# Patent

## Title
28-epirapalogs

## Abstract

Rapamycin derivatives containing substituents at C-28 in the epi orientation relative to rapamycin are disclosed, together with methods for their preparation and use, e.g. for regulation of biological phenomena in engineered cells. The compounds may contain optional additional modifications relative to rapamycin, as disclosed herein.

## Background
This application claims the priority benefit of, U.S. Ser. No. 60/150,447, filed Aug. 24, 1999 the full contents of which are hereby expressly incoporated herein by reference.


BACKGROUND OF THE INVENTION
Rapamycin is a macrolide antibiotic produced by Streptomyces hygroscopicus. It binds to a FK506-binding protein, FKBP, with high affinity to form a rapamycin:FKBP complex. Reported Kd values for that interaction are as low as 200 pM. The rapamycin:FKBP complex binds with high affinity to the large cellular protein, FRAP, to form a tripartite, [FKBP:rapamycin]:[FRAP], complex. In that complex rapamycin acts as a dimerizer or adapter to join FKBP to FRAP.




Rapamycin is potent immunosuppressive agent and is used clinically to prevent rejection of transplanted organs.
Because it serves as an adapter to complex FKBP with FRAP, rapamycin is also capable of multimerizing appropriately designed chimeric proteins incorporating FKBP-derived domains and FRAP-derived domains. Because of that activity, rapamycin and various derivatives or analogs thereof have also been used as multimerizing agents for activating biological switches based on such chimeric proteins. See e.g., WO96/41865; WO 99/36553; Rivera et al, Proc Natl Acad Sci USA 96, 8657–8662; and Ye Xet al (1999) Science 283, 88–91. In the case of rapamycin itself, its significant biological activities, including potent immunosuppressive activity, limit its use in biological switches in certain applications, especially those in animals or animal cells which are sensitive to rapamycin.
A large number of structural variants of rapamycin have been reported, typically arising as alternative fermentation products or from synthetic efforts to improve the compound's therapeutic index as an immunosuppressive agent. For example, the extensive literature on analogs, homologs, derivatives and other compounds related structurally to rapamycin (“rapalogs”) include, among others, variants of rapamycin having one or more of the following modifications relative to rapamycin: demethylation, elimination or replacement of the methoxy at C7, C42 and/or C29; elimination, derivatization or replacement of the hydroxy at C13, C43 and/or C28; reduction, elimination or derivatization of the ketone at C14, C24 and/or C30; replacement of the 6-membered pipecolate ring with a 5-membered prolyl ring; and alternative substitution on the cyclohexyl ring or replacement of the cyclohexyl ring with a substituted cyclopentyl ring. Additional historical information is presented in the background sections of U.S. Pat. Nos. 5,525,610; 5,310,903 and 5,362,718. See also U.S. Pat. No. 5,527,907.
New rapalogs with reduced immunosuppressive activity and/or interesting pharmacokinetic or bioavailability profiles would be very desirable for use as multimerizing agents or antifungal agents.
New rapalogs with improved characteristics relative to rapamycin, e.g., in therapeutic index, bioavailability, pharmacokinetics, stability, etc., would also be of interest as immunosuppressants.
SUMMARY OF THE INVENTION
While exploring alternative Lewis acids for C7 nucleophilic substitution chemistry, we discovered that treatment of rapamycin with Ti(OiPr)4 in dichloromethane in the absence of any nucleophiles resulted in an unprecedented reaction to afford an unknown compound as the major product. Through NMR analysis followed by X-ray crystollographic analysis we determined conclusively, and to our surprise, that we had produced for the first time the novel rapalog, 28-epirapamycin:




This transfromation represents an efficient and selective epimerization method for converting rapamycin to the novel compound, 28-epirapamycin, under extremely mild and neutral conditions.

This discovery opens the door to a new and interesting class of rapalogs based on 28-epirapamycin. The new class includes 28-epirapamycin as well as derivatives and analogs thereof which are modified (with respect to the structure of rapamycin) at one or more positions in addition to C28. This invention also provides compositions and methods based on these new 28-epirapalogs for multimerizing chimeric proteins in genetically engineered cells, and in certain cases, for suppressing the immune response or treating or preventing a pathogenic fungal infection in a patient in need thereof. Compositions comprising the 28-epi compounds of this invention are preferably substantially free from the homologous C28 epimer (i.e., from the epimer having the stereochemistry of C28 found in rapamycin). In other words, preferred compositions comprising the 28-epi compounds of this invention contain no more than 20% of the naturally occurring epimer at position 28, more preferably, less than 10%, even more preferably less than 5%, and most preferably, less than 1% of the homologous C28 epimer, on either a weight or molar basis.
Compounds of this invention include 28-epi rapamycin and 28-epi rapalogs additionally modified at one or more substituents at C7, C13, C14, C24, C28, C30 and the cyclohexyl ring bearing C43. A wide variety of synthetic transformations at those sites are known in the literature and may be adapted to the present invention, e.g., by substituting 28-epirapamycin for rapamycin as the starting material. Many of those transformations are noted herein. See also WO 99/36553. In adition, numerous naturally occurring analogs of rapamycin are known in the literature which may be epimerized at position 28 as described herein. Compounds of this invention further include 28-epirapalogs which are based on a pipecolyl or prolyl ring system (i.e., “n”, as shown in the following structure, may be 1 or 2). The compounds of this invention further include pharmaceutically acceptable derivatives of the 28-epirapalogs. This is discussed in detail below. Again, numerous examples of these additional structural modifications (i.e., modifications other than epimerization at position 28), and methods for obtaining those variants of rapamycin, are known in the literature, are exemplified below and may be adapted to the present invention to provide the full family of 28-epirapalogs.
One subgenus of such compounds is illustrated by Formula I:




where

    n is 1 or 2;
    R28 and R43 are independently selected from the group consisting of H and a substituted or unsubstituted aliphatic, acyl, aroyl or heteroaroyl moiety;
    one of R7a and R7b is H and the other is halo, —RA, —ORA, —SRA, —OC(O)RA, —OC(O)NRARB, —NRARB, —NRBC(O)RA, —NRBC(O)ORA, —NRBSO2RA or —NRBSO2NRARB′; or R7a and R7b, taken together, are H in the tetraene moiety:






    where RA is H or a substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety and where RB is H, OH or a substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety.


The compound may be in the form of a substantially pure stereoisomer or mixture of stereoisomers, or a pharmaceutically acceptable derivative thereof. Preferably the compoiund is present as a substantially pure stereoisomer with respect to position 28, and more preferably with respect to both position 28 and 43.
The compounds may be based on a prolyl ring (n=1) or on a pipecolate ring (n=2), although the latter are currently of particular interest.
One subset of interest are those compounds of Formula I which retain the substituents of rapamycin at C7, i.e., in which R7a is —OMe and R7b is H. This subset includes 28-epirapamycin itself, as well as derivatives and analogs thereof which are modified at one or more positions other than C7, relative to the structure of rapamycin (e.g., at position 28 and/or 43).
Another subset of interest are those compounds of Formula I, including those subsets mentioned above and those described below, in which R28 is a moiety other than H. For instance, R28 may be alkyl, benzyl or other substituted alkyl, allyl, etc.
Another subset of interest are those compounds of Formula I, including those subsets mentioned above and those described below, in which one or both of R28 and R43 are H. This subset includes 28-epirapamycin itself, compounds further modified at C7, and others.
Another subset of interest are those 28-epi compounds of Formula I in which one or both substituents at C7 differ from the corresponding C7 substituents of rapamycin, i.e., in which R7a is a moiety other than —OMe and/or R7b is a moiety other than H. In some compounds of this subset, one of R7a and R7b is a substituted or unsubstituted aryl or heteroaryl, a ubstituted or unsubstituted unsaturated aliphatic, aryl or heteroaryl ether, a substituted or unsubstituted benzyl ether, —NRBCONRARB, —NRBC(O)RA, —NRBC(O)ORA, —NRBSO2RA or —NRBSO2NRARB. In some of those cases, as in other compounds of Formula I more generally, RB may be H, OH or alkyl. Examples of such moieties include —NH—C(O)ORA, —NH—C(O)ORA, —NH—SO2RA. etc, as well as N-alkyl (e.g., N-methyl, N-ethyl, etc) and N-hydoxyl derivatives thereof. In some embodiments of interest, RA is H, while in some others it is a substituted or unsubstituted aliphatic, e.g. alkyl, moiety. As a general rule, where this document includes a compound containing an —NH— moiety (e.g., —NHRA, —NHC(O)RA, —NHSO2RA, etc.), the related N-alkyl and N-hydroxyl compounds (e.g. —N(RA′)RA, —N(RA′)C(O)RA, —N(RA′)SO2RA, —N(OH)RA, —N(OH)C(O)RA, —N(OH)SO2RA, etc.) are also included, where RA is H or a substituted or unsubstituted aliphatic, heteroaliphatic, aryl, or heteroaryl moiety.
By way of further illustration, this subset includes 28-epirapalogs of Formula I in which C7 bears the following sort of substituents:




Literature procedures are available for attaching such substituents to the C7 position of rapamycin, and those procedures were used to make the corresponding C7 28-epirapalogs.

The foregoing subset includes 28-epirapalogs (in which n is 1 or 2) which are further modified only at C7, i.e., in which R28 and R43 are H, as well as compounds which contain modifications at one or more further positions in addition to C7 and C28. Such more highly derivatized compounds of this subset include those in which R28 is a moiety other than H.
Another interesting subset of compounds of Formula I includes those 28-epirapalogs of Formula I, including compounds of the subsets described above and below, in which R43 is a moiety other than H—i.e., with or without any further modifications disclosed herein. This subset includes among others compounds of Formula I in which R43 is an aliphatic or acyl moiety. Illustrative aliphatic moieties include substituted or unsubstituted alkyl moieties such as a hydroxyalkyl group like —CH2CH2OH, an alkoxyalkyl group such as CH30CH2—, a substituted or unsubstituted benzyl group and the like, or a substituted or unsubstituted alkenyl or alkynyl moiety such as an allyl or substituted ally moiety. Illustrative acyl moieties include moieties such as alkyl-CO—, aminoalkyl-CO—, substituted aminoalkyl-CO—, etc., including substituted or unsubstituted gylcinates (e.g., RARBN—CH2—CO—) and other substituted and unsubsituted esters at C43. Such functional groups may be used to derivatize one or more other hydroxyl moieties in the 28-epirapalog, in addition to or instead of at C43. In all cases, except as noted below, the substituent at C43 may be present in either stereochemical orientation, or the compound may be present in a mixture of both C43 stereoisomers.
Another interesting subset of compounds of Formula I include those in which n is 2, R7a is —OMe and R7b and R28 are both H.
Compounds of this invention also include 24,30-tetrahydro-28-epi rapalogs as illustrated by Formula II:




where the R groups are as described above. The parent compound, 24,30-tetrahydro-28-epirapamycin may be prepared using the literature procedure for converting rapamycin to 24,30-tetrahydro-rapamycin, but starting with 28-epirapamycin instead of rapamycin. See e.g. WO 99/36553.

These and other compounds of this invention may be based on a prolyl ring (n=1) or on a pipecolate ring (n=2), although the latter are currently of particular interest. The moiety, —OR43, may be in the S or R orientation.
One subset of interest are those compounds of Formula II which retain the substituents of rapamycin at C7, i.e., in which R7a is —OMe and R7b is H. This subset includes 24,30-tetrahydro-28-epirapamycin itself, as well as derivatives and analogs thereof which are modified at one or more positions other than C7, relative to the structure of rapamycin (e.g., at position 28 and/or 43).
Another subset of interest are those compounds of Formula II, including those subsets mentioned above and those described below, in which one or both of R28 and R43 are H. This subset includes 24,30-tetrahydro-28-epirapamycin itself, compounds further modified at C7, and others.
Another subset of interest are those 24,30-tetrahydro-28-epi compounds of Formula II in which one or both substituents at C7 differ from the corresponding C7 substituents of rapamycin, i.e., in which R7a is a moiety other than —OMe and/or R7b is a moiety other than H. Such moieties may be selected from those discussed elsewhere in this document in connection with C7 modification.
The foregoing subset includes 24,30-tetrahydro-28-epirapalogs (in which n is 1 or 2) which are further modified only at C7, i.e., in which R28 and R43 are H, as well as compounds which contain modifications at one or more further positions in addition to C7 and C28. Such more highly derivatized compounds of this subset, include those in which one or both of R28 and R43 are also modified relative to rapamycin.
Another interesting subset of compounds of Formula II includes those 24,30-tetrahydro-28-epirapalogs of Formula II, including compounds of the subsets described above and below, in which R43 is a moiety other than H—i.e., with or without any further modifications disclosed herein. This subset includes compounds of Formula II in which R43 is an aliphatic or acyl moiety. Illustrative aliphatic moieties include substituted or unsubstituted alkyl moieties such as a hydroxyalkyl group such as —CH2CH2OH, and the like or a substituted or unsubstituted alkenyl or alkynyl moiety such as an allyl or substituted ally moiety. Illustrative acyl moieties include moieties such as alkyl-CO—, aminoalkyl-CO—, substituted aminoalkyl-CO—, etc., including gylcinate and other substituted and unsubsituted esters at C43.
Another interesting subset of compounds of Formula II include those in which n is 2, R7a is —OMe and R7b and R28 are both H.
Also of interest are 28,29-bisepirapalogs which contain one or more further modifications relative to rapamycin, e.g. at one or more of C7, C13, C14, C24, C30 and the cyclohexyl ring system which in rapamycin bears the —OR43 substituent.
The various 28-epirapalogs may be formulated with one or more pharmaceutically acceptable carriers, diluents or excipients to form a pharmaceutically acceptable composition comprising one of the compounds of this invention.
Our epimerization method is broadly applicable to aldols generally and may be used to advantage in pharmaceutical and non-pharmaceutical syntheses. Thus this invention further provides a new general method for epimerizing the hydroxy group of an aldol moiety which comprises contacting a compound containing an aldol moiety with a titanium tetraalkoxide reagent under suitable conditions and for a sufficient time to permit epimerization. Preferably the reaction is run below about 75 C, more preferably below about 50 C and even more preferably below 30 C. Preferably no base is added to the reactants. Suitable titanium tetraalkoxide reagents include compounds such as titanium tetraisopropoxide. In many cases, the epimerized product will be recovered from the reaction mixture. Individual isomers may be separately recovered and purified. While the reaction may be applied to a wide variety of aldols, it is particularly useful for epimerizing aldols in sensitive molecules such as polyfunctional macrocycles and other natural products, including rapamycin and rapamycin derivatives and analogs. Depending on the choice of reaction time and conditions, the method may be used for the production of 28-epirapamycin, 28-epirapalogs, 29-epirapamycin, 29-epirapalogs, 28, 29-bis-epirapamycin and 28,29-bis-epirapalogs.
The new 28-epirapalogs of this invention may be used as antifungal agents as described for other rapalogs in WO 98/02441 (especially in the case of C7-derivatized 28-epirapalogs). They may also be used as immunosuppressants as described for rapamycin in the scientific and patent literature, examples of which are cited below (especially in the case of 28-epirapalogs with an unmodified C7 substituent relative to rapamycin, or which in any event lack a bulky replacement C7 substituent). The compounds of this invention may also be used for multimerizing chimeric proteins in cells for a variety of important purposes, as described in detail for rapamycin and other rapalogs in WO 96/41865 and WO 99/36553. The use of 28-epirapalogs to multimerize chimeric proteins in genetically engineered cells is described at further length below.
The genetically engineered cells referred to above contain one or more recombinant nucleic acid constructs encoding specialized chimeric proteins as described herein. Typically a first chimeric protein contains one or more FKBP domains which are capable of binding to a 28-epirapalog of this invention. This first chimeric protein is also referred to herein as an “FKBP fusion protein” and further comprises at least one protein domain heterologous to at least one of its FKBP domains. The complex formed by the binding of the FKBP fusion protein to the rapalog is capable of binding to a second chimeric protein which contains one or more FRB domains (the “FRB fusion protein”). The FRB fusion protein further comprises at least one protein domain heterologous to at least one of its FRB domains. In some embodiments, the FKBP fusion protein and the FRB fusion protein are different from one another. In other embodiments, however, the FKBP fusion protein is also an FRB fusion protein. In those embodiments, the chimeric protein comprises one or more FKBP domains as well as one or more FRB domains. In such cases, the first and second chimeric proteins may be the same protein, may be referred to as FKBP-FRB fusion proteins and contain at least one domain heterologous to the FKBP and/or FRB domains.
The chimeric proteins may be readily designed, based on incorporation of appropriately chosen heterologous domains, such that their multimerization triggers one or more of a wide variety of desired biological responses. The nature of the biological response triggered by rapalog-mediated complexation is determined by the choice of heterologous domains in the fusion proteins. The heterologous domains are therefore referred to as “action” or “effector” domains. The genetically engineered cells for use in practicing this invention will contain one or more recombinant nucleic acid constructs encoding the chimeric proteins, and in certain applications, will further contain one or more accessory nucleic acid constructs, such as one or more target gene constructs. Illustrative biological responses, applications of the system and types of accessory nucleic acid constructs are discussed in detail below.
A system involving related materials and methods is disclosed in WO 96/41865 and WO 99/36553 (Clackson et al) and is expected to be useful in a variety of applications including, among others, research uses and therapeutic applications. See also Rivera V M, Ye X, Courage N L, Sachar J, Cerasoli F, Wilson J M and Gilman M. (1999) Long-term regulated expression of growth hormone in mice following intramuscular gene transfer. Proc Natl Acad Sci USA 96, 8657–8662; and Ye X, Rivera V M, Zoltick P, Cerasoli F Jr, Schnell M A, Gao G-p, Hughes J V, Gilman M, and Wilson J M (1999) Regulated delivery of therapeutic proteins after in vivo somatic cell gene transfer. Science 283, 88–91.
Part of the subject invention is based upon a system similar to that disclosed in the foregoing patent documents and related scientific publications, but involves the use of the new 28-epirapalogs as the multimerizing agent. The subject invention thus provides a method for multimerizing chimeric proteins in cells which comprises (a) providing appropriately engineered cells containing nucleic acid constructs for directing the expression of the desired chimeric protein(s) and any desired accessory recombinant constructs, and (b) contacting the cells with a 28-epirapalog or a pharmaceutically acceptable derivative thereof as described herein. The rapalog forms a complex containing itself and at least two molecules of the chimeric protein(s). Improved rapalogs for use in this invention include the following.
New rapalogs which may be used in the various methods of this invention include those comprising the substructure shown in Formula III:




bearing any number of a variety of substituents, and optionally unsaturated at one or more carbon—carbon bonds. Substituent “a” is a five or six membered ring, variously subsituted, such as is depicted elsewhere in this document. Certain 28-epirapalogs of this invention, especially those which differ from rapamycin with respect to the substituents at C7, may be used in applications where it is desirable to have a substantially reduced immunosuppressive effect as compared with rapamycin. By a “substantially reduced immunosuppressive effect” we mean that the rapalog has less than 0.1, preferably less than 0.01, and even more preferably, less than 0.005 times the immunosuppressive effect observed or expected with an equimolar amount of rapamycin, as measured either clinically or in an appropriate in vitro or in vivo surrogate of human immunosuppressive activity, preferably carried out on tissues of lymphoid origin, or alternatively, that the rapalog yields an EC50 value in such an in vitro assay which is at least ten times, preferably at least 100 times and more preferably at least 250 times larger than the EC50 value observed for rapamycin in the same assay.

One appropriate in vitro surrogate of immunosuppression in a human patient is inhibition of mammalian T cell proliferation in vitro. This is a conventional assay approach that may be conducted in a number of well known variations using various human or murine T cells or cells lines, including among others human PBLs and Jurkat cells. A rapalog may thus be assayed for human immunosuppressive activity and compared with rapamycin. A decrease in immunosuppressive activity relative to rapamycin measured in an appropriate in vitro assay is predictive of a decrease in immunosuppressive activity in humans, relative to rapamycin. Such in vitro assays may be used to evaluate the rapalog's relative immunosuppressive activity.
A variety of illustrative examples of 28-epirapalogs are disclosed herein. The compounds disclosed herein may also be further derivatized, e.g. at one or more of C7, C43, C13, C24 and C30 and elsewhere, by adapting chemical transformations disclosed in WO 96/41865, WO 98/02441, WO 99/36553 and other patent documents cited herein. 28-epirapalogs of particular interest include among others, those which bind to human FKBP12, or inhibit its rotamase activity, within two, and more preferably within one order of magnitude of results obtained with rapamycin in any conventional FKBP binding or rotamase assay.
Other classes of 28-epirapalogs which may be used in practicing the methods of this invention are defined with reference to the structures shown below:




(or an otherwise derivatized 5- or 6-membered ring), other substituents are as defined previously, and, each substituent may be present in either stereochemical orientation unless otherwise indicated, and where each occurrence of R8 is H, halo, —CN, —CORA, —ORA, —NRARB, OSO2CF3, OSO2F, OSO2RB, OCORB, OCONRA′RB, or OCON(ORA)RB.

28-epirapalogs useful in practicing this invention, including rapalogs of the various foregoing formulas, may (in the absence of defined stereochemistry) contain substituents in any of the possible stereoisomeric orientations, and may comprise one stereoisomer substantially free of other stereoisomers (>90%, and preferably >95%, free from other stereoisomers on a molar basis) or may comprise a mixture of stereoisomers. Novel compounds of this invention specifically exclude 28,29-bis-epirapamycin or 28,43-bis-epirapamycin per se (i.e., absent additional modifications relative to the structure of rapamycin).
Again, the 28-epirapalogs as described herein are used in a method for multimerizing chimeric proteins in genetically engineered cells. The method involves (a) providing appropriately engineered cells containing nucleic acid constructs for directing the expression of the desired chimeric proteins (and any desired accessory recombinant constructs), and (b) contacting the cells with a 28-epirapalog or a pharmaceutically acceptable derivative thereof.
In one embodiment, at least one of the chimeric proteins contains at least one FKBP domain whose peptide sequence differs from a naturally occurring FKBP peptide sequence, e.g. the peptide sequence of human FKBP12, at up to ten amino acid residues in the peptide sequence. Preferably the number of changes in peptide sequence is limited to five, and more preferably to 1, 2, or 3.
In another embodiment, at least one of the chimeric proteins contains at least one FRB domain whose peptide sequence differs from a naturally occurring FRB peptide sequence, e.g. the FRB domain of human FRAP, at up to ten amino acid residues in the peptide sequence. Preferably the number of changes in peptide sequence is limited to five, and more preferably to 1, 2, or 3. In many cases it will be preferred that the FRB domain contains a single amino acid replacement relative to the peptide sequence of the corresponding FRB domain of human FRAP or some other mammalian FRAP/TOR species. Mutations of particular interest include replacement of one or more of T2098, D2102, Y2038, F2039, K2095 of an FRB domain derived from human FRAP with independently selected replacement amino acids, e.g. A, N, H, L, or S. Also of interest are the replacement of one or more of F1975, F1976, D2039 and N2035 of an FRB domain derived from yeast TOR1, or the replacement of one or more of F1978, F1979, D2042 and N2038 of an FRB domain derived from yeast TOR2, with independently selected replacement amino acids, e.g. H, L, S, A or V.
In certain embodiments the chimeric protein(s) contain at least one modification in peptide sequence, preferably up to three modifications, relative to naturally occurring sequences, in both one or more FKBP domains and one or more FRB domains.
As mentioned previously, in the various embodiments of this invention, the chimeric protein(s) contain one or more “action” or “effector” domains which are heterologous with respect to the FKBP and/or FRB domains. Effector domains may be selected from a wide variety of protein domains including DNA binding domains, transcription activation domains, cellular localization domains and signaling domains (i.e., domains which are capable upon clustering or multimerization, of triggering cell growth, proliferation, differentiation, apoptosis, gene transcription, etc.). A variety of illustrative effector domains which may be used in practicing this invention are disclosed in the various scientific and patent documents cited herein.
For example, in certain embodiments, one fusion protein contains at least one DNA binding domain (e.g., a GAL4 or ZFHD1 DNA-binding domain) and another fusion protein contains at least one transcription activation domain (e.g., a VP16 or p65 transcription activation domain). Ligand-mediated association of the fusion proteins represents the formation of a transcription factor complex and leads to initiation of transcription of a target gene linked to a DNA sequence recognized by (i.e., capable of binding with) the DNA-binding domain on one of the fusion proteins.
In other embodiments, one fusion protein contains at least one domain capable of directing the fusion protein to a particular cellular location such as the cell membrane, nucleus, ER or other organelle or cellular component. Localization domains which target the cell membrane, for example, include domains such as a myristoylation site or a transmembrane region of a receptor protein or other membrane-spanning protein. Another fusion protein can contain a signaling domain capable, upon membrane localization and/or clustering, of activating a cellular signal transduction pathway. Examples of signaling domains include an intracellular domain of a growth factor or cytokine receptor, an apoptosis triggering domain such as the intracellular domain of FAS or TNF-R1, and domains derived from other intracellular signaling proteins such as SOS, Raf, Ick, ZAP-70, etc. A number of signaling proteins are disclosed in PCT/US94/01617 (see e.g. pp. 23–26). In still other embodiments, each of the fusion proteins contains at least one FRB domain and at least one FKBP domain, as well as one or more heterologous domains. Such fusion proteins are capable of homodimerization and triggering signaling in the presence of the rapalog. In general, domains containing peptide sequence endogenous to the host cell are preferred in applications involving whole organisms. Thus, for human gene therapy applications, domains of human origin are of particular interest.
Recombinant nucleic acid constructs encoding the fusion proteins are also provided, as are nucleic acid constructs capable of directing their expression, and vectors containing such constructs for introducing them into cells, particularly eukaryotic cells, of which yeast and animal cells are of particular interest. In view of the constituent components of the fusion proteins, the recombinant DNA molecules which encode them are capable of selectively hybridizing (a) to a DNA molecule encoding a polypeptide comprising an FRB domain or FKBP domain and (b) to a DNA molecule encoding the heterologous domain or a protein from which the heterologous protein domain was derived. DNAs are also encompassed which would be capable of so hybridizing but for the degeneracy of the genetic code.
Using nucleic acids encoding the fusion proteins, nucleic acid constructs for directing their expression in eukaryotic cells, and vectors or other means for introducing such constructs into cells, especially animal cells, one may genetically engineer the cells, preferably mammlian cells, and most preferably human cells, for a number of important uses. To do so, one first provides an expression vector or nucleic acid construct for directing the expression in a eukaryotic (preferably animal) cell of the desired chimeric protein(s) and then introduces the recombinant DNA into the cells in a manner permitting DNA uptake and expression of the introduced DNA in at least a portion of the cells. One may use any of the various methods and materials for introducing DNA into cells for heterologous gene expression, a variety of which are well known and/or commercially available.
One object of this invention is thus a method for multimerizing fusion proteins, such as described herein, in cells, preferably animal cells. To recap, one of the fusion proteins is capable of binding to the 28-epirapalog of this invention and contains at least one FKBP domain and at least one domain heterologous thereto. The second fusion protein contains at least one FRB domain and at least one domain heterologous thereto and is capable of forming a tripartite complex with the first fusion protein and one or more molecules of the 28-epirapalog. In some embodiments one or more of the heterologous domains present on one of the fusion proteins are also present on the other fusion protein, i.e., the two fusion proteins have one or more common heterologous domains. In other embodiments, each fusion protein contains one or more different heterologous domains.
The method comprises contacting appropriately engineered cells with the 28-epirapalog by adding the rapalog to the culture medium in which the cells are located or administering the rapalog to the organism in which the cells are located. The cells are preferably eukaryotic cells, more preferably animal cells, and most preferably mammalian cells. Primate cells, especially human cells, are of particular interest. Administration of the 28-epirapalog to a human or non-human animal may be effected using any pharmaceutically acceptable formulation and route of administration. Oral administration of a pharmaceutically acceptable composition containing the 28-epirapalog together with one or more pharmaceuticaly acceptable carriers, buffers or other excipients is currently of greatest interest.
One object of this invention is a method, as otherwise described above, for inducing transcription of a target gene in a rapalog-dependent manner. The cells typically contain recombinant DNAs encoding the two fusion proteins, and a target gene construct comprising a target gene operably linked to a DNA sequence which is responsive to the presence of a complex of the fusion proteins with the 28-epirapalog. The target gene construct may be recombinant, and the target gene and/or a regulatory nucleic acid sequence linked thereto may be heterologous with respect to the host cell. In certain embodiments the cells are responsive to contact with the rapalog which binds to the FKBP fusion protein and participates in a complex with a FRB fusion protein with a detectable preference over binding to endogenous FKBP and/or FRB-containing proteins of the host cell.
Another specific object of this invention is a method, as otherwise described above, for inducing cell death in a rapalog-dependent manner. In such cells, at least one of the heterologous domains on at least one fusion protein, and usually two fusion proteins, is a domain such as the intracellular domain of FAS or TNF-R1, which, upon clustering, triggers apoptosis of the cell.
Another specific object of this invention is a method, as otherwise described above, for inducing cell growth, differentiation or proliferation in a rapalog-dependent manner. In such cells, at least one of the heterologous domains of at least one of the fusion proteins is a signaling domain such as, for example, the intracellular domain of a receptor for a hormone which mediates cell growth, differentiation or proliferation, or a downstream mediator of such a receptor. Cell growth, differentiation and/or proliferation follows clustering of such signalling domains. Such clustering occurs in nature following hormone binding, and in engineered cells of this invention following contact with a 28-epirapalog.
Cells of human origin are preferred for human gene therapy applications, although cell types of various origins (human or other species) may be used, and may, if desired, be encapsulated within a biocompatible material for use in human subjects.
Also provided are materials and methods for producing the foregoing engineered cells. This object is met by providing recombinant nucleic acids, typically DNA molecules, encoding the fusion proteins, together with any desired ancillary recombinant nucleic acids such as a target gene construct, and introducing the recombinant nucleic acids into the host cells under conditions permitting nucleic acid uptake by cells. Such transfection may be effected ex vivo, using host cells maintained in culture. Cells that are engineered in culture may subsequently be introduced into a host organism, e.g. in ex vivo gene therapy applications. Doing so thus constitutes a method for providing a host organism, preferably a human or non-human mammal, which is responsive (as described herein) to the presence of a 28-epirapalog as provided herein. Alternatively transfection may be effected in vivo, using host cells present in a human or non-human host organism. In such cases, the nucleic acid molecules are introduced directly into the host organism under conditions permitting uptake of nucleic acids by one or more of the host organism's cells. This approach thus constitutes an alternative method for providing a host organism, preferably a human or non-human mammal, which is responsive (as described herein) to the presence of a 28-epirapalog. Various materials and methods for the introduction of DNA and RNA into cells in culture or in whole organisms are known in the art and may be adapted for use in practicing this invention.
Other objects are achieved using the engineered cells described herein. For instance, a method is provided for multimerizing fusion proteins of this invention by contacting cells engineered as described herein with an effective amount of the 28-epirapalog permitting the rapalog to form a complex with the fusion proteins. In embodiments in which multimerization of the fusion proteins triggers transcription of a target gene, this constitutes a method for activating the expression of the target gene. In embodiments in which the fusion proteins contain one or more signaling domains, this constitutes a method for activating a cellular signal transduction pathway. In specific embodiments in which the signaling domains are selected based on their ability following clustering to trigger cell growth, proliferation, differentiation or cell death, 28-epirapalog-mediated clustering constitutes a method for actuating cell growth, proliferation, differentiation or cell death, as the case may be. These methods may be carried out in cell culture or in whole organisms, including human patients. In the former case, the rapamycin or rapalog is added to the culture medium. In the latter case, the rapamycin or rapalog (which may be in the form of a pharmaceutical or veterinary composition) is administered to the whole organism, e.g., orally, parenterally, etc. Preferably, the dose of the 28-epirapalog administered to an animal is below the dosage level that would cause undue immunosuppression in the recipient.
Also disclosed are kits for use in the genetic engineering of cells or human or non-human animals as described herein. One such kit contains one or more recombinant nucleic add constructs encoding fusion proteins of this invention. The recombinant nucleic acid constructs will generally be in the form of eukaryotic expression vectors suitable for introduction into animal cells and capable of directing the expression of the fusion proteins therein. Such vectors may be viral vectors as described elsewhere herein. The kit may also contain a sample of a 28-epirapalog of this invention capable of forming a complex with the encoded fusion proteins. The kit may further contain a multimerization antagonist such as FK506, FK506M, one of the many known synthetic (nonimmunosuppressive) FKBP ligands or some other compound capable of binding to one of the fusion proteins but incapable of forming a complex with both. In certain embodiments, the recombinant nucleic add constructs encoding the fusion proteins will contain a cloning site in place of DNA encoding one or more of the heterologous domains, thus permitting the practitioner to introduce DNA encoding a heterologous domain of choice. In some embodiments the kit may also contain a target gene construct containing a target gene or cloning site linked to a DNA sequence responsive to the presence of the complexed fusion proteins, as described in more detail elsewhere. The kit may contain a package insert identifying the enclosed nucleic add construct(s), and/or instructions for introducing the construct(s) into host cells or organisms.


DETAILED DESCRIPTION OF THE INVENTION
Definitions
The definitions and orienting information below will be helpful for a full understanding of this document.
FRB domains are polypeptide regions (protein “domains”), typically of at least about 89 amino acid residues, which are capable of forming a tripartite complex with an FKBP protein and rapamycin (or a 28-epirapalog of this invention). FRB domains are present in a number of naturally occurring proteins, including FRAP proteins (also referred to in the literature as “RAPT1” or RAFT”) from human and other species; yeast proteins including Tor1 and Tor2; and a Candida FRAP homolog. Information concerning the nucleotide sequences, cloning, and other aspects of these proteins is already known in the art, permitting the synthesis or cloning of DNA encoding the desired FRB peptide sequence, e.g., using well known methods and PCR primers based on published sequences.











protein source
reference/sequence accession numbers







human FRAP
Brown et al, 1994, Nature 369, 756–758;



GenBank accession #L34075, NCBI Seq ID 508481;



Chiu et al, 1994, PNAS USA 91, 12574–12578;



Chen et al, 1995, PNAS USA 92, 4947–4951


murine RAPT1
Chiu et al, supra.


yeast Tor1
Helliwell et al, 1994, Mol Cell Biol 5, 105–118;



EMBL Accession #X74857, NCBI Seq Id #468738


yeast Tor 2
Kunz et al, 1993, Cell 73, 585–596;



EMBL Accession #X71416, NCBI Seq ID 298027


Candida TOR
WO95/33052 (Berlin et al)









FRB domains for use in this invention generally contain at least about 89–100 amino acid residues. FIG. 2 of Chiu et al, supra, displays a 160-amino acid span of human FRAP, murine FRAP, S. cerevisiae TOR1 and S. cerevisiae TOR2 encompassing the conserved FRB region. Typically the FRB sequence selected for use in fusion proteins of this invention will span at least the 89-amino acid sequence Glu-39 through Lys/Arg-127, as the sequence is numbered in that figure. For reference, using the numbering of Chen et al or Sabitini et al, the 89-amino acid sequence is numbered Glu-2025 through Lys-2113 in the case of human FRAP, Glu-1965 through Lys-2053 in the case of Tor2, and Glu-1962 through Arg-2050 in the case of Tor1. An FRB domain for use in fusion proteins of this invention will be capable of binding to a complex of an FKBP protein bound to rapamycin or a 28-epirapalog of this invention (as may be determined by any means, direct or indirect, for detecting such binding, including, for example, means for detecting such binding employed in the FRAP/RAFT/RAPT and Tor-related references cited herein). The peptide sequence of such an FRB domain comprises (a) a naturally occurring peptide sequence spanning at least the indicated 89-amino acid region of the proteins noted above or corresponding regions of homologous proteins; (b) a variant of a naturally occurring FRB sequence in which up to about ten (preferably 1–5, more preferably 1–3, and in some embodiments just one) amino acids of the naturally-occurring peptide sequence have been deleted, inserted, or replaced with substitute amino acids; or (c) a peptide sequence encoded by a DNA sequence capable of selectively hybridizing to a DNA molecule encoding a naturally occurring FRB domain or by a DNA sequence which would be capable, but for the degeneracy of the genetic code, of selectively hybridizing to a DNA molecule encoding a naturally occurring FRB domain. A 2098L mutant human FRB is currently preferred for use with 28-epirapalogs bearing a C7 modification. See e.g. WO 99/36553.
FKBPs (FK506 binding proteins) are the cytosolic receptors for macrolides such as FK506, FK520 and rapamycin and are highly conserved across species lines. For the purpose of this disclosure, FKBPs are proteins or protein domains which are capable of binding to rapamycin or to a 28-epirapalog of this invention and further forming a tripartite complex with an FRB-containing protein. An FKBP domain may also be referred to as a “rapamycin binding domain”. Information concerning the nucleotide sequences, cloning, and other aspects of various FKBP species is already known in the art, permitting the synthesis or cloning of DNA encoding the desired FKBP peptide sequence, e.g., using well known methods and PCR primers based on published sequences. See e.g. Staendart et al, 1990, Nature 346, 671–674 (human FKBP12); Kay, 1996, Biochem. J. 314, 361–385 (review). Homologous FKBP proteins in other mammalian species, in yeast, and in other organisms are also known in the art and may be used in the fusion proteins disclosed herein. See e.g. Kay, 1996, Biochem. J. 314, 361–385 (review). The size of FKBP domains for use in this invention varies, depending on which FKBP protein is employed. An FKBP domain of a fusion protein of this invention will be capable of binding to rapamycin or a 28-epirapalog of this invention and participating in a tripartite complex with an FRB-containing protein (as may be determined by any means, direct or indirect, for detecting such binding). The peptide sequence of an FKBP domain of an FKBP fusion protein of this invention comprises (a) a naturally occurring FKBP peptide sequence, preferably derived from the human FKBP12 protein (exemplified below) or a peptide sequence derived from another human FKBP, from a murine or other mammalian FKBP, or from some other animal, yeast or fungal FKBP; (b) a variant of a naturally occurring FKBP sequence in which up to about ten (preferably 1–5, more preferably 1–3, and in some embodiments just one) amino acids of the naturally-occurring peptide sequence have been deleted, inserted, or replaced with substitute amino acids; or (c) a peptide sequence encoded by a DNA sequence capable of selectively hybridizing to a DNA molecule encoding a naturally occurring FKBP or by a DNA sequence which would be capable, but for the degeneracy of the genetic code, of selectively hybridizing to a DNA molecule encoding a naturally occurring FKBP.
“Capable of selectively hybridizing” as that phrase is used herein means that two DNA molecules are susceptible to hybridization with one another, despite the presence of other DNA molecules, under hybridization conditions which can be chosen or readily determined empirically by the practitioner of ordinary skill in this art. Such treatments include conditions of high stringency such as washing extensively with buffers containing 0.2 to 6×SSC, and/or containing 0.1% to 1% SDS, at temperatures ranging from room temperature to 65–75° C. See for example F. M. Ausubel et al., Eds, Short Protocols in Molecular Biology, Units 6.3 and 6.4 (John Wiley and Sons, New York, 3d Ed, 1995).
The terms “protein”, “polypeptide” and “peptide” are used interchangeably herein.
“Nucleic acid constructs”, as that term is used herein, denote nucleic acids (usually DNA, but also encompassing RNA, e.g. in a retroviral delivery system) used in the practice of this invention which are generally recombinant, as that term is defined below, and which may exist in free form (i.e., not covalently linked to other nucleic acid sequence) or may be present within a larger molecule such as a DNA vector, retroviral or other viral vector or a chromosome of a genetically engineered host cell. Nucleic acid constructs of particular interest are those which encode fusion proteins of this invention or which comprise a target gene and expression control elements. The construct may further include nucleic acid portions comprising one or more of the following elements relevant to regulation of transcription, translation, and/or other processing of the coding region or gene product thereof: transcriptional promoter and/or enhancer sequences, a ribosome binding site, introns, etc.
“Recombinant”, “chimeric” and “fusion”, as those terms are used herein, denote materials comprising various component domains, sequences or other components which are mutually heterologous in the sense that they do not occur together in the same arrangement, in nature. More specifically, the component portions are not found in the same continuous polypeptide or nucleotide sequence or molecule in nature, at least not in the same cells or order or orientation or with the same spacing present in the chimeric protein or recombinant DNA molecule of this invention.
“Transcription control element” denotes a regulatory DNA sequence, such as initiation signals, enhancers, and promoters, which induce or control transcription of protein coding sequences with which they are operably linked. The term “enhancer” is intended to include regulatory elements capable of increasing, stimulating, or enhancing transcription from a promoter. Such transcription regulatory components can be present upstream of a coding region, or in certain cases (e.g. enhancers), in other locations as well, such as in introns, exons, coding regions, and 3′ flanking sequences.
“Dimerization”, “oligomerization” and “multimerizatlon” are used interchangeably herein and refer to the association or clustering of two or more protein molecules, mediated by the binding of a drug to at least one of the proteins. In preferred embodiments, the multimerization is mediated by the binding of two or more such protein molecules to a common drug which is thus considered to be divalent or multivalent. The formation of a complex comprising two or more protein molecules, each of which containing one or more FKBP domains, together with one or more molecules of an FKBP ligand which is at least divalent (e.g. FK1012 or AP1510) is an example of such association or clustering. In cases where at least one of the proteins contains more than one drug binding domain, e.g., where at least one of the proteins contains three FKBP domains, the presence of a divalent drug leads to the clustering of more than two protein molecules. Embodiments in which the drug is more than divalent (e.g. trivalent) in its ability to bind to proteins bearing drug binding domains also can result in clustering of more than two protein molecules. The formation of a tripartite complex comprising a protein containing at least one FRB domain, a protein containing at least one FKBP domain and a molecule of rapamycin is another example of such protein clustering. In certain embodiments of this invention, fusion proteins contain multiple FRB and/or FKBP domains. Complexes of such proteins may contain more than one molecule of rapamycin or a derivative thereof (e.g., a 28-epi-rapalog) or other dimerizing agent and more than one copy of one or more of the constituent proteins. Again, such multimeric complexes are still referred to herein as tripartite complexes to indicate the presence of the three types of constituent molecules, even if one or more are represented by multiple copies. The formation of complexes containing at least one divalent drug and at least two protein molecules, each of which contains at least one drug binding domain, may be referred to as “oligomerization” or “multimerization”, or simply as “dimerization”, “clustering” or association”.
“Dimerizer” denotes a 28-epirapalog of this invention which brings together two or more proteins in a multimeric complex. The 28-epi-rapalog may be 28-epi-rapamycin or a 28-epi-rapalog with additional structural modifications relative to rapamycin.
“Activate” as applied herein to the expression or transcription of a gene denotes a directly or indirectly observable increase in the production of a gene product.
“Genetically engineered cells” denotes cells which have been modified (“transduced”) by the introduction of recombinant or heterologous nucleic acids (e.g. one or more DNA constructs or their RNA counterparts) and further includes the progeny of such cells which retain part or all of such genetic modification.
A “therapeutically effective dose” of a 28-epirapalog of this invention denotes a treatment- or prophylaxis-effective dose for a human or non-human animal containing appropriately genetically engineered cells, e.g., a dose which yields detectable target gene transcription or cell growth, proliferation, differentiation, death, etc. in the recipient, or a dose which is predicted to be treatment- or prophylaxis-effective by extrapolation from data obtained in animal or cell culture models. A therapeutically effective dose is usually preferred for the treatment of a human or non-human mammal.
This invention involves, among other applications and materials, methods and materials for multimerizing chimeric proteins in genetically engineered cells using 28-epirapalogs. The design and implementation of various dimerization-based biological switches has been reported, inter alia, in Spencer et al and in various international patent applications cited herein. Other accounts of successful application of this general approach have also been reported. Chimeric proteins containing an FRB domain fused to an effector domain has also been disclosed in Rivera et al, 1996, Nature Medicine 2, 1028–1032 and in WO 96/41865 and WO99/36553 (Clackson et al) and WO 95/33052 (Berlin et al). As noted previously, the fusion proteins are designed such that association of the effector domains, through ligand-mediated “dimerization” or “multimerization” of the fusion proteins which contain them, triggers a desired biological event such as transcription of a desired gene, cell death, cell proliferation, etc. For example, clustering of chimeric proteins containing an action domain derived from the intracellular portion of the T cell receptor CD3 zeta domain triggers transcription of a gene under the transcriptional control of the IL-2 promoter or promoter elements derived therefrom. In other embodiments, the action domain comprises a domain derived from the intracellular portion of a protein such as FAS or the TNF-alpha receptor (TNFalpha-R1), which are capable, upon oligomerization, of triggering apoptosis of the cell. In still other embodiments, the action domains comprise a DNA-binding domain such as GAL4 or ZFHD1 and a transcription activation domain such as VP16 or p65, paired such that oligomerization of the chimeric proteins represents assembly of a transcription factor complex which triggers transcription of a gene linked to a DNA sequence recognized by (capable of specific binding interaction with) the DNA binding domain.
Chimeric proteins containing one or more ligand-binding domains and one or more action domains, e.g. for activation of transcription of a target gene, triggering cell death or other signal transduction pathway, cellular localization, etc., are disclosed in PCT/US94/01617, PCT/US94/08008 and Spencer et al, supra. The design and use of such chimeric proteins for ligand-mediated gene-knock out and for ligand-mediated blockade of gene expression or inhibition of gene product function are disclosed in PCT/US95/10591. Novel DNA binding domains and DNA sequences to which they bind which are useful in embodiments involving regulated transcription of a target gene are disclosed, e.g., in Pomeranz et al, 1995, Science 267:93–96. Those references provide substantial information, guidance and examples relating to the design, construction and use of DNA constructs encoding analogous chimeras, target gene constructs, and other aspects which may also be useful to the practitioner of the subject invention.
By appropriate choice of chimeric proteins, this invention permits one to activate the transcription of a desired gene; actuate cell growth, proliferation, differentiaion or apoptosis; or trigger other biological events in engineered cells in a 28-epirapalog-dependent manner analogous to the systems described in the patent documents and other references cited above. The engineered cells, preferably animal cells, may be growing or maintained in culture or may be present within whole organisms, as in the case of human gene therapy, transgenic animals, and other such applications. The 28-epirapalog is administered to the cell culture or to the organism containing the engineered cells, as the case may be, in an amount effective to multimerize the FKBP fusion proteins and FRB fusion proteins (as may be observed indirectly by monitoring target gene transcription, apoptosis or other biological process so triggered). In the case of administration to whole organisms, the 28-epirapalog may be administered in a composition containing the 28-epirapalog and one or more acceptable verterinary or pharmaceutical diluents and/or excipients.
A compound which binds to one of the chimeric proteins but does not form tripartite complexes with both chimeric proteins may be used as a multimerization antagonist. As such it may be administered to the engineered cells, or to organisms containing them (preferably in a composition as described above in the case of administration to whole animals), in an amount effective for blocking or reversing the effect of the 28-epirapalog, i.e. for preventing, inhibiting or disrupting multimerization of the chimeras. For instance, FK506, FK520 or any of the many synthetic FKBP ligands which do not form tripartite complexes with FKBP and FRAP may be used as an antagonist.
One important aspect of this invention provides materials and methods for 28-epirapalog-dependent, direct activation of transcription of a desired gene. In one such embodiment, a set of two or more different chimeric proteins, and corresponding DNA constructs capable of directing their expression, is provided. One such chimeric protein contains as its action domain(s) one or more transcriptional activation domains. The other chimeric protein contains as its action domain(s) one or more DNA-binding domains. A 28-epirapalog of this invention is capable of binding to both chimeras to form a dimeric or multimeric complex thus containing at least one DNA binding domain and at least one transcriptional activating domain. Formation of such complexes leads to activation of transcription of a target gene linked to, and under the transcriptional control of, a DNA sequence to which the DNA-binding domain is capable of binding, as can be observed by monitoring directly or indirectly the presence or concentration of the target gene product.
Preferably the DNA binding domain, and a chimera containing it, binds to its recognized DNA sequence with sufficient selectivity so that binding to the selected DNA sequence can be observed (directly or indirectly) despite the presence of other, often numerous other, DNA sequences. Preferably, binding of the chimera comprising the DNA-binding domain to the selected DNA sequence is at least two, more preferably three and even more preferably more than four orders of magnitude greater than binding to any one alternative DNA sequence, as measured by in vitro binding studies or by measuring relative rates or levels of transcription of genes associated with the selected DNA sequence as compared with any alternative DNA sequences.
Cells which have been genetically engineered to contain such a set of constructs, together with any desired accessory constructs, may be used in applications involving ligand-mediated, regulated actuation of the desired biological event, be it regulated transcription of a desired gene, regulated triggering of a signal transduction pathway such as the triggering of apoptosis, or another event. Cells engineered for regulatable expression of a target gene, for instance, can be used for regulated production of a desired protein (or other gene product) encoded by the target gene. Such cells may be grown in culture by conventional means. Addition of the 28-epirapalog to the culture medium containing the cells leads to expression of the target gene by the cells and production of the protein encoded by that gene. Expression of the gene and production of the protein can be turned off by withholding further multimerization agent from the media, by removing residual multimerization agent from the media, or by adding to the medium a multimerization antagonist reagent.
Engineered cells of this invention can also be produced and/or used in vivo, to modify whole organisms, preferably animals, especially humans, e.g. such that the cells produce a desired protein or other result within the animal containing them. Such uses include gene therapy applications.
Embodiments involving regulatable actuation of apoptosis provide engineered cells susceptible to 28-epirapalog-inducible cell death. Such engineered cells can be eliminated from a cell culture or host organism after they have served their intended purposed (e.g. production of a desired protein or other product), if they have or develop unwanted properties, or if they are no longer useful, safe or desired. Elimination is effected by adding the 28-epirapalog to the medium or administering it to the host organism. In such cases, the action domains of the chimeras are protein domains such as the intracellular domains of FAS or TNF-R1, downstream components of their signaling pathways or other protein domains which upon oligomerization trigger apoptosis.
This invention thus provides materials and methods for achieving a biological effect in cells in response to the addition of a 28-epirapalog of this invention. The method involves providing cells engineered as described herein and exposing the cells to the 28-epirapalog.
For example, this invention provides a method for activating transcription of a target gene in cells. The method involves providing cells containing (a) DNA constructs encoding a set of chimeric proteins of this invention capable upon 28-epirapalog-mediated multimerization of initiating transcription of a target gene and (b) a target gene linked to an associated cognate DNA sequence responsive to the multimerization event (e.g. a DNA sequence recognized, i.e., capable of binding with, a DNA-binding domain of a foregoing chimeric protein. The method involves exposing the cells to a 28-epirapalog capable of binding to the chimeric proteins in an amount effective to result in expression of the target gene. In cases in which the cells are growing in culture, exposing the cells to the 28-epirapalog may be effected by adding the 28-epirapalog to the culture medium. In cases in which the cells are present within a host organism, exposing them to the 28-epirapalog is effected by administering the 28-epirapalog to the host organism. For instance, in cases in which the host organism is a human or non-human, the 28-epirapalog may be administered to the host organism by oral, buccal, sublingual, transdermal, subcutaneous, intramuscular, intravenous, intra-joint or inhalation administration in an appropriate vehicl. Again, depending on the design of the constructs for the chimeric proteins and of any accessory constructs, the 28-epirapalog-mediated biological event may be activation of a cellular function such as signal transduction leading to cell growth, cell proliferation, gene transcription, or apoptosis; deletion of a gene of interest, blockade of expression of a gene of interest, or inhibition of function of a gene product of interest; direct transcription of a gene of interest; etc.
This invention further encompasses a pharmaceutical composition comprising a 28-epirapalog of this invention in admixture with a pharmaceutically acceptable carrier and optionally with one or more pharmaceutically acceptable excipients. Such pharmaceutical compositions can be used to promote multimerization of chimeras of this invention in engineered cells in whole animals, e.g. in human gene therapy applications to achieve any of the objectives disclosed herein.
Said differently, this invention provides a method for achieving any of those objectives, e.g. activation of transcription of a target gene (typically a heterologous gene for a therapeutic protein), cell growth or proliferation, cell death or some other selected biological event, in an animal, preferably a human patient, in need thereof and containing engineered cells of this invention. That method involves administering to the animal a pharmaceutical composition containing the 28-epirapalog by a route of administration and in an amount effective to cause multimerization of the chimeric proteins in at least a portion of the engineered cells. Multimerization may be detected indirectly by observing the occurrence of target gene expression; cell growth, proliferation or death; or other objective for which the chimeras were designed and the cells genetically engineered.
This invention further encompasses a pharmaceutical composition comprising a multimerization antagonist of this invention in admixture with a pharmaceutically acceptable carrier and optionally with one or more pharmaceutically acceptable excipients for inhibiting or otherwise reducing, in whole or part, the extent of multimerization of chimeric proteins in engineered cells of this invention in a subject, and thus for de-activating the transcription of a target gene, for example, or turning off another biological result of this invention. Thus, the use of the multimerizing 28-epirapalogs and of the multimerization antagonist reagents to prepare pharmaceutical compositions and achieve their pharmacologic results is encompassed by this invention.
Also disclosed is a method for providing a host organism, preferably an animal, typically a non-human mammal or a human subject, responsive to a 28-epirapalog of this invention. The method involves introducing into the organism cells which have been engineered in accordance with this invention, i.e. containing one or more nucleic acid constructs encoding the chimeric proteins, and so forth. The engineered cells may be encapsulated using any of a variety of materials and methods before being introduced into the host organism. Alternatively, one can introduce the nucleic acid constructs of this invention into a host organism, e.g. a mammal, under conditions permitting incorporation thereof into one or more cells of the host mammal, e.g. using viral vectors, introduction of DNA by injection or via catheter, etc.
Also provided are kits for producing cells responsive to a 28-epirapalog of this invention. One such kit contains one or more nucleic acid constructs encoding and capable of directing the expression of chimeras which, upon 28-epirapalog-mediated oligomerization, trigger the desired biological response. The kit may contain a quantity of a 28-epirapalog capable of multimerizing the chimeric protein molecules encoded by the construct(s) of the kit, and may contain in addition a quantity of a multimerization antagonist. The kit may further contain a nucleic acid construct encoding a target gene (or cloning site) linked to a cognate DNA sequence which is recognized by the dimerized chimeric proteins permitting transcription of a gene linked to that cognate DNA sequence in the presence of multimerized chimeric protein molecules. The constructs may be associated with one or more selection markers for convenient selection of transfectants, as well as other conventional vector elements useful for replication in prokaryotes, for expression in eukaryotes, and the like. The selection markers may be the same or different for each different construct, permitting the selection of cells which contain each such construct(s).
The accessory construct for introducing into cells a target gene in association with a cognate DNA sequence may contain a cloning site in place of a target gene. A kit containing such a construct permits the engineering of cells for regulatable expression of a gene to be provided by the practitioner.
Other kits of this invention may contain one or two (or more) nucleic acid constructs for chimeric proteins in which one or more contain a cloning site in place of the transcriptional activator or DNA binding protein, permitting the user to insert whichever such domain s/he wishes. Such a kit may optionally include other elements as described above, e.g. a nucleic construct for a target gene with or without a cognate DNA sequence for a pre-selected DNA binding domain.
Any of the kits may also contain positive control cells which were stably transformed with constructs of this invention such that they express a reporter gene (for CAT, beta-galactosidase or any conveniently detectable gene product) in response to exposure of the cells to the 28-epirapalog. Reagents for detecting and/or quantifying the expression of the reporter gene may also be provided.
For further information and guidance on the design, construction and use of such systems or components thereof which may be adapted for use in practicing the subject invention, reference to the following publications is suggested: Spencer et al, 1993, supra; Rivera et al, 1996, supra; Spencer et al, 1996, Current Biology 6, 839–847; Luo et al, 1996, Nature, 383, 181–185; Ho et al, 1996, Nature 382, 822–826; Belshaw et al, 1996, Proc. Natl. Acad. Sci. USA 93, 4604–4607; Spencer, 1996, TIG 12(5), 181–187; Spencer et al, 1995, Proc., Natl. Acad. Sci. USA 92, 9805–9809; Holsinger et al, 1995, Proc. Natl. Acad. Sci. USA 92, 9810–9814; Pruschy et al, 1994, Chemistry & Biology 1(3), 163–172; and published international patent applications WO 94/18317, WO 95/02684, WO 95/33052, WO 96/20951 and WO 96/41865.
A key focus of the subject invention is the use of 28-epirapalogs as mediators of protein—protein interactions in applications using FKBP and FRB fusion proteins such as described above and elsewhere herein. The 28-epirapalogs may be used in the various applications of the underlying dimerization-based technology, including triggering biological events in genetically engineered cells grown or maintained in culture or present in whole organisms, including humans and other mammals. The 28-epirapalogs may thus be useful as research reagents in biological experiments in vitro, in experiments conducted on animals containing the genetically engineered cells, and as prophylactic or therapeutic agents in animal and human health care in subjects containing genetically engineered cells.
28-epi Rapalogs
“28-epirapalogs” as that term is used herein denotes a class of compounds comprising the various analogs, homologs and derivatives of rapamycin and other compounds related structurally to rapamycin (collectively, “rapalogs”) which have the opposite stereochemistry at C28 as is present in rapamycin. “28-epirapalogs” which may be used in practicing the methods of this invention include compounds which comprise the substructure shown below, bearing any number of a variety of substituents, and optionally unsaturated at one or more carbon—carbon bonds unless specified to the contrary herein.




Typically the compound will contain up to three double bonds between C1 and C7; any of the various types of C7 substituents discussed elsewhere in this document; an optional and independently chosen keto, halo, hydroxy or derivatized hydroxy (e.g. ester, amide, urea, carbamate, ether, etc.) at one or more of C14, C24 and C30; an alkoxy (usually MeO), hydroxy or H at C29, an “a” moiety as disclosed elsewhere herein; and an R28 moiety as defined elsewhere herein.

An illustrative subset of those compounds comprises the substructure:




As noted elsewhere, the R43O-substituent may be in the orientation depicted above, or, in combination with other modifications to the 28-epirapamycin relative to rapamycin, may be present in the opposite stereochemistry, or the compound may represent a mixture of the two C43 isomers.
28-epirapalogs which may be used in practicing the methods of this invention include, among others, 28-epirapamycin and variants thereof having one or more of the following modifications relative to rapamycin: demethylation, elimination or replacement of the methoxy at C7, C42 and/or C29; elimination, derivatization or replacement of the hydroxy at C13, C43 and/or C28; reduction, elimination or derivatization of the ketone at C14, C24 and/or C30; replacement of the 6-membered pipecolate ring with a 5-membered prolyl ring; and elimination, derivatization or replacement of one or more substituents of the cyclohexyl ring or replacement of the cyclohexyl ring with a substituted or unsubstituted cyclopentyl ring. Illustrative examples of previously reported rapalogs are disclosed in the documents listed in Table I. Examples of previously reported rapalogs modified at C7 are shown in Table II.












TABLE I







WO9710502
WO9425022
WO9318043
US5563172
US5362735
US5210030


WO9641807
WO9421644
WO9313663
US5561228
US5324644
US5208241


WO9635423
WO9418207
WO9311130
US5561137
US5318895
US5200411


WO9603430
WO9410843
WO9310122
US5541193
US5310903
US5198421


WO9600282
WO9409010
WO9304680
US5541189
US5310901
US5147877


WO9516691
WO94/04540
WO9214737
US5534632
US5258389
US5140018


WO9515328
WO9402485
WO9205179
US5527907
US5252732
US5116756


WO9507468
WO9402137
US5604234
US5484799
US5247076
US5109112


WO9504738
WO9402136
US5597715
US5457194
US5225403
US5093338


WO9504060
WO9325533
US5583139
US5457182
US5221625
US5091389
















TABLE II





Illustrative C7 rapalog structures


 























RC7 =




















 









 









 









 









 









 







X = O or NH


 









 









 









 







Ar = phenyl, 3-nitrophenyl, 4-chlorophenyl,3-iodo-4-diazophenyl, 3,4-dimethoxy-phenyl, or 2-methoxyphenyl


 







Ar = 3,4-dimethoxyphenyl


 



—CH3COPhenyl



—OCHO



—CH2CH2OH



—CH2CH(OH)CH2OH



—CH2CH2OCH2CH2OCH2CH2OCH3


 









 









 









 









 









 









 













 








7-oxorapamycin


 








 











See e.g.,


Luengo et al, Chemistry & Biology, 1995, 2(7):471–481; JOC, 1995, 59(22):6512–13


WO 94/02136 (SmithKline Beecham)


WO 95/16691 (Sandoz)


U.S. Pat. No. 5,583,139 (Abbott)


Grinfeld et al, 1994, Tett Letters 35(37):6835–6838


WO 96/41865 (ARIAD)
















Other illustrative rapalogs include those depicted in Table III:


























 












 












 













 


















 












 



















Other compounds of interest for the practice of various aspects of this invention include 28-epirapalogs containing one or more of the following modifications relative to rapamycin:

    (a) the cyclohexyl ring is derivatized or replaced with a 5-membered ring system, as is known for prior rapalogs (although the 43-epi hydoxyl substituent is included only in combination with additional modifications, e.g. at C7, in combination with the 24,30-tetrahydro modification, or in combination with one or more other additional changes);
    (b) alkylation (including, e.g., benzylation), arylation, acylation, aroylation, or replacement with a halogen of one or more hydroxyl moieties;
    (c) conversion of one or both carbonyls at C24 and C30 to ═NRA═NORA, ═NNHRA, —NHORA, —NHNHRA, —ORA(including among others, —OH), —OC(O)RA or —OC(O)NRA, halo or —H;
    (d) conversion of one or both hydroxyls at C13 and C28 to H, halo, —ORA, —SRA, —OC(O)RA or —OC(O)NRARB or a cyclic moiety (e.g., carbonate) bridging C28 and C30, —SC(O)RA, —SC(O)NRARB, —NRARB or —N(RB)(CO)RA(including among others, embodiments of the foregoing in which —ORA is H, —OCH2phenyl, or —OCH2Ar);
    (e) conversion of the C14 carbonyl to —ORA, —NRA, —H, ═NC(O)RA, —NRBC(O)RA, —OC(O)RA or —OC(O)NRARB;
    (f) conversion of the hydroxyl at C43 into H, halo, —CN, ═O, —OH, —NRARB, OSO2CF3, OSO2F, OSO2RA, OCORA, OCONRARB, or OCON(ORA)RB.


28-epirapalogs useful in practicing this invention may contain substituents in any of the possible stereoisomeric orientations, unless othewise specified, and may comprise one stereoisomer substantially free of other stereoisomers (>90%, and preferably >95%, free from other stereoisomers on a molar basis) or may comprise a mixture of stereoisomers.
Also included are pharmaceutically acceptable derivatives of the foregoing compounds, where the phrase “pharmaceutically acceptable derivative” denotes any pharmaceutically acceptable salt, ester, carbamate, or salt of such ester or carbamate, of such compound, or any other adduct or derivative which, upon administration to a patient, is capable of providing (directly or indirectly) a 28-epirapalog as described herein, or a metabolite or residue thereof. Pharmaceutically acceptable derivatives thus include among others pro-drugs of the rapalogs. A pro-drug is a derivative of a compound, usually with significantly reduced pharmacological activity, which contains an additional moiety which is susceptible to removal in vivo yielding the parent molecule as the pharmacologically active species. An example of a pro-drug is an ester which is cleaved in vivo to yield a compound of interest. Various pro-drugs of rapamycin and of other compounds, and materials and methods for derivatizing the parent compounds to create the pro-drugs, are known and may be adapted to the present invention.
The term “aliphatic” as used herein includes both saturated and unsaturated, straight chain (i.e., unbranched), branched, cyclic, or polycyclic aliphatic hydrocarbons, which are optionally substituted with one or more functional groups. Unless otherwise specified, alkyl, other aliphatic, alkoxy and acyl groups preferably contain 1–8, and in many cases 1–6, contiguous aliphatic carbon atoms. Illustrative aliphatic groups thus include, for example, methyl, ethyl, n-propyl, isopropyl, cyclopropyl, —CH2-cyclopropyl, allyl, n-butyl, sec-butyl, isobutyl, tert-butyl, cyclobutyl, —CH2-cyclobutyl, n-pentyl, sec-pentyl, isopentyl, tert-pentyl, cyclopentyl, —CH2-cyclopentyl, n-hexyl, sec-hexyl, cyclohexyl, —CH2-cyclohexyl moieties and the like, which again, may bear one or more substituents.
Examples of substituents include: —OH, —OR2′, —SH, —SR2′, —CHO, ═O, —COOH (or ester, carbamate, urea, oxime or carbonate thereof), —NH2 (or substituted amine, amide, urea, carbamate or guanidino derivative therof), halo, trihaloalkyl, cyano, —SO2—CF3, —OSO2F, —OS(O)2R11, —SO2—NHR11, —NHSO2—R11, sulfate, sulfonate, aryl and heteroaryl moieties. Aryl and heteroaryl substituents may themselves be substituted or unsubstituted (e.g. mono-, di- and tri-alkoxyphenyl; methylenedioxyphenyl or ethylenedioxyphenyl; halophenyl; or -phenyl-C(Me)2—CH2—O—CO—[C3–C6]alkyl or alkylamino).
The term “aliphatic” is thus intended to include alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties.
As used herein, the term “alkyl” includes both straight, branched and cyclic alkyl groups. An analogous convention applies to other generic terms such as “alkenyl”, “alkynyl” and the like. Furthermore, as used herein, the language “alkyl”, “alkenyl”, “alkynyl” and the like encompasses both substituted and unsubstituted groups.
The term “alkyl” refers to groups usually having one to eight, preferably one to six carbon atoms. For example, “alkyl” may refer to methyl, ethyl, n-propyl, isopropyl, cyclopropyl, butyl, isobutyl, sec-butyl, tert-butyl, cyclobutyl, pentyl, isopentyl tert-pentyl, cyclopentyl, hexyl, isohexyl, cyclohexyl, and the like. Suitable substituted alkyls include, but are not limited to, fluoromethyl, difluoromethyl, trifluoromethyl, 2-fluoroethyl, 3-fluoropropyl, hydroxymethyl, 2-hydroxyethyl, 3-hydroxypropyl, benzyl, substituted benzyl and the like.
The term “alkenyl” refers to groups usually having two to eight, preferably two to six carbon atoms. For example, “alkenyl” may refer to prop-2-enyl, but-2-enyl, but-3-enyl, 2-methylprop-2-enyl, hex-2-enyl, hex-5-enyl, 2,3-dimethylbut-2-enyl, and the like. The language “alkynyl,” which also refers to groups having two to eight, preferably two to six carbons, includes, but is not limited to, prop-2-ynyl, but-2-ynyl, but-3-ynyl, pent-2-ynyl, 3-methylpent-4-ynyl, hex-2-ynyl, hex-5-ynyl, and the like.
The term “cycloalkyl” as used herein refers specifically to groups having three to seven, preferably three to ten carbon atoms. Suitable cycloalkyls include, but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and the like, which, as in the case of other aliphatic or heteroaliphatic or heterocyclic moieties, may optionally be substituted.
The term “heteroaliphatic” as used herein refers to aliphatic moieties which contain one or more oxygen, sulfur, nitrogen, phosphorous or silicon atoms, e.g., in place of carbon atoms. Heteroaliphatic moieties may be branched, unbranched or cyclic and include heterocycles such as morpholino, pyrrolidinyl, etc.
The term “heterocycle” as used herein refers to cyclic heteroaliphatic groups and preferably three to ten ring atoms total, includes, but is not limited to, oxetane, tetrahydrofuranyl, tetrahydropyranyl, aziridine, azetidine, pyrrolidine, piperidine, morpholine, piperazine and the like.
The terms “aryl” and “heteroaryl” as used herein refer to stable mono- or polycyclic, heterocyclic, and polyheterocyclic unsaturated moieties having 3–14 carbon atoms which may be substituted or unsubstituted. Substituents include any of the previously mentioned substituents. Non-limiting examples of useful aryl ring groups include phenyl, halophenyl, alkoxyphenyl, dialkoxyphenyl, trialkoxyphenyl, alkylenedioxyphenyl, naphthyl, phenanthryl, anthryl, phenanthro and the like. Examples of typical heteroaryl rings include 5-membered monocyclic ring groups such as thienyl, pyrrolyl, imidazolyl, pyrazolyl, furyl, isothiazolyl, furazanyl, isoxazolyl, thiazolyl and the like; 6-membered monocyclic groups such as pyridyl, pyrazinyl, pyrimidinyl, pyridazinyl, triazinyl and the like; and polycyclic heterocyclic ring groups such as benzo[b]thienyl, naphtho[2,3-b]thienyl, thianthrenyl, isobenzofuranyl, chromenyl, xanthenyl, phenoxathienyl, indolizinyl, isoindolyl, indolyl, indazolyl, purinyl, isoquinolyl, quinolyl, phthalazinyl, naphthyridinyl, quinoxalinyl, quinazolinyl, benzothiazole, benzimidazole, tetrahydroquinoline cinnolinyl, pteridinyl, carbazolyl, beta-carbolinyl, phenanthridinyl, acridinyl, perimidinyl, phenanthrolinyl, phenazinyl, isothiazolyl, phenothiazinyl, phenoxazinyl, and the like (see e.g. Katritzky, Handbook of Heterocyclic Chemistry). The aryl or heteroaryl moieties may be substituted with one to five members selected from the group consisting of hydroxy, C1–C8 alkoxy, C1–C8 branched or straight-chain alkyl, acyloxy, carbamoyl, amino, N-acylamino, nitro, halo, trihalomethyl, cyano, and carboxyl. Aryl moieties thus include, e.g. phenyl; substituted phenyl bearing one or more substituents selected from groups including: halo such as chloro or fluoro, hydroxy, C1–C6 alkyl, acyl, acyloxy, C1–C6 alkoxy (such as methoxy or ethoxy, including among others dialkoxyphenyl moieties such as 2,3-, 2,4-, 2,5-, 3,4- or 3,5-dimethoxy or diethoxy phenyl or such as methylenedioxyphenyl, or 3-methoxy-5-ethoxyphenyl; or trisubstituted phenyl, such as trialkoxy (e.g., 3,4,5-trimethoxy or ethoxyphenyl), 3,5-dimethoxy-4-chloro-phenyl, etc.), amino, —SO2NH2, —SO2NH(aliphatic), —SO2N(aliphatic)2, —O-aliphatic-COOH, and —O-aliphatic-NH2 (which may contain one or two N-aliphatic or N-acyl substituents).
A “halo” substituent according to the present invention may be a fluoro, chloro, bromo or iodo substituent. Fluoro is often the preferred halogen.
28-epirapalogs may differ from 28-epirapamycin with respect to one, two, three, four, five, six or seven substituent moieties. This class includes among others 28-epirapalogs with modifications, relative to rapamycin, at C7 and C13; C7 and C14; C7 and a; C7 and C43; C7 and C24; C7 and C28; C7 and C30; C7, C13 and C14; C7, C13 and a; C7, C13 and C43; C7, C13 and C24; C7, C13 and C28; C7, C13 and C30; C7, C14 and a; C7, C14 and C43; C7, C14 and C24; C7, C14 and C28; C7, C14 and C30; C7, a and C24; C7, a and C28; C7, a and C30; C7, C24 and C30; C7, C24, C30 and a; C7, C24, C30 and C13; C7, C24, C30 and C14; C24, C30 and C13; C24, C30 and a; C24, C30 and C14; and C24, C30, C13 and a. Modifications in rapalog structure are known for a number of previously known rapalogs (see e.g. WO 99/36553, Table III and Liberles et al, 1997, Proc Natl Acad Sci USA 94:7825–7830 and infra) and may be readily adapted to the present invention.
One subset of 28-epirapalogs of special interest for practicing the methods of this invention are those 28-epirapalogs (or pharmaceutically acceptable derivatives thereof) in which RC7a is a moiety other than OMe. This subset (“C7 28-epirapalogs”) includes compounds in which one of R7a and R7b is H and the other is selected from —RA, —Z—RA, —Z—(CO)RA, —Z—(CO)Z′RA, —NRASO2RA′ and —NSO2RA, where Z and Z′ are independently O, S or NRA. Illustrating this subset are the 28-epirapalogs bearing a C7 substituent selected from the following group: aryl; heteroaryl; aryl, heteroaryl or benzyl ether; and —NH(CO)ORA, —NH(CO)RA, —NH(SO2)RA or —NH(SO2)NHRA(where RA is a substituted or unsubstituted lower alkyl, e.g., methyl, ethyl, iPr, butyl, benzyl, etc. or is a substituted or unsubstituted phenyl (e.g., p-tolyl); In certain embodiments of this subset, R7a and R7b are independently selected from the following groups: H; a substituted or unsubstituted two to eight carbon straightchain, branched or cyclic alkenyl, alkoxyl or alkylmercapto; and a substituted or unsubstituted aryl, heteroaryl, aryloxy or heteroaryloxy, arylmercapto or heteroarylmercapto. Compounds of this subset include among others those in which R7a is H; (together with R7b)═O; alkoxy; alkylmercapto; amino (1°, 2° or 3°); amido; carbamate; aryl or substituted aryl; phenyl or substituted phenyl; substituted or unsubstituted heteroaryl such as substituted or unsubstituted thiophenyl, furyl, indolyl, etc.; or benzyloxy or substituted benzyloxy. Other illustrative C7 28-epirapalogs which may be used in practicing the methods of this invention include those in which one of R7a and R7b is H and the other is selected from —OEt, —O-propyl, —O-butyl, —OCH2CH2—OH, —O-benzyl, —O-substituted benzyl (including e.g., 3-nitro-, 4-chloro-, 3-iodo-4-diazo-, 3,4-dimethoxy-, and 2-methoxy-), —S—Me, —S-phenyl, —O(CO)Me, -allyl, —CH2C(Me)═CH2, —OCH2—CCH, —OCH2—CC—Me, —OCH2—CC—Et, —OCH2—CC—CH2OH, or -2,4-dimethoxyphenyl, 2,4,6-trimethoxyphenyl, furanyl, thiophen-yl, methylthiophen-yl, pyrolyl and indolyl. C7-modified 28-epirapalogs of particular interest are those bearing a substituted or unsubstituted aromatic ether, a substituted or unsubstituted benzyl ether or a carbamate moiety at C7. In C7-modified embodiments, the hydroxy substituent at C43 may be present in either stereochemical orientation (or as a mixture of isomers) or may be modified as described elsewhere herein. C7 28-epirapalogs may further vary from C7-modified 28-epirapamycin at one, two, three, four, five or more other positions as well.
28-epirapamycin and C7 28-epirapalogs of Formulas I, II and III are of particular interest and are encompassed by this invention as compositions of matter per se.
Another subset of 28-epirapalogs of special interest in the practice of the various methods of the invention are those of formula I, II or III in which the substituents at C24 and C30 are both other than (═O). Of special interest are those C30 and C24 substituents disclosed in WO 99/36553. This subset includes among others all 28-epirapalogs in which RC30 and RC24 are OH and one of RC7a and RC7b comprises any of the replacement substituents at that position specified for formula II, including any of the C7 substituents identified in compounds of Tables II or III. This subset includes among others 28-epirapalogs which differ from rapamycin with respect to the moiety a. For instance, this subset includes compounds of the formula:




where at least one of RC7a and RC7b is other than —OMe. Alternative substituents for RC7a and/or RC7b are as disclosed elsewhere herein. Of special interest are compounds in which one of RC7a and RC7b is cyclic aliphatic, aryl, heterocyclic or heteroaryl, which may be optionally substituted. Other compounds within this subset include those in which one, two, three, four or five of the hydroxyl groups is epimerized, fluorinated, alkylated, acylated or otherwise modified via other ester, carbamate, carbonate or urea formation. An illustrative compound for example is the 28-epirapalog in which the hydroxyl group at C43 is epimerized and the hydroxyl groups at C28 and C30 are alkylated, acylated or linked via carbonate formation.

Another subset of 28-epirapalogs of special interest are the mono-, di- and trifluoro-28-epirapalogs which contain an F at one or more of C13, C43, and C28, as disclosed in WO 99/36553, with or without additional changes elsewhere in the 28-epirapalog molecule.
Another subset of 28-epirapalogs of interest are those compounds of formula II in which RC24 is other than ═O, again, with or without one or more other modifications at other positions relative to rapamycin.
Other 28-epirapalogs of interest include 28-epirapalogs in which RC14 is OH.
Furthermore, this invention encompasses 28-epirapalogs in which one or more of the carbon—carbon double bonds at the 1,2, 3,4 or 5,6 positions in rapamycin are saturated, alone or in combination with a modification elsewhere in the molecule, e.g. at one or more of C7, C13, C43, C24 C28 and/or C30. It should also be appreciated that the C3,C4 double bond may be epoxidized; that the C6 methyl group may be replaced with —CH2OH or —CH2OMe; that the C43 hydroxy may be converted to F, Cl or H or other substituent; and that the C42 methoxy moiety may be demethylated, in any of the compounds disclosed herein, using methods known in the art. Likewise, moiety “a” may be replaced with any of the following




Synthetic Guidance

The production of rapamycin by fermentation and by total synthesis is known. The production of a number of rapalogs as fermentation products is also known. These include among others rapalogs bearing alternative moieties to the characteristic cyclohexyl ring or pipecolate ring of rapamycin, as well as C7-desmethyl-rapamycin, C29-desmethyl-rapamycin and C29-desmethoxyrapamycin.
The conversion of rapamycin to 28-epirapamycin can be readily carried out using Ti(OiPr)4 in dichloromethane at room temperature. The 28-epirapamycin so produced can than be further modified using methods and materials that have been used with rapamycin and other rapalogs. Alternatively, in some cases (not those involving modification to the C30 keto moiety) desired transformations can be carried out with rapamycin or a derivative thereof, and the penultimate product can then be epimerized at C28 and the desired product can be separately recovered from other products of the reaction mixture by the methods disclosed herein, although this approach is often not preferred.
Methods and materials for effecting various chemical transformations of rapamycin and structurally related macrolides are known in the art, as are methods for obtaining rapamycin and various rapalogs by fermentation. Many such chemical transformations of rapamycin and various rapalogs are disclosed in the patent documents identified in Table I, above, which serve to illustrate the level of skill and knowledge in the art of chemical synthesis and product recovery, purification and formulation which may be applied in practicing the subject invention. The following representative transformations and/or references which can be employed to produce the desired rapalogs are illustrative:











ring position



modified
literature reference







C7
Luengo, et al. JOC 59, 6512 (1995); Chem & Biol 2(7),



471–481 (1995)


C-13
C13 → F: protect C28 and C43, rxn at 0°


C-14
Schubert, et al. Angew Chem Int Ed Engl 23, 167 (1984).


C-20
Nelson, U.S. Pat. No. 5,387,680


C-24
U.S. Pat. No. 5,373,014; 5,378,836



Lane, et al. Synthesis 1975, p136.


C-30
Luengo et al. Tet. Lett. 35, 6469 (1994)


various
Or et al, U.S. Pat. Nos. 5,527,907 and 5,583,139; Luengo,


positions
WO 94/02136; Cottens et al, WO 95/16691; Clackson et al,



WO 96/41865 and WO99/36553









Additionally, it is contemplated that 28-epirapalogs for use in this invention as well as intermediates for the production of such 28-epirapalogs may be prepared by directed biosynthesis, e.g. as described by Katz et al, WO 93/13663 and by Cane et al, WO 9702358. See also Khaw et al, 1998, J. Bacteriology 180(4):809–814 for additional biological methods.
Novel 28-epirapalogs of this invention may be prepared by one of ordinary skill in this art relying upon methods and materials known in the art as guided by the disclosure presented herein. For instance, methods and materials may be adapted from known methods set forth or referenced in the documents cited above, the full contents of which are incorporated herein by reference. Additional guidance and examples are provided herein by way of illustration and further guidance to the practitioner. It should be understood that the chemist of ordinary skill in this art would be readily able to make modifications to the foregoing, e.g. to add appropriate protecting groups to sensitive moieties during synthesis, followed by removal of the protecting groups when no longer needed or desired, and would be readily capable of determining other synthetic approaches.
FKBP Domains and Fusion Proteins
The FKBP fusion protein comprises at least one FKBP domain containing all or part of the peptide sequence of an FKBP domain and at least one heterologous action domain. This chimeric protein must be capable of binding to a 28-epirapalog of this invention, preferably with a Kd value below about 100 nM, more preferably below about 10 nM and even more preferably below about 1 nM, as measured by direct binding measurement (e.g. fluorescence quenching), competition binding measurement (e.g. versus FK506), inhibition of FKBP enzyme activity (rotamase), or other assay methodology. Typically the chimeric protein will contain one or more protein domains comprising peptide sequence selected from that of a naturally occurring FKBP protein such as human FKBP12, e.g. as described in International Patent Application PCT/US94/01617. That peptide sequence may be modified to adjust the binding specificity, usually with replacement, insertion or deletion of 10 or fewer, preferably 5 or fewer, amino acid residues. Such modifications are elected in certain embodiments to yield one or both of the following binding profiles: (a) binding of a 28-epirapalog to the modified FKBP domain, or chimera containing it, preferably at least one, and more preferably at least two, and even more preferably three or four or more, orders of magnitude better (by any measure) than to FKBP12 or the FKBP endogenous to the host cells to be engineered; and (b) binding of the FKBP:28-epirapalog complex to the FRB fusion protein, preferably at least one, and more preferably at least two, and even more preferably at least three, orders of magnitude better (by any measure) than to the FRAP or other FRB-containing protein endogenous to the host cell to be engineered.
The FKBP chimera also contains at least one heterologous action domain, i.e., a protein domain containing non-FKBP peptide sequence. The action domain may be a DNA-binding domain, transcription activation domain, cellular localization domain, intracellular signal-transduction domain, etc., e.g. as described elsewhere herein or in PCT/US94/01617 or the other cited references. Generally speaking, the action domain is capable of directing the chimeric protein to a selected cellular location or of initiating a biological effect upon association or aggregation with another action domain, for instance, upon multimerization of proteins containing the same or different action domains.
A recombinant nucleic acid encoding such a fusion protein will be capable of selectively hybridizing to a DNA encoding the parent FKBP protein, e.g. human FKBP12, or would be capable of such hybridization but for the degeneracy of the genetic code. Since these chimeric proteins contain an action domain derived from another protein, e.g. Gal4, VP16, FAS, CD3 zeta chain, etc., the recombinant DNA encoding the chimeric protein will also be capable of selectively hybridizing to a DNA encoding that other protein, or would be capable of such hybridization but for the degeneracy of the genetic code.
FKBP fusion proteins of this invention, as well as FRB fusion proteins discussed in further detail below, may contain one or more copies of one or more different ligand binding domains and one or more copies of one or more action domains. The ligand binding domain(s) (i.e., FKBP and FRB domains) may be N-terminal, C-terminal, or interspersed with respect to the action domain(s). Embodiments involving multiple copies of a ligand binding domain usually have 2, 3 or 4 such copies. For example, an FKBP fusion protein may contain 2, 3 or 4 FKBP domains. The various domains of the FKBP fusion proteins (and of the FRB fusion proteins discussed below) are optionally separated by linking peptide regions which may be derived from one of the adjacent domains or may be heterologous.
Illustrative examples of FKBP fusion proteins useful in the practice of this invention include the FKBP fusion proteins disclosed in PCT/US94/01617 (Stanford & Harvard), PCT/US94/08008 (Stanford & Harvard), Spencer et al (supra), PCT/US95/10591 (ARIAD), PCT/US95/06722 (Mitotix, Inc.) and other references cited herein; the FKBP fusion proteins disclosed in the examples which follow; variants of any of the foregoing FKBP fusion proteins which contain up to 10 (preferably 1–5) amino acid insertions, deletions or substitutions in one or more of the FKBP domains and which are still capable of binding to rapamycin or to a 28-epirapalog; variants of any of the foregoing FKBP fusion proteins which contain one or more copies of an FKBP domain which is encoded by a DNA sequence capable of selectively hybridizing to a DNA sequence encoding a naturally occurring FKBP domain and which are still capable of binding to rapamycin or to a 28-epirapalog; variants of any of the foregoing in which one or more heterologous action domains are deleted, replaced or supplemented with a different heterologous action domain; variants of any of the foregoing FKBP fusion proteins which are capable of binding to rapamycin or a 28-epirapalog and which contain an FKBP domain derived from a non-human source; and variants of any of the foregoing FKBP fusion proteins which contain one or more amino acid residues corresponding to Tyr26, Phe36, Asp37, Arg42, Phe46, Phe48, Glu54, Val55, or Phe99 of human FKBP12 in which one or more of those amino acid residues is replaced by a different amino acid, the variant being capable of binding to rapamycin or a 28-epirapalog.
For instance, in a number of cases the FKBP fusion proteins comprise multiple copies of an FKBP domain containing amino acids 1–107 of human FKBP12, separated by the 2-amino acid linker Thr-Arg encoded by ACTAGA, the ligation product of DNAs digested respectively with the restriction endonucleases Spel and Xbal. The following table provides illustrative subsets of mutant FKBP domains based on the foregoing FKBP12 sequence:










Illustrative Mutant FKBPs




















F36A
Y26V
F46A
W59A



F36V
Y26S
F48H
H87W



F36M
D37A
F48L
H87R



F36S
I90A
F48A
F36V/F99A



F99A
I91A
E54A
F36V/F99G



F99G
F46H
E54K
F36M/F99A



Y26A
F46L
V55A
F36M/F99G







note: Entries identify the native amino acid by single letter code and sequence position, followed by the replacement amino acid in the mutant. Thus, F36V designates a human FKBP12 sequence in which phenylalanine at position 36 is replaced by valine. F36V/F99A indicates a double mutation in which phenylalanine at positions 36 and 99 are replaced by valine and alanine, respectively.






FRB Domains and Fusion Proteins

The FRB fusion protein comprises at least one FRB domain (which may comprise all or part of the peptide sequence of a FRAP protein or a variant thereof, as described elsewhere) and at least one heterologous effector domain.
Generally speaking, the FRB domain, or a chimeric protein encompassing it, is encoded by a DNA molecule capable of hybridizing selectively to a DNA molecule encoding a protein comprising a naturally occurring FRB domain, e.g. a DNA molecule encoding a human or other mammalian FRAP protein or one of yeast proteins, Tor-1 or Tor-2 or the previously mentioned Candida FRB-containing protein. FRB domains of this invention include those which are capable of binding to a complex of an FKBP protein and a 28-epirapalog of this invention.
The FRB fusion protein must be capable of binding to the complex formed by the FKBP fusion protein with a 28-epirapalog of this invention. Preferably, the FRB fusion protein binds to that complex with a Kd value below 200 μM, more preferably below 10 μM, as measured by conventional methods. The FRB domain will be of sufficient length and composition to maintain high affinity for a complex of the 28-epirapalog with the FKBP fusion protein. In some embodiments the FRB domain spans fewer than about 150 amino acids in length, and in some cases fewer than about 100 amino acids. One such region comprises a 133 amino acid region of human FRAP extending from Val2012 through Tyr2144. See Chiu et al, 1994, Proc. Natl. Acad. Sci. USA 91:12574–12578. An FRB region of particular interest spans Glu2025 through Gln2114 of human FRAP and retains affinity for a FKBP12-rapamycin complex or for FKBP-28-epirapalog complex. In some embodiments Q2214 is removed from the 90-amino acid sequence rendering this an 89-amino acid FRB domain. The FRB peptide sequence may be modified to adjust the binding specificity, usually with replacement, insertion or deletion, of or fewer, preferably 5 or fewer, amino acids. Such modifications are elected in certain embodiments to achieve a preference towards formation of the complex comprising one or more molecules of the FKBP fusion protein, FRB fusion protein and a 28-epirapalog over formation of complexes of endogenous FKBP and FRAP proteins with the rapalog. Preferably that preference is at least one, and more preferably at least two, and even more preferably three, orders of magnitude (by any measure).
A recombinant DNA encoding such a protein will be capable of selectively hybridizing to a DNA encoding a FRAP species, or would be capable of such hybridization but for the degeneracy of the genetic code. Again, since these chimeric proteins contain an effector domain derived from another protein, e.g. Gal4, VP16, Fas, CD3 zeta chain, etc., the recombinant DNA encoding the chimeric protein will be capable of selectively hybridizing to a DNA encoding that other protein, or would be capable of such hybridization but for the degeneracy of the genetic code.
Illustrative examples of FRB chimeras useful in the practice of this invention include those disclosed in the examples which follow, variants thereof in which one or more of the heterologous domains are replaced with alternative heterologous domains or supplemented with one or more additional heterologous domains, variants in which one or more of the FRB domains is a domain of non-human peptide sequence origin (such as Tor 2 or Candida for example), and variants in which the FRB domain is modified by amino acid substitution, replacement or insertion as described herein, so long as the chimera is capable of binding to a complex formed by an FKBP protein and a 28-epirapalog of this invention. An illustrative FRB fusion protein contains one or more FRBs of at least 89-amino acids, containing a sequence spanning at least residues 2025–2113 of human FRAP, separated by the linker Thr-Arg formed by ligation of Spel-Xbal sites as mentioned previously. It should be appreciated that such restriction sites or linkers in any of the fusion proteins of this invention may be deleted, replaced or extended using conventional techniques such as site-directed mutagenesis.
Mixed Chimeric Proteins
A third type of chimeric protein comprises one or more FKBP domains, one or more heterologous effector domains, and one or more FRB domains as described for the FRB fusion proteins.
Mixed chimeric protein molecules are capable of forming homodimeric or homomultimeric protein complexes in the presence of a 28-epirapalog to which they bind. Embodiments involving mixed chimeras have the advantage of requiring the introduction into cells of a single recombinant nucleic acid construct in place of two recombinant nucleic acid constructs otherwise required to direct the expression of both an FKBP fusion protein and a FRB fusion protein.
A recombinant DNA encoding a mixed chimeric protein will be capable of selectively hybridizing to a DNA encoding an FKBP protein, a DNA encoding FRAP, and a heterologous DNA sequence encoding the protein from which one or more effector domains is derived (e.g. Gal4, VP16, Fas, CD3 zeta chain, etc.), or would be capable of such hybridization but for the degeneracy of the genetic code.
Heterologous Domains
As mentioned above, the heterologous effector domains of the FKBP and FRB fusion proteins are protein domains which, upon mutual association of the chimeric proteins bearing them, are capable of triggering (or inhibiting) DNA-binding and/or transcription of a target gene; actuating cell growth, differentiation, proliferation or apoptosis; directing proteins to a particular cellular location; or actuating other biological events.
Embodiments involving regulatable gene transcription involve the use of target gene constructs which comprise a target gene (which encodes a polypeptide, antisense RNA, ribozyme, etc. of interest) under the transcriptional control of a DNA element responsive to the association or multimerization of the heterologous domains of the 1st and 2d chimeric proteins.
In embodiments of the invention involving direct activation of transcription, the heterologous domains of the 1st and 2d chimeric proteins comprise a DNA binding domain such as Gal4 or a chimeric DNA binding domain such as ZFHD1, discussed below, and a transcriptional activating domain such as those derived from VP16 or p65, respectively. The multimerization of a chimeric protein containing such a transcriptional activating domain to a chimeric protein containing a DNA binding domain targets the transcriptional activator to the promoter element to which the DNA binding domain binds, and thus activates the transcription of a target gene linked to that promoter element. Foregoing the transcription activation domain or substituting a repressor domain (see PCT/US94/01617) in place of a transcription activation domain provides an analogous chimera useful for inhibiting transcription of a target gene. Composite DNA binding domains and DNA sequences to which they bind are disclosed in Pomerantz et al, 1995, supra, the contents of which are incorporated herein by reference. Such composite DNA binding domains may be used as DNA binding domains in the practice of this invention, together with a target gene construct containing the cognate DNA sequences to which the composite DBD binds.
In embodiments involving indirect activation of transcription, the heterologous domains of the chimeras are effector domains of signaling proteins which upon aggregation or multimerization trigger the activation of transcription under the control of a responsive promoter. For example, the signaling domain may be the intracellular domain of the zeta subunit of the T cell receptor, which upon aggregation, triggers transcription of a gene linked to the IL-2 promoter or a derivative thereof (e.g. iterated NF-AT binding sites).
In another aspect of the invention, the heterologous domains are protein domains which upon mutual association are capable of triggering cell death. Examples of such domains are the intracellular domains of the Fas antigen or of the TNF R1. Chimeric proteins containing a Fas domain can be designed and prepared by analogy to the disclosure of PCT/US94/01617.
Engineered Receptor Domains
As noted previously, the FKBP and FRB domains may contain peptide sequence selected from the peptide sequences of naturally occurring FKBP and FRB domains. Naturally occurring sequences include those of human FKBP12 and the FRB domain of human FRAP. Alternatively, the peptide sequences may be derived from such naturally occurring peptide sequences but contain generally up to 10, and preferably 1–5, mutations in one or both such peptide sequences. As disclosed in greater detail elswhere herein, such mutations can confer a number of important features. For instance, an FKBP domain may be modified such that it is capable of binding a 28-epirapalog preferentially, i.e. at least one, preferably two, and even more preferably three or four or more orders of magnitude more effectively, with respect to 28-epirapalog binding by the unmodified FKBP domain. An FRB domain may be modified such that it is capable of binding a (modified or unmodified) FKBP:28-epirapalog complex preferentially, i.e. at least one, preferably two, and even more preferably three orders of magnitude more effectively, with respect to the unmodified FRB domain. FKBP and FRB domains may be modified such that they are capable of forming a tripartite complex with a 28-epirapalog, preferentially, i.e. at least one, preferably two, and even more preferably three orders of magnitude more effectively, with respect to unmodified FKBP and FRB domains.
(a) FKBP
Methods for identifying FKBP mutations that confer enhanced ability to bind derivatives of FK506 containing various substituents (“bumps”) were disclosed in PCT/US94/01617. Similar strategies can be used to obtain modified FKBPs that preferentially bind bumped rapamycin derivatives, i.e., 28-epirapalogs. The structure of the complex between rapamycin and FKBP12 is known (see for example Van Duyne et al., J. Am. Chem. Soc. (1991) 113, 7433–7434). Such data can be used to reveal amino acid residues that would clash with various 28-epirapalog substituents. In this approach, molecular modelling is used to identify candidate amino acid substitutions in the FKBP domain that would accommodate the 28-epirapalog substituent(s), and site-directed mutagenesis may then be used to engineer the protein mutations so identified. The mutants are expressed by standard methods and their binding affinity for the 28-epirapalogs measured, for example by inhibition of rotamase activity, or by competition for binding with a molecule such as FK506, if the mutant retains appropriate activity/affinity.
More particularly, we contemplate that certain 28-epirapalogs of this invention, e.g. 28-epirapalogs with modifications relative to rapamycin at C-13 or C-14 bind preferentially to FKBPs in which one or more of the residues, Tyr26, Phe36, Asp37, Tyr82 and Phe99, are substituted with amino acids that have smaller side chains (such as Gly, Ala, Val, Met and Ser). Examples of mutant FKBPs with modifications at positions 26 or 36 are noted in the “Illustrative Mutant FKBPs” table above. Similarly, we contemplate that 28-epirapalogs with modifications at C20 (i.e., 28-epirapalogs in which R4 is other than —H) bind preferentially to FKBPs in which Tyr82 and/or Ile56 are replaced by other amino acids, especially those with smaller side chains. In a further example, we contemplate that 28-epirapalogs bearing modifications at C24 (i.e., in which W is other than ═O) bind preferentially to FKBPs in which one or more of Phe46, Phe48 and Val55 are replaced by other amino acids, again especially those with smaller side chains. Moreover, we envisage that 28-epirapalogs with modifications at C28 and/or C30 bind preferentially to FKBPs in which Glu54 is replaced by another amino acid, especially one with a smaller side chain. In all of the above examples, single or multiple amino acid substitutions may be made. Again, specific examples are noted in the previous table.
An alternative to iterative engineering and testing of single or multiple mutants is to co-randomize structurally-identified residues that are or would be in contact with or near one or more 28-epirapalog or rapamycin substituents. A collection of polypeptides containing FKBP domains randomized at the identified positions (such as are noted in the foregoing paragraph) is prepared e.g. using conventional synthetic or genetic methods. Such a collection represents a set of FKBP domains containing replacement amino acids at one or more of such positions. The collection is screened and FKBP variants are selected which possess the desired 28-epirapalog binding properties. In general, randomizing several residues simultaneously is expected to yield compensating mutants of higher affinity and specificity for a given bumped rapalog as it maximizes the likelihood of beneficial cooperative interactions between sidechains. Techniques for preparing libraries randomized at discrete positions are known and include primer-directed mutagenesis using degenerate oligonucleotides, PCR with degenerate oligonucleotides, and cassette mutagenesis with degenerate oligonucleotides (see for example Lowman, H. B, and Wells, J. A. Methods: Comp. Methods Enzymol. 1991. 3, 205–216; Dennis, M. S. and Lazarus, R. A. 1994. J. Biol. Chem. 269, 22129–22136; and references therein).
We further contemplate that in many cases, randomization of only the few residues in or near direct contact with a given position in rapamycin may not completely explore all the possible variations in FKBP conformation that could optimally accommodate a 28-epirapalog substituent (bump). Thus the construction is also envisaged of unbiased libraries containing random substitutions that are not based on structural considerations, to identify subtle mutations or combinations thereof that confer preferential binding to bumped 28-epirapalogs. Several suitable mutagenesis schemes have been described, including alanine-scanning mutagenesis (Cunningham and Wells (1989) Science 244, 1081–1085), PCR misincorporation mutagenesis (see eg. Cadwell and Joyce, 1992, PCR Meth. Applic. 2, 28–33), and ‘DNA shuffling’ (Stemmer, 1994, Nature 370, 389–391 and Crameri et al, 1996, Nature Medicine 2, 100–103). These techniques produce libraries of random mutants, or sets of single mutants, that are then searched by screening or selection approaches.
In many cases, an effective strategy to identify the best mutants for preferential binding of a given bump is a combination of structure-based and unbiased approaches. See Clackson and Wells, 1994, Trends Biotechnology 12, 173–184 (review). For example we contemplate the construction of libraries in which key contact residues are randomized by PCR with degenerate oligonucleotides, but with amplification performed using error-promoting conditions to introduce further mutations at random sites. A further example is the combination of component DNA fragments from structure-based and unbiased random libraries using DNA shuffling.
Screening of libraries for desirable mutations may be performed by use of a yeast 2-hybrid system (Fields and Song (1989) Nature 340, 245–246). For example, an FRB-VP16 fusion may be introduced into one vector, and a library of randomized FKBP sequences cloned into a separate GAL4 fusion vector. Yeast co-transformants are treated with 28-epirapalog, and those harboring complementary FKBP mutants are identified by for example beta-galactosidase or luciferase production (a screen), or survival on plates lacking an essential nutrient (a selection), as appropriate for the vectors used. The requirement for bumped rapamycin to bridge the FKBP-FRAP interaction is a useful screen to eliminate false positives.
A further strategy for isolating modified ligand-binding domains from libraries of FKBP (or FRB) mutants utilizes a genetic selection for functional dimer formation described by Hu et. al. (Hu, J. C., et al. 1990. Science. 250:1400–1403; for review see Hu, J. C. 1995. Structure. 3:431–433). This strategy utilizes the fact that the bacteriophage lambda repressor cl binds to DNA as a homodimer and that binding of such homodimers to operator DNA prevents transcription of phage genes involved in the lytic pathway of the phage life cycle. Thus, bacterial cells expressing functional lambda repressor are immune to lysis by superinfecting phage lambda. Repressor protein comprises an amino terminal DNA binding domain (amino acids 1–92), joined by a 40 amino acid flexible linker to a carboxy terminal dimerization domain. The isolated N-terminal domain binds to DNA with low affinity due to inefficient dimer formation. High affinity DNA binding can be restored with heterologous dimerization domains such as the GCN4 “leucine zipper”. Hu et al have described a system in which phage immunity is used as a genetic selection to isolate GCN4 leucine zipper mutants capable of mediating lambda repressor dimer formation from a large population of sequences (Hu et. al., 1990).
For example, to use the lambda repressor system to identify FRAP mutants complementary to bumped 28-epirapalogs, lambda repressor-FRAP libraries bearing mutant FRAP sequences are transformed into E. coli cells expressing wildtype lambda repressor-FKBP protein. Plasmids expressing FRAP mutants are isolated from those colonies that survive lysis on bacterial plates containing high titres of lambda phage and “bumped” rapamycin compounds. Alternatively, to isolate FKBP mutants, the above strategy is repeated with lambda repressor-FKBP libraries bearing mutant FKBP sequences transformed into E. coli cells expressing wildtype lambda repressor-FRAP protein.
A further alternative is to clone the randomized FKBP sequences into a vector for phage display, allowing in vitro selection of the variants that bind best to the 28-epirapalog. Affinity selection in vitro may be performed in a number of ways. For example, 28-epirapalog is mixed with the library phage pool in solution in the presence of recombinant FRAP tagged with an affinity handle (for example a hexa-histidine tag, or GST), and the resultant complexes are captured on the appropriate affinity matrix to enrich for phage displaying FKBP harboring complementary mutations. Techniques for phage display have been described, and other in vitro selection selection systems can also be contemplated (for example display on lambda phage, display on plasmids, display on baculovirus). Furthermore, selection and screening strategies can also be used to improve other properties of benefit in the application of this invention, such as enhanced stability in vivo. For a review see Clackson, T. & Wells, J. A. 1994. Trends Biotechnol. 12, 173–184.
(b) FRAP
Similar considerations apply to the generation of mutant FRB domains which bind preferentially to 28-epirapalogs containing modifications (i.e., are ‘bumped’) relative to rapamycin in the FRAP-binding portion of the macrocycle. For example, one may obtain preferential binding using 28-epirapalogs bearing substituents other than —OMe at the C7 position with FRBs based on the human FRAP FRB peptide sequence but bearing amino acid substitutions for one of more of the residues Tyr2038, Phe2039, Thr2098, Gln2099, Trp2101 and Asp2102. Exemplary mutations include Y2038H, Y2038L, Y2038V, Y2038A, F2039H, F2039L, F2039A, F2039V, D2102A, T2098A, T2098N, and T2098S, 28-epirapalogs bearing substituents other than —OH at C28 and/or substituents other than ═O at C30 may be used to obtain preferential binding to FRAP proteins bearing an amino acid substitution for Glu2032. Examplary mutations include E2032A and E2032S. Proteins comprising an FRB containing one or more amino acid replacements at the foregoing positions, libraries of proteins or peptides randomized at those positions (i.e., containing various substituted amino acids at those residues), libraries randomizing the entire protein domain, or combinations of these sets of mutants are made using the procedures described above to identify mutant FRAPs that bind preferentially to bumped 28-epirapalogs.
The affinity of candidate mutant FRBs for the complex of an FKBP protein complexed with a 28-epirapalog may be assayed by a number of techniques; for example binding of in vitro translated FRB mutants to GST-FKBP in the presence of drug (Chen et al. 1995. Proc. Natl. Acad. Sci. USA 92, 4947–4951); or ability to participate in a 28-epirapalog-dependent transcriptionally active complex with an appropriate FKBP fusion protein in a yeast two-hybrid assay.
FRB mutants with desired binding properties may be isolated from libraries displayed on phage using a variety of sorting strategies. For example, a 28-epirapalog is mixed with the library phage pool in solution in the presence of recombinant FKBP tagged with an affinity handle (for example a hexa-histidine tag, or GST), and the resultant complexes are captured on the appropriate affinity matrix to enrich for phage displaying FRAP harboring complementary mutations.
An additional feature of the FRB fusion protein that may vary in the various embodiments of this invention is the exact sequence of the FRB domain used. In some applications it may be preferred to use portions of an FRB which are larger than the minimal (89 amino acid) FRB domain. These include extensions N-terminal to residue Glu2025 (preferably extending to at least Arg2018 or Ile2021), as well as C-terminal extensions beyond position 2113, e.g. to position 2113, 2141 or 2174 or beyond), which may in some cases improve the stability of the folded FRB domain and/or the efficiency of expression. Other applications in which different FRB sequence termini may be used include those in which a long linker is desired for steric reasons on one or both sides of the FRB domain, for example to accommodate the distortions of the polypeptide chain required for FRB-mediated protein—protein association at the cell membrane or on DNA. Conversely, in other applications short linkers on one or both sides of the FRB domain may be preferred or required to present the heterologous effector domain(s) appropriately for biological function. In human gene therapy applications the use of naturally occurring human FRAP sequence for such linkers will generally be preferred to the introduction of heterologous sequences, or reduce the risk of provoking an immune response in the host organism.
Some 28-epirapalogs, especially rapalogs with modifications or substituents (relative to rapamycin) at positions believed to lie near the boundary between the FKBP binding domain and the FRAP binding domain, such as those on C28, C30, C7 and C24, possess reduced ability, relative to rapamycin, to form complexes with both mammalian FKBP and FRB domains, in particular, with those domains containing naturally occurring human peptide sequence. That reduced ability may be manifested as a reduced binding affinity as determined by any of the direct or indirect assay means mentioned herein or as reduced immunosuppressive activity as determined in an appropriate assay such as a T cell proliferation assay. In such cases, iterative procedures may be used to identify pairs of mutant FKBPs and mutant FRBs that are capable of complexing with the rapalog more effectively than the corresponding domains containing naturally occurring human peptide sequence. For example, one may first identify a complementary modified FKBP domain capable of binding to the rapalog, as discussed previously, and then using this mutant FKBP domain as an affinity matrix in complex with the rapalog, one may select a complementary modified FRB domain capable of associating with that complex. Several cycles of such mutagenesis and screening may be performed to optimize the protein pair.
For some embodiments, it will be desirable to use FRB and/or FKBP domains containing mutations that can affect the protein—protein interaction. For instance, mutant FKBP domains which when bound to a given rapalog are capable of complexing with an endogenous FRB measurably less effectively than to a mutant FRB are of particular interest. Also of interest are mutant FRB domains which are capable of associating with a complex of a mutant FKBP with a given rapalog measurable more effectively than with a complex of an endogenous FKBP with the rapalog. Similar selection and screening approaches to those delineated previously can be used (i) to identify amino acid substitutions, deletions or insertions to an FKBP domain which measurably diminish the domain's ability to form the tripartite complex with a given rapalog and the endogenous FRB; (ii) to identify amino acid substitutions, deletions or insertions to an FRB domain which measurably diminish the domain's ability to form the tripartite complex with a given rapalog and the endogenous FKBP; and (iii) to select and/or otherwise identify compensating mutation(s) in the partner protein. As examples of suitable mutant FKBPs with diminished effectiveness in tripartite complex formation, we include mammalian, preferably human FKBP in which one or both of His87 and Ile90 are replaced with amino acids such as Arg, Trp, Phe, Tyr or Lys which contain bulky side chain groups; FRB domains, preferably containing mammalian, and more preferably of human, peptide sequence may then be mutated as described above to generate complementary variants which are capable of forming a tripartite complex with the mutant FKBP and a given rapalog. Illustrative FRB mutations which may be useful with H87W or H87R hFKBP12s include human FRBs in which Y2038 is replaced by V, S, A or L; F2039 is replaced by A; and/or R2042 is replaced by L, A or S. Illustrative FRB mutations which may be useful with 190W or 190R hFKBP12s include human FRBs in which K2095 is replaced with L, S, A or T.
Additionally, in optimizing the receptor domains of this invention, it should be appreciated that immunogenicity of a polypeptide sequence is thought to require the binding of peptides by MHC proteins and the recognition of the presented peptides as foreign by endogenous T-cell receptors. It may be preferable, at least in human gene therapy applications, to tailor a given foreign peptide sequence, including junction peptide sequences, to minimize the probability of its being immunologically presented in humans. For example, peptide binding to human MHC class I molecules has strict requirements for certain residues at key ‘anchor’ positions in the bound peptide: eg. HLA-A2 requires leucine, methionine or isoleucine at position 2 and leucine or valine at the C-terminus (for review see Stern and Wiley (1994) Structure 2, 145–251). Thus in engineering proteins in the practice of this invention, this periodicity of these residues is preferably avoided, especially in human gene therapy applications. The foregoing applies to all protein engineering aspects of the invention, including without limitation the engineering of point mutations into receptor domains, and to the choice or design of boundaries between the various protein domains.
Other Components, Design Features and Applications
The chimeric proteins may contain as a heterologous domain a cellular localization domain such as a membrane retention domain. See e.g. PCT/US94/01617, especially pages 26–27. Briefly, a membrane retention domain can be isolated from any convenient membrane-bound protein, whether endogenous to the host cell or not. The membrane retention domain may be a transmembrane retention domain, i.e., an amino acid sequence which extends across the membrane as in the case of cell surface proteins, incluing many receptors. The transmembrane peptide sequence may be extended to span part or all of an extracellular and/or intracellular domain as well. Alternatively, the membrane retention domain may be a lipid membrane retention domain such as a myristoylation or palmitoylation site which permits association with the lipids of the cell surface membrane. Lipid membrane retention domains will usually be added at the 5′ end of the coding sequence for N-terminal binding to the membrane and, proximal to the 3′ end for C-terminal binding. Peptide sequences involving post-translational processing to provide for lipid membrane binding are described by Carr, et al., PNAS USA (1988) 79, 6128; Aitken, et al., FEBS Lett. (1982) 150, 314; Henderson, et al., PNAS USA (1983) 80, 319; Schulz, et al., Virology (1984), 123, 2131; Dellman, et al. Nature (1985) 314, 374; and reviewed in Ann. Rev. of Biochem. (1988) 57, 69. An amino acid sequence of interest includes the sequence M-G-S—S-K-S-K-P-K-D-P—S-Q-R. Various DNA sequences can be used to encode such sequences in the various chimeric proteins of this invention. Other localization domains include organelle-targeting domains and sequences such as -K-D-E-L and -H-D-E-L which target proteins bearing them to the endoplasmic reticulum, as well as nuclear localization sequences which are particularly useful for chimeric proteins designed for (direct) transcriptional regulation. Various cellular localization sequences and signals are well known in the art.
Further details which may be used in the practice of the subject invention relating to the design, assembly and use of constructs encoding chimeric proteins containing various effector domains including cytoplasmic signal initiation domains such as the CD3 zeta chain, nuclear transcription factor domains including among others VP16 and GAL4, domains capable of triggering apoptosis including the Fas cytoplasmic domain and others are disclosed in PCT/US94/01617 and PCT/US95/10591. The latter international application further discloses additional features particularly applicable to the creation of genetically engineered animals which may be used as disease models in biopharmaceutical research. Those features include the use of tissue specific regulatory elements in the constructs for expression of the chimeric proteins and the application of regulated transcription to the expression of Cre recombinase as the target gene leading to the elimination of a gene of interest flanked by loxP sequences. Alternatively, flp and its cognate recognition sequences may be used instead of Cre and lox. Those features may be adapted to the subject invention.
In various cases, especially in embodiments involving whole animals containing cells engineered in accordance with this invention, it will often be preferred, and in some cases required, that the various domains of the chimeric proteins be derived from proteins of the same species as the host cell. Thus, for genetic engineering of human cells, it is often preferred that the heterologous domains (as well as the FKBP and FRB domains) be of human origin, rather than of bacterial, yeast or other non-human source.
We also note that epitope tags may also be incorporated into chimeric proteins of this invention to permit convenient detection.
Tissue-Specific or Cell-Type Specific Expression
It will be preferred in certain embodiments, that the chimeric proteins be expressed in a cell-specific or tissue-specific manner. Such specificity of expression may be achieved by operably linking one ore more of the DNA sequences encoding the chimeric protein(s) to a cell-type specific transcriptional regulatory sequence (e.g. promoter/enhancer). Numerous cell-type specific transcriptional regulatory sequences are known. Others may be obtained from genes which are expressed in a cell-specific manner. See e.g. PCT/US95/10591, especially pp. 36–37.
For example, constructs for expressing the chimeric proteins may contain regulatory sequences derived from known genes for specific expression in selected tissues. Representative examples are tabulated below:












Tissue
Gene
Reference







lens
g2-crystallin
Breitman, M. L., Clapoff, S., Rossant, J.,




Tsui, L. C., Golde, L. M., Maxwell, I. H.,




Bernstin, A. (1987) Genetic Ablation: tar-




geted expression of a toxin gene causes




microphthalmia in transgenic mice.




Science 238: 1563–1565



aA-crystallin
Landel, C. P., Zhao, J., Bok, D., Evans, G.




A. (1988) Lens-specific expression of a




recombinant ricin induces developmental




defects in the eyes of transgenic mice.




Genes Dev. 2: 1168–1178




Kaur, S., key, B., Stock, J., McNeish, J. D.,




Akeson, R., Potter, S. S. (1989) Targeted




ablation of alpha-crystallin-synthesizing cells




produces lens-deficient eyes in transgenic




mice. Development 105: 613–619


pituitary-
Growth
Behringer, R. R., Mathews, L. S., Palmiter,


somatrophic
hormone
R. D., Brinster, R. L. (1988) Dwarf mice


cells

produced by genetic ablation of growth




hormone-expressing cells. Genes Dev. 2:




453–461


pancreas
Insulin-
Ornitz, D. M., Palmiter, R. D., Hammer, R.



Elastase -
E., Brinster, R. L., Swift, G. H.,



acinar cell
MacDonald, R. J. (1985) Specific expression



specific
of an elastase-human growth fusion in pan-




creatic acinar cells of transgeneic mice.




Nature 131: 600–603




Palmiter, R. D., Behringer, R. R., Quaife,




C. J., Maxwell, F., Maxwell, I. H., Brinster,




R. L. (1987) Cell lineage ablation in trans-




geneic mice by cell-specific expression of




a toxin gene. Cell 50: 435–443


T cells
lck promoter
Chaffin, K. E., Beals, C. R., Wilkie, T. M.,




Forbush, K. A., Simon, M. I., Perlmutter,




R. M. (1990) EMBO Journal 9: 3821–3829


B cells
Immuno-
Borelli, E., Heyman, R., Hsi, M., Evans, R.



globulin
M. (1988) Targeting of an inducible toxic



kappa light
phenotype in animal cells. Proc. Natl. Acad.



chain
Sci. USA 85: 7572–7576




Heyman, R. A., Borrelli, E., Lesley, J.,




Anderson, D., Richmond, D. D., Baird,




S. M., Hyman, R., Evans, R. M. (1989)




Thymidine kinase obliteration: creation




of transgenic mice with controlled immuno-




deficiencies. Proc. Natl. Acad. Sci.




USA 86: 2698–2702


Schwann
P0 promoter
Messing, A., Behringer, R. R., Hammang, J.


cells

P. Palmiter, R D, Brinster, R L, Lemke, G. ,




P0 promoter directs espression of reporter




and toxin genes to Schwann cells of




transgenic mice. Neuron 8: 507–520 1992



Myelin basic
Miskimins, R. Knapp, L., Dewey, M J,



protein
Zhang, X. Cell and tissue-specific expression




of a heterologous gene under control of the




myelin basic protein gene promoter in trans-




genic mice. Brain Res Dev Brain Res 1992




Vol 65: 217–21


spermatids
protamine
Breitman, M. L., Rombola, H., Maxwell, I.




H., Klintworth, G. K., Bernstein, A. (1990)




Genetic ablation in transgenic mice with




attenuated diphtheria toxin A gene. Mol.




Cell. Biol. 10: 474–479


lung
Lung
Ornitz, D. M., Palmiter, R. D., Hammer, R.



surfacant
E., Brinster, R. L., Swift, G. H.,



gene
MacDonald, R. J. (1985) Specific expression




of an elastase-human growth fusion in




pancreatic acinar cells of transgenic mice.




Nature 131: 600–603


adipocyte P2

Ross, S. R, Braves, R A, Spiegelman, B M




Targeted expression of a toxin gene to




adipose tissue: transgenic mice resistant to




obesity Genes and Dev 7: 1318–24 1993


muscle
myosin light
Lee, K J, Ross, R S, Rockman, H A, Harris,



chain
A N, O'Brien, T X, van-Bilsen, M., Shu-




beita, H E, Kandolf, R., Brem, G., Prices




et alJ. Blol. Chem. 1992 Aug. 5, 267:




15875–85



Alpha actin
Muscat, G E., Perry, S. , Prentice, H. Kedes,




L. The human skeletal alpha-actin gene is




regulated by a muscle-specific enhancer




that binds three nuclear factors. Gene




Expression 2, 111–26, 1992 . . . / . . .


neurons
neuro-
Reeben, M. Halmekyto, M. Alhonen, L.



filament
Sinervirta, R. Saarma, M. Janne, J. Tissue-



proteins
specific expression of rat light neurofilament




promoter-driven reporter gene in transgenic




mice. BBRC 1993: 192: 465–70


liver
tyrosine



aminotrans-



ferase,



albumin,



apolipo-



proteins









Target Gene Constructs

In embodiments of the invention in which the chimeric proteins are designed such that their multimerization activates transcription of a target gene, an appropriate target gene construct is also used in the engineered cells. Appropriate target gene constructs are those containing a target gene and transcriptional control elements such as a promoter and/or enhancer which is responsive to the multimerization of the chimeric proteins. In embodiments involving direct activation of transcription, that responsiveness may be achieved by the presence in the target gene construct of one or more DNA sequences recognized by the DNA-binding domain of a chimeric protein of this invention (i.e., a DNA sequence to which the chimeric protein binds). In such embodiments, the target gene construct typically comprises a synthetic transcription unit typically consisting of: (1) one copy or multiple copies of a DNA sequence recognized with high-affinity by the component DNA binding domain of one of the fusion proteins; (2) a promoter sequence consisting minimally of a TATA box and initiator sequence but optionally including other transcription factor binding sites; (3) sequence encoding the desired product, including sequences that promote the initiation and termination of translation, if appropriate; (4) an optional sequence consisting of a splice donor, splice acceptor, and intervening intron DNA; and (5) a sequence directing cleavage and polyadenylation of the resulting RNA transcript. Typically the gene construct contains a copy of the target gene to be expressed, operably linked to a transcription control sequence comprising a minimal promoter and one or more copies of a DNA recognition sequence responsive to the transcription factor. In embodiments involving indirect activation of transcription, responsiveness may be achieved by the presence in the target gene construct of a promoter and/or enhancer sequence which is activated by an intracellular signal generated by multimerization of the chimeric proteins. For example, where the chimeric proteins contain the TCR zeta chain intracellular domain, the target gene is linked to and under the expression control of the IL-2 promoter region.
A wide variety of genes can be employed as the target gene, including genes that encode a therapeutic protein, antisense sequence or ribozyme of interest. The target gene can be any sequence of interest which provides a desired phenotype. It can encode a surface membrane protein, a secreted protein, a cytoplasmic protein, or there can be a plurality of target genes encoding different products. The target gene may be an antisense sequence which can modulate a particular pathway by inhibiting a transcriptional regulation protein or turn on a particular pathway by inhibiting the translation of an inhibitor of the pathway. The target gene can encode a ribozyme which may modulate a particular pathway by interfering, at the RNA level, with the expression of a relevant transcriptional regulator or with the expression of an inhibitor of a particular pathway. The proteins which are expressed, singly or in combination, can involve homing, cytotoxicity, proliferation, immune response, inflammatory response, clotting or dissolving of clots, hormonal regulation, etc. The proteins expressed may be naturally-occurring proteins, mutants of naturally-occurring proteins, unique sequences, or combinations thereof.
Various secreted products include hormones, such as insulin, human growth hormone, glucagon, pituitary releasing factor, ACTH, melanotropin, relaxin, etc.; growth factors, such as EGF, IGF-1, TGF-alpha, -beta, PDGF, G-CSF, M-CSF, GM-CSF, FGF, erythropoietin, thrombopoietin, megakaryocytic stimulating and growth factors, etc.; interleukins, such as IL-1 to -13; TNF-alpha and -beta, etc.; and enzymes and other factors, such as tissue plasminogen activator, members of the complement cascade, performs, superoxide dismutase, coagulation factors, antithrombin-III, Factor VIIIc, vWF, Factor IX, alpha-anti-trypsin, protein C, protein S, endorphins, dynorphin, bone morphogenetic protein, CFTR, etc.
The gene can encode a naturally-occurring surface membrane protein or a protein made so by introduction of an appropriate signal peptide and transmembrane sequence. Various such proteins include homing receptors, e.g. L-selectin (Mel-14), blood-related proteins, particularly having a kringle structure, e.g. Factor VIIIc, Factor VIIIvW, hematopoietic cell markers, e.g. CD3, CD4, CD8, B cell receptor, TCR subunits alpha, beta, gamma or delta, CD10, CD19, CD28, CD33, CD38, CD41, etc., receptors, such as the interleukin receptors IL-2R, IL-4R, etc., channel proteins, for influx or efflux of ions, e.g. H+, Ca+2, K+, Na+, Cl−, etc., and the like; CFTR, tyrosine activation motif, zap-70, etc.
Proteins may be modified for transport to a vesicle for exocytosis. By adding the sequence from a protein which is directed to vesicles, where the sequence is modified proximal to one or the other terminus, or situated in an analogous position to the protein source, the modified protein will be directed to the Golgi apparatus for packaging in a vesicle. This process in conjunction with the presence of the chimeric proteins for exocytosis allows for rapid transfer of the proteins to the extracellular medium and a relatively high localized concentration.
Also, intracellular proteins can be of interest, such as proteins in metabolic pathways, regulatory proteins, steroid receptors, transcription factors, etc., depending upon the nature of the host cell. Some of the proteins indicated above can also serve as intracellular proteins.
By way of further illustration, in T-cells, one may wish to introduce genes encoding one or both chains of a T-cell receptor. For B-cells, one could provide the heavy and light chains for an immunoglobulin for secretion. For cutaneous cells, e.g. keratinocytes, particularly stem cells keratinocytes, one could provide for protection against infection, by secreting alpha, beta or gamma interferon, antichemotactic factors, proteases specific for bacterial cell wall proteins, etc.
In addition to providing for expression of a gene having therapeutic value, there will be many situations where one may wish to direct a cell to a particular site. The site can include anatomical sites, such as lymph nodes, mucosal tissue, skin, synovium, lung or other internal organs or functional sites, such as clots, injured sites, sites of surgical manipulation, inflammation, infection, etc. By providing for expression of surface membrane proteins which will direct the host cell to the particular site by providing for binding at the host target site to a naturally-occurring epitope, localized concentrations of a secreted product can be achieved. Proteins of interest include homing receptors, e.g. L-selectin, GMP140, CLAM-1, etc., or addressing, e.g. ELAM-1, PNAd, LNAd, etc., clot binding proteins, or cell surface proteins that respond to localized gradients of chemotactic factors. There are numerous situations where one would wish to direct cells to a particular site, where release of a therapeutic product could be of great value.
This invention encompasses a variety of configurations for the chimeric proteins. In all cases involving the activation of target gene transcription, however, the chimeric proteins share an important characteristic: cells containing constructs encoding the chimeras and a target gene construct express the target gene at least one, preferably at least two, and more preferably at least three or four or more orders of magnitude more in the presence of the multimerizing ligand than in its absence. Optimally, expression of the selected gene is not observed unless the cells are or have been exposed to a multimerizing ligand.
To recap, the chimeric proteins are capable of initiating a detectable level of transcription of target genes within the engineered cells upon exposure of the cells to the a 28-epirapalog, i.e., following multimerization of the chimeras. Thus, transcription of target genes is activated in genetically engineered cells of this invention following exposure of the cells to a 28-epirapalog capable of multimerizing the chimeric protein molecules. Said differently, genetically engineered cells of this invention contain chimeric proteins as described above and are responsive to the presence and/or concentration of a 28-epirapalog which is capable of multimerizing those chimeric protein molecules. That responsiveness is manifested by the activation of transcription of a target gene. Such transcriptional activity can be readily detected by any conventional assays for transcription of the target gene. In other embodiments, the biological response to ligand-mediated multimerization of the chimeras is cell death or other biological events rather than direct activation of transcription of a target gene.
Design and Assembly of the DNA Constructs
Constructs may be designed in accordance with the principles, illustrative examples and materials and methods disclosed in the patent documents and scientific literature cited herein, each of which is incorporated herein by reference, with modifications and further exemplification as described herein. Components of the constructs can be prepared in conventional ways, where the coding sequences and regulatory regions may be isolated, as appropriate, ligated, cloned in an appropriate cloning host, analyzed by restriction or sequencing, or other convenient means. Particularly, using PCR, individual fragments including all or portions of a functional unit may be isolated, where one or more mutations may be introduced using “primer repair”, ligation, in vitro mutagenesis, etc. as appropriate. In the case of DNA constructs encoding fusion proteins, DNA sequences encoding individual domains and sub-domains are joined such that they constitute a single open reading frame encoding a fusion protein capable of being translated in cells or cell lysates into a single polypeptide harboring all component domains. The DNA construct encoding the fusion protein may then be placed into a vector that directs the expression of the protein in the appropriate cell type(s). For biochemical analysis of the encoded chimera, it may be desirable to construct plasmids that direct the expression of the protein in bacteria or in reticulocyte-lysate systems. For use in the production of proteins in mammalian cells, the protein-encoding sequence is introduced into an expression vector that directs expression in these cells. Expression vectors suitable for such uses are well known in the art. Various sorts of such vectors are commercially available.
Constructs encoding the chimeric proteins and target genes of this invention can be introduced into the cells as one or more DNA molecules or constructs, in many cases in association with one or more markers to allow for selection of host cells which contain the construct(s). The construct(s) once completed and demonstrated to have the appropriate sequences may then be introduced into a host cell by any convenient means. The constructs may be incorporated into vectors capable of episomal replication (e.g. BPV or EBV vectors) or into vectors designed for integration into the host cells' chromosomes. The constructs may be integrated and packaged into non-replicating, defective viral genomes like Adenovirus, Adeno-associated virus (AAV), r Herpes simplex virus (HSV) or others, including retroviral vectors, for infection or transduction into cells. Viral delivery systems are discussed in greater detail below. Alternatively, the construct may be introduced by protoplast fusion, electroporation, biolistics, calcium phosphate transfection, lipofection, microinjection of DNA or the like. The host cells will in some cases be grown and expanded in culture before introduction of the construct(s), followed by the appropriate treatment for introduction of the construct(s) and integration of the construct(s). The cells will then be expanded and screened by virtue of a marker present in the constructs. Various markers which may be used successfully include hprt, neomycin resistance, thymidine kinase, hygromycin resistance, etc., and various cell-surface markers such as Tac, CD8, CD3, Thy1 and the NGF receptor.
In some instances, one may have a target site for homologous recombination, where it is desired that a construct be integrated at a particular locus. For example, one can delete and/or replace an endogenous gene (at the same locus or elsewhere) with a recombinant target construct of this invention. For homologous recombination, one may generally use either Ω or O-vectors. See, for example, Thomas and Capecchi, Cell (1987) 51, 503–512; Mansour, et al., Nature (1988) 336, 348–352; and Joyner, et al., Nature (1989) 338, 153–156.
The constructs may be introduced as a single DNA molecule encoding all of the genes, or different DNA molecules having one or more genes. The constructs may be introduced simultaneously or consecutively, each with the same or different markers.
Vectors containing useful elements such as bacterial or yeast origins of replication, selectable and/or amplifiable markers, promoter/enhancer elements for expression in procaryotes or eucaryotes, and mammalian expression control elements, etc. which may be used to prepare stocks of construct DNAs and for carrying out transfections are well known in the art, and many are commercially available.
Delivery of Nucelc Acid: Ex Vivo and In Vivo
Any means for the introduction of heterologous nucleic acids into host cells, especially eucaryotic cells, an in particular animal cells, preferably human or non-human mammalian cells, may be adapted to the practice of this invention. For the purpose of this discussion, the various nucleic acid constructs described herein may together be referred to as the transgene. Ex vivo approaches for delivery of DNA include calcium phosphate precipitation, electroporation, lipofection and infection via viral vectors. Two general in vivo gene therapy approaches include (a) the delivery of “naked”, lipid-complexed or liposome-formulated or otherwise formulated DNA and (b) the delivery of the heterologous nucleic acids via viral vectors. In the former approach, prior to formulation of DNA, e.g. with lipid, a plasmid containing a transgene bearing the desired DNA constructs may first be experimentally optimized for expression (e.g., inclusion of an intron in the 5′ untranslated region and elimination of unnecessary sequences (Felgner, et al., Ann NY Acad Sci 126–139, 1995). Formulation of DNA, e.g. with various lipid or liposome materials, may then be effected using known methods and materials and delivered to the recipient mammal.
While various viral vectors may be used in the practice of this invention, retroviral-, AAV- and adenovirus-based approaches are of particular interest. See, for example, Dubensky et al. (1984) Proc. Natl. Acad. Sci. USA 81, 7529–7533; Kaneda et al., (1989) Science 243,375–378; Hiebert et al. (1989) Proc. Natl. Acad. Sci. USA 86, 3594–3598; Hatzoglu et al. (1990) J. Biol. Chem. 265, 17285–17293 and Ferry, et al. (1991) Proc. Natl. Acad. Sci. USA 88, 8377–8381. The following additional guidance on the choice and use of viral vectors may be helpful to the practitioner.
Retroviral Vectors
Retroviruses are a class of RNA viruses in which the RNA genome is reversely transcribed to DNA in the infected cell. The retroviral genome can integrate into the host cell genome and requires three viral genes, gag, pol and env, as well as the viral long terminal repeats (LTRs). The LTRs also act as enhancers and promoters for the viral genes. The packaging sequence of the virus, (Y), allows the viral RNA to be distinguished from other RNAs in the cell (Verma et al., Nature 389:239–242, 1997). For expression of a foreign gene, the viral proteins are replaced with the gene of interest in the viral vector, which is then transfected into a packaging line containing the viral packaging components. Packaged virus is secreted from the packaging line into the culture medium, which can then be used to infect cells in culture. Since retroviruses are unable to infect non-dividing cells, they have been used primarily for ex vivo gene therapy.
AAV Vectors
Adeno-associated virus (AAV)-based vectors are of general interest as a delivery vehicle to various tissues, including muscle and lung. AAV vectors infect cells and stably integrate into the cellular genome with high frequency. AAV can infect and integrate into growth-arrested cells (such as the pulmonary epithelium), and is non-pathogenic.
The AAV-based expression vector to be used typically includes the 145 nucleotide AAV inverted terminal repeats (ITRs) flanking a restriction site that can be used for subcloning of the transgene, either directly using the restriction site available, or by excision of the transgene with restriction enzymes followed by blunting of the ends, ligation of appropriate DNA linkers, restriction digestion, and ligation into the site between the ITRs. The capacity of AAV vectors is about 4.4 kb. The following proteins have been expressed using various MV-based vectors, and a variety of promoter/enhancers: neomycin phosphotransferase, chloramphenicol acetyl transferase, Fanconi's anemia gene, cystic fibrosis transmembrane conductance regulator, and granulocyte macrophage colony-stimulating factor (Kotin, R. M., Human Gene Therapy 5:793–801, 1994, Table I). A transgene incorporating the various DNA constructs of this invention can similarly be included in an MV-based vector. As an alternative to inclusion of a constitutive promoter such as CMV to drive expression of the recombinant DNA encoding the fusion protein(s), an AAV promoter can be used (ITR itself or AAV p5 (Flotte, et al. J. Biol. Chem. 268:3781–3790, 1993).
Such a vector can be packaged into AAV virions by reported methods. For example, a human cell line such as 293 can be co-transfected with the MV-based expression vector and another plasmid containing open reading frames encoding MV rep and cap under the control of endogenous AAV promoters or a heterologous promoter. In the absence of helper virus, the rep proteins Rep68 and Rep78 prevent accumulation of the replicative form, but upon superinfection with adenovirus or herpes virus, these proteins permit replication from the ITRs (present only in the construct containing the transgene) and expression of the viral capsid proteins. This system results in packaging of the transgene DNA into MV virions (Carter, B. J., Current Opinion in Biotechnology 3:533–539, 1992; Kotin, R. M, Human Gene Therapy 5:793–801, 1994)). Methods to improve the titer of MV can also be used to express the transgene in an AAV virion. Such strategies include, but are not limited to: stable expression of the ITR-flanked transgene in a cell line followed by transfection with a second plasmid to direct viral packaging; use of a cell line that expresses MV proteins inducibly, such as temperature-sensitive inducible expression or pharmacologically inducible expression. Additionally, one may increase the efficiency of AAV transduction by treating the cells with an agent that facilitates the conversion of the single stranded form to the double stranded form, as described in Wilson et al., WO96/39530.
Concentration and purification of the virus can be achieved by reported methods such as banding in cesium chloride gradients, as was used for the initial report of AAV vector expression in vivo (Flotte, et al. J. Biol. Chem. 268:3781–3790, 1993) or chromatographic purification, as described in O'Riordan et al., WO97/08298.
For additional detailed guidance on AAV technology which may be useful in the practice of the subject invention, including methods and materials for the incorporation of a transgene, the propagation and purification of the recombinant AAV vector containing the transgene, and its use in transfecting cells and mammals, see e.g. Carter et al, U.S. Pat. No. 4,797,368 (10 Jan. 1989); Muzyczka et al, U.S. Pat. No. 5,139,941 (18 Aug. 1992); Lebkowski et al, U.S. Pat. No. 5,173,414 (22 Dec. 1992); Srivastava, U.S. Pat. No. 5,252,479 (12 Oct. 1993); Lebkowski et al, U.S. Pat. No. 5,354,678 (11 Oct. 1994); Shenk et al, U.S. Pat. No. 5,436,146 (25 Jul. 1995); Chatterjee et al, U.S. Pat. No. 5,454,935 (12 Dec. 1995), Carter et al WO 93/24641 (published 9 Dec. 1993), and Flotte et al., U.S. Pat. No. 5,658,776 (19 Aug. 1997).
Adenovirus Vectors
Various adenovirus vectors have been shown to be of use in the transfer of genes to mammals, including humans. Replication-deficient adenovirus vectors have been used to express marker proteins and CFTR in the pulmonary epithelium. The first generation E1a deleted adenovirus vectors have been improved upon with a second generation that includes a temperature-sensitive E2a viral protein, designed to express less viral protein and thereby make the virally infected cell less of a target for the immune system (Goldman et al., Human Gene Therapy 6:839–851, 1995). More recently, a viral vector deleted of all viral open reading frames has been reported (Fisher et al., Virology 217:11–22, 1996). Moreover, it has been shown that expression of viral IL-10 inhibits the immune response to adenoviral antigen (Qin et al., Human Gene Therapy 8:1365–1374, 1997).
DNA sequences of a number of adenovirus types are available from Genbank. The adenovirus DNA sequences may be obtained from any of the 41 human adenovirus types currently identified. Various adenovirus strains are available from the American Type Culture Collection, Rockville, Md., or by request from a number of commercial and academic sources. A transgene as described herein may be incorporated into any adenoviral vector and delivery protocol, by the same methods (restriction digest, linker ligation or filling in of ends, and ligation) used to insert the CFTR or other genes into the vectors. Hybrid Adenovirus-AAV vectors represented by an adenovirus capsid containing selected portions of the adenovirus sequence, 5′ and 3′ AAV ITR sequences flanking the transgene and other conventional vector regulatory elements may also be used. See e.g. Wilson et al, International Patent Application Publication No. WO 96/13598. For additional detailed guidance on adenovirus and hybrid adenovirus-AAV technology which may be useful in the practice of the subject invention, including methods and materials for the incorporation of a transgene, the propagation and purification of recombinant virus containing the transgene, and its use in transfecting cells and mammals, see also Wilson et al, WO 94/28938, WO 96/13597 and WO 96/26285, and references cited therein.
Generally the DNA or viral particles are transferred to a biologically compatible solution or pharmaceutically acceptable delivery vehicle, such as sterile saline, or other aqueous or non-aqueous isotonic sterile injection solutions or suspensions, numerous examples of which are well known in the art, including Ringer's, phosphate buffered saline, or other similar vehicles.
Preferably, in gene therapy applications, the DNA or recombinant virus is administered in sufficient amounts to transfect cells at a level providing therapeutic benefit without undue adverse effects. Optimal dosages of DNA or virus depends on a variety of factors, as discussed elsewhere, and may thus vary somewhat from patient to patient. Again, therapeutically effective doses of viruses are considered to be in the range of about 20 to about 50 ml of saline solution containing concentrations of from about 1×107 to about 1×1010 pfu of virus/ml, e.g. from 1×108 to 1×109 pfu of virus/ml.
Host Cells
This invention is particularly useful for the engineering of animal cells and in applications involving the use of such engineered animal cells. The animal cells may be insect, worm or mammalian or other animal cells. While various mammalian cells may be used, including, by way of example, equine, bovine, ovine, canine, feline, murine, and non-human primate cells, human cells are of particular interest. Among the various species, various types of cells may be used, such as hematopoietic, neural, glial, mesenchymal, cutaneous, mucosal, stromal, muscle (including smooth muscle cells), spleen, reticuloendothelial, epithelial, endothelial, hepatic, kidney, gastrointestinal, pulmonary, fibroblast, and other cell types. Of particular interest are hematopoietic cells, which may include any of the nucleated cells which may be involved with the erythroid, lymphoid or myelomonocytic lineages, as well as myoblasts and fibroblasts. Also of interest are stem and progenitor cells, such as hematopoietic, neural, stromal, muscle, hepatic, pulmonary, gastrointestinal and mesenchymal stem cells.
The cells may be autologous cells, syngeneic cells, allogeneic cells and even in some cases, xenogeneic cells with respect to an intended host organism. The cells may be modified by changing the major histocompatibility complex (“MHC”) profile, by inactivating beta2-microglobulin to prevent the formation of functional Class I MHC molecules, inactivation of Class II molecules, providing for expression of one or more MHC molecules, enhancing or inactivating cytotoxic capabilities by enhancing or inhibiting the expression of genes associated with the cytotoxic activity, or the like.
In some instances specific clones or oligoclonal cells may be of interest, where the cells have a particular specificity, such as T cells and B cells having a specific antigen specificity or homing target site specificity.
Constructs encoding the chimeric transcription factors or other fusion proteins and constructs comprising target genes can be introduced into the cells as one or more DNA molecules or constructs, in many cases in association with one or more markers to allow for selection of host cells which contain the construct(s). The construct(s) once completed and demonstrated to have the appropriate sequences may then be introduced into a host cell by any convenient means. The constructs may be incorporated into vectors capable of episomal replication (e.g. BPV or EBV vectors) or into vectors designed for integration into the host cells' chromosomes. The constructs may be integrated and packaged into non-replicating, defective viral genomes like Adenovirus, Adeno-associated virus (AAV), or Herpes simplex virus (HSV) or others, including retroviral vectors, for infection into cells. Viral delivery systems are discussed in greater detail below. Alternatively, the construct may be introduced by protoplast fusion, electroporation, biolistics, calcium phosphate transfection, lipofection, microinjection of DNA or the like. The host cells will in some cases be grown and expanded in culture before introduction of the construct(s), followed by the appropriate treatment for introduction of the construct(s) and integration of the construct(s). The cells will then be expanded and screened by virtue of a marker present in the constructs. Various markers which may be used successfully include hprt, neomycin resistance, thymidine kinase, hygromycin resistance, etc., and various cell-surface markers such as Tac, CD8, CD3, Thy1 and the NGF receptor.
In some instances, one may have a target site for homologous recombination, where it is desired that a construct be integrated at a particular locus. For example, one can delete and/or replace an endogenous gene (at the same locus or elsewhere) with a recombinant target construct of this invention. For homologous recombination, one may generally use either Ω or O-vectors. See, for example, Thomas and Capecchi, Cell (1987) 51, 503–512; Mansour, et al., Nature (1988) 336, 348–352; and Joyner, et al., Nature (1989) 338, 153–156.
The constructs may be introduced as a single DNA molecule encoding all of the genes, or different DNA molecules having one or more genes. The constructs may be introduced simultaneously or consecutively, each with the same or different markers.
Vectors containing useful elements such as bacterial or yeast origins of replication, selectable and/or amplifiable markers, promoter/enhancer elements for expression in prokaryotes or eukaryotes, and mammalian expression control elements, etc. which may be used to prepare stocks of construct DNAs and for carrying out transfections are well known in the art, and many are commercially available.
Introduction of Constructs into Animals
Cells which have been modified ex vivo with the DNA constructs may be grown in culture under selective conditions and cells which are selected as having the desired construct(s) may then be expanded and further analyzed, using, for example, the polymerase chain reaction for determining the presence of the construct in the host cells and/or assays for the production of the desired gene product(s). Once modified host cells have been identified, they may then be used as planned, e.g. grown in culture or introduced into a host organism.
Depending upon the nature of the cells, the cells may be introduced into a host organism, e.g. a mammal, in a wide variety of ways. Hematopoietic cells may be administered by injection into the vascular system, there being usually at least about 104 cells and generally not more than about 1010 cells. The number of cells which are employed will depend upon a number of circumstances, the purpose for the introduction, the lifetime of the cells, the protocol to be used, for example, the number of administrations, the ability of the cells to multiply, the stability of the therapeutic agent, the physiologic need for the therapeutic agent, and the like. Generally, for myoblasts or fibroblasts for example, the number of cells will be at least about 104 and not more than about 109 and may be applied as a dispersion, generally being injected at or near the site of interest. The cells will usually be in a physiologically-acceptable medium.
Cells engineered in accordance with this invention may also be encapsulated, e.g. using conventional biocompatible materials and methods, prior to implantation into the host organism or patient for the production of a therapeutic protein. See e.g. Hguyen et al, Tissue Implant Systems and Methods for Sustaining viable High Cell Densities within a Host, U.S. Pat. No. 5,314,471 (Baxter International, Inc.); Uludag and Sefton, 1993, J. Biomed. Mater. Res. 27(10):1213–24 (HepG2 cells/hydroxyethyl methacrylate-methyl methacrylate membranes); Chang et al, 1993, Hum Gene Ther 4(4):433–40 (mouse Ltk-cells expressing hGH/immunoprotective perm-selective alginate microcapsules; Reddy et al, 1993, J Infect Dis 168(4):1082–3 (alginate); Tai and Sun, 1993, FASEB J 7(11):1061–9 (mouse fibroblasts expressing hGH/alginate-poly-L-lysine-alginate membrane); Ao et al, 1995, Transplanataion Proc. 27(6):3349, 3350 (alginate); Rajotte et al, 1995, Transplantation Proc. 27(6):3389 (alginate); Lakey et al, 1995, Transplantation Proc. 27(6):3266 (alginate); Korbutt et al, 1995, Transplantation Proc. 27(6):3212 (alginate); Dorian et al, U.S. Pat. No. 5,429,821 (alginate); Emerich et al, 1993, Exp Neurol 122(1):37–47 (polymer-encapsulated PC12 cells); Sagen et al, 1993, J Neurosci 13(6):2415–23 (bovine chromaffin cells encapsulated in semipermeable polymer membrane and implanted into rat spinal subarachnoid space); Aebischer et al, 1994, Exp Neurol 126(2):151–8 (polymer-encapsulated rat PC12 cells implanted into monkeys; see also Aebischer, WO 92/19595); Savelkoul et al, 1994, J Immunol Methods 170(2):185–96 (encapsulated hybridomas producing antibodies; encapsulated transfected cell lines expressing various cytokines); Winn et al, 1994, PNAS USA 91(6):2324–8 (engineered BHK cells expressing human nerve growth factor encapsulated in an immunoisolation polymeric device and transplanted into rats); Emerich et al, 1994, Prog Neuropsychopharmacol Biol Psychiatry 18(5):935–46 (polymer-encapsulated PC 2 cells implanted into rats); Kordower et al, 1994, PNAS USA 91(23):10898–902 (polymer-encapsulated engineered BHK cells expressing hNGF implanted into monkeys) and Butler et al WO 95/04521 (encapsulated device). The cells may then be introduced in encapsulated form into an animal host, preferably a mammal and more preferably a human subject in need thereof. Preferably the encapsulating material is semipermeable, permitting release into the host of secreted proteins produced by the encapsulated cells. In many embodiments the semipermeable encapsulation renders the encapsulated cells immunologically isolated from the host organism in which the encapsulated cells are introduced. In those embodiments the cells to be encapsulated may express one or more chimeric proteins containing component domains derived from proteins of the host species and/or from viral proteins or proteins from species other than the host species. For example in such cases the chimeras may contain elements derived from GAL4 and VP16. The cells may be derived from one or more individuals other than the recipient and may be derived from a species other than that of the recipient organism or patient.
Instead of ex vivo modification of the cells, in many situations one may wish to modify cells in vivo. For this purpose, various techniques have been developed for genetic modification of target tissue and cells in vivo. A number of viral vectors have been developed, such as adenovirus, adeno-associated virus, and retroviruses, which allow for transduction and, in some cases, integration of the virus into the host. See, for example, Dubensky et al. (1984) Proc. Natl. Acad. Sci. USA 81, 7529–7533; Kaneda et al., (1989) Science 243,375–378; Hiebert et al. (1989) Proc. Natl. Acad. Sci. USA 86, 3594–3598; Hatzoglu et al. (1990) J. Biol. Chem. 265, 17285–17293 and Ferry, et al. (1991) Proc. Natl. Acad. Sci. USA 88, 8377–8381. The vector may be administered by injection, e.g. intravascularly or intramuscularly, inhalation, or other parenteral mode. Non-viral delivery methods such as administration of the DNA via complexes with liposomes or by injection, catheter or biolistics may also be used. See e.g. WO 96/41865, PCT/US97/22454 and U.S. Ser. No. 60/084,819, for example, for additional guidance on formulation and delivery of recombinant nucleic acids to cells and to organisms. Those references as well as the references cited previously, including those relating to tetR-based systems, progesterone-r-based systems and ecdysone-based systems provide detailed additional guidance on the preparation, formulation and delivery of various ligands to cells in vitro and to organisms. As mentioned elsewhere, the contents of those cited documents are incorporated herein by reference.
In accordance with in vivo genetic modification, the manner of the modification will depend on the nature of the tissue, the efficiency of cellular modification required, the number of opportunities to modify the particular cells, the accessibility of the tissue to the DNA composition to be introduced, and the like. By employing an attenuated or modified retrovirus carrying a target transcriptional initiation region, if desired, one can activate the virus using one of the subject transcription factor constructs, so that the virus may be produced and transfect adjacent cells.
The DNA introduction need not result in integration in every case. In some situations, transient maintenance of the DNA introduced may be sufficient. In this way, one could have a short term effect, where cells could be introduced into the host and then turned on after a predetermined time, for example, after the cells have been able to home to a particular site.
Binding Properties, Assays
Rapamycin is known to bind to the human protein, FKBP12 and to form a tripartite complex with hFKBP12 and FRAP, a human counterpart to the yeast proteins TOR1 and TOR2. Rapalogs may be characterized and compared to rapamycin with respect to their ability to bind to human FKBP12 and/or to form tripartite complexes with human FKBP12 and human FRAP (or fusion proteins or fragments containing its FRB domain). See WO 96/41865 (Clackson et al). That application discloses various materials and methods which can be used to quantify the ability of a compound to bind to human FKBP12 or to form a tripartite complex with (i.e., “heterodimerize”) proteins comprising human FKBP12 and the FRB domain of human FRAP, respectively. Such assays include fluorescence polarization assays to measure binding. Also included are cell based transcription assays in which the ability of a compound to form the tripartite complex is measured indirectly by correlation with the observed level of reporter gene product produced by engineered mammalian cells in the presence of the compound. Corresponding cell-based assays may also be conducted in engineered yeast cells. See e.g. WO 95/33052 (Berlin et al).
It will often be preferred that the rapalogs of this invention be physiologically acceptable (i.e., lack undue toxicity toward the cell or organism with which it is to be used), can be taken orally by animals (i.e., is orally active in applications in whole animals, including gene therapy), and/or can cross cellular and other membranes, as necessary for a particular application.
In addition, in some cases, preferred rapalogs are those which bind preferentially to mutant immunophilins (by way of non-limiting example, a human FKBP in which Phe36 is replaced with a different amino acid, preferably an amino acid with a less bulky R group such as valine or alanine) over native or naturally-ocurring immunophilins. For example, such compounds may bind preferentially to mutant FKBPs at least an order of magnitude better than they bind to human FKBP12, and in some cases may bind to mutant FKBPs greater than 2 or even 3 or more orders of magnitude better than they do to human FKBP12, as determined by any scientifically valid or art-accepted assay methodology.
Binding affinities of various rapalogs of this invention with respect to human FKBP12, variants thereof or other immunophilin proteins may be determined by adaptation of known methods used in the case of FKBP. For instance, the practitioner may measure the ability of a compound of this invention to compete with the binding of a known ligand to the protein of interest. See e.g. Sierkierka et al, 1989, Nature 341, 755–757 (test compound competes with binding of labeled FK506 derivative to FKBP).
One set of preferred rapalogs of this invention which binds, to human FKBP12, to a mutant thereof as discussed above, or to a fusion protein containing such FKBP domains, with a Kd value below about 200 nM, more preferably below about 50 nM, even more preferably below about 10 nM, and even more preferably below about 1 nM, as measured by direct binding measurement (e.g. fluorescence quenching), competition binding measurement (e.g. versus FK506), inhibition of FKBP enzyme activity (rotamase), or other assay methodology. In one subset of such compounds, the FKBP domain is one in which phenylalanine at position 36 has been replaced with an amino acid having a less bulky side chain, e.g. alanine, valine, methionine or serine.
A Competitive Binding FP Assay is described in detail in WO99/36553 and WO96/41865. That assay permits the in vitro measurement of an IC50 value for a given compound which reflects its ability to bind to an FKBP protein in competition with a labeled FKBP ligand, such as, for example, FK506.
One preferred class of compounds of this invention are those rapalogs which have an IC50 value in the Competitive Binding FP Assay better than 1000 nM, preferably better than 300 nM, more preferably better than 100 nM, and even more preferably better than 10 nM with respect to a given FKBP domain and ligand pair, e.g. human FKBP12 or a variant thereof with up to 10, preferably up to amino acid replacements, with a flouresceinated FK506 standard.
The ability of the rapalogs to multimerize chimeric proteins may be measured in cell-based assays by measuring the occurrence of an event triggered by such multimerization. For instance, one may use cells containing and capable of expressing DNA encoding a first chimeric protein comprising one or more FKBP-domains and one or more effector domains as well as DNA encoding a second chimeric protein containing an FRB domain and one or more effector domains capable, upon multimerization, of actuating a biological response. We prefer to use cells which further contain a reporter gene under the transcriptional control of a regulatory element (i.e., promoter) which is responsive to the multimerization of the chimeric proteins. The design and preparation of illustrative components and their use in so engineered cells is described in WO99/36553 and WO96/41865 and the other international patent applications referred to in this and the foregoing section. (See also WO99/10510 for additional guidance on the design, assembly and delivery of nucleic acids to render cells and animals responsive to rapalogs of interest and for additional guidance on applications of such systems.) The cells are grown or maintained in culture. A rapalog is added to the culture medium and after a suitable incubation period (to permit gene expression and secretion, e.g. several hours or overnight) the presence of the reporter gene product is measured. Positive results, i.e., multimerization, correlates with transcription of the reporter gene as observed by the appearance of the reporter gene product. The reporter gene product may be a conveniently detectable protein (e.g. by ELISA) or may catalyze the production of a conveniently detectable product (e.g. colored). Materials and methods for producing appropriate cell lines for conducting such assays are disclosed in the international patent applications cited above in this section. Typically used target genes include by way of example SEAP, hGH, beta-galactosidase, Green Fluorescent Protein and luciferase, for which convenient assays are commercially available.
Another preferred class of compounds of this invention are those which are capable of inducing a detectable signal in a 2-hybrid transcription assay based on fusion proteins containing an FKBP domain. Preferably, the FKBP domain is an FKBP domain other than wild-type human FKBP12.
Another assay for measuring the ability of the rapalogs to multimerize chimeric proteins, like the FKBP-based transcription assay, is a cell-based assay which measures the occurrence of an event triggered by such multimerization. In this case, one uses cells which constitutively express a detectable product. The cells also contain and are capable of expressing DNAs encoding chimeric proteins comprising one or more immunophilin-derived ligand binding domains and one or more effector domains, such as the intracellular domain of FAS, capable, upon multimerization, of triggering cell death. The design and preparation of illustrative components and their use in so engineering cells is described in WO95/02684. See also WO96/41865. The cells are maintained or cultured in a culture medium permitting cell growth or continued viability. The cells or medium are assayed for the presence of the constitutive cellular product, and a base-line level of reporter is thus established. One may use cells engineered for constitutive production of hGH or any other conveniently detectable product to serve as the reporter. The compound to be tested is addded to the medium, the cells are incubated, and the cell lysate or medium is tested for the presence of reporter at one or more time points. Decrease in reporter production indicates cell death, an indirect measure of multimerization of the fusion proteins.
Another preferred class of compounds of this invention are those which are capable of inducing a detectable signal in such an FKBP/FRB-based apoptosis assay. Preferably, the FKBP domain is an FKBP domain other than wild-type human FKBP12. In some cases, the FKBP domain is modified, as discussed above. Also preferably, the FRB domain is an FRB domain other than wild-type FRB from human FRAP. In some cases, the FRB domain is modified at position 2098, as described above.
Conducting such assays permits the practitioner to select rapalogs possessing the desired IC50 values and/or binding preference for a mutant FKBP over wild-type human FKBP12. The Competitive Binding FP Assay permits one to select rapalogs which possess the desired IC50 values and/or binding preference for a mutant FKBP or wild-type FKBP relative to a control, such as FK506.
Applications
In addition to use as immunosuppressants and antifungal agents, the 28-epirapalogs can be used as described in WO94/18317, WO95/02684, WO96/20951, WO95/41865, and WO99/36553 e.g. to regulatably activate the transcription of a desired gene, delete a target gene, actuate apoptosis, or trigger other biological events in engineered cells growing in culture or in whole organisms, including in gene therapy applications. The following are non-limiting examples of applications of the subject invention.
1. Regulated gene therapy. In many instances, the ability to switch a therapeutic gene on and off at will or the ability to titrate expression with precision are important for therapeutic efficacy. This invention is particularly well suited for achieving regulated expression of a therapeutic target gene in the context of human gene therapy. One example uses a pair of chimeric proteins (one containing at least one FRB domain, the other containing at least one FKBP domain), a 28-epirapalog of this invention capable of dimerizing the chimeras, and a target gene construct to be expressed. One of the chimeric proteins comprises a DNA-binding domain, preferably a composite DNA-binding domain as described in Pomerantz et al, supra, as the heterologous effector domain. The second chimeric protein comprises a transcriptional activating domain as the heterologous effector domain. The 28-epirapalog is capable of binding to both chimeras and thus of effectively cross-linking the chimeras. DNA molecules encoding and capable of directing the expression of these chimeric proteins are introduced into the cells to be engineered. Also introduced into the cells is a target gene linked to a DNA sequence to which the DNA-binding domain is capable of binding. Contacting the engineered cells or their progeny with the 28-epirapalog (by administering it to the animal or patient) leads to assembly of the transcription factor complex and hence to expression of the target gene. The design and use of similar components is disclosed in PCT/US93/01617 and in WO 96/41865 (Clackson et al). In practice, the level of target gene expression should be a function of the number or concentration of chimeric transcription factor complexes, which should in turn be a function of the concentration of the 28-epirapalog. Dose (of 28-epirapalog)-responsive gene expression is typically observed.
The 28-epirapalog may be administered to the patient as desired to activate transcription of the target gene. Depending upon the binding affinity of the 28-epirapalog, the response desired, the manner of administration, the biological half-life of the rapalog and/or target gene mRNA, the number of engineered cells present, various protocols may be employed. The 28-epirapalog may be administered by various routes, including parenterally or orally. The number of administrations will depend upon the factors described above. The 28-epirapalog may be taken orally as a pill, powder, or dispersion; buccally; sublingually; injected intravascularly, intraperitoneally, intramuscularly, subcutaneously; by inhalation, or the like. The 28-epirapalog (and monomeric antagonist compound) may be formulated using conventional methods and materials well known in the art for the various routes of administration. The precise dose and particular method of administration will depend upon the above factors and be determined by the attending physician or human or animal healthcare provider. For the most part, the manner of administration will be determined empirically.
In the event that transcriptional activation by the 28-epirapalog is to be reversed or terminated, adminstration of the 28-epirapalog is terminated. Furthermore, if desired, a monomeric compound which can compete with the 28-epirapalog may be administered. Thus, in the case of an adverse reaction or the desire to terminate the therapeutic effect, an antagonist to the dimerizing agent can be administered in any convenient way, particularly intravascularly, if a rapid reversal is desired. Alternatively, one may provide for the presence of an inactivation domain (or transcriptional silencer) with a ligand binding domain. In another approach, cells may be eliminated through apoptosis via signalling through Fas or TNF receptor as described elsewhere. See International Patent Applications PCT/US94/01617 and PCT/US94/08008.
The particular dosage of the 28-epirapalog for any application may be determined in accordance with the procedures used for therapeutic dosage monitoring, where maintenance of a particular level of expression is desired over an extended period of times, for example, greater than about two weeks, or where there is repetitive therapy, with individual or repeated doses of 28-epirapalog over short periods of time, with extended intervals, for example, two weeks or more. A dose of the 28-epirapalog within a predetermined range would be given and monitored for response, so as to obtain a time-expression level relationship, as well as observing therapeutic response. Depending on the levels observed during the time period and the therapeutic response, one could provide a larger or smaller dose the next time, following the response. This process would be iteratively repeated until one obtained a dosage within the therapeutic range. Where the 28-epirapalog is chronically administered, once the maintenance dosage of the 28-epirapalog is determined, one could then do assays at extended intervals to be assured that the cellular system is providing the appropriate response and level of the expression product.
It should be appreciated that the system is subject to many variables, such as the cellular response to the 28-epirapalog, the efficiency of expression and, as appropriate, the level of secretion, the activity of the expression product, the particular need of the patient, which may vary with time and circumstances, the rate of loss of the cellular activity as a result of loss of cells or expression activity of individual cells, and the like.
2. Production of recombinant proteins and viruses. Production of recombinant therapeutic proteins for commercial and investigational purposes is often achieved through the use of mammalian cell lines engineered to express the protein at high level. The use of mammalian cells, rather than bacteria or yeast, is indicated where the proper function of the protein requires post-translational modifications not generally performed by heterologous cells. Examples of proteins produced commercially this way include erythropoietin, tissue plasminogen activator, clotting factors such as Factor VIII:c, antibodies, etc. The cost of producing proteins in this fashion is directly related to the level of expression achieved in the engineered cells. A second limitation on the production of such proteins is toxicity to the host cell: Protein expression may prevent cells from growing to high density, sharply reducing production levels. Therefore, the ability to tightly control protein expression, as described for regulated gene therapy, permits cells to be grown to high density in the absence of protein production. Only after an optimum cell density is reached, is expression of the gene activated and the protein product subsequently harvested.
A similar problem is encountered in the construction and use of “packaging lines” for the production of recombinant viruses for commercial (e.g., gene therapy) and experimental use. These cell lines are engineered to produce viral proteins required for the assembly of infectious viral particles harboring defective recombinant genomes. Viral vectors that are dependent on such packaging lines include retrovirus, adenovirus, and adeno-associated virus. In the latter case, the titer of the virus stock obtained from a packaging line is directly related to the level of production of the viral rep and core proteins. But these proteins are highly toxic to the host cells. Therefore, it has proven difficult to generate high-titer recombinant AAV viruses. This invention provides a solution to this problem, by allowing the construction of packaging lines in which the rep and core genes are placed under the control of regulatable transcription factors of the design described here. The packaging cell line can be grown to high density, infected with helper virus, and transfected with the recombinant viral genome. Then, expression of the viral proteins encoded by the packaging cells is induced by the addition of dimerizing agent to allow the production of virus at high titer.
3. Biological research. This invention is applicable to a wide range of biological experiments in which precise control over a target gene is desired. These include: (1) expression of a protein or RNA of interest for biochemical purification; (2) regulated expression of a protein or RNA of interest in tissue culture cells (or in vivo, via engineered cells) for the purposes of evaluating its biological function; (3) regulated expression of a protein or RNA of interest in transgenic animals for the purposes of evaluating its biological function; (4) regulating the expression of a gene encoding another regulatory protein, ribozyme or antisense molecule that acts on an endogenous gene for the purposes of evaluating the biological function of that gene. Transgenic animal models and other applications in which the components of this invention may be adapted include those disclosed in PCT/US95/10591.
This invention further provides kits useful for the foregoing applications. Such kits contain DNA constructs encoding and capable of directing the expression of chimeric proteins of this invention (and may contain additional domains as discussed above) and, in embodiments involving regulated gene transcription, a target gene construct containing a target gene linked to one or more transcriptioal control elements which are activated by the multimerization of the chimeric proteins. Alternatively, the target gene construct may contain a cloning site for insertion of a desired target gene by the practitioner. Such kits may also contain a sample of a dimerizing agent capable of dimerizing the two recombinant proteins and activating transcription of the target gene.
Formulations, Dosage and Administration
By virtue of its capacity to promote protein—protein interactions, a rapalog of this invention may be used in pharmaceutical compositions and methods for promoting formation of complexes of chimeric proteins of this invention in a human or non-human mammal containing genetically engineered cells of this invention.
The preferred method of such treatment or prevention is by administering to the mammal an effective amount of the compound to promote measurable formation of such complexes in the engineered cells, or preferably, to promote measurable actuation of the desired biological event triggered by such complexation, e.g. transcription of a target gene, apoptosis of engineered cells, etc.
Therapeutic/Prophylactic Administration & Pharmaceutical Compositions
The rapalogs can exist in free form or, where appropriate, in salt form. Pharmaceutically acceptable salts of many types of compounds and their preparation are well-known to those of skill in the art. The pharmaceutically acceptable salts of compounds of this invention include the conventional non-toxic salts or the quaternary ammonium salts of such compounds which are formed, for example, from inorganic or organic acids of bases.
The compounds of the invention may form hydrates or solvates. It is known to those of skill in the art that charged compounds form hydrated species when lyophilized with water, or form solvated species when concentrated in a solution with an appropriate organic solvent.
This invention also relates to pharmaceutical compositions comprising a therapeutically (or prophylactically) effective amount of the compound, and one or more pharmaceutically acceptable carriers and/or other excipients. Carriers include e.g. saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof, and are discussed in greater detail below. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. The composition can be a liquid solution, suspension, emulsion, tablet, pill, capsule, sustained release formulation, or powder. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Formulation may involve mixing, granulating and compressing or dissolving the ingredients as appropriate to the desired preparation. In another approach, the composition may be formulated into nanoparticles.
The pharmaceutical carrier employed may be, for example, either a solid or liquid.
Illustrative solid carrier include lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, stearic acid and the like. A solid carrier can include one or more substances which may also act as flavoring agents, lubricants, solubilizers, suspending agents, fillers, glidants, compression aids, binders or tablet-disintegrating agents; it can also be an encapsulating material. In powders, the carrier is a finely divided solid which is in admixture with the finely divided active ingredient. In tablets, the active ingredient is mixed with a carrier having the necessary compression properties in suitable proportions, and compacted in the shape and size desired. The powders and tablets preferably contain up to 99% of the active ingredient. Suitable solid carriers include, for example, calcium phosphate, magnesium stearate, talc, sugars, lactose, dextrin, starch, gelatin, cellulose, methyl cellulose, sodium carboxymethyl cellulose, polyvinylpyrrolidine, low melting waxes and ion exchange resins.
Illustrative liquid carriers include syrup, peanut oil, olive oil, water, etc. Liquid carriers are used in preparing solutions, suspensions, emulsions, syrups, elixirs and pressurized compositions. The active ingredient can be dissolved or suspended in a pharmaceutically acceptable liquid carrier such as water, an organic solvent, a mixture of both or pharmaceutically acceptable oils or fats. The liquid carrier can contain other suitable pharmaceutical additives such as solubilizers, emulsifiers, buffers, preservatives, sweeteners, flavoring agents, suspending agents, thickening agents, colors, viscosity regulators, stabilizers or osmo-regulators. Suitable examples of liquid carriers for oral and parenteral administration include water (partially containing additives as above, e.g. cellulose derivatives, preferably sodium carboxymethyl cellulose solution), alcohols (including monohydric alcohols and polyhydric alcohols, e.g. glycols) and their derivatives, and oils (e.g. fractionated coconut oil and arachis oil). For parenteral administration, the carrier can also be an oily ester such as ethyl oleate and isopropyl myristate. Sterile liquid carriers are useful in sterile liquid form compositions for parenteral administration. The liquid carrier for pressurized compositions can be halogenated hydrocarbon or other pharmaceutically acceptable propellant. Liquid pharmaceutical compositions which are sterile solutions or suspensions can be utilized by, for example, intramuscular, intraperitoneal or subcutaneous injection. Sterile solutions can also be administered intravenously. The compound can also be administered orally either in liquid or solid composition form.
The carrier or excipient may include time delay material well known to the art, such as glyceryl monostearate or glyceryl distearate along or with a wax, ethylcellulose, hydroxypropylmethylcellulose, methylmethacrylate and the like. When formulated for oral administration, 0.01% Tween 80 in PHOSAL PG-50 (phospholipid concentrate with 1,2-propylene glycol, A. Nattermann & Cie. GmbH) has been recognized as providing an acceptable oral formulation for other compounds, and may be adapted to formulations for various compounds of this invention.
A wide variety of pharmaceutical forms can be employed. If a solid carrier is used, the preparation can be tableted, placed in a hard gelatin capsule in powder or pellet form or in the form of a troche or lozenge. The amount of solid carrier will vary widely but preferably will be from about 25 mg to about 1 g. If a liquid carrier is used, the preparation will be in the form of a syrup, emulsion, soft gelatin capsule, sterile injectable solution or suspension in an ampule or vial or nonaqueous liquid suspension.
To obtain a stable water soluble dosage form, a pharmaceutically acceptable salt of the multimerizer may be dissolved in an aqueous solution of an organic or inorganic acid, such as a 0.3M solution of succinic acid or citric acid. Alternatively, acidic derivatives can be dissolved in suitable basic solutions. If a soluble salt form is not available, the compound is dissolved in a suitable cosolvent or combinations thereof. Examples of such suitable cosolvents include, but are not limited to, alcohol, propylene glycol, polyethylene glycol 300, polysorbate 80, glycerin, polyoxyethylated fatty acids, fatty alcohols or glycerin hydroxy fatty acids esters and the like in concentrations ranging from 0–60% of the total volume.
Various delivery systems are known and can be used to administer the multimerizer, or the various formulations thereof, including tablets, capsules, injectable solutions, encapsulation in liposomes, microparticles, microcapsules, etc. Methods of introduction include but are not limited to dermal, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, pulmonary, epidural, ocular and (as is usually preferred) oral routes. The compound may be administered by any convenient or otherwise appropriate route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local. For treatment or prophylaxis of nasal, bronchial or pulmonary conditions, preferred routes of administration are oral, nasal or via a bronchial aerosol or nebulizer.
In certain embodiments, it may be desirable to administer the compound locally to an area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, by injection, by means of a catheter, by means of a suppository, or by means of a skin patch or implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers.
In a specific embodiment, the composition is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
Administration to an individual of an effective amount of the compound can also be accomplished topically by administering the compound(s) directly to the affected area of the skin of the individual. For this purpose, the compound is administered or applied in a composition including a pharmacologically acceptable topical carrier, such as a gel, an ointment, a lotion, or a cream, which includes, without limitation, such carriers as water, glycerol, alcohol, propylene glycol, fatty alcohols, triglycerides, fatty acid esters, or mineral oils.
Other topical carriers include liquid petroleum, isopropyl palmitate, polyethylene glycol, ethanol (95%), polyoxyethylene monolaurate (5%) in water, or sodium lauryl sulfate (5%) in water. Other materials such as anti-oxidants, humectants, viscosity stabilizers, and similar agents may be added as necessary. Percutaneous penetration enhancers such as Azone may also be included.
In addition, in certain instances, it is expected that the compound may be disposed within devices placed upon, in, or under the skin. Such devices include patches, implants, and injections which release the compound into the skin, by either passive or active release mechanisms.
Materials and methods for producing the various formulations are well known in the art and may be adapted for practicing the subject invention. See e.g. U.S. Pat. Nos. 5,182,293 and 4,837,311 (tablets, capsules and other oral formulations as well as intravenous formulations) and European Patent Application Publication Nos. 0 649 659 (published Apr. 26, 1995; illustrative formulation for IV administration) and 0 648 494 (published Apr. 19, 1995; illustrative formulation for oral administration).
The effective dose of the compound will typically be in the range of about 0.01 to about 50 mg/kgs, preferably about 0.1 to about 10 mg/kg of mammalian body weight, administered in single or multiple doses. Generally, the compound may be administered to patients in need of such treatment in a daily dose range of about 1 to about 2000 mg per patient.
The amount of compound which will be effective in the treatment or prevention of a particular disorder or condition will depend in part on the characteristics of the fusion proteins to be multimerized, the characteristics and location of the genetically engineered cells, and on the nature of the disorder or condition, which can be determined by standard clinical techniques. In addition, in vitro or in vivo assays may optionally be employed to help identify optimal dosage ranges. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems. The precise dosage level should be determined by the attending physician or other health care provider and will depend upon well known factors, including route of administration, and the age, body weight, sex and general health of the individual; the nature, severity and clinical stage of the disease; the use (or not) of concomitant therapies; and the nature and extent of genetic engineering of cells in the patient.
The invention also provides a pharmaceutical pack or kit comprising one or more containers containing one or more of the ingredients of the pharmaceutical compositions of the invention. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceutical or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration. The notice or package insert may contain instructions for use of a 28-epirapalog of this invention, consistent with the disclsoure herein.
The following examples contain important additional information, exemplification and guidance which can be adapted to the practice of this invention in its various embodiments and the equivalents thereof. The examples are offered by way illustration should not be construed as limiting in any way. Numerous modifications and variations of the present invention should be apparent to one of skill in the art. Such modifications and variations, including design choices in selecting, preparing, formulating and administering a 28-epirapalog, and in the choice of heterologous action domain, fusion protein design, DNA formulation, viral vector or other DNA delivery means, manner and route of transgene administration, etc. are intended to be encompassed by the scope of the invention and of the appended claims.
The contents of all cited references including literature references, issued patents, and published patent applications as cited throughout this document are hereby expressly incorporated by reference. The practice of the present invention will employ, unless otherwise indicated, conventional techniques of synthetic organic chemistry, including product recovery, purification and formulation, as well as of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the patent and scientific literature. See, for example, in the case of biological techniques: Molecular Cloning†A Laboratory†Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I–IV (D. M. Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).
EXAMPLES
Example 1
The Discovery and Analysis of 28-epirapamycin
While exploring alternative Lewis acids for C7 nucleophilic substitution chemistry, we discovered that treatment of rapamycin with Ti(OiPr)4 in dichloromethane in the absence of any nucleophiles resulted in an unprecedented reaction to afford an unknown compound 2 as the major product (over 60% isolated yield) with the same molecular weight as rapamycin (scheme 1).
Preliminary NMR analysis revealed changes in the proton resonance at C26, C28 and C29 suggesting a possible epimerization at either C28, C29 or both. Compound 2 and rapamycin 1 were separately subjected to the identical retroaldol reaction conditions (ZnCl2, THF, 50 −0C, 4 hr). As shown by HPLC (reverse phase, 85:15 MeOH:H2O) and 1H NMR analysis, both reactions generated the ring opened secorapamycin 3 proving that the C28 and/or the C29 stereocenter was epimerized.




Both compound 2 and rapamycin were subjected to extensive NMR analysis (COSY, ROESY, TOCSY, NOESY, HETCOR and HMBC). The NMR assignment of rapamycin agreed very well with that reported in the literature. Both HMBC and NOESY data of 2 indicate the stereochemistry at C28 had been reversed.
Compound 2 was recrystallized from methanol/water and the X-ray crystal structure was determined. It unambiguously confirmed the newly isolated product as the C28 epimer of rapamycin.
Besides 2 and residual rapamycin, a few minor side products (less than 5% each by HPLC) were also isolated from the reaction. They were found to be secorapamycin 3,29-epirapamycin 4 and 28,29-bisepirapamycin 5 as determined by the NMR analyses similar to that applied to 28-epirapamycin.




The presence of a trace amount of secorapamycin 3 in the crude reaction mixture suggests the mechanistic route may occur through a retroaldol of rapamycin and realdol macrolization affected by Ti(OiPr)4.
The titanium (IV) complexed retroaldol intermediate can be trapped by benzaldehyde when the epimerization reaction is carried out in the presence of five equivalents of benzaldehyde. A mixture of diastereomers 6 from aldol condensation between benzaldehyde and retroaldol intermediate were afforded in good yields (scheme 2).




The reaction process can be monitored closely by HPLC (both normal and reverse phase). Secorapamycin 3 was detectable immediately after Ti(OiPr)4 was introduced and it remained at a constant yet minimal level ( ̃1%) throughout the reaction, while rapamycin converted to its various diastereomers. When pure 28-epirapamycin 2,29-epirapamycin 4 and 28,29-bisepirapamycin 5 were individually subjected to the epimerization conditions, the same products ratios were observed as that of rapamycin. These experiments suggested that the retroaldol of titanium (IV) complexed rapamycin was the rate limiting step of the reaction. Once generated, the opened-ring intermediate complexed to titanium (IV) quickly realdolizes. This retroaldol and realdol process continues until the reaction reaches equilibrium. The final product distribution indicates 28-epirapamycin 2 as the thermodynamically most stable diastereomer.
This novel retroaldol and realdol equilibration of β-hydroxy ketones mediated by Ti(OiPr)4 under neutral condition is not specific to rapamycin as described here. Preliminary data confirmed that it is also applicable to β-hydroxy ketones in an acyclic system. Treatment of a 2:1 mixture (syn/anti) of 1-hydroxy-1-phenyl-2-methyl-3-pentanone with Ti(OiPr)4 resulted in a 4:5 (syn/anti) mixture, favoring the thermodanamically more stable anti isomer. The equilibration of aldolates by metals such as Zn (II), Mg (II) and Ba (II) have been reported in the literature. However, the equilibration needs strong basic conditions and often results in the retroaldol products as demonstrated by Hayward in the total synthesis of rapamycin.
28-Epirapamycin was subjected to biological assays in comparison with rapamycin. The affinity of 28-epirapamycin towards FKBP is about 5 times weaker than that of rapamycin as measured in a fluorescence polarization competition assay, possibly because of the loss of the hydrogen bonding between C28 hydroxy group and the main chain carbonyl of Glu54 on FKBP as conceivable from the x-ray crystal structure of rapamycin bound to FKBP. In accordance with its reduced binding affinity towards FKBP, the immunosuppressive activity of 2 is more than an order of magnitude reduced from that of rapamycin in a splenocyte proliferation assay. Comparative data is shown in Example 5.
Thus, a novel selective epimerization reaction of the immunosuppressive natural product rapamycin has been discovered and the structures of the epimerization products have been confirmed through both NMR and X-ray crystallographic analyses. 28-Epirapamycin was assayed in vitro and found to possess less potent immunosuppressive activity. This extremely mild and efficient retroaldol and realdol epimerization condition can also be applied to acyclic β-hydroxyketone to generate the thermodynamically more stable stereoisomer. This methodology should be broadly applicable to other natural products and compounds bearing β-hydroxy ketones.
Example 2
Synthesis of 28-epirapamycin and C43-modified 28-epirapalogs
2.0 28-epirapamycin
General Methods. All reagents and solvents were analytical grade and used as purchased without further purification. 1H and 13C NMR spectra were recorded on a Bruker ARX-300 or DRX-600 instrument. Chemical shifts are reported in ppm downfield from tetramethylsilane. In cases where a mixture of rotamers is present, only the chemical shifts of the major rotamer are reported. Low resolution mass spectra (LRMS) were obtained on a Micromass Platform II quadrupole mass spectrometer operating in electrospray mode. Flash chromatography was performed on silica gel (Merck, 230–400 mesh). Analytical TLC was performed on silica gel 60 F254 plates (Merck). Rapamycin related reactions were monitored by both normal phase and reverse phase analytical HPLC at 280 nm wavelength. The normal phase HPLC uses Kromasil silica column (4.6 mm×25 cm) with 4.0/42.5/50/200:MeOH/EtOAc/Hexanes/CH2C12 as the eluent at 1.0 mL/min flow rate at room temperature. The reverse phase HPLC uses Kromasil C18 column (4.6 mm×25 cm) with 80/20:MeOH/H2O as the eluent at 1.0 mL/min flow rate at 50° C. Preparative HPLC separations were carried out on a Kromasil silica column (21.4 mm×25 cm) at 20 mL/min flow rate.
General procedure for epimerization of rapamycin. To a solution of rapamycin (510 mg, 0.56 mmol) in CH2C12 (35.2 mL), Ti(OiPr)4 (494 μL, 1.67 mmol) was added dropwise at room temperature. The reaction mixture turned pale yellow. After 30 min, the solution was poured into a separatory funnel containing a heterogeneous mixture of 1 N HC1 and EtOAc. The organic layer was sequentially washed with saturated aqueous NaHCO3, H2O, brine, dried over Na2SO4, filtered and concentrated under vacuum. The retention time for all the products are listed below.













Normal Phase
Reverse Phase


Compound
retention time (min)
retention time (min)







28-secorapamycin (3)
15.89
13.80


28,29-bisepirapamycin (5)
24.51
14.24


29-epirapamycin (4)
25.88
13.11


rapamycin (1)
30.95
11.60


28-epiramycin (2)
33.21
13.80


rapamycin tautomer
39.68
14.79


28-epirapamycin tautomer
43.26
14.54









2.1 C43 O-allyl C28 Epi Procedure (One Pot)

Rapamycin (219 mg, 0.240 mmoles) was dissolved in dichloromethane (12.3 mL) and stirred at room temperature. Ti(OiPr)4 (212 mL, 0.720 mmoles) was added producing a pale yellow solution. After 75 min at rt, the solution was cooled to −78° C. followed by addition of 2,6-lutidine (156 mL, 1.2 mmoles) and allyl triflate. The reaction was stirred for 100 min at −78° C., then warmed to 0° C. After 2 h, the solution was quenched into a separatory funnel containing a heterogeneous solution of 1 N HCl and CH2C12. The organic layer was washed with NaHCO3, brine and water, dried over NaSO4, filtered and concentrated under vacuum to approximately 2 mL. Purification with silica gel flash chromatography (3/1 Hexane/Acetone) followed by Semi Preparative HPLC (4.0:42.5:50:200/MeOH:EtOAc:Hexane:CH2C12) yielded clean 28epi-43-O-allyl rapamycin (14%: 41% based on conversion). MS: (M—H)—: 952.44.
2.2 C43 O-allyl C28 Epi Procedure (from Clean 28-Epi Rapamycin)
A solution of allyl alcohol (15.5 mL 0.228 mmoles) and 2,6-di-t-butyl pyridine (46 mg, 0.225 mmoles) in CH2C12 (1.12 mL) was added to a second solution of triflic anhydride (38.0 mL, 0.229 mmoles) dissolved in CH2C12 (546 mL) stirring at −78° C. After 90 min, a solution of 28-epirapamycin (101 mg, 0.111 mmoles), and 2,6-di-t-butyl pyridine (46 mg, 0.225 mmoles) in CH2C12 (7.0 mL) was added to the solution of allyl triflate. The reaction stirred for 30 min at −78° C. then warmed to 0° C. and stirred for an additional 7 h. The solution was added to a separatory funnel containing a heterogenoues solution of EtOAc and 5% HCl. The organic layer was washed with NaHCO3, brine and water, dried over NaSO4 filtered and concentrated. Purification by silica gel flash chromatography (gradient of 2/1 to 3/2 hexane/ethyl acetate) yielded 28-epi 43-O-allyl-rapamycin as a white solid (59% based on recovered starting material). MS: (M−H)−: 952.44.
2.3 C43 O-methyl C28 Epi Procedure (One Pot)
Rapamycin (1.39 g 1.52 mmoles) was dissolved in CH2C12. Titanium isopropoxide (1.35 mL, 4.57 mmoles) was added dropwise quickly. The solution stirred at room temperature for 30 min then cooled to 0° C. 2.6 Lutidine (994 mL 7.61 mmoles) and methyl triflate (861 mL, 7.61) were added simultaneously. The reaction stirred for 110 min, quenched by adding to a separatory funnel containing a heterogeneous mixture of 1 N HCl and CH2C12, extracted, washed with NaHCO3, brine and water, dried over NaSO4, filtered and concentrated. Purification via silica gel flash chromatography (3/1 to 1/1 hexane/acetone) followed by preparatory HPLC (4.0/42.5/50.0/200:MeOH/EtOAc/Hex/CH2C12) yielded 28-epirapmycin-43-O-allyl as a white solid (24% yield based on recovered starting material). MS: (M−H)−: 926.71.
2.4 Other C-43-modified 28-epirapalogs
43-O-benzyl-28-epirapamycin, 43-O-methoxymethylene-28-epirapamycin, and 43-N,N-dimethylgylcinate-28-epirapamycin may be prepared using known transformations, starting with 28-epirapamycin. 28-epirapalogs containing modifications at C7 and C43 may be prepared analogously, starting with the C7 28-epirapalog (See Example 4, below) corresponding to the desired product.
2.5 Comparative Characteristics of Several C-43-Modified 28-eplrapalogs














FKBP





binding1
txn 2098L2
Spienocyte3


Cmpd
IC50 (nM)
EC50 (nM)
IC50 (nM)


















rapamycin
1.7
7–10
0.1–0.3


28-epirapamycin
8, 17
8
0.9–3.5


43-O-MOM-28-epirapamycin
27
7
0.6–1.6


43-O-methyl-28-epirapamycin
34
3
20–31


43-O-allyl-28-epirapamycin
65
8
641–684


43-O-benzyl-28-epirapamycin
63
12
~1200





1Affinities of rapalogs for FKBP may determined using a previously reported competitive binding assay based on fluorescence polarization (FP). A fluorescein-labelled FK506 probe (AP1491) is used, and the increase in the polarization of its fluorescence provides a direct readout of % bound probe in an equilibrium binding experiment containing sub-saturating FKBP and variable amounts of rapalog as competitor. See e.g., WO 99/36553, Example 11, pages 119–120


2EC50 values of the various compounds was measured in a transcription assay using genetically engineered HD1080 cells which constitutively express transcriptional switch components containing FKBP and 2098L mutant FRB domains, respectively and which regulatably express secreted alkaline phosphatase (SEAP) in the presence of a compound which multimerizes the switch components. The assay is a literature assay. See WO 99/36553, e.g. Example 12, pages 120–121 (& FIG. 2D)


3Conventional murine splenocyte assay for immunosuppressive activity.






Example 3
Synthesis of Representative C-24 modified 28-epirapalogs
Methods for preparing the E and Z forms of C-24 oximes of rapamycin are known. See e.g. WO96/41865 and WO99/36553. Using those methods, but substituting 28-epirapamycin for rapamycin yields the corresponding oximes of 28-epirapamycin:




where, for the purpose of this Example, RB is —OH, —OMe, —OEt, —OisoBu, —OtBu, —Obenzyl, —OCH2CO2H, —OCH2CONH2.

Example 4
Synthesis of C7 28-epirapalogs
WO96/41865 and WO99/36553 disclose the synthesis of a series of C7 analogs of rapamycin containing various C7 substituents including, among others, branched and unbranched alkoxy, arylalkyloxy, —NHCO-Oalkyl, —NHSO2 alkyl and substituted aryl and heteroaryl moieties, using chemistry generally as described in the literature except as noted (see e.g., Luengo et al. 1995. Chemistry and Biology 2, 471–481, and the references cited in Table II for additional background). Using the same methods, but substituting 28-epirapamycin for rapamycin yields the corresponding C7 derivatives of 28-epirapamycin, e.g, compounds of the following structure:




where one of R7a and R7b is H, and the other is —OEt, —OiPr, —Obenzyl, —NH—CO—OMe, —NH—SO2—Me, -furanyl, -methylthiophene, -ethylthiophene, -tertbutyl thiophene, -o,p-dimethoxyphenyl, -indolyl, -o,p-diethoxyphenyl, -methylthiophene, -N-methylpyrrole and the like.

Example 5
Comparative Characteristics of Several C-7-modified 28-epirapalogs
A diverse group of C7-modified 28-epirapalogs were prepared as described in Example 4. Representative examples are listed on the table set forth on the next two pages, with comparative data for FKBP binding, activity in a cellular transcription assay, and activity in a mouse splenocyte assay using methods discussed in Example 2.5, above.














FKBP





IC50 
TXN 2098L
Splenocyte


Description
(nM)
EC50 (nM)
IC50 (nM)


















Rapamycin
1.7
7–10
0.1–0.3


28-EPI FAMILY


28-epirapamycin
8, 17
 8
0.9–3.5


7-Alkyl/Aryl


28-epi-7S-dimethoxyphenyl
31
50
 598–1064


28-epi-7R-dimethoxyphenyl
54
26
22–28


28-epi-7R-methylthiophene
120
22
394–424


28-epi-7S-methylthiophene
86
25
170–242


28-epi-7S-dimethylthiophene
78
30
1242–1541


7-Ethers


28-epi-7S-allyloxy
18
 8
1802


28-epi-7R-allyloxy
11
25
3402


28-epi-7S-benzyloxy
70
18
93


28-epi-7R-benzyloxy
9.1
14
313


28-epi-7S-(3′-methyl)-but-4′-
27
16
718


enyloxy


28-epi-7R-(3′-methyl)-but-4′-
13
35
3156.3


enyloxy


28-epi-7S-phenyloxy
36
 8(−)
 478–2502


28-epi-7R-phenyloxy
19
 9(−)
 200–1954


28-epi-7S-2′-methoxybenzyloxy
33
15
25


28-epi-7R-2′-methoxybenzyloxy
4.6
24
653


28-epi-7S-2′-methylphenyloxy
17
14
710, 1700


28-epi-7R-2′-methylphenyloxy
8.1
 8(+)
802, 3113


28-epi-7S-cyclohexylethyloxy

76


28-epi-7S-isopropyloxy
49
29


28-epi-7R-isopropyloxy


28-epi-7S-ethoxy

15
801.3


28-epi-7R-ethoxy

33


28-epi-7R-methoxy

 46(+)


ThioEthers


28-epi-7S-isopropylthioether
15
 31(+)


28-epi-7S-isopropylthioether
21
15


7-Carbamates


28-epi-7S-ethylcarbamate
13
10
>5000


28-epi-7R-ethylcarbamate
7.5
  9(+)
>5000


28-epi-7S-benzylcarbamate
40
15
3448


28-epi-7R-benzylcarbamate
12
  9(+)
2256


28-epi-7S-phenylcarbamate
18
 14(+)
>5000


28-epi-7R-phenylcarbamate
9
 10(+)
>5000


28-epi-7S-isobutylcarbamate


28-epi-7R-isobutylcarbamate


7-N-AlkylCarbamates


28-epi-7R-N-methyl-ethylcarba-
120
 9
255


mate


28-epi-7S-N-methyl-ethylcarba-
30
 12(−)
2292


mate


28-epi-7S-N-Me-isobutylcarba-
19
40
1381


mate


28-epi-7R-N-Me-isobutylcarba-
109
15
587


mate


28-epi-7S-N-Me-benzylcarbamate
40
 9
158


28-epi-7R-N-Me-benzylcarbamate
163
  8(−)
1154


28-epi-7S-N-Me-p-tolylcarbamate
54
25
50


28-epi-7R-N-Me-p-tolylcarbamate
119
70
393


7-Sulfonamides


28-epi-7S-butanesulfonamide
9.2
 11(+)
152


28-epi-7R-butanesulfonamide
11
20
0.16


28-epi-7S-methanesulfonamide
16
24
7


28-epi-7R-methanesulfonamide
7.2
24
91


7-N-AlkylSulfonamides


28-epi-7R-N-Me-p-toluenesulfon-
34
 8
12


amide


28-epi-7S-N-Me-methanesulfona-
21
 27(+)
140


mide


28-epi-7R-N-Me-methanesulfona-
37
 8
166


mide


28-epi-7S-N-Et-methanesulfona-
31
  8(+)
1362


mide


28-epi-7R-N-Et-methanesulfona-
31
  8(+)
189


mide


28-epi-7S-N-Me-propanesulfona-
19
 35(+)
2629


mide


28-epi-7R-N-Me-propanesulfona-
148
 9
1372


mide


7-Sulfamides


28-epi-7S-methylphenylsulfamide
11
28
564


28-epi-7R-methylphenylsulfamide
38
27
22


28-epi-7S-dimethylsulfamide
13
 20(+)
879


28-epi-7R-dimethylsulfamide
29
 20(+)
1844


28-epi-7-N-AkylSulfamides


28-epi-7S-N-Me-methylphenylsul-

26


famide


28-epi-7R-N-Me-methylphenylsul-
74
 8


famide


28-epi-7R-N-Me-dimethylsulfa-

 8
653


mide





(+)peak was >125% rapamycin peak


(−)peak was <80% rapamycin peak






Example 6
Preparation of 24(S),30(S)-tetrahydro- and 30-dihydro- 28-epirapamycin
WO99/36553 discloses the synthesis and characterization of 24(S),30(S)-tetrahydro rapamycin. Using the same methods, but substituting 28-epirapamycin for rapamycin yields 24(S),30(S)-tetrahydro-28-epirapamycin




28-epi-30-dihydro rapamycin was also prepared using conventional methods but substituting 28-epirapamycin for rapamycin as the starting material.

Example 7
Preparation of 28-epirapalogs modified at C24, C30 and C7
24(S), 30(S)-tetrahydro-28-epirapamycin prepared as in Example 6, may be modified at C7 using approaches illustrated in the prior C7 rapalog examples. For example:




24(S), 30(S)-tetrahydro-28-epirapamycin (20 mg, 0.022 mmol) is dissolved in dichloro-methane (1.0 mL). 1,3-dimethoxybenzene (0.20 mL, 1.5 mmol) is added, and the solution is cooled to −60° C. Trifluoroacetic acid (0.030 mL, 0.39 mmol) is added, and the reaction mixture is stirred for 1 h at −60° C., then partitioned between ethyl acetate (10 mL) and saturated aqueous sodium bicarbonate (1 mL). The organic phase is washed with water (2 mL) and brine (1 mL), dried over anhydrous magnesium sulfate, filtered, and concentrated. The product is recovered using flash chromatography (silica gel, 15:75:50:200 methanol:ethyl acetate:hexane:dichloromehane)—lit. ref. Luengo, J. I.; Konialian-Beck, A.; Rozamus, L. W.; Holt, D. A. J. Org. Chem. 1994, 59, 6512–6513.

By analogous means, one may produce 24(S), 30(S)-tetrahydro 28-epirapamycins bearing other C7 substituents as described elsewhere herein, e.g., containing alternatively substituted aryl groups, heteroaryl, —O-aliphatic groups, thioethers, or any of the other types of moieties designated previously for RC7a or RC7b. These compounds may be obtained by reduction at C24 and C30 of the appropriate C7 28-epirapalog, or by transformation at C7 of C24, C30-tetrahydro 28-epirapamycin. Illustrative examples follow.
Rapalogs modified at C24, C30 and C7 may also be differ from rapamycin at the various positions discussed herein, e.g. with respect to one or more of RC13, RC43, RC28, RC29, R4, “a”, etc. By way of example, starting with 13-F-rapamycin in place of rapamycin yields the corresponding 13-fluoro analog.
Other illustrative compounds which may be analgously prepared include:


    7-ethoxy-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-i-propoxy-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-benzyloxy-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-methylcarbamate7-(7-demethoxy)-24(S), 30(S)-tetrahydro-28-epirapamycin
    7-methanesulfonamide-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-furanyl-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-methylthiophene-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-ethylthiophene-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-tertbutylthiophene-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-indolyl-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-o,p-diethoxyphenyl-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-(N-methylpyrrole)-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin
    7-(2,4,6-trimethoxyphenyl)-(7-demethoxy)-24(S),30(S)-tetrahydro-28-epirapamycin


Example 8
For detailed information on the design of nucleic acid constructs for engineering cells or animals to be responsive to rapalogs such as disclosed herein, and for detailed guidance on the assembly, delivery to cells and animals, and evaluation of such nucleic acids, see e.g. WO99/36553, the contents of which are specifically incorporated herein. Examples 8–10 of that document disclose examples of the use of rapamycin for activating target gene transcription in cells and in animals, while example 14 thereof discloses the use of rapamycin to activate signal transduction in engineered cells. Those examples are also specifically incorporated by reference herein. That guidance may be adapted for analogous use in connection with the 28-epirapalogs of this invention.

## Claims

1. A compound of the formula I or II:




wherein
n is 1 or 2;
R28 and R43 are independently selected from the group consisting of H and an aliphatic or acyl moiety;
one of R7a and R7b is H and the other is halo, —RA, —ORA, —SRA, —OC(O)RA, —OC(O)NRARB—NRARB, —NRBC(O)RA, —NRBC(O)ORA, —NRBSO2RA, —NRBSO2NRARB′ or —NRBC(O)NRARB′; or
R7a and R7b taken together, are H in the tetraene moiety:




where RA is H or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where RB is H, OH or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where each aliphatic moiety is an independently chosen saturated or unsaturated, branched or unbranched, cyclic or polycyclic, aliphatic hydrocarbon containing 1–8 contiguous aliphatic carbon atoms;
where each heteroaliphatic moiety is an independently chosen 2–8-membered non-cyclic or 3–10-membered cyclic aliphatic moiety which contains one or more oxygen, sulfur, nitrogen, phosphorous or silicon atoms;
where each aryl moiety is an independently chosen 6–14-membered mono- or polycyclic unsaturated moiety;
where each heteroaryl moiety is an independently chosen 5–6-membered monocyclic or 9–14-membered polycyclic unsaturated moiety which contains one or more oxygen, sulfur or nitrogen atoms; and
where each acyl moiety is an independently chosen —OCR group where R is an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
or a pharmaceutically acceptable salt thereof.

2. A compound of the formula I or II:




wherein
n is 1 or 2;
R28 and R43 are independently selected from the group consisting of H and an aliphatic or acyl moiety;
one of R7a and R7b is H and the other is halo, —RA, ORA, SRA, OC(O)RA, —OC(O)NRARB, —NRARB, —NRBC(O)RA, —NRBC(O)ORA, —NRBSO2RA, —NRBSO2NRARB′ or —NRBC(O)NRARB′; or
R7a and R7b taken together, are H in the tetraene moiety:




where RA is H or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where RB is H, OH or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where each aliphatic moiety is an independently chosen saturated or unsaturated, branched or unbranched, cyclic or polycyclic, aliphatic hydrocarbon containing 1–8 contiguous aliphatic carbon atoms;
where each heteroaliphatic moiety is an independently chosen 2–8-membered non-cyclic or 3–10-membered cyclic aliphatic moiety which contains one or more oxygen, sulfur, nitrogen, phosphorous or silicon atoms;
where each aryl moiety is an independently chosen 6–14-membered mono- or polycyclic unsaturated moiety;
where each heteroaryl moiety is an independently chosen 5–6-membered monocyclic or 9–14-membered polycyclic unsaturated moiety which contains one or more oxygen, sulfur or nitrogen atoms;
where each acyl moiety is an independently chosen —OCR group where R is an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
wherein each aliphatic, acyl, heteroaliphatic, aryl, or heteroaryl moiety contains one or more optional substituents selected from the group consisting of —OH, —OR2, —SH, —SR2, —CHO, ═O, —COOH (or ester, carbamate, urea, oxime or carbonate thereof), —NH2 (or substituted amine, amide, urea, carbamate or guanidino derivative thereof), halo, trihaloalkyl, cyano, —SO2—CF3, —OSO2F, —OS(O)2R11, —SO2—NHR11, —NHSO2—R11, sulfate, sulfonate, aryl and heteroaryl moieties;
where R2 is an aliphatic, heteroaliphatic, aryl, heteroaryl or alkylaryl moiety; and
where R11 is H or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety;
or a pharmaceutically acceptable salt thereof.

3. A compound of the formula I or II:




wherein
n is 1 or 2;
R28 and R43 are independently selected from the group consisting of H and an aliphatic or acyl moiety;
one of R7a and R7b is H and the other is halo, —RA, —ORA, —SRA, —OC(O)RA, —OC(O)NRARB′, —NRARB, —NRBC(O)RA, —NRBC(O)ORA, —NRBSO2RA, —NRBSO2NRARB′ or NRBC(O)NRARB′; or
R7a and R7b taken together, are H in the tetraene moiety:




where RA is H or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where RB is H, OH or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where each aliphatic moiety is an independently chosen saturated or unsaturated, branched or unbranched, cyclic or polycyclic, aliphatic hydrocarbon containing 1–8 contiguous aliphatic carbon atoms;
where each heteroaliphatic moiety is an independently chosen 2–8-membered non-cyclic or 3–10-membered cyclic aliphatic moiety which contains one or more oxygen, sulfur, nitrogen, phosphorous or silicon atoms;
where each aryl moiety is an independently chosen 6–14-membered mono- or polycyclic unsaturated moiety;
where each heteroaryl moiety is an independently chosen 5–6-membered monocyclic or 9–14-membered polycyclic unsaturated moiety which contains one or more oxygen, sulfur or nitrogen atoms;
where each acyl moiety is an independently chosen —OCR group where R is an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
wherein each aryl or heteroaryl moiety contains one or more optional substituents selected from the group consisting of hydroxy, C1–C8 alkoxy, C1–C8 branched or straight-chain alkyl, acyloxy, carbamoyl, amino, N-acylamino, nitro, halo, trihalomethyl, cyano, and carboxyl;
or a pharmaceutically acceptable salt thereof.

4. The compound of claim 1, 2 or 3 wherein n is 2, R28 is H, R7a is —OMe, R7b is H and R43 is an aliphatic moiety.

5. The compound of claim 1, 2 or 3 wherein R7a is —OMe and R7b is H.

6. The compound of claim 1, 2 or 3 wherein R28 is H.

7. The compound of claim 1, 2 or 3 wherein R43 is H.

8. The compound of claim 1, 2 or 3 wherein either R7a is a moiety other than —OMe or R7b is a moiety other than H.

9. The compound of claim 8 wherein one of R7a and R7b is —NRBC(O)RA, —NRBC(O)ORA, —NRBSO2RA, —NRBSO2NRARB′ or —NRBC(O)NRARB′.

10. The compound of claim 9 in which RB is H, OH or alkyl.

11. The compound of claim 1, 2 or 3 wherein R43 is an aliphatic moiety.

12. The compound of claim 11 wherein R43 is an alkyl moiety.

13. The compound of claim 1, 2 or 3 wherein R43 is a hydroxyalkyl moiety.

14. The compound of claim 11 wherein R43 is an alkenyl moiety.

15. The compound of claim 14 wherein the alkenyl moiety is an allyl group.

16. The compound of claim 1, 2 or 3 wherein R43 is an acyl moiety.

17. The compound of claim 16 wherein R43 is an acyl moiety of the formula RARBN-alkyl-C(O)—.

18. The compound of claim 4, wherein R28 and R43 are H, R7a is —OMe, and R7b is H.

19. The compound of claim 8 wherein n is 2, and R28 and R43 are H.

20. The compound of claim 1, 2 or 3 wherein n is 2.

21. The compound of claim 1, 2 or 3 wherein the compound has the formula II in which —OR43 is in the S orientation.

22. The compound of claim 1, 2 or 3 wherein the compound has the formula II in which —OR43 is in the R orientation.

23. A composition comprising a compound of claim 1, 2 or 3 and one or more pharmaceutically acceptable carriers, diluents or excipients.

24. A method for producing a compound of claim 1, 2 or 3 which comprises contacting a homologous C28 epimer with a titanium tetraalkoxide reagent under suitable conditions and for a sufficient time to permit epimerization.

25. The method of claim 24 wherein the titanium tetraalkoxide reagent is titanium tetraisopropoxide.

26. The method of claim 24 which further comprises recovering the epimerized product.

27. The method of claim 24 wherein the homologous C28 epimer is rapamycin.

28. A compound of the formula I or II:




wherein
n is 1 or 2;
R28 is selected from the group consisting of H and an aliphatic or acyl moiety;
R43 is an alkyl, alkenyl or acyl moiety;
one of R7a and R7b is H and the other is halo, —RA, —ORA, —SRA, —OC(O)RA, —OC(O)NRARB, —NRARB, —NRBC(O)RA, —NRBC(O)ORA, —NRBSO2RA, —NRBSO2NRARB′ or —NRBC(O)NRARB′; or
R7a and R7b taken together, are H in the tetraene moiety:




where RA is H or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where RB is H, OH or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where each aliphatic moiety is an independently chosen saturated or unsaturated, branched or unbranched, cyclic or polycyclic, aliphatic hydrocarbon containing 1–8 contiguous aliphatic carbon atoms;
where each heteroaliphatic moiety is an independently chosen 2–8-membered non-cyclic or 3–10-membered cyclic aliphatic moiety which contains one or more oxygen, sulfur, nitrogen, phosphorous or silicon atoms;
where each aryl moiety is an independently chosen 6–14-membered mono- or polycyclic unsaturated moiety;
where each heteroaryl moiety is an independently chosen 5–6-membered monocyclic or 9–14-membered polycyclic unsaturated moiety which contains one or more oxygen, sulfur or nitrogen atoms;
where each acyl moiety is an independently chosen —OCR group where R is an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
wherein each alkyl, alkenyl or acyl moiety contains one or more optional substituents selected from the group consisting of —OH, —OR2, —SH, —SR2, —CHO, ═O, —COOH (or ester, carbamate, urea, oxime or carbonate thereof), —NH2 (or substituted amine, amide, urea, carbamate or guanidino derivative thereof), halo, trihaloalkyl, cyano, —SO2—CF3, —OSO2F, —OS(O)2R11, —SO2—NHR11, —NHSO2—R11, sulfate, sulfonate, aryl and heteroaryl moieties;
where R2 is an aliphatic, heteroaliphatic, aryl, heteroaryl or alkylaryl moiety; and
where R11 is H or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety;
or a pharmaceutically acceptable salt thereof.

29. 28-epirapamycin or a pharmaceutically acceptable salt thereof.

30. 29-epirapamycin or a pharmaceutically acceptable salt thereof.

31. 28,29-bis-epirapamycin or a pharmaceutically acceptable salt thereof.

32. A compound having the structure of 28-epirapamycin, 29-epirapamycin or 28,29-bis-epirapamycin except that the hydroxyl group at position 43 is replaced with OR43 wherein R43 is an aliphatic or acyl moiety;
where an aliphatic moiety is a saturated or unsaturated, branched or unbranched, cyclic or polycyclic, aliphatic hydrocarbon containing 1–8 contiguous aliphatic carbon atoms;
where an acyl moiety is an —OCR group where R is an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where a heteroaliphatic moiety is a 2–8-membered non-cyclic or 3–10-membered cyclic aliphatic moiety which contains one or more oxygen, sulfur, nitrogen, phosphorous or silicon atoms;
where an aryl moiety is a 6–14-membered mono- or polycyclic unsaturated moiety;
where a heteroaryl moiety is a 5–6-membered monocyclic or 9–14-membered polycyclic unsaturated moiety which contains one or more oxygen, sulfur or nitrogen atoms; and
or a pharmaceutically acceptable salt thereof.

33. A compound having the structure of 28-epirapamycin, 29-epirapamycin or 28,29-bis-epirapamycin except that the hydroxyl group at position 43 is replaced with OR43 wherein R43 is an aliphatic or acyl moiety;
where an aliphatic moiety is a saturated or unsaturated, branched or unbranched, cyclic or polycyclic, aliphatic hydrocarbon containing 1–8 contiguous aliphatic carbon atoms;
where an acyl moiety is an —OCR group where R is an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where a heteroaliphatic moiety is a 2–8-membered non-cyclic or 3–10-membered cyclic aliphatic moiety which contains one or more oxygen, sulfur, nitrogen, phosphorous or silicon atoms;
where an aryl moiety is a 6–14-membered mono- or polycyclic unsaturated moiety;
where a heteroaryl moiety is a 5–6-membered monocyclic or 9–14-membered polycyclic unsaturated moiety which contains one or more oxygen, sulfur or nitrogen atoms;
wherein each aliphatic or acyl, moiety contains one or more optional substituents selected from the group consisting of —OH, —OR2, —SH, —SR2, —CHO, ═O, —COOH (or ester, carbamate, urea, oxime or carbonate thereof), —NH2 (or substituted amine, amide, urea, carbamate or guanidino derivative thereof), halo, trihaloalkyl, cyano, —SO2—CF3, —OSO2F, —OS(O)2R11, —SO2—NHR11, —NHSO2—R11, sulfate, sulfonate, aryl and heteroaryl moieties;
where R2 is an aliphatic, heteroaliphatic, aryl, heteroaryl or alkylaryl moiety; and
where R11 is H or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety;
or a pharmaceutically acceptable salt thereof.

34. A compound having the structure of 28-epirapamycin, 29-epirapamycin or 28,29-bis-epirapamycin except that the hydroxyl group at position 43 is replaced with OR43 wherein R43 is an aroyl or heteroaroyl moiety;
where an aroyl moiety is an —OCR group where R is an aryl moiety;
where a heteroaroyl moiety is an —OCR group where R is a heteroaryl moiety;
where an aryl moiety is a 6–14-membered mono- or polycyclic unsaturated moiety;
where a heteroaryl moiety is a 5–6-membered monocyclic or 9–14-membered polycyclic unsaturated moiety which contains one or more oxygen, sulfur or nitrogen atoms; and
wherein each aroyl or heteroaroyl moiety contains one or more optional substituents selected from the group consisting of hydroxy, C1–C8 alkoxy, C1–C8 branched or straight-chain alkyl, acyloxy, carbamoyl, amino, N-acylamino, nitro, halo, trihalomethyl, cyano, and carboxyl;
or a pharmaceutically acceptable salt thereof.

35. The compound of claim 33
wherein R43 is a hydroxyalkyl moiety.

36. A compound having the structure of 28-epirapamycin, 29-epirapamycin or 28,29-bis-epirapamycin except that the hydroxyl group at position 43 is replaced with OR43 wherein R43 is an acyl moiety;
where an acyl moiety is an —OCR group where R is an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety;
where an aliphatic moiety is a saturated or unsaturated, branched or unbranched, cyclic or polycyclic, aliphatic hydrocarbon containing 1–8 contiguous aliphatic carbon atoms;
where a heteroaliphatic moiety is a 2–8-membered non-cyclic or 3–10-membered cyclic aliphatic moiety which contains one or more oxygen, sulfur, nitrogen, phosphorous or silicon atoms;
where an aryl moiety is a 6–14-membered mono- or polycyclic unsaturated moiety;
where a heteroaryl moiety is a 5–6-membered monocyclic or 9–14-membered polycyclic unsaturated moiety which contains one or more oxygen, sulfur or nitrogen atoms;
wherein each acyl moiety contains one or more optional substituents selected from the group consisting of —OH, —OR2, —SH, —SR2, —CHO, ═O, —COOH (or ester, carbamate, urea, oxime or carbonate thereof), —NH2 (or substituted amine, amide, urea, carbamate or guanidino derivative thereof), halo, trihaloalkyl, cyano, —SO2—CF3, —OSO2F, —OS(O)2R11, —SO2—NHR11, —NHSO2—R11, sulfate, sulfonate, aryl and heteroaryl moieties;
where R2 is an aliphatic, heteroaliphatic, aryl, heteroaryl or alkylaryl moiety; and
where R11 is H or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety;
or a pharmaceutically acceptable salt thereof.

37. The compound of claim 1, 2 or 3, wherein the compound has the formula I.

38. The compound of claim 1, 2 or 3, wherein the compound has the formula II.

39. The compound of claim 1, 2 or 3, wherein R28 and R43 are independently selected from the group consisting of H and an aliphatic, aroyl or heteroaroyl moiety.

40. The compound of claim 28, wherein R28 is selected from the group consisting of H and an aliphatic, aroyl or heteroaroyl moiety.

41. The compound of claim 32 or 33, wherein R43 is an aliphatic, aroyl or heteroaroyl moiety.

42. The compound of claim 36, wherein R43 is an aroyl or heteroaroyl moiety.