# Patent

## Title
Compounds for enhancing p21 expression and methods of use thereof

## Abstract

The present invention relates to a method for identifying a drug candidate for enhancing expression of p21cip1/waf1 in a human patient suffering from a medical condition that can be treated by enhancing expression of p21Cφ1/waf1. The method includes (a) providing a cell line comprising a nucleic acid sequence that comprises a p21cip1/waf1 promoter operationally ligated to a reporter domain; (b) exposing the cell line to a compound; and (c) identifying a compound that induces expression of the reporter domain. The compound that induces expression of the reporter domain is a drug candidate for treating a medical condition that can be treated by enhancing expression of p21cip1/waf1.

## Background
This application asserts priority to U.S. Provisional Application No. 60/933,366, filed on Jun. 5, 2007, which is hereby incorporated by reference in its entirety.


The invention was also made with funds from New York State Department of Health, contract number CO19772. New York State has certain rights in this invention.
BACKGROUND OF THE INVENTION
p21cip1/waf1, is an important intermediate by which p53 mediates its role as an inhibitor of cellular proliferation in response to DNA damage. p21cip1/waf1 may bind to and inhibit cyclin-dependent kinase activity, preventing the phosphorylation of critical cyclin-dependent kinase substrates and blocking cell cycle progression, and thus proliferation. Induction or overexpression of p21cip1/waf1 leads to cell cycle inhibition and growth suppression in cells.
In many cells, p21cip1/waf1 is increased in response to different types of stress, such as oxidative stress, x-ray radiation, and DNA damage. Oxidative stress is reported to be associated with numerous diseases and conditions, including stroke, hypoxia, ischemia, spinal cord injury and neurodegenerative conditions. Accordingly, compounds that enhance the expression of p21cip1/waf1 and methods of identifying such compounds are beneficial for treating conditions and diseases that can be treated by enhancing expression of p21cip1/waf1 or by inhibiting cell cycle progression.
SUMMARY OF THE INVENTION
In one aspect, the present invention relates to a method for identifying a drug candidate for enhancing expression of p21cip1/waf1 in a human patient suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1. The method includes (a) providing a cell line comprising a nucleic acid sequence that comprises a p21cip1/waf1 promoter operationally ligated to a reporter domain; (b) exposing the cell line to a compound; and (c) identifying a compound that induces expression of the reporter domain. The compound that induces expression of the reporter domain is a drug candidate for treating a medical condition that can be treated by enhancing expression of p21cip1/waf1.
In another aspect, the invention relates to a method for enhancing expression of p21cip1/waf1 in a human patient suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1. The method includes administering to the patient an effective amount of one of the following compounds: ciclopirox olamine, dihydrocelastrol, colistimethate sodium, lycorine, diphenylurea, and acetylcysteine, chloroquine diphosphate, and 4′-methoxyflavone (acacetin).



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1A. GenBank Accession No. U24170 (SEQ ID NO: 1) (nucleotide numbers 1-2460). Nucleotide sequence of human p21cip1/waf1 gene.
FIG. 1B. GenBank Accession No. U24170 (SEQ ID NO: 1) (nucleotide numbers 2461-5143). Nucleotide sequence of human p21cip1/waf1 gene.
FIG. 2A. GenBank Accession No. U24171 (SEQ ID NO: 2) (nucleotide numbers 1-2700). Nucleotide sequence of Mus musculus p21cip1/waf1 gene.
FIG. 2B. GenBank Accession No. U24171 (SEQ ID NO: 2) (nucleotide numbers 2701-5006). Nucleotide sequence of Mus musculus p21cip1/waf1 gene.
FIG. 3. 60 bp murine p21cip1/waf1 promoter sequence from GenBank accession number U24171 (SEQ ID NO: 2). The sequence was sub-cloned in to pGL3 Luciferase Reporter Vector (Promega Corp. WI). Double underline represents an Sp1 binding site. Single underline represents TATA-box.
FIG. 4. 2,400 bp human p21cip1/waf1 promoter sequence from GenBank accession number U24170 (SEQ ID NO: 1). The sequence was sub-cloned in to pGL3 Luciferase Reporter Vector (Promega Corp. WI). Double underline represents an Sp1 binding site. Single underline represents TATA-box.
FIG. 5. Realtime PCR results. Cultured rat primary cortical neurons were treated with the respective drug for 12 hours. Neurons were harvested and RNA extracted using TriZolTM reagent (Invitrogen). cDNA was synthesized by standard reverse-transcriptase protocol. Realtime PCR performed using Applied Biosystems Realtime PCR cycler and rat p21-specific TaqMan primer and probe set. Data is displayed as fold induction relative to control (1-fold), which received vehicle only (no drug).



METHOD FOR IDENTIFYING DRUG CANDIDATES
In one aspect of the invention, a method is provided for identifying a drug candidate for enhancing expression of p21cip1/waf1 in human patients suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1. The method includes providing a cell line comprising a nucleic acid sequence that comprises a p21cip1/waf1 promoter operationally ligated to a reporter domain; exposing (treating) the cells to a chemical compound; and identifying a compound that induces expression of the reporter. The compound that induces expression of the reporter is a drug candidate for treating a medical condition that can be treated by (i.e., benefits from) enhancing expression of p21cip1/waf1. Preferably, the compound that induces expression of the reporter is a drug candidate for treating a medical condition that inhibits cell cycle progression.
The p21cip1/waf1 protein is also known as cyclin-dependent kinase inhibitor 1A (CDKN1A). The p21cip1/waf1 expression can be enhanced in any cell that expresses p21 in the patient, and, most advantageously, in a damaged or injured cell.
As used herein, enhancing expression of p21cip1/waf1 refers to increasing a level of measurable p21cip1/waf1 in a given assay in the presence of a drug candidate relative to a measurable level of p21cip1/waf1 in the absence of the drug candidate, when tested under the same conditions.
Expression of p21cip1/waf1 is considered enhanced if expression under the same conditions is enhanced at least about 10% greater, preferably at least about 25% greater, more preferably at least about 50% greater, even more preferably at least about 75% greater, most preferably at least about 90% greater, or more than in the absence of the drug candidate.
Expression of p21cip1/waf1 can be enhanced by any mechanism, and the invention is not limited to any particular mechanism. For example, expression of p21cip1/waf1 can be enhanced by transcriptional induction of the cognate messenger RNA (mRNA) of p21cip1/waf1 increased stability of p21cip1/waf1 mRNA, increased translation of p21cip1/waf1 mRNA into p21cip1/waf1 increased stability of p21cip1/waf1 increased p21cip1/waf1 activity (in the presence or absence of increased protein), increased induction of p21cip1/waf1 promoter activity, or any other mechanism.
Gene expression can be assessed by direct detection of protein product. Protein can be detected by methods known in the art, for example, by protein gel-electrophoresis or immunological methods. Protein can also be detected by detection of the corresponding mRNA products of transcription.
A drug candidate refers to a compound that may have activity in enhancing expression of p21cip1/waf1 human patients in need thereof. The drug candidate may be identified for enhancing expression of p21cip1/waf1 in any cell (in vitro) or mammal (in vivo).
Examples of cells in which the drug candidate enhances expression of p21cip1/waf1 include neuronal cells (e.g., neurons, ganglia, Schwann cells, astrocytes, oligodendrocytes, and microglia), brain cells, spinal cord cells, kidney cells, intestinal cells, heart and cardiac muscle cells such as myocytes, skin cells, etc. Examples of mammals in which the drug candidate enhances expression of p21cip1/waf1 include laboratory mammals, such as mice, rats, rodents, monkeys, baboons, etc.
A traditional paradigm for drug discovery and development typically involves three phases. During the early stages of drug discovery, large compound libraries of compounds (chemical molecules, biological molecules, small molecules, for example) are screened or tested in vitro for biological activity at a molecular target in order to identify potential new drugs, or lead compounds.
The active compounds, or hits, from this initial screening process are then tested through a series of other in vitro and in vivo tests to further characterize the active compounds. The in vivo tests at this phase may include tests in non-human mammals such as typical laboratory animals, for example, in mice, rats, rodents, monkeys, baboons, etc. If a compound meets the standards for continued development as a drug following in vitro and in vivo tests, the compound is typically selected for testing in humans.
A progressively smaller number of lead compounds at each stage are selected for testing in the next stage. The series of tests eventually leads to one or a few drug candidates being selected to proceed to testing in human clinical trials. The human clinical trials may include studies in a human suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1.
Many drug candidates, however, fail to gain marketing approval by the U.S. Food and Drug Administration (FDA). Accordingly, the drug candidate as used herein is preferably, but not necessarily, approved by a governmental entity responsible for approving drugs (e.g., U.S. FDA) for use in a pharmaceutical.
Cell Line
A step in the method for identifying drug candidates is providing a cell line that includes a nucleic acid sequence that includes a p21cip1/waf1 promoter operationally ligated to a reporter domain.
As used herein, a cell line refers to a population of cells capable of continuous or prolonged growth and division in vitro. Potentially any cell line that is capable of expressing a p21cip1/waf1/reporter domain construct could be used for this screen. The cell line preferably has the properties of being immortalized and is capable of being replicated.
The cell line can be derived from any mammal, such as a mouse, rat, or human. Preferably, the cell line is derived from a human. Preferentially, the cell lines are neural. Some specific examples of cell lines include HT22 mouse hippocampal cell line, human cortical neuron cell line HCN-2, human cerebellum cell lines PFSK-1, D283 Med, and D341 Med, rat neuroblastoma cell line B35 and pheochromocytoma cell line PC12.
Preferably, the cell line includes cells that are capable of replicating a vector and expressing a heterologous gene encoded by a sequence in the vector. The vector optionally expresses a nucleic acid sequence that includes a p21cip1/waf1 promoter/reporter domain construct.
A vector as used herein refers to a nucleic acid construct, generated recombinantly or synthetically, with a series of nucleic acid elements that permit transcription of a particular nucleic acid in a cell that hosts the vector. The vector can be part of a plasmid, virus, or nucleic acid fragment.
Any vector or plasmid DNA may be used as a backbone for carrying the nucleic acid sequence that comprises a p21cip1/waf1 promoter operationally ligated to a reporter domain. Examples of suitable vectors include pGL3 vector (Promega, Madison, Wis.), pCAT3 vector (Promega, Madison, Wis.), and pSEAP2 Vector (Clontech).
Nucleic Acid Sequence
As stated above, the cell line includes a nucleic acid sequence that includes a p21cip1/waf1 promoter operationally ligated to a reporter domain. Nucleic acid includes polyribonucleic acid (RNA) and polydeoxyribonucleic acid (DNA), both of which may be single-stranded or double-stranded.
The term operationally ligated refers to a linkage of nucleotide elements in a functional relationship. A nucleic acid sequence is “operationally ligated” when it is placed into a functional relationship with another nucleic acid sequence. For example, a promoter or enhancer is operationally ligated to a coding sequence if it affects the transcription of the coding sequence. The nucleic acid sequences that are operationally ligated are typically contiguous and, where necessary to join two protein coding regions, contiguous and in reading frame.
The term promoter refers to a nucleic acid sequence capable of initiating and controlling expression of a coding sequence or functional RNA. The wild-type p21cip1/waf1 promoter is the promoter that is typically located upstream of (5′ to) the p21cip1/waf1 coding sequence. The sequence of full length wild-type p21cip1/waf1 promoter is well-known in the art. See, for example, NCBI GenBank accession number U24170 (SEQ ID NO: 1), by 2141-4656, shown in FIG. 1. See also FIG. 4, which shows a 2,400 bp human p21cip1/waf1 promoter sequence that was sub-cloned in to pGL3 Luciferase Reporter Vector (Promega Corp. WI).
The wild-type p21cip1/waf1 promoter is approximately 2.4 kb in size. It typically contains a TATA box, two p53-binding sites and six conserved GC boxes that are binding sites for the transcription factor Sp1. The six conserved binding sites for Sp1 are known in the art as Sp1-1, Sp1-2, Sp1-3, Sp1-4, Sp1-5 and Sp1-6. The binding sites for Sp1-5 and Sp1-6 overlap. The promoter may include additional recognition or binding sites for other factors involved in regulation of transcription of the gene.
As used herein, the term p21cip1/waf1 promoter refers to the full length wild-type p21cip1/waf1 promoter or a truncated p21cip1/waf1 promoter. The full length wild-type p21cip1/waf1 promoter is described above.
A truncated p21cip1/waf1 promoter has contiguous nucleotides removed from the 5′ end of the full length wild-type p21cip1/waf1 promoter, and must include at least a TATA box element. Truncated p21cip1/waf1 promoters are well-known in the art. For example, a truncated p21cip1/waf1 promoter may include a nucleic acid sequence of the full length wild-type p21cip1/waf1 promoter that lacks contiguous nucleotides from the 5′ end up to and including the two p53 binding sites (e.g., up to approximately −124 bp upstream, relative to the TATA box). Other examples include nucleic acid sequences of the full length wild-type p21cip1/waf1 promoter that lack contiguous nucleotides from the 5′ end up to and including the Sp1-1 site (e.g., up to approximately −110 bp upstream, relative to the TATA box), up to and including the Sp1-2 site (e.g., up to approximately −101 bp upstream, relative to the TATA box), up to and including the Sp1-3 site (e.g., up to approximately −70 bp upstream, relative to the TATA box), or up to and including the Sp1-4 site (e.g., up to approximately −60 bp upstream, relative to the TATA box).
Most preferably, the truncated p21cip1/waf1 promoter contains −60 bp upstream, relative to the TATA box. Such a preferred truncated p21cip1/waf1 promoter lacks the p53 binding sites and Sp1-1, Sp1-2, Sp1-3, and Sp-4 binding sites, but includes the Sp1-5 and Sp1-6 binding site and TATA box elements. See, for example, NCBI GenBank accession number U24171 (SEQ ID NO: 2), by 4593-4812, shown in FIG. 2. See also FIG. 3 which shows a 60 bp murine p21cip1/waf1 promoter sequence that was sub-cloned into pGL3 luciferase reporter vector (Promega Corp., WI).
The full length wild-type p21cip1/waf1 promoter necessarily encompasses regions of a truncated p21cip1/waf1 promoter, described above. Accordingly, compounds that induce a truncated p21cip1/waf1 promoter also induce the full length wild-type p21cip1/waf1 promoter. However, compounds that induce the full length wild-type p21cip1/waf1 promoter may not induce a truncated p21cip1/waf1 promoter.
Therefore, in one embodiment, the method for identifying drug candidates further includes providing an additional cell line comprising a second nucleic acid sequence that comprises a p21cip1/waf1 promoter operationally ligated to a reporter domain. For example, the method may include providing a first cell line that comprises a nucleic acid sequence that comprises a full length wild-type p21cip1/waf1 promoter operationally ligated to a reporter domain, and a second cell line that comprises a nucleic acid sequence that comprises a truncated wild-type p21cip1/waf1 promoter operationally ligated to a reporter domain. By providing more than one nucleic acid construct, a compound may be distinguished based on the mechanism (or binding site on the promoter) with which they induce expression of the reporter.
For purposes of the claimed invention, the p21cip1/waf1 promoter may be derived from any mammal, e.g., a mouse, rat, or human. Preferably, the full length wild-type p21cip1/waf1 promoter and cell line are derived from a human.
A reporter domain (or reporter) refers to a nucleic acid sequence that encodes a protein that is readily detectable, either by its presence or activity. The reporter domain is typically maintained under control of the promoter. Molecules used as reporters are well-known to one of skill in the art, and expression of a reporter domain in the cell-based reporter-gene assays may be detected by any technique well-known to one of skill in the art. Methods for detecting the expression of a reporter domain will vary with the reporter gene used.
Assays for the various reporter genes are well-known to one of skill in the art. For example, luciferase, beta-galactosidase (“b-gal”), beta-glucoronidase (“GUS”), beta-lactamase, chloramphenicol acetyltransferase (“CAT”), and alkaline phosphatase (“AP”) are enzymes that can be analyzed in the presence of a substrate and could be amenable to high throughput screening. For example, the reaction products of luciferase, beta-galactosidase (“b-gal”), and alkaline phosphatase (“AP”) are assayed by changes in light imaging (e.g., luciferase), spectrophotometric absorbance (e.g., b-gal), or fluorescence (e.g., AP). Assays for changes in light output, absorbance, and/or fluorescence are easily adapted for high throughput screening. For example, b-gal activity can be measured with a microplate reader. Green fluorescent protein (“GFP”) activity can be measured by changes in fluorescence. For example, in the case of mutant GFPs that fluoresce at 488 nm, standard fluorescence activated cell sorting (“FACS”) equipment can be used to separate cells based upon GFP activity.
Alterations in the expression of a reporter gene may be determined by comparing the level of expression of the reporter gene to a negative control (e.g., PBS or another agent that is known to have no effect on the expression of the reporter gene) and optionally, a positive control (e.g., an agent that is known to have an effect on the expression of the reporter gene, preferably an agent that effects untranslated region-dependent expression). Alternatively, alterations in the expression of a reporter gene may be determined by comparing the level of expression of the reporter gene to a previously determined reference range.
Nucleic acid sequences that include a p21cip1/waf1 promoter operationally ligated to a reporter domain are prepared by methods well-known in the art. The nucleic acid sequence can be incorporated into a vector or chromosomal DNA in the cells of the cell line.
Exposing the Cell to a Compound
Another step in the method for identifying drug candidates is exposing (treating) the cell to a compound. The term exposing refers to affecting an interaction or contact between the cell and compound, either directly or indirectly.
The cell can be exposed to a compound by any method. Suitable methods are known to those in the art. For example, the cell can be exposed to a compound by incubating the cell and compound in vitro.
The cell can also be exposed to the compound in vivo in a mammal, for example, in a laboratory mammal or in a human as part of clinical trials, as described above. The cell can be exposed to a compound in vivo by administering the compound to the mammal by methods known in the art, including the administration methods described below.
Identifying a Compound that Induces Expression of the Reporter
Another step in the method for identifying drug candidates is identifying a compound that induces expression of the reporter. A compound that induces expression of a reporter domain refers to a compound that is capable of increasing transcription or expression of a reporter gene.
The transcription or expression is increased relative to some base level of transcription or expression. The base level of transcription or expression is in the absence of the compound. Expression of the reporter is considered induced if the expression is increased by at least about 10%, preferably at least about 25%, more preferably at least about 50%, even more preferably at least about 75%, and most preferably at least about 90%, or more relative to some base level of transcription or expression.
A compound that activates a p21cip1/waf1 promoter initiates expression of p21cip1/waf1 Enhancing expression of p21cip1/waf1 inhibits cell cycle progression because p21cip1/waf1 is a key regulator of cell cycle entry, progression, and withdrawal. Therefore, a compound that induces expression of the reporter is a drug candidate for treating a medical condition that can be treated by (e.g., benefits from) inhibiting cell cycle progression.
The term treating or treated refers to relieving the condition by causing regression of the condition, preventing the condition from occurring in a mammal that may be predisposed to the condition, arresting the development of the condition, or ameliorating the condition or at least one symptom of the condition.
The term inhibiting cell cycle progression refers to slowing or preventing the process of passing through the cell cycle as compared to normal cells.
The term cell cycle progression refers to the process of passing through the different cell cycle phases. The cell cycle refers to the cyclic biochemical and structural events occurring during growth and division of cells. The phases of the cell cycle include G0 (Gap 0; rest phase), G1 (Gap1), S phase (DNA synthesis), G2 (Gap 2), and M phase (mitosis).
Medical conditions in which inhibiting cell cycle progression is desired as a treatment include a wide variety of conditions. Examples include various cancers and leukemias, cardiovascular conditions, neurodegenerative diseases of the nervous system (described below), including stroke, spinal cord injury, trauma, insult to the central nervous system, Alzheimer's disease, Parkinson's disease, Huntington's chorea, amylotrophic lateral sclerosis, etc., and spinocerebellar degenerations. Further examples include medical conditions that can be treated by enhancing expression of p21cip1/waf1.
A human patient suffering from a medical condition refers to a patient that has one or more symptoms of the stated medical condition or has a positive diagnosis based on one or more diagnostic tests.
Method for Enhancing p21cip1/waf1 Expression
In another aspect, the invention relates to a method for enhancing expression of p21cip1/waf1 protein in a human patient in need thereof. A patient in need thereof includes a patient suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1. The method includes administering to the patient an effective amount of a compound selected from the group consisting of ciclopirox olamine, dihydrocelastrol, colistimethate sodium, lycorine, diphenylurea, and acetylcysteine, chloroquine diphosphate, and 4′-methoxyflavone (acacetin).
In another embodiment, the method includes administering to the patient an effective amount of a compound selected from the group consisting of ciclopirox olamine, dihydrocelastrol, colistimethate sodium, lycorine, diphenylurea, and acetylcysteine.
In yet another embodiment, the method includes administering to the patient an effective amount of a compound selected from the group consisting of chloroquine diphosphate and 4′-methoxyflavone (acacetin).
Method for Enhancing p21cip1/waf1 Expression in Humans Suffering from Neurodegenerative Disease or Condition
p21cip1/waf1 protect cortical neurons from oxidative stress-induced death. p21cip1/waf1 can also promote neurite remodeling and axonal regeneration. See, for example, Langley B, et al. Pulse inhibition of HDACs induces complete resistance to oxidative death in cortical neurons without toxicity and reveals a role for cytoplasmic p21cip1/waf1 in cell cycle independent neuroprotection. J. Neuroscience. 28(1):163-176.
Accordingly, in another aspect, the human patient suffers from a neurodegenerative disease or condition. A neurodegenerative disease or condition typically refers to a disorder characterized by gradual and progressive loss of cells of the central or peripheral nervous system, which may lead to gradual and progressive loss of the corresponding tissue and/or organs. Examples of such cells include neurons, ganglia, Schwann cells, astrocytes, oligodendrocytes and microglia. Examples of corresponding tissue and organs include the brain and spinal cord.
For example, the neurodegenerative disease or condition can be an acute condition. Acute conditions generally occur as a result of trauma to a cell, tissue and/or organ of the nervous system. The trauma can, for example, partially or completely block blood flow to the cell, tissue and/or organ. Examples of acute neurodegenerative conditions include head injury and brain injury.
Alternatively, the neurodegenerative disease or condition can be a chronic neurodegenerative condition. Examples of chronic neurodegenerative diseases and conditions include Parkinson's disease, Alzheimer's disease, Huntington's disease and Amyotrophic Lateral Sclerosis (also known as Lou Gherig's disease).
Method for Enhancing p21cip1/waf1 Expression in Humans Suffering from Stroke
In a further aspect, the human patient suffers from the consequences of a stroke. Stroke generally involves the interruption of blood flow to and/or within the brain. The interruption of blood flow can be due to, for example, a blockage or rupture of an artery or vessel. The blockage typically occurs from a blood clot. As a result of the interruption of blood flow, the brain does not receive sufficient amounts of blood.
A loss of p21cip1/waf1 increases the amount of damage that stroke causes to the brain. Accordingly, in one aspect of the invention, a method for enhancing expression of p21cip1/waf1 in a human patient suffering from stroke is provided.
Method for Enhancing p21cip1/waf1 Expression in Humans Suffering from Spinal Cord Injury
In still a further aspect, the human patients suffer from spinal cord injury. Spinal cord injury refers to any damage to the spinal cord. The damage typically results in loss of function, such as mobility or feeling. Damage to the spinal cord can occur, for example, as a result or trauma (car accident, gunshot, falls, etc.) or disease (polio, spina bifida, Friedreich's Ataxia, etc).
Any injury to the spinal cord can be treated in accordance with the method of the present invention. For example, the injury can be a complete injury to the spinal cord. Complete injury typically refers to the lack of function (e.g., no sensation and no voluntary movement) below the site of injury. Both sides of the body are usually affected.
Alternatively, the injury may be an incomplete injury to the spinal cord. An incomplete injury generally refers to some function below the site of injury. For instance, a person with an incomplete injury may be able to move one limb more than another, may be able to feel parts of the body that cannot be moved, or may have more functioning on one side of the body than the other, etc.
Compounds
The drug candidate can be any chemical or biological molecule, including a small molecule. The drug candidate can be a salt of any such compounds.
A biological molecule is any molecule which contains a nucleic acid or amino acid sequence and has a molecular weight greater than 450. Examples of a biological molecule include nucleic acid molecules, oligonucleotides, oligopeptides, polypeptides, or proteins including antisense and dominant negative molecules; polypeptides, peptides, and proteins.
Small molecules include organic compounds, organometallic compounds, salts of organic and organometallic compounds, saccharides, amino acids, and nucleotides. Small molecules can further include molecules that would otherwise be considered biological molecules, except their molecular weight is not greater than 450. Thus, small molecules may be lipids, oligosaccharides, oligopeptides, and oligonucleotides, and their derivatives, having a molecular weight of 450 or less.
It is emphasized that small molecules can have any molecular weight. They are merely called small molecules because they typically have molecular weights less than 450. Small molecules include compounds that are found in nature as well as synthetic compounds.
Compounds useful in the methods of the present invention and processes to produce such compounds are known. For example, known compounds useful in the methods of the present invention preferably include ciclopirox olamine, dihydrocelastrol, colistimethate sodium, lycorine, diphenylurea, and acetylcysteine. Some additional compounds include chloroquine diphosphate and 4′-methoxyflavone (acacetin).
The compounds can be in the form of a pharmaceutically acceptable salt. The term “pharmaceutically acceptable salt” refers to a well-tolerated, nontoxic salt prepared from any one of the compounds mentioned above that have a basic and/or an acidic group, and an acid or base, respectively.
The acids may be inorganic or organic acids of any one of the compounds mentioned above. Examples of inorganic acids include hydrochloric, hydrobromic, nitric hydroiodic, sulfuric, and phosphoric acids. Examples of organic acids include carboxylic and sulfonic acids. The radical of the organic acids may be aliphatic or aromatic. Some examples of organic acids include formic, acetic, phenylacetic, propionic, succinic, glycolic, glucuronic, maleic, furoic, glutamic, benzoic, anthranilic, salicylic, phenylacetic, mandelic, embonic (pamoic), methanesulfonic, ethanesulfonic, panthenoic, benzenesulfonic, stearic, sulfanilic, alginic, tartaric, citric, gluconic, gulonic, arylsulfonic, and galacturonic acids.
Appropriate organic bases may be selected, for example, from N,N-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine (N-methylglucamine), and procaine.
Administration
The compounds are administered to a human patient suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1 or by inhibiting cell cycle progression. The compound can be administered by any method known to those skilled in the art. Some examples of suitable modes of administration include systemic administration. Systemic administration can be enteral or parenteral, and preferably is oral administration. Liquid or solid formulations can be employed for systemic administration. Some suitable formulations include tablets, capsules, such as gelatin capsules, pills, troches, elixirs, suspensions, syrups, and wafers. Parenteral administration of the compound includes, for example, intravenous, intramuscular, and subcutaneous injections.
The compound is preferably in a suitable pharmaceutical composition comprising a pharmaceutical carrier. In this specification, a pharmaceutical carrier is considered to be synonymous with a vehicle or an excipient as is understood by practitioners in the art. Examples of carriers include starch, milk, sugar, certain types of clay, gelatin, stearic acid or salts thereof, magnesium or calcium stearate, talc, vegetable fats or oils, gums and glycols.
The pharmaceutical composition may also comprise one or more of the following: a stabilizer, a surfactant, preferably a nonionic surfactant, and optionally a salt and/or a buffering agent.
The stabilizer may, for example, be an amino acid, such as for instance, glycine; or an oligosaccharide, such as for example, sucrose, tetralose, lactose or a dextran. Alternatively, the stabilizer may be a sugar alcohol, such as for instance, mannitol; or a combination thereof. Preferably the stabilizer or combination of stabilizers constitutes from about 0.1% to about 10% weight for weight of the compound.
The surfactant is preferably a nonionic surfactant, such as a polysorbate. Some examples of suitable surfactants include Tween 20, Tween 80; a polyethylene glycol or a polyoxyethylene polyoxypropylene glycol, such as Pluronic F-68 at from about 0.001% (w/v) to about 10% (w/v).
The salt or buffering agent may be any salt or buffering agent. Suitable salts include, for example, sodium or potassium chloride. Suitable buffers include, for example, mixtures of citric acid and sodium or potassium citrate, and sodium or potassium bicarbonate or biphosphate. Preferably, the buffering agent maintains the pH of the pharmaceutical composition in the range of about 5.5 to about 7.5. The salt and/or buffering agent is also useful to maintain the osmolality at a level suitable for administration to a mammal. Preferably the salt or buffering agent is present at a roughly isotonic concentration of about 150 mM to about 300 mM.
A compound may be administered to a mammal by controlled release, as is known in the art. Controlled release administration is a method of drug delivery to achieve a certain level of the drug over a particular period of time. Suitable controlled release formulations include delayed, sustained, and immediate (i.e., instantaneous) release. Methods for controlled release of drugs are well known in the art, and are described in, for example, U.S. Pat. Nos. 5,567,439; 6,838,094; 6,863,902; and 6,905,708, which are hereby incorporated by reference.
The compound is administered to the patient in an amount effective in achieving its purpose. For example, an effective amount may include an amount exposed to a cell that is sufficient to enhance expression of p21cip1/waf1 The effective amount of the compound to be administered can be readily determined by those skilled in the art during pre-clinical trials and clinical trials by methods familiar to physicians and clinicians. Typical daily doses include approximately 1 mg to 1000 mg.
In one aspect, the compound is considered to be effective in enhancing p21cip1/waf1 expression if the expression of p21cip1/waf1 is enhanced by at least about 10%, preferably at least about 25%, more preferably at least about 50%, even more preferably at least about 75%, and most preferably at least about 90%. The p21cip1/waf1 expression is considered enhanced relative to some base level of expression. The base level of expression is a level of induction that occurs in the absence of the compound.
The pharmaceutical composition may additionally contain one or more conventional additives. Some examples of such additives include a solubilizer such as, for example, glycerol; an antioxidant such as for example, benzalkonium chloride (a mixture of quaternary ammonium compounds, known as “quart”), benzyl alcohol, chloretone or chlorobutanol; anaesthetic agent such as for example a morphine derivative; or an isotonic agent etc., such as those described above. As a further precaution against oxidation or other spoilage, the compound may be stored under nitrogen gas in vials sealed with impermeable stoppers.
EXAMPLES
Example 1
A 2000 compound library was tested to identify drug candidates that enhance expression of p21cip1/waf1. The library tested was The Sprectrum CollectionTM from MicroSource Discovery System, Inc. (Groton, Conn.). The 2000 compounds in the library are primarily Food and Drug Administration (FDA)-approved compounds or natural products. An alphabetical list of the compounds is available at the MicroSource Discovery website at www.msdiscovery.com/spect.html, which is incorporated by reference. The compounds are supplied as 10 mM solutions in dimethyl sulfoxide (DMSO).
The library was screened using murine hippocampal HT22 cells transfected with a p21cip1/waf1 promoter-luciferase construct. Compounds that induced expression of the reporter at a level approximately 2-fold above the base level were identified.
Example 2
In another analysis, realtime PCR was performed. Cultured rat primary cortical neurons were treated with the respective drug for 12 hours. Neurons were harvested and RNA extracted using TriZolTM reagent (Invitrogen). cDNA was synthesized by standard reverse-transcriptase protocol. Realtime PCR performed using Applied Biosystems Realtime PCR cycler and rat p21-specific TaqMan primer and probe set. Data is displayed as fold induction relative to control (1-fold), which received vehicle only (no drug). See FIG. 5.
Example 3
Based on available dosing data, rats were dosed with 1, 5, 10, 15 or 30 mg/kg ciclopirox (intraperiotoneal; 3 animals per concentration). Spinal cord, liver and skeletal muscle tissue was harvested 6-hours after drug delivery. Real-time rt-PCR was performed on RNA extracted from tissues to examine the expression of p21waf1/cip1, arginase-1, and VEGF in order to determine what might be the most efficacious dose.
Microarray gene analysis was also performed on spinal cord tissue RNA to determine gene expression changes that correlate with treatment and dose in an unbiased manner. These studies revealed that the arylhydrocarbon receptor (AHR) was a dose-dependent ciclopirox-regulated gene, in vivo, and provided confidence that ciclopirox could penetrate the blood brain barrier and could induce transcription in the spinal cord.
Results from these studies show that ciclopirox given as single 30 mg/kg intraperiotoneal injection 30 minutes after a contusion injury at the level of T-8, can provide significant protection (reduced lesion volume). The effects of a single injection after injury on behavior showed little functional improvement.
Example 4
High Throughput Screen for p21 Activators
To identify novel activators of p21, fragments of the mouse or human p21 promoter were subcloned into the pGL3 basic promoter-reporter construct (see promoter sequence information). The resultant p21-luciferase reporter plasmids were each then stably transfected into a mouse hippocampal cell line, HT22. Several lines were generated and each showed predicted increases in p21-luciferase in response to the known p21 inducer trichostatin A (a HDAC inhibitor). Drugs were added to cells stably expressing p21-luciferase in a 96 well format. The HDAC inhibitor trichostatin A was used as a positive control. After 12 hours of drug treatment, the cells were lysed and luciferase activity was measured using a desktop luminometer. Cell viability was monitored in parallel, so that agents that induce toxicity can quickly be eliminated. Secondary screens including real time PCR or Western blots of p21 were monitored in primary neurons.
Example 5
Survival Assays—Oxidative Stress
Primary cortical neurons from E17 rat embryos were prepared according to a well-established papain dissociation method as described previously (Ratan, R. R., Murphy, T. H., Baraban, J. M. Oxidative stress induces apoptosis in embryonic cortical neurons. J Neurochem, 62, 376-379, (1994)). These neurons were plated on poly-D-lysine (Sigma) coated cell culture plates at a density of 1×106 cells/ml in minimal essential medium (MEM, Gibco BRL) with 5.5 g/l glucose, 10% FCS, 2 mM L-glutamine, 100 μM cysteine. 24 h after plating, neurons were rinsed with warm phosphate buffered saline and incubated with media containing HCA (2.5 or 5 mM). Control neurons were supplied media without HCA. In parallel, cortical neurons were co-treated with the “compounds/drugs” at the time of HCA exposure to evaluate neuronal protection. A concentration range was used to ensure a therapeutic dose. After incubation with treatment media for 24 h cells were assayed for viability. Calcein-acetoxymethy 1 ester (AM)/ethidium homodimer-1 staining (live/dead assay) (Molecular Probes, Eugene, Oreg.) under fluorescence microscopy and the MTT assay (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) (Promega, Madison, Wis.) methods were used as measures of cell viability and death. Testing of the compounds was performed in 48-well cell culture plates with 4-6 wells per treatment and repeated four times.
SEQUENCE LISTING
Incorporated herein by reference in its entirety is the attached Sequence Listing, which was created on Jun. 5, 2008.

## Claims

1. A method for enhancing expression of p21cip1/waf1 in a human patient suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1, the method comprising administering to the patient an effective amount of a compound selected from a group consisting of dihydrocelastrol, colistimethate sodium, lycorine, diphenylurea and chloroquine diphosphate, wherein expression of p21cip1/waf1 is enhanced in the patient suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1.

2. The method according to claim 1, wherein the compound is selected from the group consisting of dihydrocelastrol, colistimethate sodium, lycorine, and diphenylurea.

3. The method according to claim 1, wherein the medical condition is spinal cord injury.

4. The method according to claim 1, wherein the medical condition is stroke, trauma, or insult to the central nervous system.

5. The method according to claim 1, wherein the medical condition is a neurodegenerative disease.

6. The method according to claim 1, wherein the neurodegenerative disease is Parkinson's disease, Alzheimer's disease, Huntington's disease or amyotrophic lateral sclerosis.

7. The method according to claim 1, wherein the compound is selected from the group consisting of dihydrocelastrol, colistimethate sodium, lycorine, and diphenylurea.

8. The method according to claim 1, wherein the compound is dihydrocelastrol.

9. The method according to claim 1, wherein the compound is chloroquine diphosphate.

10. The method according to claim 1, wherein the compound is colistimethate sodium.

11. The method according to claim 1, wherein the compound is lycorine.

12. The method according to claim 1, wherein the compound is diphenylurea.

13. A method for enhancing expression of p21cip1/waf1 in a human patient suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1, the method comprising administering to the patient an effective amount of colistimethate sodium, wherein expression of p21cip1/waf1 is enhanced in the patient suffering from a medical condition that can be treated by enhancing expression of p21cip1/waf1, wherein the medical condition is selected from the group consisting of spinal cord injury, stroke, trauma, Parkinson's disease, Alzheimer's disease, Huntington's disease and amyotrophic lateral sclerosis.