# Patent

## Title
PNA conjugate for the treatment of diseases associated with HIV

## Abstract

The invention relates to peptide nucleic acid (PNA) conjugates which can be used for treating diseases correlated with HIV, wherein the peptide nucleic acid (PNA) inhibits the gene expression of HIV. The conjugates comprise the following components: (a) a transport mediator for the cell membrane, (b) an address protein or peptide for the import into the cell nucleus, and (c) a peptide nucleic acid (PNA) which is to be transported and can be hybridized with an HIV gene and can inhibit the expression of the HIV gene.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is filed under the provisions of 35 U.S.C. §371 and claims the priority of International Patent Application No. PCT/DE02/02564 filed Jul. 12, 2002, which in turn claims priority of German Patent Application No. 101 33 307.2 filed Jul. 12, 2001.
FIELD OF THE INVENTION
Background of the Invention
The present invention relates to peptide nucleic acid (PNA) conjugates which can be used for treating diseases correlated with HIV, the peptide nucleic acid (PNA) inhibiting the gene expression of HIV.
The incidence of the human immunodeficiency virus (HIV) is increasing world-wide in spite of the previous intensive research efforts made as to the development of effective treatment methods. HIV is counted among the lentiviral group of retroviruses and is one of the most intensively studied viruses. The HIV infection cycle starts with binding viral particles to the cell membrane of the target cells by means of a viral coat protein gp120/gp41. The virus initially binds to the CD4 protein, followed by binding to the obligatory co-receptor which is a member of the chemokin-receptor family. Main objectives of the HIV infection are T-helper cells and macrophages. Here, the viral core complex penetrates the cell and the virus is integrated into the viral genome in several steps (reverse transcription, introduction into the cell nucleus, integration into the chromosomes of the host cells as a DNA double strand). From this point of time, HIV is a permanent component of the cellular genome and can be considered an acquired genetic disease. HIV cannot replicate in the CD4+ cell and for the “priming” of its promoters in the regulatory region (LTR) it requires cellular transcription factor for the transcription of early regulatory mRNAs which code for Tat, Rev and Nef proteins. The transactivator protein Tat is of special significance in the early phase of HIV-RNA synthesis. The Tat protein concentration correlates directly with the HIV-RNA amount. The interaction between Tat and TAR can also result in a strongly increased trans-activation of the viral gene expression by inducing the initiation of transcription as well as elongation.
Previous therapy approaches which aimed at a causal treatment have not brought about a decisive breakthrough in combating infections. Drug therapies have not yet been able to either stop HIV infections or heal diseases caused by them. Immunological strategies, e.g. inoculations, have not yet been successful on account of the high variability of the expression patterns of the HIV virus coat proteins and it seems that they will not be very promising in the future either. Another theoretical therapy approach is based on a molecular virus inactivation, e.g. via antisense RNAs for blocking viral nucleic acids. Although this therapy approach offers itself particularly for HIV, it appears to be highly problematic on account of the transient control of the HIV infection cycle and the presently almost unknown viral expression pattern. It also seems that a HIV proliferation control by ribozymes is very difficult to realize because special suitable CUG sequences of the virus genome have to be identified for such a strategy (since the ribozymes only cleave at this sequence motif), which appears to be extremely difficult, above all with respect to the very high HIV mutation rate.
The problem of an effective introduction of the antisense or ribozyme molecules into the target location also arises in connection with all of the above discussed procedures. The vectors previously used for this purpose, e.g. adeno-associated viruses (AAVs) have numerous drawbacks. AAVs are small parvoviruses having a single-stranded DNA. Their potential is their ability of infecting both dividing and non-dividing cells and penetrating the host genome. However, their major drawback is the lack of synthesis of sufficient amounts and lack of stability as a vector for hematopoietic cells. Vectors based on MLV (murine leukemia virus) have also been tested in numerous clinical studies. Although they seem to be non-toxic and theoretically suited as possible carriers for antisense constructs, they have the drawback that only very low titers are achieved in the host. Finally, vectors based on LV (lentiviruses) might also come into consideration, however, their major drawback is that they can only infect non-proliferating cells. Although this property would permit the superinfection of HIV-infected cells, they are nevertheless unsuited on account of their natural viral tropism.
SUMMARY OF THE INVENTION
The present invention is thus based on the technical problem of providing products which permit a specific and efficient therapy based on an inhibition of the HIV gene expression.
This technical problem is solved by providing the embodiments characterized in the claims.
In order to obtain a solution to the technical problem, the inventors developed a conjugate comprising the following components:

    
    
        a transport mediator for the cell membrane (“P”),
        an address protein or peptide (“AP”) for the import into the cell nucleus, and
        a peptide nucleic acid which is to be transported and can be hybridized with a HIV gene and inhibits the expression thereof (“PNA”).
    
    


This modular conjugate has two decisive advantages:

    
    
        (a) An efficient and site-directed PNA transport to the target location and thus a gene therapy is enabled by means of the components “P” and “AP”. These components do not only permit a rapid and effective transport of macromolecules such as PNA through cell membranes of living cells into the cytoplasm but, following a cytoplasmic activation of address peptide sequences, also an efficient transport into the cell nucleus.
        (b) The use of the protease-resistant and nuclease-resistant peptide nucleic acids (PNAs) which are oligonucleotide derivatives whose sugar phosphate backbone is preferably substituted by ethyl-amine-linked α-amino-ethyl-glycine units permits a stable and efficient blocking of the transcription of the desired gene under physiological conditions on account of their physicochemical properties. An anti-gene strategy based on the antisense principle is pursued by these PNAs. However, in this strategy, the target is not the mRNA but the gene itself, e.g. a viral DNA intermediate or the viral DNA integrated into the genomic host DNA. Here, the PNAs hybridize via the formation of a triple helix to the target DNA. The target region can be a transcribed region of the target DNA, on the one hand, or a regulatory region the blocking of which via the PNAs also inhibits the transcription, on the other hand.
    
    


Regarding methods as to the production of the individual components of the conjugates and their linkage reference is made to German patent application No. 199 33 492.7. The synthesis of PNAs is known to a person skilled in the art and also described in Nielsen et al., Science 254 (1991), 1497-1500, for example.
The structure of the conjugate according to the invention is preferably:










P - AP −(HIV-PNA)







more preferably with a spacer (“SP”):











P - AP - SP - (HIV-PNA)







The transport mediator for the cell membrane (abbreviated as “P” above) represents a peptide or protein which can pass through the plasma membrane. The length of this peptide or protein is not limited as long as it has the above property. Examples of “P” originate preferably from the penetratin family (Derossi et al., Trends Cell Biol. 8 (1988), pages 84-87) or are transportan or parts thereof (Pooga et al., The Faseb Journal 12 (1998), page 68 et seq.), those of the penetratin family being preferred. An example of “P” is a penetratin having the following sequence:










NH2-RQIKIWFQNRRMKWKK-




(SEQ ID NO: 1)






The select “P” sequence is produced biologically (purification of natural transport mediator proteins or cloning and expression of the sequence in a eukaryotic or prokaryotic expression system) and preferably synthetically, e.g. according to the Merrifield method (Merrifield, J. Am. Chem. Soc. 85 (1963), 2149).
For the selection of the address protein peptide (abbreviated by “AP” above) the person skilled in the art can chose controlling peptides or polypeptides by means of the known amino acid sequences for the import into the cell nucleus. In principle, the length of this address peptide or protein is not limited as long as it has the property of ensuring a cell nucleus-specific transport. In general “APs”, which contain a cell nucleus-specific recognition signal and thus direct the PNAs into the cell nucleus, are generally selected for the introduction of the PNAs. Fundamentally, the mere address sequence is sufficient for a transport into the cell nucleus. However, it is also possible to select “APs” which have a cell nucleus-specific peptidase cleavage site. Most favorably, this cleavage site is within the signal sequence but may also be attached thereto by additional amino acids to ensure the cleavage of the address sequence after reaching the cell nucleus. The select “AP” sequence is produced biologically (purification of natural transport mediator proteins or cloning and expression of the sequence in a eukaryotic or prokaryotic expression system) and preferably synthetically, e.g. according to the Merrifield method (Merrifield, J. Am. Chem. Soc. 85 (1963), 2149). Examples of suitable address proteins or peptides are:








-Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val;



(SEQ ID NO: 2)


and


 


H3N+-Pro-Lys-Lys-Lys-Arg-Lys-Val-


(SEQ ID NO: 3)


 


(SEQ ID NO: 3 is a = nuclear localization sequence


from SV40 T-antigen).






Furthermore, the conjugate can optionally contain a spacer (abbreviated by “SP” above) which is preferably located between the address protein/peptide and the peptide nucleic acid (PNA) to be transported. However, it may also be present additionally or alternatively between the transport mediator and the address protein. The spacer serves for eliminating or favorably influencing optionally existing steric interactions between the components. The spacer can be selected from e.g.: glycine, polylysine, polyethylene glycol (PEG), derivatives of polymethacrylic acid or polyvinyl pyrrolidone (PVP).
A redox cleavage site, e.g. -cysteine-S—S-cysteine-O—N—H, is preferably found between the transport mediator and the address protein/peptide. The bond forming between transport mediator and address protein is a redox coupling (mild cell-immanent linkage by means of DMSO; Rietsch and Beckwith, Annu. Rev. Genet. 32 (1998), 163-84):

    
    
        Cysteine-SH SH-cysteinecysteine-S—S-cystine
    
    


The peptide nucleic acid (PNA) permits the inhibition of the transcription of genes essential for HIV, e.g. in that it hybridizes with a gene region which is transcribed or a regulatory region, i.e. a region which is responsible for the activation of the expression of a certain gene or certain genes. Suitable genes and suitable regions can be identified by the person skilled in the art by means of the previously known HIV genes or the function thereof. The peptide nucleic acids preferably have a length of at least 18 bases, peptide nucleic acids with a length of at least 20 bases being particularly preferred. The peptide nucleic acid can also optionally be labeled, e.g. radioactively (e.g. linked with an alpha-, beta- or gamma radiator), with a dyestuff, with biotin/avidine, etc.
The conjugate constituents “P” and “AP” are synthesized preferably synthetically according to the Merrifield method (Merrifield, J. Am. Chem. Soc. 85 (1963), 2149). The other constituents (e.g. spacers and/or PNAs) are linked thereto by covalent chemical bond. The redox cleavage site is inserted between “P” and “AP” chemically by the above mentioned redox coupling. A covalent bond, preferably an acid amide bond, is also present between an optionally present spacer and the PNA or the address protein and the PNA. Possible alternatives are ether or ester bonds, depending on the functional group(s) existing in the substance to be conjugated.
In a particularly preferred embodiment of the conjugate according to the invention the peptide nucleic acid (PNA) hybridizes with the HIV-tat gene or HIV-rev gene. Based on the special viral HIV cycle the tat and rev genes are two preferred molecular targets for an anti-HIV therapy. The products of both genes act as essential regulatory proteins for trans-activating the HIV gene expression by binding to HIV-mRNA. Tat binds to TAR (“trans-activating-response-element”) near the HIV-RNA 5′ end and Rev interacts with RRE (“Rev-responsive-element”) of the env gene.
The genomic organization of HIV-1 is shown in FIG. 1.
The sequences coding for HIV-1 are published in Ratner et al., Nature 313, pp. 277-284 (1985).
In a particularly preferred embodiment of the conjugate according to the invention, the PNAs hybridize with sequences of the HIV-1 LTR region (FIG. 2). Advantageous PNAs comprise the below sequences:










TTATTTCCTCTTTTGTTG




(SEQ ID NO: 4)



 



ATTAC*TAC*GTC*TC*TC*C*GTT



(SEQ ID NO: 5)



 



TATC*GGTTTTTAAC*GTC*C*C*



(SEQ ID NO: 6)



 



TC*C*TTTTC*C*C*C*GAC*AAC*C*TTTAC*



(SEQ ID NO: 7)



C* = is pseudoisocytosine






The use of pseudoisocytosine has the advantage that pH-independent hybridization is possible.
In another preferred embodiment, the PNAs are directed against the polypurine tract, central DNA flap, Nef or NCp7 (Vpr, Vpu [see FIG. 7]. For this purpose, the inventors conducted various experiments which are shown in FIGS. 9 to 13.
Preferred PNAs against the above-mentioned regions are as follows:
Sequences HIV-1 (Reference is made Herein to FIGS. 7-13)
Abbreviations:


    L=linker
    J=pseudoisocytosine or cytosine











For HIV:




c-PPT and 3′-PPT 4821-36/9116-31 (general sequence):
PNA I


 


(Polypurine tract)


N-TCC CCC CTT TTC TTT T-L-TTT TJT T


(SEQ ID NO: 8)


 


c-PPt target:


DNA (+) or RNA 4821-39


N-CA ATC CCC CCT TTT CTT T-L-TT TJT TT
PNA Ia


(SEQ ID NO: 9)
1) nbIaNLS+



2) nbIaNLS−


 


N-CA ATC CCC CCT TTT CTT T
PNA Ib


(SEQ ID NO: 10)
3) nbIbNLS+


(the same sequence without linker part)
4) nbIbNLS−


 


DNA (−) 4800-20


N-GTA TTC ATC CAC AAT TTT
PNA II


(SEQ ID NO: 11)
5) nbIIaNLS+



6) nbIIbNLS−


 


DNA (+) 4800-20


N-AAA TTG TGG ATG AAT ACT
PNA III


(SEQ ID NO: 12)
7) nbIIIaNLS+



8) nbIIIbNLS−


 


Flap:
PNA IV


DNA(−) 4861-80


N-TAG TAG ACA TAA TAG CAA
PNA IVa


(SEQ ID NO: 13)
9) nbIVaNLS−


 


Another DNA (−) between c-PPT and Tar to shorten the “flap” length:


DNA (+) 4841-60


N-TCC CCT GCA CTG TAC CCC
PNA IVb


(SEQ ID NO: 14)
10) nbVbNLS−


 


Nef:


DNA (−) 9095-9115


N-AGA TCT TAG CCA CTT TTT-C
PNA Va


(SEQ ID NO: 15)
11) nbVaNLS+


 


9136-56


N-GGC TAA TTC ACT CCC AAC-C
PNA Vb


(SEQ ID NO: 16)
12) nbVbNLS+


 


IN site (3′) 9746-66:


N-TAG AGA TTT TCC ACA CTG
PNA Vc


(SEQ ID NO: 17)
13) nbVcNLS+


 


Seq is directed against the start of gag:


N-cac cca tct ctc tcc ttc (no linker)
PNA VI


(SEQ ID NO: 18)
14) nbVINLS−


 


Splice acceptor site:


N-jtt jtt-L-ttc ttc ctg cca tag
PNA VII


(SEQ ID NO: 55)
15) nbXNLS+



16) nbXNLS−


 


TAR:


N-cag gct caa atc tgg tct-L-tjt
PNA VII


(SEQ ID NO: 19)
17) nbXNLS−


 


NCp7:


N-ATT ACT ACG TCT CTC CGT (not tested)
PNA VIII


(SEQ ID NO: 20)


N-TAT CGG TTT TTA ACG TCC
18) smVIIIaNLS+


(SEQ ID NO: 21)


N T TTT JJT-linker-TCC TTT TCC CCG ACA ACC
19) smVIIIaNLS+


(SEQ ID NO: 22)
20) smVIIIcNLS+


 


Random sequence as a control:


N-CAT ACT TGA CTC GTT ATC-C
PNA IX


(SEQ ID NO: 23)


N-CAT ACT TGA CTC GTT ATC-C
21) IX NLS−


(SEQ ID NO: 24)
22) IX NLS+


 







BDV PNA: (This sequence was tested for BDV spreading; FIG. 8)


N-TCC CTA CGC CGC CTT CTC-C terminus


(SEQ ID NO: 25)






In another preferred embodiment the PNAs (e.g. PNA VI above) are directed against the viral RNA, the molecular target representing the Gag-splice acceptor site.
Finally, the present invention also relates to a medicament containing a conjugate according to the invention, optionally together with a suitable carrier, and to the use thereof for an HIV therapy. In this connection, in particular the parenteral or intravenous application has proved suited.



The invention is further described by means of the figures wherein:
FIG. 1 shows the genomic organization of HIV-1
FIG. 2 shows sequences of the HIV-1LTR region
FIG. 3 shows a plasmid map of pEGFP-C3
FIG. 4 shows viral sites of attack of the pseudo-isocytosine-containing PNAs
FIG. 5 shows CLSM pictures (non-activated control in HeLa)
FIG. 6 shows CLSM pictures (after activation in HeLa)
FIG. 7 shows PNA targets
FIG. 8 shows studies of BDV (Borna disease virus; retrovirus) instead of HIV to prove that other retroviruses can also be inhibited by PNA constructs
FIG. 9 shows the efficiency of PNA in the early phase of viral infection The biological effect was measured by transactivation of a reporter gene construct (LacZ)
FIG. 10 shows the results of the reporter gene assay after treatment with different PNAs. Significant results were observed with PNAs against cPPT (polypurine tract)
FIG. 11 shows the use of PNAs in the early and late phases of viral infection; testing by ELISA against p24 virus protein. Different PNAs against cPPT/flap/Nef/gag/random were capable of drastically reducing the viral p24
FIG. 12 shows the reporter gene assay with anti-FLAP PNA combined with other PNAs. The combination of PNA[IVb]+PNA[IIINLS]+PNA[Vb] (500 nM concentration) resulted in an optimum β-Gal reduction.
FIG. 13 shows that chronically HIV-infected cells were studied by viral p24 ELISA following PNA treatment (72 and 144 h after the PNA application). The best effect was obtained with cPPT (polypurine tract) by PNA[IINLS].



The invention is further described by means of the below examples.
EXAMPLE 1
The HIV-1 “long terminal repeat” (LTR) codes for the transcription promoter. Sequence analyses prove the existence of a single LTR enhancer promoter configuration for all of the presently studied HIV-1 subtypes. Transcription studies using EGF reporter constructs show its functionality.
LTR-EGF construct:
Based on biocomputing data, the sequence AC S72615, which relates to the HIV subtype HIV4B6 was selected representatively using the HUSAR program of DKFZ, the SRS (sequence Retrieval System) and the multiple alignment algorithm (MALIGN) (Shiramizu et al., Cancer Res. 65, pp. 2069-2072 (1994)).










HIV4B6-LTR:





CCAATAAAGG
AGAAAACAAC
TGCTTGTTAC


 


ACCC(−18)TATAAG
CCAGCATAAA
GC(+1)ATG GA


(SEQ ID NO: 26)






The Ase I (8/−52)-Nhe I (64/+1)-LTR fragment was synthesized according to the known phosphoramidite method and cloned into a pEGFP-C3/Variant (without PCMV) (FIG. 3) (Clontech company, Heidelberg).
Cloned Fragment:

























Then, the plasmid DNA was replicated in E. coli in LB-Amp culture medium under ampicillin selection pressure. The isolation and preparation of the plasmid DNA were carried out with the Mini-Prep-DNA kit (Clontech company) according to the manufacturer's instructions.
Cell culture and transfection assay:
The human cervical carcinoma suspension cell line HeLa-S (tumor bank DKFZ) was used. The cells were cultured in MEM“Joklik” (Minimal Essential Medium; Sigma company) with 10% FCS (Sigma company), glutamine (Gibco company) in a CO2 atmosphere at 37° C.
The following shuttle construct was produced:

























This construct was transfected into the HeLa cells according to the Britten and Kohne protocol (Science, Vol. 161, No. 3841, pp. 529-540, 1986). HeLa-S is transfected by direct addition of the shuttle construct to the culture medium at a concentration of 100 pM at 37° C. for 3 hours under incubation in 5% CO2 atmosphere. Then, the hybridization was carried out with the LTR-EGF construct analogously to the above mentioned Britten and Kohne protocol. The following complex forms:

























The HeLa-S cells are cultured in 8-chamber glass plates in Petri dishes under 5% CO2 at 370 for 48 hours.
In order to activate the plasmid, it is necessary to separate the shuttle system from the plasmid DNA. For this purpose, the plates are heated to 45° C. in a water bath for 1 minute. Having changed the medium, the HeLa-S cells are further cultured. The transcription determination of GFP under LTR control is effected by means of fluorescence reader analysis after 48, 72 and 96 hours (excitation: 488 nm; emission: 520 nm). GFP is localized by means of confocal laser scanning microscopy (CLSM) analogously but in 8-chamber glass plates in Petri dishes under 5% CO2 at 37° C. for 48, 72 and 96 hours (excitation: 488 nm; emission: 520 nm). The results are shown in FIGS. 5 and 6.
EXAMPLE 2
Here, a method is described which permits to determine a PNA effect in an early infection phase of HIV-1. Reference is made to FIGS. 9-11.
HeLa cells which were transfected with a stably expressed LacZ reporter gene were used as a model. The test was carried out in a 96-well plate. HeLa cells are suspended in RPMI medium and plated out. The cell number was 20000 cells per well. The pipetting volume is 100 μl/well. 18 different PNA sequences (see FIG. 10) plus one control were tested (X=further viral control (e.g. BDV)). The PNA construct concentrations were 10 pM, 100 pM and 1 nM. The PNA constructs were produced in analogy with Example 1. After one hour, the viral infection was effected. The viral effect on the LTR promoter was determined via LacZ activity by means of a photometer.

## Claims

1. A conjugate for mediating a cell nucleus-specific transport of a peptide nucleic acid (PNA) which hybridizes to DNA of HIV and inhibits the transcription of the DNA of a transcribable HIV gene or a HIV gene involved in the regulation of gene expression or a part thereof, wherein the conjugate comprises the following components:
a) a transport peptide or protein which can pass through the plasma cell membrane,
b) an address protein or peptide for the import into the cell nucleus which contains a nucleus-recognition signal, and
c) a peptide nucleic acid (PNA) comprising a sequence selected from SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, TTATTTCCTCTTTTGTTG (SEQ ID NO: 4), ATTAC*TAC*GTC*TC*TC*C*GTT (SEQ ID NO: 5), TATC *GGTTTTTAAC*GTC*C*C* (SEQ ID NO: 6), and, TC*C*TTTTC*C*C*C*GAC*AAC*C*TTTAC* (SEQ ID NO: 7), wherein C* is pseudoisocytosine, wherein the PNA is to be transported and hybridizes to DNA of HIV and inhibits the transcription thereof, wherein said DNA is selected from the group consisting of polypurine tract, central DNA flap, Nef, NCp7 and LTR region.

2. The conjugate according to claim 1 wherein the transport protein or peptide has the following sequence: NH2-RQIKIWFQNRRMKWKK-(SEQ ID NO: 1) and wherein the address protein or peptide is selected from:










Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val; and




(SEQ ID NO: 2)



 



H3N+-Pro-Lys-Lys-Lys-Arg-Lys-Val,



(SEQ ID NO: 3)






wherein SEQ ID NO: 3 is the nuclear localization sequence from SV40-T antigen.

3. The conjugate according to claim 1, wherein the conjugate has the following structure:
transport peptide or protein-address protein-peptide nucleic acid (PNA).

4. The conjugate according to claim 1, wherein the peptide nucleic acid is protease-resistant and nuclease-resistant.

5. The conjugate according to claim 1, wherein the peptide nucleic acid has a sugar phosphate backbone substituted by ethyl-amine-linked α-amino-ethyl-glycine units.

6. The conjugate according to claim 1, wherein a redox-cleavage site is between the transport protein/peptide and the address peptide.

7. The conjugate according to claim 1, wherein the PNA has a length of at least 18 bases.