The invention discloses polypeptides encoded by an alternative reading frame of a pathogenic virus, which polypeptides--start with a methionine amino acid residue,--comprise an antigenic determinant and--comprise more than 7 amino acid residues and fragments of said polypeptides comprising more than 7 amino acids.

Description of the Invention

This application is a national phase application under 35 U.S.C. .sctn. 317 of International Application No. PCT/EP2003/008112 filed 24 Jul. 2003, which claims priority to Austrian Application No. A 1124/2002 filed 24 Jul. 2002 and European Patent Application No. 03450171.8 filed 11 Jul. 2003.

The Sequence Listing is submitted on one compact disc (Copy 1), together with a duplicate thereof (Copy 2), each created on Jul. 21, 2005, and each containing one 2,190 kb file entitled "SONN060SEQ.txt." The material contained on the compact disc is specifically incorporated herein by reference.

The invention relates to peptides derived from pathogenic viruses.

For several viral infections it has become more and more clear that an early effective and strong CTL response to most encoded viral proteins is critical to overcome or clear a viral infection from the host.

Selection for mutations within CTL epitopes of HIV demonstrates that CTL exert pressure on virus replication in vivo, and studies in macaques have provided compelling in vivo data for the role of CD8+ T cells in controlling viremia in both acute and chronic simian immunodeficiency virus (SIV) infection. HIV-infected individuals who are treated during acute infection show enhancement of both CTL and T helper cell responses against HIV associated with subsequent viral control after treatment interruption.

Therefore the identification of precise epitopes from most (if not all) viral proteins is a major goal in view of understanding the hosts immune response and most important for the design of new and effective vaccines against those pathogens.

As up to now, most research for the identification of those epitopes has focused mainly on those proteins of the viruses which are encoded in the actually transcribed open reading frames (ORF's), i.e. the structural proteins and the proteins which have a certain function for the virus, e.g. for its regulation, replication or reproduction.

Although some research has been performed in investigating in potential alternative reading frames of pathogens, the topic of such alternative reading frames has up to now only been regarded as relevant for tumor antigens, but not for viral pathogens, despite some reports about overlapping reading frames in HCV (see Walewski et al. (RNA 7 (2001) 710-721) and WO99/63941) and other viruses or antigens (Bullock et al. (J. Exp. Med. 186(7) (1997), 1051-1058), Malarkannan et al. (Immunity 10(1999) 681-690) and Shastri et al. (J. Biol. Chem. 270(3) (1995) 1088-1091). All these reported viral polypeptides have starting codons other than AUG or ATG leading to peptides starting with e.g. Ala, Leu, Pro or Gly. Moreover these viral peptides according to the prior art were no T cell epitopes, but--at best--were able to elicit an antibody response.

It is an object of the present invention to provide further means for combating viral infections. It is a further object to provide means for replacing or improving existing or proposed vaccines against viral pathogens, especially human pathogens. A specific aim is to provide effective T cell epitopes against viral pathogens.

Therefore, the present invention provides a polypeptide encoded by an alternative reading frame of a pathogenic virus, characterized in that said polypeptide starts with a methionine amino acid residue, comprises an antigenic determinant and comprises more than 7 amino acid residues and fragments of said polypeptide comprising more than 7 amino acids.

Surprisingly, such epitopes (antigenic determinants) proved to be highly relevant in infections with pathogenic viruses. Indeed, T cell responses against such alternatively encoded epitopes are detectable in patients suffering such infections. It seems that upon infection of a virus into a host cell, not only those ORFs of the viral genome, which give rise to the viral proteins, are transcribed, but also some of those proteins or fragments which are encoded by other frames of the genome.

Such a polypeptide according to the present invention may be defined as an antigenic sequence within an ORF of the genome but outside the primarily (main) transcribed ORF of a given pathogenic virus.

Alternative reading frame as used in the context of the present invention is defined as a reading frame which is different from the open reading frames (=main frames) which encode utilized codons of an organism or virus for the expression of e.g. structural proteins or non structural proteins.

Typically but not exclusively a main frame starts with the first coding start codon, e.g. AUG or GUG of a nucleic acid eg. of a messenger RNA or an RNA from a positive/negative stranded RNA virus. Alternative frames described in this invention do not use these start codons or any other codon used by the main frames, respectively.

The present invention considers 5 such alternative reading frames which by a second name are also called non-coding open reading frames (ncORFs), to be distinctive from the main frames as described above. One such alternative reading frame is the +1 frame, which uses codons that start with the next nucleotide 3' prime of the 5' prime nucleotide of a main frame codon. A second such frame is the +2 frame which uses codons of which the 5' prime nucleotide is identical with a 3' prime nucleotide of a codon of the main coding frame. Alternative reading frames 4, 5 and six are encoded by a nucleic acid which is complementary to a nucleic acid, encoding alternative reading frames 1 and 2 respectively. The 5' prime nucleotide of a frame 4 codon is complementary to a middle nucleotide of a codon of a +1 frame. The 5' prime nucleotide of a frame 5 codon is complementary to the 5' prime nucleotide of a +1 frame codon and the 5' prime nucleotide of a frame 6 codon is complementary to a 3' prime nucleotide of a +2 frame codon.

Furthermore, alternative reading frames might be located in regions of the genome which are not involved in main frame translations, eg. so called non translated 5' prime or 3' prime regions.

Although these "ncOrfs" ("non coding ORFs") do not display a (yet) known function for the pathogen, they encode for antigenic determinants (B- or T-cell epitopes)

In contrast to all enabling reports about alternatively encoded ORFs in HCV (see Walewski et al., WO99/63941) and other viruses or antigens (Bullock et al., Malarkannan et al., Shastri et al.) the polypeptides according to the present invention have all an AUG or ATG (encoding Methionin) as start codon. Moreover the peptides provided with the present invention contain T cell epitopes as antigenic determinants and are not intended to exclusively elicit an antibody response.

The principle provided with the present invention seems to be a general one in viral infections. It is therefore not restricted to certain viruses or certain groups of viruses. Regarding this, preferred polypeptide or fragments according to the present invention are those from major and prominent (human) pathogenic viruses or pathogenic virus for which currently no proper treatment or active immunisation protocol exists, such as Hepatitis A virus (HAV), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Hepatitis D virus (HDV), Hepatitis E virus (HEV), Hepatitis F virus (HFV) Hepatitis G virus (HGV) Human Immunodeficiency viruses (e.g HIV-1 and HIV-2), Influenza virus, Foot and Mouth Disease virus (FMDV), Ebola virus, HTLV I, HTLV II, SIV, Parvovirus, Papilloma virus, Rotavirus, Adenovirus, Cytomegalovirus, Feline Immunodeficiency virus (FIV), Epstein-Barr virus (EBV), Herpes simplex virus (HSV), Herpes zoster virus (HZV), Measles virus and oncogenic viruses.

With the present invention, a completely new generation of immunogenic epitopes are provided which according to a preferred embodiment are characterized in that the polypeptides and fragments according to the present invention comprise at least one cytotoxic T lymphocyte (CTL-) epitope.

Preferably the polypeptide or fragments according to the present invention comprise a cytotoxic T lymphocyte (CTL-) epitope for a HLA allele selected from the group consisting of A0201, A1, A24, A3, A31, B3501, B4403, B7, B8, especially A0201, or mixtures thereof.

According to a preferred embodiment, the polypeptide or fragments according to the present invention comprise at least one T helper cell epitope.

Preferably, the polypeptide or fragments according to the present invention comprise a T helper cell epitope for a HLA allele selected from the group consisting of DP, DQ, DR or mixtures thereof.

Preferred epitopes according to the present invention are selected from the group listed in table 2a)-n) (Seq.ID No.1-822 (see Original Patent)) or a fragment of said polypeptide comprising more than 7 amino acids and/or epitopes comprising or consisting of a fragment selected from the group listed in table 4a)-n (see Original Patent)), preferable fragments with a score of 50 or more, more preferred with a score of more than 200, especially fragments with a score of more than 500 (according to the scores given in the table which were determined according to the algorithm reported by Parker et al. (J. Immunol. 152 (1994) 163)).

Further preferred epitopes according to the present invention are the polypeptides selected from the group listed in table 6 (see Original Patent) and comprising more than 7 amino acid residues (Seq.ID No.823-874) or a fragment of said polypeptide comprising more than 7 amino acid residues.

The polypeptides or fragments according to the present invention may be conjugated to a carrier, especially to an immunomodulating substance. For certain applications, such conjugations result in an improved action of these peptides. It may also be preferred to couple selected hydrophobic (F, I, L, A, Y, W, C) or acidic amino (D or E) acid residues N- and/or C-terminally to the peptides as described in WO 01/78767.

Preferred polypeptides or fragments therefore comprise a tail consisting of two to seven amino acids, said amino acids being selected from F, I, L, A, Y, W or C, at least one of its N- or C-terminus; or a tail consisting of two to seven amino acids, said amino acids being selected from E or D, at least one of its N- or C-terminus.

In specifically preferred conjugates, the polypeptides or fragments according to the present invention are conjugated to an immunomodulating substance selected from the group comprising polycationic substances, especially polycationic polypeptides, and immunomodulating nucleic acids, especially deoxyinosine- and/or deoxyuridine containing oligodeoxynucleotides.

Preferably the polycationic substance is a polymer, preferably a polycationic peptide, especially polyarginine, polylysine or an antimicrobial peptide.

The polycationic compound(s) to be used according to the present invention may be any polycationic compound which shows the characteristic effect according to the WO 97/30721. Preferred polycationic compounds are selected from basic polypeptides, organic polycations, basic polyaminoacids or mixtures thereof. These polyaminoacids should have a chain length of at least 4 amino acid residues. Especially preferred are substances containing peptidic bonds, like polylysine, polyarginine and polypeptides containing more than 20%, especially more than 50% of basic amino acids in a range of more than 8, especially more than 20, amino acid residues or mixtures thereof. Other preferred polycations and their pharmaceutical compositions are described in WO 97/30721 (e.g. polyethyleneimine) and WO 99/38528. Preferably these polypeptides contain between 20 and 500 amino acid residues, especially between 30 and 200 residues.

These polycationic compounds may be produced chemically or recombinantly or may be derived from natural sources.

Cationic (poly)peptides may also be polycationic anti-bacterial microbial peptides. These (poly)peptides may be of prokaryotic or animal or plant origin or may be produced chemically or recombinantly. Peptides may also belong to the class of defensines. Such host defense peptides or defensines are also a preferred form of the polycationic polymer according to the present invention. Generally, a compound allowing as an end product activation (or down-regulation) of the adaptive immune system, preferably mediated by APCs (including dendritic cells) is used as polycationic polymer.

Especially preferred for use as polycationic substance in the present invention are cathelicidin derived antimicrobial peptides or derivatives thereof (WO 02/13857, incorporated herein by reference), especially antimicrobial peptides derived from mammal cathelicidin, preferably from human, bovine or mouse, or neuroactive compounds, such as (human) growth hormone (as described e.g. in WO01/24822).

Polycationic compounds derived from natural sources include HIV-REV or HIV-TAT (derived cationic peptides, antennapedia peptides, chitosan or other derivatives of chitin) or other peptides derived from these peptides or proteins by biochemical or recombinant production. Other preferred polycationic compounds are cathelin or related or derived substances from cathelin, especially mouse, bovine or especially human cathelins and/or cathelicidins. Related or derived cathelin substances contain the whole or parts of the cathelin sequence with at least 15-20 amino acid residues. Derivations may include the substitution or modification of the natural amino acids by amino acids which are not among the 20 standard amino acids. Moreover, further cationic residues may be introduced into such cathelin molecules. These cathelin molecules are preferred to be combined with the antigen/vaccine composition according to the present invention. However, these cathelin molecules surprisingly have turned out to be also effective as an adjuvant for a antigen without the addition of further adjuvants. It is therefore possible to use such cathelin molecules as efficient adjuvants in vaccine formulations with or without further immunactivating substances.

Another preferred polycationic substance to be used according to the present invention is a synthetic peptide containing at least 2 KLK-motifs separated by a linker of 3 to 7 hydrophobic amino acids, especially L (WO 02/32451, incorporated herein by reference).

The immunomodulating nucleic acids to be used according to the present invention can be of synthetic, prokaryotic and eukaryotic origin. In the case of eukaryotic origin, DNA should be derived from, based on the phylogenetic tree, less developed species (e.g. insects, but also others). In a preferred embodiment of the invention the immunogenic oligodeoxynucleotide (ODN) is a synthetically produced DNA-molecule or mixtures of such molecules. Derivates or modifications of ODNs such as thiophosphate substituted analogues (thiophosphate residues substitute for phosphate) as for example described in US patents U.S. Pat. Nos. 5,723,335 and 5,663,153, and other derivatives and modifications, which preferably stabilize the immunostimulatory composition(s) but do not change their immunological properties, are also included. A preferred sequence motif is a six base DNA motif containing an (unmethylated) CpG dinucleotide flanked by two 5' purines and two 3' pyrimidines (5'-Pur-Pur-C-G-Pyr-Pyr-3'). The CpG motifs contained in the ODNs according to the present invention are more common in microbial than higher vertebrate DNA and display differences in the pattern of methylation. Surprisingly, sequences stimulating mouse APCs are not very efficient for human cells. Preferred palindromic or non-palindromic ODNs to be used according to the present invention are disclosed e.g. in Austrian Patent applications A 1973/2000, A 805/2001, EP 0 468 520 A2, WO 96/02555, WO 98/16247, WO 98/18810, WO 98/37919, WO 98/40100, WO 98/52581, WO 98/52962, WO 99/51259 and WO 99/56755 all incorporated herein by reference. Apart from stimulating the immune system certain ODNs are neutralizing some immune responses. These sequences are also included in the current invention, for example for applications for the treatment of autoimmune diseases. ODNs/DNAs may be produced chemically or recombinantly or may be derived from natural sources. Preferred natural sources are insects.

Alternatively, also nucleic acids based on hypoxanthine and cytosine (as e.g. described in the WO 01/93905) or deoxynucleic acids containing deoxyinosine and/or deoxyuridine residues (described in the PCT/EP02/05448, incorporated herein by reference) may preferably be used as immunostimulatory nucleic acids for the present invention.

Of course, also mixtures of different immunogenic nucleic acids may be used according to the present invention.

The above mentioned substances may be used as conjugates with the present peptides or fragments or as mixtures. The mixtures may either be provided in a form already mixed or as a kit of single components intended to be mixed before application.

The preferred polypeptides or fragments according to the present invention comprise a T cell epitope.

Surprisingly, with the present invention not only polypeptides or fragments having a shifted reading frame (i.e. reading frame 2 and 3) are provided as clinically relevant peptides, but also such peptides and fragments being encoded by an alternative reading frame which reads on the complementary strand as the functional reading frame of said pathogenic virus, i.e. generally referred to as reading frame 4 to 6 in the present specification. This means that also such reading frames proved to be of importance which are located at the opposite end of the known (functional or structural) gene or e.g. its regulating elements.

Therefore, one further aspect of the present invention consists in all antigens being encoded by alternative reading frames of pathological viruses which read on the complementary strand as the functional reading frame of said pathogenic virus, i.e. generally referred to as reading frame 4 to 6.

Preferred polypeptides or fragments according to the present invention comprise at least one peptide selected from the group of peptides listed in table 4a, 4c, 4e, 4g, 4i, 4k and 4m (see Original Patent) having a score of 50 or more, more preferred with a score of more than 200, especially with a score of more than 500.

According to a preferred aspect of the present invention the present polypeptides or fragments are used as a therapeutic agent. It is known that especially T cell epitopes may be used as vaccines for prophylactic uses. However, with the peptides and fragments according to the present invention, especially with the HCV derived peptides i.a. in reading frames 2 and 3, also a therapeutic tool for combatting (chronic) infections with such pathogenic viruses, such as HCV, is provided.

The peptides and fragments according to the present invention also include modified epitopes wherein preferably one or two of the amino acids of a given epitope are modified or replaced according to the rules disclosed in e.g. Tourdot et al. (Eur. J. Immunol. 30 (2000), 3411-3421), as well as the nucleic acid sequences encoding such modified epitopes.

According to a preferred aspect, the present invention also relates to a pharmaceutical composition comprising one or more polypeptides or fragments according to the present invention. This pharmaceutical composition may be used for both, prophylactic as well as therapeutic purposes.

As stated above, the present pharmaceutical compositions preferably further comprise an immunomodulating substance, preferably selected from the group comprising polycationic substances, especially polycationic polypeptides, and immunomodulating nucleic acids, especially deoxyinosine- and/or deoxyuridine containing oligodeoxynucleotides.

In the present pharmaceutical compositions, the peptides or fragments according to the present invention may be used alone or in combination with "normal" polypeptides (epitopes, antigenic determinants) of a given pathogenic virus (or combinations of antigens of different pathogens). A preferred embodiment therefore further comprises structural or functional polypeptides of a pathogenic virus or fragments thereof, especially structural or functional polypeptides or fragments thereof comprising an antigenic determinant.

The administration of the pharmaceutical compositions according to the present invention may be performed according to the administration of other known polypeptide vaccines. Preferably, the composition contains per administrable dose 1 ng to 1 g, preferably 100 ng to 10 mg, especially 10 .mu.g to 1 mg, of one or more polypeptides or fragments according to the present invention.

Preferably, the pharmaceutical composition is formulated as a vaccine.

It is preferred that the pharmaceutical composition according to the present invention comprises further active ingredients, especially immunopotentiating cytokines, anti-inflammatory substances, antimicrobial substances or combinations thereof.

It is further preferred that the present pharmaceutical composition further comprises a polycationic polymer selected from the group consisting of a polycationic peptide, especially polyarginine, polylysine or an antimicrobial peptide, especially a cathelicidin-derived antimicrobial peptide, or a growth hormone, especially a human growth hormone.

Additionally, auxiliary substances, especially a pharmaceutically acceptable carrier, buffer substances, stabilizers or combinations thereof are provided with the pharmaceutical composition.

According to another aspect, the present invention also relates to the use of a polypeptide or fragments according to the present invention for the manufacture of a medicament for treating or preventing an infection with said pathogenic virus.

It was not foreseeable within the prior art that upon infection of a virus into a host cell, not only those ORF's of the viral genome, which give rise to the viral proteins, are transcribed, but also some of those proteins or fragments which are encoded by other frames of the genome. This was even more surprising for reading frames 4 to 6.
 

Claim 1 of 41 Claims

1. An isolated polypeptide encoded by an alternative reading frame of an influenza virus, wherein said polypeptide comprises the sequence VTILNLALL (SEQ ID NO: 1042) and starts with a methionine amino acid residue, or a fragment of said polypeptide comprising the sequence VTILNLALL (SEQ ID NO: 1042).

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