 11B isoforms are also expected at different developmental stages). The mutation results in a truncation described as W1689X (SEQ ID NO: 8). The present invention also provides a second mutation in the gene encoding SCN9A which is responsible for congenital indifference to pain in a different family (CIP-14). The nucleic acid sequence of this second mutation, C984A, is set out in SEQ ID NO: 9 (herein shown in the 5N/11 isoform) and the corresponding mutant protein, Y328X, is described in SEQ ID NO: 10. The present invention also provides a third mutation in the gene encoding SCN9A which is responsible for congenital indifference to pain in a third family (CIP-08). The nucleic acid sequence of this second mutation, C2488T, is set out in SEQ ID NO: 11 (herein shown in the 5N/11 isoform) and the corresponding mutant protein, R830X, is described in SEQ ID NO: 12.
This invention also provides human BAC clone RP11-437H3 (AC108146) which carries the complete human genomic fragment bearing the SCN9A gene. This BAC may be obtained commercially from well known sources. A short part of this BAC bearing the nucleotide sequence from the 3′ end of exon 4 to the 5′ end of exon 6, including exon 5A and exon 5N, is set forth at SEQ ID No. 13. The promoter region of SCN9A, including both genomic sequence and the 5′UTR of SCN9A is set forth at SEQ ID No. 14.
This invention also provides SCN9A from mouse (M. musculus) and various isoforms in Table 2 below.







TABLE 2







Isoforms of Mouse SCN9A disclosed








SEQ ID No.
Mouse SCN9A isoform





15
Mouse 11B nt


16
Mouse 11B a.a.


17
Mouse 5A nt


18
Mouse 5A a.a.


19
Mouse 5N nt


20
Mouse 5N a.a.









Thus the invention thus discloses several novel isoforms and mutants of human and mouse SCN9A.
In aspects of the invention relating to the use of SCN9A, such as in screening assays, or for the development of antibodies, etc., etc., the inventors recognize that those skilled in the art may prefer to use forms of SCN9A corresponding to the sequences disclosed herein, although not necessarily the same. For example, screening assays may utilize SCN9A from a different organism, preferably a vertebrate, and most preferably from a mammalian species. The shared technical features of these forms of SCN9A, are that, when expressed, they have sodium channel activity, and that they share functional similarity with SCN9A, such as may be determined by those skilled in the art. Thus the invention encompasses the use of, for example, sheep, dog or horse SCN9A, for the same purposes as set out more specifically herein for human or mouse SCN9A.
As used herein, the term “correspond” means that the gene has the indicated nucleotide sequence or that it encodes the same RNA as would be encoded by the indicated sequence, including splice variants thereof.
Because of the processing that may take place in transforming the initial RNA transcript into the final mRNA, the sequences disclosed herein may represent less than the full genomic sequence. They may also represent sequences derived from alternate splicing of exons, ribosomal and/or transfer RNAs. Consequently, the genes present in the cell (and representing the genomic sequences) and the sequences disclosed herein, which are mostly cDNA sequences, may be identical or may be such that the cDNAs contain less than the full genomic sequence. Such genes and cDNA sequences are still considered corresponding sequences because they both encode similar RNA sequences. Thus, by way of non-limiting example only, a gene that encodes an RNA transcript, which is then processed into a shorter mRNA, is deemed to encode both such RNAs and therefore encodes an RNA complementary to (using the usual Watson-Crick complementarity rules), or that would otherwise be encoded by, a cDNA (for example, a sequence as disclosed herein). (Those skilled in the art understand that the word “encode” and its derivatives mean, in this field “can be transcribed into”.) Thus, the sequences disclosed herein correspond to genes contained in the cells and are used to determine relative levels of expression because they represent the same sequences or are complementary to RNAs encoded by these genes. Such genes also include different alleles and splice variants that may occur in the cells used in the processes of the invention.
Thus, the polynucleotides, such as the genes disclosed herein, for use in the screening assays of the invention “correspond to” the polynucleotide encoding SCN9A mRNA (processed or unprocessed, including naturally occurring splice variants and alleles) at least 60%, preferably at least 70%, even more preferably at least 80%, or even at least 85%, most preferably at least 90%, or even at least 95%, or most especially at least 98%, with the especially preferred embodiment of identical to, and especially having the sequence of, an RNA that would be encoded by, or be complementary to, such as by hybridization under reasonably stringent conditions, with a SCN9A polynucleotide (SEQ ID NO: 1). In addition, sequences encoding the same polypeptides and proteins as any of these sequences, regardless of the percent identity of such sequences, are also specifically contemplated by any of the methods of the present invention that rely on any or all of said sequences, regardless of how they are otherwise described or limited. Thus, any such sequences are available for use in carrying out any of the methods disclosed according to the invention. Such sequences also include any open reading frames, as defined herein, present within an SCN9A polynucleotide.
As used herein, the term “percent identity” or “percent identical,” when referring to a sequence, means that a sequence is compared to a claimed or described sequence after alignment of the sequence to be compared (the “Compared Sequence”) with the described or claimed sequence (the “Reference Sequence”). The Percent Identity is then determined according to the following formula:

Percent Identity=100[1−(C/R)]

wherein C is the number of differences between the Reference Sequence and the Compared Sequence over the length of alignment between the Reference Sequence and the Compared Sequence wherein (i) each base or amino acid in the Reference Sequence that does not have a corresponding aligned base or amino acid in the Compared Sequence and (ii) each gap in the Reference Sequence and (iii) each aligned base or amino acid in the Reference Sequence that is different from an aligned base or amino acid in the Compared Sequence, constitutes a difference; and R is the number of bases or amino acids in the Reference Sequence over the length of the alignment with the Compared Sequence with any gap created in the Reference Sequence also being counted as a base or amino acid.

If an alignment exists between the Compared Sequence and the Reference Sequence for which the percent identity as calculated above is about equal to or greater than a specified minimum Percent Identity then the Compared Sequence has the specified minimum percent identity to the Reference Sequence even though alignments may exist in which the hereinabove calculated Percent Identity is less than the specified Percent Identity.
As used herein, the terms “portion,” “segment,” and “fragment,” when used in relation to polypeptides, refer to a continuous sequence of nucleotide residues, sequence forms a subset of a larger sequence. Such terms include the products produced by treatment of said polynucleotides with any of the common endonucleases, or any stretch of polynucleotides that could be synthetically synthesized. These may include exonic and intronic sequences of the corresponding genes.
Identification of SCN9A Modulating Agents
The present invention readily affords different means for identification of SCN9A modulating agents which are useful as therapeutic agents. One such protocol involves the screening of chemical agents for ability to modulate the activity of SCN9A thereby identifying an SCN9A modulating agent. SCN9A modulating agents so identified are then tested in a variety of in vivo models so as to determine if they alleviate pain, especially chronic pain or other disorders. In a preferred embodiment the agent modulates the activity of SCN9A downwards.
Thus, in one aspect the present invention relates to a method for identifying an agent that modulates the activity of a polynucleotide whose expression contributes to pain sensation or whose non-expression contributes to lack of pain sensation, comprising:
a) contacting under physiological conditions a chemical agent with a polynucleotide corresponding to a promoter of the SCN9A gene, preferably having the sequence of SEQ. ID NO. 14, under conditions promoting such contacting; and
b) detecting a change in the expression of said polynucleotide as a result of said contacting;
thereby identifying an agent that modulates said polynucleotide activity.
Such modulation is preferably a decrease in expression. In preferred embodiments, such expression is measured by measuring the amount of an expression product encoded by said polynucleotide, most preferably an RNA or a polypeptide. In a preferred embodiment the promoter sequence is operably linked to a reporter gene, and the assay measures relative expression of the reporter gene or its gene product.
In preferred embodiments, the polynucleotide whose expression is to be measured or monitored is present in an intact cell, preferably a mammalian cell, most preferably a neuronal cell, and may include a recombinant cell. In preferred embodiments, such an intact cell is a cell that has been engineered to comprise said polynucleotide, such as by genetic engineering, most preferably wherein the cell does not express the subject gene or polynucleotide absent having been engineered to do so.
Agents that alter the activity of SCN9A or active fragments or portions of said gene, or that may modulate the activity of polypeptides encoded by SCN9A, or polypeptides that act as transcription factors to modulate the activity of such genes, or other related gene segments, such as enhancers or other regulatory genetic elements that modulate the activity of SCN9A, acting either in cis or trans fashion, are thereby identified and may prove useful in treating chronic and other types of pain. Related genes might include those with high sequence homology, perhaps at least 98%, to the sequences disclosed herein and would, preferably, have sequences identical to the sequences disclosed herein.
In another aspect, the present invention relates to a method for identifying an agent that modulates the activity of a polypeptide encoded by a polynucleotide as disclosed herein, comprising:
a) contacting under physiological conditions a chemical agent with a polypeptide encoded by a polynucleotide corresponding to a SCN9A gene, preferably having the sequence of SEQ. ID NO. 1, 3, 5, 15, 17, 19; and
b) detecting a change in the activity of said polypeptide as a result of said contacting;
thereby identifying an agent that modulates said polypeptide activity.
In a preferred embodiment, the observed change in activity in step (b) is a decrease in activity, most preferably wherein said change in activity is the result of binding to or interacting with said polypeptide by said chemical agent of step (b), especially where the polypeptide is an ion channel, and the ion channel is blocked by said binding. In a further preferred embodiment, the polypeptide is a sodium channel, and said blocking is voltage dependent. A preferred therapeutic agent may be an irreversible binding agent or it may be a reversible binding agent.
In additional preferred embodiments, the polypeptide is part of a lipid bilayer, such as an intact cell, preferably a mammalian cell, such as a neuronal cell, most preferably a recombinant cell. In one such embodiment, a cell that has been engineered to comprise said polypeptide, including by genetic engineering, especially where the cell does not possess the polypeptide absent said engineering.
In another embodiment, the polypeptide is part of a cell, tissue, cell-line, immortalized cell or the like, which carries the gene and that expresses it, either naturally or upon induction. In this embodiment, the expressed gene is non-recombinant. As a non-limiting example, the PC-12 cell line derived from a transplantable rat pheochromocytoma responds reversibly to nerve growth factor (NGF) by induction of the neuronal phenotype and SCN9A expression. See Toledo-Aral J J, et al. Proc Natl Acad Sci USA. 1997 Feb. 18; 94(4):1527-32.
In one preferred embodiment of such method, the SCN9A polypeptide is a polypeptide corresponding to a polypeptide having the amino acid sequence of SEQ ID NO: 2, 4, 6, 16, 18, or 20.
Thus, the present invention specifically contemplates embodiments in which the cell is engineered by other than genetic engineering, such as where the activity of a polypeptide is to be enhanced and the cell has been engineered to contain, or have on its surface, said polypeptide but wherein the polypeptide is present due to physical insertion of the polypeptide into the membrane or cytoplasm of the cell and not through expression of a gene contained in the cell. Such engineering includes direct insertion of the polypeptide into the lipid bilayer, such as where a lipid bilayer comprising the polypeptide is fused to a membrane, such as that of an intact cell, resulting in the cell membrane comprising the polypeptide. Methods well known in the art, such as use of polyethylene glycol, viruses, and the like, are available to effect such insertions and the details of such procedures need not be further described herein.
In one preferred embodiment of such method, the polypeptide is a polypeptide that reacts with an antibody that reacts with, or is specific for, a polypeptide having an amino acid sequence at least 95% identical to, more preferably at least 98% identical to, the sequence of SEQ ID NO: 2 and where any difference in amino acid sequence is due only to conservative amino acid substitutions. In an especially preferred embodiment, the polypeptide has the amino acid sequence of SEQ ID NO: 2.
In a further aspect, the present invention relates to a method for identifying an analgesic agent, comprising:
a) administering to an animal an agent found to have activity using an assay or screening method as disclosed herein, and
b) detecting in said animal a decrease in response to a pain stimulus following said administering and due thereto,
thereby identifying an analgesic agent.
Preferably, the animal is a mammal, such as a human being. In specific embodiments, the pain stimulus is a heat stimulus and reaction or sensitivity to hot and/or cold may be measured. In another embodiment, an electrical stimulus may be used. In all cases, the stimulus may be represented as a sharp or dull sensation. In some cases, the animal may otherwise react normally to such stimulus so that a decrease in normal response due to the test agent is being measured whereas in other cases the animal may initially possess a heightened sensitivity to the stimulus prior to administering the test agent. In all cases, observation of an analgesic effect need not necessarily involve a reduced sensitivity or response to pain but may involve simply a reduced sensation of a particular stimulus. The analgesics identified by the methods of the invention may induce general analgesia in an animal or may have more localized analgesic or anesthetic effects.
Further embodiments of the assays useful for identifying modulators of SCN9A are set out further below in this specification.
Selectivity for SCN9A Over Other Sodium Channels
The present invention specifically contemplates the identification of chemical agents, especially small organic molecules, that inhibit the expression of an SCN9A gene or the activity of an SCN9A polypeptide, with high specificity and/or selectivity and that have limited effect on other sodium channel genes and/or expression products. The inventors recognize on the basis of their discovery that selective inhibition of SCN9A as opposed to any of the other sodium channels leads to the therapeutically desirable outcomes observed in C-I-P. Because the other sodium channels are implicated in other essential physiological processes, such as heart activity, muscle contraction, and various neurological processes, it is highly desirable to avoid modulation of these other sodium channels.
This invention thus sets forth, for the first time, a scientifically justified rationale for the pursuit and discovery of sodium channel blockers which are highly selective for SCN9A for use as analgesics and to induce other symptomatic responses observed in C-I-P. The invention herein provides a solution to the problems posed in Anger et al. (2001. J. Med. Chem. 44(2):115-137) about the lack of information concerning which sodium channel sub-type to pursue and about the significant uncertainty in the art regarding the extent of selectivity required.
Also, by identifying SCN9A as the therapeutic target of choice in humans, the invention overcomes prior art teachings which suggested, but did not prove, that SCN9A may be involved in essential bodily functions such as bladder control and temperature control. SCN9A was believed to be the primary sodium channel of unmyelinated sensory and autonomic nerve cells. This prior art work led the field to believe that SCN9A was to be avoided as a target for therapeutic modulation because such modulation would negatively effect these essential bodily functions. However, the instant invention teaches, for the first time, that in humans, modulation of SCN9A can provide a highly desirable result, namely the treatment of pain, evidently without other physiological or autonomic impacts.
Thus, in a preferred embodiment of the invention, the compound identified which modulates SCN9A gene expression or SCN9A polypeptide activity is selective for SCN9A as opposed to other sodium channel alpha subunits (i.e. SCN1A to SCN8A, SCN10A to SCN12A). Such selectivity of modulation is preferably at least 10%, 50%, 100%, 10 times, 20 times, 100 times, 1000 times, 10,000 times or higher for SCN9A over any other sodium channel alpha subunit. Alternatively, a compound which is selective for SCN9A may not demonstrate an absolute preference for SCN9A, but the compound may show a preference for modulating SCN9A compared to any other sodium channel which preference is greater than any other prior art sodium channel blocker.
In another preferred embodiment, the methods disclosed herein for identifying an agent that modulates, preferably inhibits, expression or activity of a gene or polypeptide corresponding to SCN9A comprise first identifying such agent and then testing such agent for effects on expression or activity of at least one other sodium channel gene or polypeptide, as the case may be, preferably at least two other such genes, or polypeptides, with little or no effect. A preferred compound identified herein normally demonstrates no more than 25% of the effect that any compound heretofore measured has on the other sodium channel gene and/or polypeptide, preferably no more than 10% of such activity, most preferably no more than 5% of such activity and especially exhibiting no more than 1% of such activity. In such cases, the activity may be measured as the rate at which sodium ions are transported under the actions of the polypeptide or the amount of RNA expressed by said gene, especially on a weight-to-weight basis, or the nanomole ratio of RNA products produced by transcription of the gene.
Thus, the agents contemplated by the present invention are highly selective for the SCN9A gene or protein and administration of such an agent to a human or other animal in need thereof generates a temporary condition which mimics the Congenital Indifference to Pain phenotype to the highest degree possible, or aspects thereof. For example, it mimics the effects of one or more of the mutated forms of the gene as disclosed herein. In a preferred embodiment, the agent generates indifference to pain, but does not diminish sensations which are available to patients with CIP, such as but not limited to heat/cold sensing, pressure sensing, sharp/dull sensations, and does not diminish physiological responses such as sweating, heart rate, muscle activity and the like. For example, indifference to pain without any concomitant numbness or loss of sensation would represent a useful manifestation of the results to be achieved.
It is a preferred embodiment of this invention to use the screening assays of the invention to identify potential therapeutic agents, or analogs thereof, that are selective for the SCN9A sodium channel ahead of other sodium channels, in humans and other animals. It will therefore be apparent to those skilled in the art that a series of assays for measuring differential interaction with other sodium channels would provide the tools necessary to identify selective agents for SCN9A. In this embodiment, a first screening assay employing SCN9A is used to identify compounds which inhibit SCN9A activity. A suite of secondary assays are then employed, each containing one or more different sodium channels selected from among Nav1.1 (SCN1A); Nav1.2 (SCN2A), Nav1.3 (SCN3A), Nav1.4 (SCN4A), Nav1.5 (SCN5A), Nav1.6 (SCN8A), Nav1.8 (SCN10A), Nav1.9 (SCN11A), and Nax (SCN6A, SCN7A) (for consensus nomenclature see Goldin, A L. 2001. Ann. Rev. Physiol. 63:871-894). Compounds which were found to inhibit SCN9A expression or activity, are systematically tested against the assays for the other sodium channels. Those compounds which are more selective for SCN9A over other channels than current sodium channel blocking compounds used in the art are preferred compounds.
The other sodium channels can be incorporated into screening assays according to methods disclosed herein, or as disclosed elsewhere in the art or as later discovered or invented. As such, the Nav1.1, Nav1.2 and Nav1.3 screening assays set out in WO 01/38564 (Rouleau et al, published 31 May 2001) may be used to effectively distinguish compounds which are broadly selective for sodium channels from those that are specific and selective exclusively for SCN9A.
Some of the standard screening assays for a protein like SCN9A are set out in U.S. Pat. No. 6,110,672 (a US counterpart of WO 96/14077), incorporated herein by reference in its entirety. These assays provide for basic analysis of agents which interact with a protein like SCN9A (although the reference provides no guidance on achieving selectivity among sodium channels). The genetic and phenotypic information provided in the instant patent application now provides therapeutic agents which effectively mimic the Congenital Indifference to Pain phenotype, by selecting those compounds which are selective for SCN9A over other sodium channel family members. The invention provides a compound which, while not necessarily being selective for the peripheral nervous system over the central nervous system (as prescribed in WO 96/14077), the compound is specific for SCN9A ahead of all other sodium channels. Such a compound provides analgesic relief without side-effects such as nausea, tremor and irritability.
The benefits of the present invention and the value of selectivity for SCN9A over other sodium channels for the treatment of pain is further illustrated in Table 4 below. Table 4 sets out the known phenotypic or disease consequences of mutations in various known sodium channels in rodents and humans. As can be seen, modulation of the activity of almost all the other sodium channels results in severe and undesirable physiological consequences. For example, inhibitory mutations in human SCN1A result in a type of epilepsy. Gain of function mutations in rodent SCN2A result in behavioral disorders. Loss of function mutations in rodent SCN2A result in severe neurological disorders. SCN2A mutations in humans also result in a type of epilepsy. The list leads to the conclusion that a compound which selectively inhibits SCN9A will be a useful treatment for pain, and will not cause the undesirable consequences of modulation of the other sodium channels.











TABLE 4








Human Disease or



Gene
Protein
Rodent Phenotype
Phenotype
Reference







SCN1A
Na(v)1.1
Unknown
Generalized epilepsy with
1, 2, 3,





febrile seizures plus type II





(OMIM 604233); severe





myoclonic epilepsy of





infancy (OMIM 607208)


SCN2A2,
Na(v)1.2
Transgenic Mouse -
Generalized epilepsy with
4, 25


SCN2A

seizures, focal motor
febrile seizures plus (OMIM




abnormalities, behavioral
604233)




arrest and stereotyped




repetitive behaviors;




Knock-Out Mouse - perinatal




lethal with severe hypoxia




and massive neuronal




apoptosis in the brainstem


SCN3A
Na(v)1.3
Unknown
Unknown


SCN4A
Na(v)1.4
Unknown
Hyper-(and hypo-) kalemic
10, 11





periodic paralysis (OMIM





170500, 170400





paramyotonia congenita





(OMIM 168300, 168350)


SCN5A
Na(v)1.5
Knock-In Mice - arrhythmias;
Long QT syndrome-3
12, 13, 14, 15,




Knock-Out mice (−/−) -
(OMIM 603830), Brugada
16, 17, 26




intrauterine lethality with
syndrome (601144); heart




defective ventricular
block (OMIM 113900;




morphogenesis;
paroxysmal familial




Knock-Out mice (+/−) -
ventricular fibrillation (OMIM




arrhythmias
603829)


SCN8A
Na(v)1.6
Various spontaneous
Unknown
5, 6, 7, 8, 9




mutations result in: motor




endplate disease -




progressive paralysis and




juvenile lethality in C57BL/6J




mice; Viable adults with




dystonia in C3H mice; Jolting




mice - cerebellar ataxia;




DMU mice - skeletal and




cardiac muscle degeneration;




heterozygotes unaffected


SCN10A
Na(v)1.8
Knock-out mice mechanical
Unknown
18, 19, 20,




analgesia, reduced thermal

21, 22




hyperalgesia, and delayed




inflammatory hyperalgesia,




but normal neuropathic pain




perception (heterozygotes




like wild-type);




Knock-down mice - reduced




inflammatory hyperalgesia




and neuropathic pain (note




discrepancy with above)


SCN12A,
Na(v)1.9
Knock-down in rat: No effect
Unknown
23


SCN11A

on nerve-injury induced




behavior responses


SCN6A,
Na(x)
Knock-out: Altered salt
Unknown
24


SCN7A

intake


SCN9A
Na(v)1.7
Unknown
Congenital indifference to
This work





pain (OMIM 243000)









The emphasis noted herein on the preferred selectivity for SCN9A over other sodium channels, should also be understood to include selectivity over other ion channels and related proteins and genes. Preferred selective SCN9A modulating agents have limited or no effect on the activity of ion channels such as potassium, calcium, ion co-transporters and the like, nor does it effect the hERG channel or other physiologically relevant channels. The emphasis on sodium channel selectivity is based on the high degree of similarity among sodium channels among which selectivity is technically more challenging to achieve than with less closely related proteins/genes.
On another note, this invention also establishes that improved therapeutic agents for the treatment of pain must take advantage of the dynamic state of a sodium channel. Therapeutic agents can now be identified with entirely novel modes of action against the channel. A sodium channel cycles from the open (activated) state to the closed (inactivated) state, then to the resting (closed but capable of being activated) state, where it waits for an electrical signal to convert to the open state and allow passage of sodium ions. The transition from open to closed may be by fast inactivation or slow inactivation. Previous knowledge of the SCN9A channel did not allow for the identification of which state or transition state of the channel was preferred for therapeutic intervention. The instant invention now establishes that the Y328X or the W1689X mutation causes the desired channel behavior to generate the desirable indifference to pain in humans. An irreversible binding agent may be as suitable for use as a reversible binding agent. This invention therefore provides mutant proteins which may be used in the screening assays to assist in the identification of therapeutic agents or their analogs which mimic the truncation mutations of the invention. It also teaches a functional description about what the binding agent/blocking agent must do to achieve analgesia.
Further Assays
Stated broadly, the screening assays of the invention simplify the identification, evaluation and development of classes of compounds which are suitable for use as analgesic agents and for the reduction of adverse pain responses to disease, such as chronic disease, for example cancer. In general, these screening methods provide a ready means for selecting either natural product extracts or synthetic compounds of interest from a large population (i.e. a chemical library, for example, one produced by combinatorial means). As stated previously, an assay is first designed which measures SCN9A expression or activity. Exemplary methods useful for the identification of such compounds are detailed herein, although those skilled in the art will be aware of alternative means. In a first step, compounds are sequentially tested against the assay to determine whether they influence a measurable biological activity of the assay.
Functional assays may be based one or more of the diverse measurable biological activities of a gene or polypeptide corresponding to SCN9A. “SCN9A activity” as used herein, especially relating to screening assays, is to be interpreted broadly and contemplates all directly or indirectly measurable and identifiable biological activities of the SCN9A gene and protein. Relating to the purified SCN9A protein, SCN9A activity includes, but is not limited to, all those biological processes, interactions, binding behavior, binding-activity relationships, pKa, pD, enzyme kinetics, stability, and functional assessments of the protein. Relating to SCN9A activity in cell fractions, reconstituted cell fractions or whole cells, these activities include, but are not limited to the rate at which the SCN9A channel transports sodium, guanidine, lithium or other ions across a membrane, or the dynamics of this transport (such as voltage dependence, rate of transition between states) and all measurable consequences of these effects, including cell growth, development or behavior and other direct or indirect effects of SCN9A activity. Relating to SCN9A genes and transcription, SCN9A activity includes the rate, scale or scope of transcription of genomic DNA to generate RNA; the effect of regulatory proteins on such transcription, the effect of modulators of such regulatory proteins on such transcription; plus the stability and behavior of mRNA transcripts, post-transcription processing, mRNA amounts and turnover, and all measurements of translation of the mRNA into polypeptide sequences. Relating to SCN9A activity in organisms, this includes but is not limited biological activities which are identified by their absence or deficiency in disease processes or disorders caused by aberrant SCN9A biological activity in those organisms. Broadly speaking, SCN9A biological activity can be determined by all these and other means for analyzing biological properties of proteins and genes that are known in the art.
The invention therefore provides numerous assays which measure an activity of SCN9A and are useful for the testing of chemical compounds to identify which ones effect such activity. The invention also invites those skilled in the art to develop further SCN9A activity assays which go beyond those disclosed herein, for use in the screening compound libraries.
A typical assay uses patch-clamp techniques to study the behavior of channels. Such techniques are known to those skilled in the art, and may be developed, using current technologies, into low or medium throughput assays for evaluating compounds for their ability to modulate sodium channel behavior.
A competitive binding assay with known sodium channel toxins such as tetrodotoxin, alpha-scorpion toxins, and the like, may be suitable for identifying potential therapeutic agents with high selectivity for SCN9A.
In still another assay, uptake of radioactive isotopes into or out of a vesicle can be measured. The vesicles are separated from the extra-vesicular medium and the radioactivity in the vesicles and in the medium is quantitated and compared.
Other typical assays employ drug screening technology such as (but not limited to) radioactive, colorimetric or fluorescent based measurements. A classic colorimetric assay measures the ability of a dye to change color in response to changes in assay conditions resulting from the activity of the polypeptides. A useful instrument for the study of ion channels, including sodium channels is the ICR 8000 available from Aurora Biomed Inc. (Vancouver, BC).
Functional drug screening assays can also be based upon the ability of SCN9A polypeptides to interact with other proteins. Such interacting proteins can be identified by a variety of methods known in the art, including, for example, radioimmunoprecipitation, co-immunoprecipitation, co-purification, and yeast two-hybrid screening. Such interactions can be further assayed by means including but not limited to fluorescence polarization or scintillation proximity methods. Drug screens can also be based upon functions of the polypeptides deduced upon X-ray crystallography of the protein and comparison of their 3-D structure to that of proteins with known functions. Drug screens can be based upon a function or feature apparent upon creation of a transgenic or knockout mouse, or upon overexpression of the protein or protein fragment in mammalian cells in vitro. Moreover, expression of mammalian (e.g., human) polypeptides in yeast or C. elegans allows for screening of candidate compounds in wild-type and mutant backgrounds, as well as screens for mutations that enhance or suppress a low pain sensitivity phenotype. Modifier screens can also be performed in transgenic or knock-out mice.
Additionally, drug screening assays can also be based upon polypeptide functions deduced upon antisense interference with the gene function. Intracellular localization of SCN9A polypeptides, or effects which occur upon a change in intracellular localization of such proteins, can also be used as an assay for drug screening. Immunocytochemical methods may be used to determine the exact location of the pain-related polypeptides.
Polypeptides encoded by the polynucleotides disclosed herein can be used as an antigen to raise antibodies, including monoclonal antibodies. Such antibodies will be useful for a wide variety of purposes, including but not limited to functional studies and the development of drug screening assays and diagnostics. Monitoring the influence of agents (e.g., small organic compounds) on the expression or biological activity of the pain-related polypeptides identified according to the invention can be applied not only in basic drug screening, but also in clinical trials. For example, the effectiveness of an agent determined by a screening assay as described herein to increase or decrease gene expression, protein levels, or biological activity can be monitored in clinical trails of subjects exhibiting symptoms of chronic or persistent pain due to inadequate gene expression, protein levels, or biological activity (for example, the individuals studied herein. Alternatively, the effectiveness of an agent determined by a screening assay to modulate expression of SCN9A, as well as structurally and functionally related genes, including genes with high homology thereto, and including protein levels, or biological activity can be monitored in clinical trials of subjects exhibiting decreased altered gene expression, protein levels, or biological activity. In such clinical trials, the expression or activity of the genes or polypeptides disclosed herein and, preferably, other genes that have been implicated in, for example, congenital indifference to pain stimuli, can be used to ascertain the effectiveness of a particular analgesic drug.
As a non-limiting example, genes that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) that modulates the activity of the SCN9A gene, or any expression products thereof, or polypeptides that modulate the activity of SCN9A (e.g., identified in a screening assay as described herein) can be identified. Preferably, such cells are recombinant cells engineered to express a polynucleotide or polypeptide as disclosed herein. Thus, such recombinant cells are prepared and RNA isolated and analyzed for the levels of expression of SCN9A after contacting said cells with agents that may have analgesic properties. The levels of gene expression can be quantified by Northern blot analysis or RT-PCR, or, alternatively, by measuring the amount of protein produced, by one of a number of methods known in the art, or by measuring the levels of biological activity of polypeptides encoded thereby or other genes. In this way, the gene expression can serve as a marker, indicative of the physiological response of the cells to the agent. Accordingly, this response state may be determined before, and at various points during, treatment of the individual with the agent.
In another aspect, the invention provides a method for computationally identifying a compound having analgesic properties. The method involves (a) determining crystal structure and preferably the active site of a SCN9A protein (i.e. through x-ray crystallography or other techniques); and (b) through computational modeling, identifying a compound which interacts with the active site, thereby identifying a compound, or its analog, as a compound which is useful for modulating the activity of such a polypeptide. Useful screening assays may also be performed in silico using available computerized databases for the identification of such compounds.
In a preferred embodiment, the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) including the steps of (i) determining that a patient exhibits discomfort due to a disease or disorder that causes some type of painful stimulus; (ii) administering an effective amount of an agent identified using one of the screening assays disclosed herein; (iii) ascertaining a reduction to pain or other stimuli following said administration and (iv) altering the administration of the agent to the subject accordingly. For example, increased administration of the agent may be desirable to decrease the expression or activity of gene or encoded polypeptide, i.e., to increase the effectiveness of the agent.
Where the patient is non-human, biopsy samples can be taken to show a decrease in gene expression, such as by measuring levels of protein, mRNA, or genomic DNA post-administration samples and comparing the level of expression or activity of said protein, mRNA, or genomic DNA in the pre-administration sample with that of the corresponding post administration sample or samples, thereby showing the effects of drug administration on one or more of the genes disclosed herein and concomitant reduction in pain response and/or sensitivity.
The gene disclosed herein as being involved in congenital indifference to pain in an animal can be used, or a fragment thereof can be used, as a tool to express a protein, where such genes encode a protein, in an appropriate cell in vitro, or can be cloned into expression vectors which can be used to produce large enough amounts of protein to use in in vitro assays for drug screening. Expression systems which may be employed include baculovirus, herpes virus, adenovirus, adeno-associated virus, bacterial systems, and eucaryotic systems such as CHO cells, HEK cells and other cells commonly available. Naked DNA and DNA-liposome complexes can also be used.
Candidate modulators may be purified (or substantially purified) molecules or may be one component of a mixture of compounds (e.g., an extract or supernatant obtained from cells). In a mixed compound assay, SCN9A activity is tested against progressively smaller subsets of the candidate compound pool (e.g., produced by standard purification techniques, e.g., HPLC or FPLC; Ausubel et al.) until a single compound or minimal compound mixture is demonstrated to modulate gene or protein activity or expression in a manner having analgesic effects.
Specific compounds which will modulate the gene expression or gene transcript levels in a cell of SCN9A include antisense nucleic acids, ribozymes and other nucleic acid compositions which specifically hybridize with SCN9A (including exons or introns of such genes, promoters, 3′ tails, etc.). These specific compounds are compounds of the invention, and are useful for treating the diseases discussed previously. Design and manufacturing of such compounds are well known to those skilled in the art.
Specific compounds which modulate the activity of a SCN9A polypeptide include antibodies (polyclonal or monoclonal) which specifically bind to an epitope of said polypeptide. These specific compounds are compounds of the invention, and are useful for inducing resistance of tolerance to pain stimuli. Design and manufacturing of such compounds are well known to those skilled in the art.
Specific compounds which modulate the activity of SCN9A in the body include gene therapy vectors comprising all or a part of the SCN9A gene sequence or mutant SCN9A sequence. As is well known to those skilled in the art, gene therapy allows the delivery of the SCN9A gene in an organism to cells where it is taken up and expressed, thus changing the level or amount of SCN9A protein in such cell. These vectors thereby modulate the activity of SCN9A in the body and are useful for the therapeutic indications disclosed herein.
In accordance with the foregoing, the present invention provides the amino acid sequence of a protein, designated SCN9A, that is a known ion channel structure found in neuronal cells (SEQ ID NO: 2) and which is associated with hereditary transmission of indifference to pain. In addition, a mutation, here a truncation, has been found in this sequence derived from individuals found to have such indifference to pain. Thus, agents that mimic the phenotypic effects of this truncation, such as aberrant protein structure and decreased, or absent, function represent candidate compounds for evaluation as analgesic agents. In addition, agents that have the effect of reducing the half-life of such polypeptide in cells would also act to induce decreased sensitivity to pain and thereby achieve analgesia.
By way of non-limiting example, cells expressing a wild-type SCN9A polypeptide are transiently metabolically labeled during translation, contacted with a candidate compound, and the half-life of the polypeptide is determined using standard techniques. Compounds that decrease the half-life of the polypeptide are useful compounds in the present invention.
In other embodiments, treatment with an antagonist of the invention may be combined with other analgesics to achieve a combined, possibly even synergistic, effect.
The ability of analgesic compounds to modulate polypeptides as disclosed herein, such as SCN9A, can be determined by any number of different binding assays, including use of a solid support, either as part of a column or as a batch procedure. Such support may be composed of plastic or glass, and includes standard resins and resin beads. Such assays are also available to test the ability of polypeptides, such as SCN9A, including mutated and/or truncated forms thereof, to bind to such test compounds or to other proteins present in cells, thereby identifying modulators of SCN9A activity according to the invention.
In one such assay for which the polypeptides encoded by genes disclosed herein are useful, the polypeptide (or a polypeptide fragment thereof or an epitope-tagged form or fragment thereof) is bound to a suitable support (e.g., nitrocellulose or an antibody or a metal agarose column in the case of, for example, a his-tagged form of said polypeptide). Binding to the support is preferably done under conditions that allow proteins associated with the polypeptide to remain associated with it. Such conditions may include use of buffers that minimize interference with protein-protein interactions. If desired, other proteins (e.g., a cell lysate) are added, and allowed time to associate with the polypeptide. The immobilized polypeptide is then washed to remove proteins or other cell constituents that may be non-specifically associated with it the polypeptide or the support. The immobilized polypeptide can then be used for multiple purposes. In a compound screening embodiment, compounds can be tested for their ability to interfere with interactions between SCN9A and other bound molecules (which are presumably SCN9A interacting proteins). Compounds which can successfully displace interacting proteins are thereby identified as SCN9A modulating agents of the invention.
In an alternative embodiment designed to identify the SCN9A interacting proteins, the immobilized polypeptide is dissociated from its support, and proteins bound to it are released (for example, by heating), or, alternatively, associated proteins are released from the polypeptide without releasing the latter polypeptide from the support. The released proteins and other cell constituents can be analyzed, for example, by SDS-PAGE gel electrophoresis, Western blotting and detection with specific antibodies, phospho-amino acid analysis, protease digestion, protein sequencing, or isoelectric focusing. Normal and mutant forms of such polypeptide can be employed in these assays to gain additional information about which part of the polypeptide a given factor is binding to. In addition, when incompletely purified polypeptide is employed, comparison of the normal and mutant forms of the protein can be used to help distinguish true binding proteins. Such an assay can be performed using a purified or semipurified protein or other molecule that is known to interact with a polypeptide encoded by a SCN9A polynucleotide.
This assay may include the following steps.
1. Harvest the encoded polypeptide and couple a suitable fluorescent label to it;
2. Label an interacting protein (or other molecule) with a second, different fluorescent label. Use dyes that will produce different quenching patterns when they are in close proximity to each other vs. when they are physically separate (i.e., dyes that quench each other when they are close together but fluoresce when they are not in close proximity);
3. Expose the interacting molecule to the immobilized polypeptide in the presence or absence of a compound being tested for its ability to interfere with an interaction between the two; and
4. Collect fluorescent readout data.
An alternative assay for such protein interaction is the Fluorescent Resonance Energy Transfer (FRET) assay. This assay can be performed as follows.
1. Provide the encoded protein or a suitable polypeptide fragment thereof and couple a suitable FRET donor (e.g., nitro-benzoxadiazole (NBD)) to it;
2. Label an interacting protein (or other molecule) with a FRET acceptor (e.g., rhodamine);
3. Expose the acceptor-labeled interacting molecule to the donor-labeled polypeptide in the presence or absence of a compound being tested for its ability to interfere with an interaction between the two; and
4. Measure fluorescence resonance energy transfer.
Quenching and FRET assays are related. Either one can be applied in a given case, depending on which pair of fluorophores is used in the assay.
One or more of the genes disclosed herein may act by altering membrane permeability, such as the permeability of membranes to ions, an example being the SCN9A gene disclosed herein. Such activity may be assayed for using vesicles, such as liposomes or intact cells, wherein such structures comprise one or more of the polypeptides of the invention, which polypeptides are expressed in such vesicle, preferably an intact cell, such as a mammalian recombinant cell, and the permeability of the membrane of the cell is determined in the presence or absence of such expression. In the same way, such permeability can then be assayed in the presence and absence of chemical agents known to modulate the activity of one or more of the genes disclosed herein. Thus, the utility of these agents in enhancing the activity of proteins known to affect such membrane transport can be readily determined. In the same way, the ability of these agents to affect the transport of other molecules, such as lipids, amino acids, and the like, across such membranes is readily determined.
In performing such assays, the test cell, such as a mammalian recombinant cell expressing SCN9A, or a polynucleotide corresponding to such gene, is loaded with a reporter molecule (such as a fluorescent ion indicator whose fluorescent properties change when it binds a particular ion) that can detect ions (to observe outward movement), or alternatively, the external medium is loaded with such a molecule (to observe inward movement). A molecule which exhibits differential properties when it is inside the vesicle compared to when it is outside the vesicle is preferred. For example, a molecule that has quenching properties when it is at high concentration but not when it is at another low concentration would be suitable. The movement of the charged molecule (either its ability to move or the kinetics of its movement) in the presence or absence of a compound being tested for its ability to affect this process can be determined.
Throughput of test compounds is an important consideration in the choice of screening assay to be used. In some strategies, where hundreds of thousands of compounds are to be tested, it is not desirable to use low throughput means. In other cases, however, low throughput is satisfactory to identify important differences between a limited number of compounds. Often it will be necessary to combine assay types to identify preferred SCN9A modulating compounds
In brief, electrophysiology using patch clamp techniques is accepted as a gold standard for detailed characterization of sodium channel compound binding. There is a manual low-throughput screening (LTS) method which can compare 2-10 compounds per day; a recently developed system for automated medium-throughput screening (MTS) at 20-50 patches (i.e. compounds) per day; and a technology reportedly in development from Molecular Devices Corporation (Sunnyvale, Calif.) which permits automated high-throughput screening (HTS) at 1000-3000 patches (i.e. compounds) per day.
Binding Assays are also available, however these are of only limited functional value and information content. Designs include traditional radioactive filter based binding assays or the confocal based fluorescent system available from Evotec OAI group of companies (Hamburg, Germany), both of which are HTS.
Radioactive flux assays can also be used. In this assay, channels are stabilized in an open state with veratridine, and channel blockers are identified by their ability to prevent ion influx. The assay can use radioactive 22[Na] and 14[C] guanidinium ions as tracers. FlashPlate & Cytostar-T plates in living cells avoids separation steps and are suitable for HTS. Scintillation plate technology has also advanced this method to HTS suitability. Because of the functional aspects of the assay, the information content is reasonably good.
Yet another format measures the redistribution of membrane potential using the FLIPR system membrane potential kit (HTS) available from Molecular Dynamics (a division of Amersham Biosciences, Piscataway, N.J.). Again, in this assay channels are stabilized in an open state with veratridine, and channel blockers are identified. The assay can use radioactive 22[Na] and 14[C] guanidinium ions as tracers. This method is limited to slow membrane potential changes. Some problems may result from the fluorescent background of compounds. Test compounds may also directly influence the fluidity of the cell membrane and lead to an increase in intracellular dye concentrations. Still, because of the functional aspects of the assay, the information content is reasonably good.
Sodium dyes can be used to measure the rate or amount of sodium ion influx through a channel. This type of assay provides a very high information content regarding potential channel blockers. The assay is functional and would measure Na influx directly. CoroNa Red, SBFI and/or sodium green (Molecular Probes, Inc. Eugene Oreg.) can be used to measure Na influx; all are Na responsive dyes. They can be used in combination with the FLIPR instrument. The use of these dyes in a screen has not been previously described in the literature. Calcium dyes may also have potential in this format.
In a further embodiment, FRET based voltage sensors are used to measure the ability of a test compound to directly block Na influx. Commercially available HTS systems include the VIPRTM II FRET system (Aurora Biosciences Corporation, San Diego, Calif., a division of Vertex Pharmaceuticals, Inc.) which may be used in conjunction with FRET dyes, also available from Aurora Biosciences. This assay measures sub-second responses to voltage changes. There is no requirement for a modifier of channel function. The assay measures depolarization and hyperpolarizations, and provides ratiometric outputs for quantification. A somewhat less expensive MTS version of this assay employs the FLEXstationTM (Molecular Devices Corporation) in conjunction with FRET dyes from Aurora Biosciences.
The present invention also relates to assays that may employ transcription factors for one or more of the genes disclosed herein. The effect of a test compound on the relative ability of such transcription factor to modulate transcription of the SCN9A gene is assessed by means of such an assay. In accordance with the disclosure herein, untranslated regions and promoter regions of SCN9A are provided or readily obtained. Such genomic or untranslated regions may be included in plasmids comprising the identified gene, such as in assays to identify compounds which modulate expression thereof. In one such assay, 1-5 kilobases of upstream genomic region of SCN9A is operably linked (i.e. ligated) to a reporter gene, and incorporated into an expression plasmid. The plasmid is transfected into a cell, and the recombinant cell is exposed to test compound(s). Those compounds which increase or decrease the expression of the reporter gene are then modulators of the SCN9A gene/protein, and are considered therapeutic agents of the invention.
Those skilled in the art are familiar with typical and easily measured reporter genes, such as luciferase, chloramphenicol acetyl-transferase (CAT), and other luminescent or fluorescent assays.
Thus, in one aspect the present invention relates to a method for identifying an agent that modulates the activity of a polynucleotide whose expression contributes to pain sensation or whose non-expression contributes to lack of pain sensation, comprising:
a) contacting under physiological conditions a chemical agent with a polynucleotide corresponding to a promoter of the SCN9A gene, preferably having the sequence of SEQ. ID NO. 14, under conditions promoting such contacting; and
b) detecting a change in the expression of said polynucleotide as a result of said contacting;
thereby identifying an agent that modulates said polynucleotide activity.
Medicinal Chemistry and Lead Optimization
While this invention discloses a wide variety of assays for measuring the effect of a compound on SCN9A expression or activity, it is important to note that this compound detection is merely the first step in the industrial process of identification of an approvable therapeutic agent. The library screening accomplished with the first screening assay may be low, medium or high-throughput screening. It identifies “hits” or individual compounds from the library which cause the desired modulation of SCN9A expression or activity. The hits are further evaluated at a chemical structure level, and, if possible, are organized according to shared core structures, which presumably define chemical features required to achieve the desired modulation of SCN9A. This process, sometimes called lead identification, may involve a structure-activity relationship (or SAR) analysis. Various cycles of medicinal chemistry or focussed library generation may then be employed to generate multiple analogs of such core structures in a process called lead optimization. Finally, those skilled in the art know how to identify and test those preferred analogs (optimized leads) which have improved characteristics as therapeutic agents, generally through a series of in vitro and in vivo analyses.
In general, novel agents having SCN9A modulating properties are identified from large libraries of both natural product or synthetic (or semi-synthetic) extracts or chemical libraries according to methods known in the art. Those skilled in the field or drug discovery and development will understand that the precise source of test extracts or compounds is not critical to the screening procedure(s) of the invention. Accordingly, virtually any number of chemical extracts or compounds can be screened using the exemplary methods described herein. Examples of such extracts or compounds include, but are not limited to, plant-, fungal-, prokaryotic- or animal-based extracts, fermentation broths, and synthetic compounds, as well as modification of existing compounds. Numerous methods are also available for generating random or directed synthesis (e.g., semi-synthesis or total synthesis) of any number of chemical compounds, including, but not limited to, saccharide-, lipid-, peptide-, and nucleic acid-based compounds. Synthetic compound libraries are commercially available from Brandon Associates (Merrimack, N.H.) and Aldrich Chemical (Milwaukee, Wis.). Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant, and animal extracts are commercially available from a number of sources, including Biotics (Sussex, UK), Xenova (Slough, UK), Harbor Branch Oceangraphics Institute (Ft. Pierce, Fla.), and PharmaMar, U.S.A. (Cambridge, Mass.). In addition, natural and synthetically produced libraries are produced, if desired, according to methods known in the art, e.g., by standard extraction and fractionation methods. Furthermore, if desired, any library or compound is readily modified using standard chemical, physical, or biochemical methods.
In addition, those skilled in the art of drug discovery and development readily understand that methods for dereplication (e.g., taxonomic dereplication, biological dereplication, and chemical dereplication, or any combination thereof) or the elimination of replicates or repeats of materials already known for their analgesic and/or anesthetic activities should be employed whenever possible.
When a crude extract is found to have SCN9A modulating activity, further fractionation of the positive lead extract is necessary to isolate chemical constituent responsible for the observed effect. Thus, the goal of the extraction, fractionation, and purification process is the careful characterization and identification of a chemical entity within the crude extract having potential therapeutic activities. The same assays described herein for the detection of activities in mixtures of compounds can be used to purify the active component and to test derivatives thereof. Methods of fractionation and purification of such heterogeneous extracts are known in the art.
In an alternative strategy, if a compound is identified which is known to modulate expression or activity of a polynucleotide or polypeptide corresponding to SCN9A, analogs of that compound can be developed and tested for improved selectivity, potency, binding affinity or the like against the target gene/protein. According to the invention, such analogs will also be tested against other sodium channels (such as NaV 1.1 to 1.6 and NaV 1.8 to 1.12) to identify analogs which are preferentially selective towards blocking NaV 1.7 and which do not interact with the others. Such improved analogs, which are compounds of the invention, are expected to demonstrate reduced side effects and improved analgesic effects in human patients as compared to their parent compounds.
In an alternative embodiment, an investigator may desire to initiate research with known sodium channel blockers and to develop analogs of the blocker which are more selective for SCN9A. Known sodium channel modulators that may be selectively improved to increase specificity for SCN9A include:














Drug/clinical candidate
Company









AWD-140-190
ASTA Medica AG



AWD-33-173
ASTA Medica AG



BIA-2-024
Boehringer Ingelheim



BIA-2-093
Boehringer Ingelheim



Co-102862
University of Saskatchewan



Conopeptides
Cognetix Inc



DCUKA
Lohocla Research Corp



felbamate
Carter-Wallace Inc



fosphenytoin
InterX Research Corp



GW-273293
Glaxo Wellcome plc



lamotrigine
Glaxo Wellcome plc



OROS (phenytoin)
ALZA Corp



oxcarbazepine
Novartis AG



rufinamide
Novartis AG



safinamide
Pharmacia & Upjohn AB



topiramate
Johnson & Johnson



valproate semisodium
Abbott Laboratories



vinpocetine
Richter Gedeon VG



ZM-227189
Zeneca Group plc



zonisamide
Dainippon Pharmaceutical Co Ltd.










Improved analogs may also include compounds with improved stability, biodistribution, pharmacokinetics or other desirable features for therapeutic agents which are not directly related to modulation of the therapeutic target.
In a preferred embodiment, the improved analog of the invention is effectively delivered, either by physiological means or assisted means, to cells of the body expressing the SCN9A protein.
Compounds identified as having potential therapeutic value are subsequently analyzed using any standard in vitro assay or in vivo animal model for the disease indication known in the art.
Method of Treatment
In a further aspect, the present invention relates to a method for treating a condition in an animal afflicted with a source of chronic pain comprising administering to said animal an effective amount of an analgesic agent first identified by an assay method of the invention. Preferably, said animal is a human patient, such as a patient afflicted with a chronic ailment, such as a cancerous condition.
Therapeutic Use of Selective SCN9A Modulators
In a preferred embodiment, the agent generates indifference to pain, but does not diminish sensations which are available to patients with CIP, such as but not limited to hot/cold sensing, pressure sensing and sharp/dull sensations. For example, indifference to pain without any concomitant numbness or loss of sensation would represent an important use of the compounds of the invention. In an alternative embodiment, a preferred therapeutic agent is useful in humans or other animals for treating pain, inducing analgesia or anesthesia, or another disorder which is connected to the C-I-P phenotype.
Compounds first identified as useful in reducing sensitivity to pain stimuli using one or more of the assays of the invention may be administered with a pharmaceutically-acceptable diluent, carrier, or excipient, in unit dosage form. Conventional pharmaceutical practice may be employed to provide suitable formulations or compositions to administer such compositions to patients. Although oral administration is preferred, any appropriate route of administration may be employed, for example, intravenous, parenteral, subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intrathecal, epidural, intracisternal, intraperitoneal, intranasal, or aerosol administration. Therapeutic formulations may be in the form of liquid solutions or suspension; for oral administration, formulations may be in the form of tablets or capsules; and for intranasal formulations, in the form of powders, nasal drops, or aerosols.
Methods well known in the art for making formulations are found in, for example, Remington: The Science and Practice of Pharmacy, (19th ed.) ed. A. R. Gennaro A R., 1995, Mack Publishing Company, Easton, Pa. Formulations for parenteral administration may, for example, contain excipients, sterile water, or saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated napthalenes. Biocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compounds. Other potentially useful parenteral delivery systems for agonists of the invention include ethylenevinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation may contain excipients, or example, lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate and deoxycholate, or may be oily solutions for administration in the form of nasal drops, or as a gel.
The methods of the invention simplify the evaluation, identification and development of active agents for the treatment and prevention of conditions of chronic or other types of pain while not necessarily treating the causative condition. Of course, both may be treated simultaneously as contemplated by the invention. For example, an analgesic agent identified by one of the screening methods disclosed herein may be administered along with an agent intended to treat a coincident conditions, such as where analgesic and antitumor agents are given together or contemporaneously.
Process of Data Transfer
The present invention also relates to a process that comprises a method for producing a product comprising identifying an agent according to one of the disclosed processes for identifying such an agent (i.e., the therapeutic agents identified according to the assay procedures disclosed herein) wherein said product is the data collected with respect to said agent as a result of said identification process, or assay, and wherein said data is sufficient to convey the chemical character and/or structure and/or properties of said agent. For example, the present invention specifically contemplates a situation whereby a user of an assay of the invention may use the assay to screen for compounds having the desired enzyme modulating activity and, having identified the compound, then conveys that information (i.e., information as to structure, dosage, etc) to another user who then utilizes the information to reproduce the agent and administer it for therapeutic or research purposes according to the invention. For example, the user of the assay (user 1) may screen a number of test compounds without knowing the structure or identity of the compounds (such as where a number of code numbers are used the first user is simply given samples labeled with said code numbers) and, after performing the screening process, using one or more assay processes of the present invention, then imparts to a second user (user 2), verbally or in writing or some equivalent fashion, sufficient information to identify the compounds having a particular modulating activity (for example, the code number with the corresponding results). This transmission of information from user 1 to user 2 is specifically contemplated by the present invention.
In one embodiment of the foregoing, the present invention relates to a method for producing test data with respect to the SCN9A polynucleotide modulating activity of a compound, comprising
a) contacting a chemical agent with a polynucleotide corresponding to a SCN9A polynucleotide, or corresponding to a SCN9A promoter sequence polynucleotide and under conditions promoting expression of such polynucleotide;
b) detecting a change in the expression of said polynucleotide as a result of said contacting; and
(c) producing test data with respect to the SCN9A polynucleotide modulating activity of said compound based on a change in the expression of the determined SCN9A polynucleotide modulating activity indicating such modulating activity.
Diagnostics and Pharmacogenomics
In a further embodiment, the invention relates to diagnostic and pharmacogenomic compounds, kits and methods. This aspect relates to analysis SCN9A for the diagnosis of insensitivity or indifference to pain, other pain disorder, or in the selection of a therapeutic agent for a patient (i.e. pharmacogenomics).
For example, nucleic acid analysis can be used to identify the G5067A or the C984A mutation thus confirming the diagnosis of congenital indifference to pain. Many nucleic acid diagnostic techniques are well known to those skilled in the art. Such techniques include DNA sequencing, hybridization probing, single stranded conformational analysis, PCR based techniques such as mismatch amplification, and myriad other well known methods. All such analysis can be performed on a small sample of blood, saliva, urine or other tissue provided by the patient.
Alternatively, protein based analyses such as antibody based assays (Elisa, Radioimmunoassay and the like) can be employed to identify the expression, amount or presence or absence of a mutant SCN9A protein, such as the W1689X or Y328X mutant.
Gene expression, both comparable and absolute, as well as biological activity, and mutational analysis can each serve as a diagnostic tool for pain disorders; thus determination of the amount of SCN9A mRNA can be used to diagnose the presence or absence of a mutation correlated with such pain disorder.
Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons (Eichelbaum, M., Clin. Exp. Pharmacol. Physiol., 23:983-985, 1996; Linder, M. W., Clin. Chem., 43:254-266, 1997). In general, two types of pharmacogenetic conditions can be differentiated. Genetic conditions transmitted as a single factor altering the way drugs act on the body (altered drug action) or genetic conditions transmitted as single factors altering the way the body acts on drugs (altered drug metabolism). Altered drug action may occur in a patient having a polymorphism (e.g., an single nucleotide polymorphism or SNP) in promoter, intronic, or exonic sequences of SCN9A. Thus by determining the presence and prevalence of polymorphisms allow for prediction of a patient's response to a particular therapeutic agent.
This pharmacogenomic analysis can lead to the tailoring of drug treatments according to patient genotype, including prediction of side effects upon administration of therapeutic agents, particularly therapeutic agents for treating disorders disclosed in this specification. Pharmacogenomics allows for the selection of agents (e.g., drugs) for therapeutic or prophylactic treatment of an individual based on the genotype of the individual (e.g., the genotype of the individual is examined to determine the ability of the individual to respond to a particular agent).
Diagnostics employing a gene or protein corresponding to SCN9A can also be useful in selecting patients for clinical trials of a potential therapeutic agent. Patients can be stratified according to the DNA or protein sequence of SCN9A and their response to drug treatment can be evaluated. Such stratification can greatly reduce the number of patients required to establish efficacy for a potential therapeutic agent.
Sequences 1 to 20 have the following identifications:
SEQ ID NO: 1—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), mRNA sequence
SEQ ID NO: 2—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), protein sequence
SEQ ID NO: 3—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), mRNA sequence, predicted splice variant
SEQ 4—SCN9A predicted splice variant
SEQ 5—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), mRNA, alternately spliced transcript using exon 5N and alternate splice donor site for exon 11 (11B)
SEQ 6—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), protein sequence, alternately spliced isoform using exon 5N and alternate splice donor site for exon 11 (11B)
SEQ 7—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), mRNA sequence, CIP-10 mutant
SEQ 8—SCN9A W1689X protein sequence
SEQ 9—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), mRNA sequence, CIP-14 mutant
SEQ ID NO: 10—SCN9A Y328X protein sequence
SEQ ID NO: 11—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), mRNA sequence, c.2488C>T mutation in CIP-08
SEQ ID NO: 12—Homo sapiens sodium channel, voltage-gated, type IX, alpha polypeptide (SCN9A), protein sequence, R830X CIP-08 mutation
SEQ ID No. 13—Partial Sequence from human BAC clone RP11-437H3 (AC108146) showing genomic arrangement of Exon 5A and Exon 5N. The first exon is the 3′ end of Exon 4 (residues 1-16). Next Exon is Exon 5N (residues 1479-1570). The one following is Exon 5A (residues 1686-1777). The final exon is the 5′ end of Exon 6 (residues 2506-2521).

SEQ ID NO: 14—human genomic sequence containing the SCN9A promoter region ending with the ATG of the initiator methionine codon; a partial cDNA sequence appears as residues 9913-9963.

SEQ ID NO: 15—predicted mouse SCN9A 11B isoform

SEQ ID NO: 16—predicted mouse SCN9A 11B isoform

SEQ ID NO: 17—predicted mouse SCN9A 5A isoform

SEQ ID NO: 18—predicted—1 mouse SCN9A 5A isoform

SEQ ID NO: 19—predicted mouse SCN9A 5N isoform

SEQ ID NO: 20—predicted mouse SCN9A 5N isoform

In carrying out the procedures of the present invention it is of course to be understood that reference to particular buffers, media, reagents, cells, culture conditions and the like are not intended to be limiting, but are to be read so as to include all related materials that one of ordinary skill in the art would recognize as being of interest or value in the particular context in which that discussion is presented. For example, it is often possible to substitute one buffer system or culture medium for another and still achieve similar, if not identical, results. Those of skill in the art will have sufficient knowledge of such systems and methodologies so as to be able, without undue experimentation, to make such substitutions as will optimally serve their purposes in using the methods and procedures disclosed herein.
The invention is described in more detail in the following non-limiting examples. It is to be understood that these methods and examples in no way limit the invention to the embodiments described herein and that other embodiments and uses will no doubt suggest themselves to those skilled in the art.
Example 1
Identification of the Genetic Mutation Responsible for Congenital Indifference to Pain (CIP) in Humans
We collected a multigenerational family with 3 affecteds (CIP-14) FIG. 1 and a smaller family with 1 affected (CIP-10) FIG. 2 reported previously (Guillermo A. and A. Grinspan. 1970. Rev Neurol (Paris) 123(6): p. 434-5.)
31 family members from CIP-14 were genotyped at 763 autosomal markers and at 48× markers. A genome-wide two-point analysis identified 8 regions with LOD scores >1.0. A region on chromosome 2 had two consecutive markers—D2S2330-D2S335—spanning 6cM, with positive scores. A LOD score of 1.51 at zero recombination was obtained at D2S2330. Multi-point analysis of this region was consistent with linkage to CIP. The CIP-14 pedigree contains 3 affecteds, one issued from a consanguineous marriage, and two expected to share one allele identical by descent with the first case and one allele identical by descent between themselves. Because the pedigree comes from an isolated population, it can be expected that there would be linkage disequilibrium at the disease gene, and that all 3 affecteds would share alleles. However, as there was only one allele that could be assumed to be inherited identically by descent to the 3 affecteds, a scoring method was designed to assign scores to allele sharing taking that into consideration. The allele sharing algorithm identified 4 regions as having two-point LOD scores >1.0, and identified 3 additional regions that had not been excluded in two-point linkage analysis.
Haplotype construction using 12 polymorphic markers in candidate regions identified by 2-point linkage analysis and allele-sharing methods suggested that only the D2S2330-D2S335 region was consistent with linkage to CIP. All 3 affecteds shared one chromosome in common inherited from 3006/3009. Individuals 0000 and 0002 share another chromosome in common inherited from a 3004/3005. A005 has a chromosome introduced through 1020 that appears to be identical by state (and potentially identical by descent) to the one inherited from 3006/3009, which may be explained by the consanguinity of the population. The homozygous haplotypes in the 3 affecteds could represent multiple copies of a single ancestral chromosome. Recombination with the proximal marker D2S306, and the distal marker, D2S2188, is seen in 2002 and 0002/A006, respectively, provided centromeric and telomeric boundaries for the disease gene at the 2q24-31 locus.
Definition of the CIP Minimal Genomic Region
The interval between D2S306 and D2S2188 corresponds to a genetic size of  ̃16cM. To increase the resolution of the interval, we performed fine mapping with 32 additional markers, including several novel dinucleotide-repeat markers identified from genomic sequence. Haplotype construction using 41 polymorphic markers revealed one proximal and 5 distal recombinations. Of the 6 recombinant individuals, one was affected and 5 were carriers. The additional data narrowed the boundaries defined in 2002 and A006 to approximately 11.2 MB, between CA1AC010876 and D2S1267.
To assess whether the disease in CIP-10 maps to the 2q24-31 locus, five family members were genotyped using the 41 polymorphic markers described above. The proband was homozygous for markers between D2S2299 and D2S2177, and the genotypic data was consistent with linkage to CIP. Haplotype construction revealed a candidate interval of  ̃19cM defined by inferred recombination events that must have occurred in the untyped generations.
Use of genetic data from CIP-14 and CIP-10 together provided a centromeric boundary at CA1AC010876 (based a meiotic recombination in CIP14-2002) and a telomeric boundary at D2S2177 (based on the haplotype sharing data of CIP-10).
Mutation Analysis
We next embarked on a positional cloning effort. According to the UCSC August 2001 genomic sequence assembly, the CIP genomic region contains 26 known genes, five of which code for alpha polypeptides of voltage-gated sodium channels. We initiated sequencing of the coding regions of SCN9A and SCN3A in CIP-14-A005 and CIP-10-503, theorizing that selective expression in dorsal root ganglia and upregulation in models of neuropathic pain, respectively, made them interesting candidate genes. In CIP-10-503, we detected a homozygous nucleotide change of G>A at nt 5067 in SCN9A that resulted in a change to a stop codon at tryptophan 1689 (FIG. 4a). The stop codon results in deletion of 289 amino acids at the C-terminal of SCN9A, including the last transmembrane domain of the fourth channel domain. In CIP-14-A005 we detected a homozygous nucleotide change of 984C>A in SCN9A that resulted in a change to a stop codon at tyrosine 328 (FIG. 4b). We developed PCR-RFLP assays and showed that both mutations cosegregated perfectly with the disease and the affected haplotypes. Both mutations were absent in 142 control chromosomes from individuals of similar ancestral background. A third mutation was identified in a CIP proband descended from first cousins in another previously identified family. FIG. 3 (See Lievre J A, et al. 1968. Bull Mem Soc Med Hop Paris. 1968 Mar. 15; 119(5):447-56.) Patient CIP-08-11:1 is homozygous for a C>T substitution at nt 2488 that corresponds to a change to a stop codon at arginine 830 (FIG. 4c).
Alternative Exons 5N and 5A
The rabbit SCN9A gene (NaS), the rat and human SCN2A and SCN3A genes, and the human SCN8A gene contain two alternatively spliced exons encoding segments S3 and S4 of channel domain I. (See Belcher S M, et al. Proc Natl Acad Sci USA. 1995 Nov. 21; 92(24):11034-8; Sarao R, et al. Nucleic Acids Res. 1991 Oct. 25; 19(20):5673-9; Gustafson T A, et al. J Biol. Chem. 1993 Sep. 5; 268(25):18648-53; Lu C M, and Brown G B. J Mol Neurosci 1998 February; 10(1):67-70; and Plummer N W, et al. Genomics. 1998 Dec. 1; 54(2):287-96.) The two exons are separated by introns of  ̃90-150 bp. The isoforms are believed to be developmentally regulated, and without being bound to theory, it is suggested that the upstream exon (N) is predominantly expressed during the neonatal period, while the downstream exon (A) is expressed in adult brain. To determine whether this organization is conserved in human SCN9A, we aligned the genomic sequence from BAC clone RP11-437H3 (Genbank accession #AC108146) SEQ ID No. 13, with the human and rabbit coding sequences, and found that two potential copies of exon 5 are separated by 115 bp (FIG. 5). The exons contain two predicted amino acid differences. Alternative splicing for these exons is illustrated in FIG. 5. Residue 201 in the second exon is valine rather than leucine and residue 206 (corresponding to 209 in SCN2A and 208 in SCN3A) is aspartic acid rather than asparagine. A species and channel comparison in FIG. 6 shows the conserved relationship between isoforms. Because their physical arrangement and amino acid sequence correspond to those in other sodium channel genes, they are designated exons 5N and 5A. It has been suggested that the proximity of the residue 206 in these exons and the positively charged residues of the voltage sensor in transmembrane segment IS4 (see FIG. 7) may alter the voltage dependence or permeability of the neonatal and adult channels. Plummer NW, supra.
We used PCR to amplify the region of human SCN9A described above from total RNA of adult dorsal root ganglia (DRG) to examine exon usage within intact cDNAs. Primers designed to specifically bind cDNAs containing either exon 5A or exon 5N produced fragments of the expected size and sequencing confirmed mutually exclusive use of both exons.
Alternative Splice Donor for Exon 11
Two clones containing exons 1-13 of SCN9A amplified from human DRG were sequenced. One clone contained an additional 33 nucleotides located between the sequences of exon 11 and exon 12. To identify the origin of the extra 33 bp in the novel transcript, we examined the genomic sequence of the human SCN9A gene. Two alternative splice donor sites separated by 33 bp were identified. Splicing at the downstream site generates the novel transcript that encodes a protein with 11 additional amino acids in cytoplasmic loop 1 (FIG. 8). The sequence of the additional amino acids is conserved in rat and rabbit SCN9A and additional members of the channel gene family (FIG. 9).
Example 2
RT-PCR Analysis of Relative SCN9A Expression
cDNAs from a variety of human tissues were used to perform relative quantitative RT-PCR with primers and conditions that specifically amplified the SCN9A transcript (FIG. 10). Experiments to determine the tissue distribution of SCN9A were performed with three separate primer sets. Dorsal root ganglia was included as a positive control and β-actin was included as an internal standard. We found highest levels of SCN9A relative to the β-actin standard in dorsal root ganglia and medulla oblongata. Lower levels of SCN9A product were detected in the samples from temporal lobe, thymus, hippocampus, cerebral cortex, amygdala, frontal lobe, spinal cord, occipital lobe, cerebellum, thalamus, and ovary. SCN9A expression was not detected in cDNA from parietal lobe, corpus callosum, cerebral peduncles, pons, thyroid, or placenta. The sequences of the RT-PCR products amplified from dorsal root ganglia and medulla oblongata were identical to human SCN9A cDNA. Previous studies have reported low levels of SCN9A in the CNS relative to the PNS, but we have detected significant levels in the CNS, and particularly high levels in the medulla oblongata.
This expression profile teaches those skilled in the art where compounds which modulate SCN9A gene expression or SCN9A protein activity are likely to have effect. For example, expression of SCN9A in the CNS may support a role for this gene in central perception of pain, although alternative theories are suggested. It also is strongly suggestive of the other therapeutic indications for SCN9A modulating agents.
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## Claims

1. A method for reducing pain in a mammal afflicted therewith, comprising administering to said mammal an effective amount of an agent that selectively decreases SCN9A-mediated ion flux activity in said mammal.

2. The method of claim 1, wherein said agent is a voltage dependent blocker of SCN9A.

3. The method of claim 2, wherein said agent decreases the amount of SCN9A-mediated ion flux activity in said mammal.

4. The method of claim 2, wherein said agent decreases the rate of SCN9A-mediated ion flux activity in said mammal.

5. The method of claim 2, wherein said agent decreases the ion flux activity of SCN9A polypeptide in said mammal.

6. The method of claim 5, wherein said polypeptide comprises the amino acid sequence encoded by SEQ. ID NO. 1, 3, 5, 15, 17, or 19.

7. The method of claim 1, wherein said mammal is a human patient.

8. The method of claim 1, wherein said pain is chronic pain.

9. The method of claim 8, wherein said chronic pain is due to a cancerous condition.

10. The method of claim 8, wherein said chronic pain is neuropathic pain.