Combination comprising immunostimulatory oligonucleotides
11578331 · 2023-02-14
Assignee
Inventors
- Matthias Schroff (Berlin, DE)
- Manuel Schmidt (Berlin, DE)
- Kerstin Kapp (Berlin, DE)
- Alfredo Zurlo (Berlin, DE)
Cpc classification
A61K31/7088
HUMAN NECESSITIES
C12N2310/344
CHEMISTRY; METALLURGY
A61K39/3955
HUMAN NECESSITIES
C12N15/117
CHEMISTRY; METALLURGY
C12N15/111
CHEMISTRY; METALLURGY
A61K39/3955
HUMAN NECESSITIES
A61K2300/00
HUMAN NECESSITIES
A61K2300/00
HUMAN NECESSITIES
International classification
C12N15/117
CHEMISTRY; METALLURGY
C07K16/28
CHEMISTRY; METALLURGY
C12N15/11
CHEMISTRY; METALLURGY
A61K39/395
HUMAN NECESSITIES
A61K39/00
HUMAN NECESSITIES
A61K31/7088
HUMAN NECESSITIES
Abstract
The invention relates to a combination and its use for the treatment of diseases. The instant disclosure provides a combination of a so-called T-cell regulator selected from the group comprising PD1, PD-L1, OX40, TIM-3, LAG3, CD137(4-1BB) and a non-coding immunomodulating DNA.
Claims
1. A linear open-chained non-coding sequence of deoxyribonucleic acids selected from SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID NO: 9.
2. The linear open-chained non-coding sequence of claim 1, consisting of SEQ ID NO: 7.
3. The linear open-chained non-coding sequence of claim 1, consisting of SEQ ID NO: 8.
4. The linear open-chained non-coding sequence of claim 1, consisting of SEQ ID NO: 9.
Description
BRIEF DESCRIPTION OF THE FIGURES
(1) The invention will be described on the basis of figures. It will be understood that the embodiments and aspects of the invention described in the figures are only examples and do not limit the protective scope of the claims in any way. The invention is defined by the claims and their equivalents. It will be understood by the skilled artisan that features of one aspect or embodiment of the invention can be combined with a feature of a different aspect or aspects of other embodiments of the invention. It shows:
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DETAILED DESCRIPTION OF THE INVENTION
(15) The instant invention provides a combination of a molecule binding to a so called T-cell regulator and a non coding sequence of deoxyribonucleic acids.
(16) Within the meaning of the present disclosure a linear open-chained DNA sequence is designated as oligonucleotide, abbreviated with ODN. Said DNA sequence can be single-stranded or partially or completely double-stranded. The terms oligo, oligonucleotide and oligodeoxynucleotide are used synonymously and do not indicate a limitation of the length of the corresponding DNA sequence. The single components of oligonucleotides are nucleotides.
(17) An oligo can be manufactured synthetically or be partially or completely of biological origin, wherein a biological origin includes genetically based methods of manufacture of DNA sequences.
(18) L-DNA or nucleotides in L-conformation refer to nucleotides, which comprises L-deoxyribose as the sugar residue instead of the naturally occurring D-deoxyribose. L-deoxyribose is the enantiomer (mirror-image) of D-deoxyribose. Oligonucleotides partially or completely consisting of nucleotides in L-conformation can be partially or completely single- or double-stranded; however, nucleotides in L-conformation cannot hybridize to nucleotides in D-conformation (Hauser et al., Nucleic Acid Res. 2006 34: 5101-11). L-DNA is equally soluble and selective as D-DNA. Yet, L-DNA is resistant towards enzymatic exoactivity of naturally occurring enzymes, especially exonucleases, so L-DNA is protected against intracellular degradation (Urata et al., Nucleic Acids Res. 1992 20: 3325-32). Therefore, L-DNA is very widely applicable.
(19) A “stem” according to the present disclosure shall be understood as a DNA double strand formed by base pairing either within the same oligonucleotide (which is then partially self-complementary) or within different oligonucleotides (which are partially or completely complementary). Intramolecular base-pairing designates base-pairing within the same oligonucleotide and base-pairing between different oligonucleotides is termed as intermolecular base-pairing.
(20) A “loop” within the meaning of the present disclosure shall be understood as an unpaired, single-stranded region either within or at the end of a stem structure. A “hairpin” is a distinct combination of a stem and a loop, which occurs when two self-complementary regions of the same oligonucleotide hybridize to form a stem with an unpaired loop at one end.
(21) A “solid phase” to which the nucleotides are covalently or non-covalently attached refers to, but is not restricted to, a column, a matrix, beads, glass including modified or functionalized glass, silica or silica-based materials including silicon and modified silicon, plastics (comprising polypropylene, polyethylene, polystyrene and copolymers of styrene and other materials, acrylics, polybutylene, polyurethanes etc.), nylon or nitrocellulose, resins, polysaccharides, carbon as well as inorganic glasses and plastics. Thus, microtiter plates are also within the scope of a solid phase according to the present disclosure.
(22) Immunomodulation according to the present disclosure refers to immunostimulation and immunosuppression. Immunostimulation means preferentially that effector cells of the immune system are stimulated in order to proliferate, migrate, differentiate or become active in any other form. B cell proliferation for instance can be induced without co-stimulatory signals by immunostimulatory oligonucleotides, which normally require a co-stimulatory signal from helper thymocytes.
(23) Immunosuppression on the other hand shall be understood as reducing the activation or efficacy of the immune system. Immunosuppression is generally deliberately induced to prevent for instance the rejection of a transplanted organ, to treat graft-versus-host disease after a bone marrow transplant, or for the treatment of autoimmune diseases such as, for example, rheumatoid arthritis or Crohn's disease.
(24) In this context, immunomodulation may also refer to the influence of the nature or the character of an immune reaction, either by affecting or modifying an immune reaction, which is still developing or maturing or by modulating the character of an established immune reaction. Thus, affecting means in the context of checkpoint inhibitors to suppress their inhibitory effect, and in the context of co-stimulatory molecules to activate them.
(25) The term “cancer” comprises cancerous diseases or a tumor being treated or prevented that is selected from the group comprising mammary carcinomas, melanoma, skin neoplasms, gastrointestinal tumors, including colon carcinomas, stomach carcinomas, pancreas carcinomas, colon cancer, small intestine cancer, ovarial carcinomas, cervical carcinomas, lung cancer, prostate cancer, kidney cell carcinomas and/or liver metastases.
(26) Autoimmune diseases according to the present disclosure comprise rheumatoid arthritis, Crohn's disease, systemic lupus (SLE), autoimmune thyroiditis, Hashimoto's thyroiditis, multiple sclerosis, Graves' disease, myasthenia gravis, celiac disease and Addison's disease.
(27) An agonist within the meaning of the instant disclosure and in accordance with its common definition represents a chemical or molecule that binds to another molecule, like a receptor or ligand and thus activates the molecule. In contrast to an agonist that activates, an antagonist shall be understood as a chemical or molecule that blocks the interaction of the molecule to which the antagonist binds with a respective agonist. Depending on the context, an antagonist in the understanding of the instant invention may also result in the activation of a process, because the antagonist blocks the interaction of another antagonist with a receptor for instance.
(28) The term “pharmaceutically applicable or acceptable salts” as used herein includes salts of a compound of the combination, which are prepared with relatively nontoxic (i.e. pharmaceutically acceptable) acids or bases, depending on the particular substituents found on the compounds of the present invention. If, for example, compounds of the present invention contain acidic functionalities, base addition salts may be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent. Non-limiting examples of pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt. If compounds of the present invention contain basic functionalities, acid addition salts may be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent. Non-limiting examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, phosphoric, partially neutralized phosphoric acids, sulfuric, partially neutralized sulfuric, hydroiodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic. malonic, benzoic, succinic, suberic, fumaric, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like. Also included are salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunornic acids and the like. Certain specific compounds of the present invention may contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts. Contacting the salt with a base may regenerate the neutral forms of the compounds of the present invention or acid and isolating the parent compound in the conventional manner. The parent form of the compound differs from the various salt forms in certain physical properties, such as solubility in polar solvents, but otherwise the salts are equivalent to the parent form of the compound for the purposes of the present invention. The compounds of the present invention may possess chiral or asymmetric carbon atoms (optical centers) and/or double bonds. The racemates, diastereomers, geometric isomers and individual optical isomers are encompassed by the present invention. The compounds of the present invention may exist in unsolvated forms as well as solvated forms, including hydrated forms. In general, the solvated forms are equivalent to unsolvated forms and are also encompassed by the present invention. The compounds of the present invention may furthermore exist in multiple crystalline or amorphous forms.
(29) Deoxyribonucleic acid molecules, consisting of a partially single-stranded, dumbbell-shaped, covalently closed chain of deoxyribonucleoside residues, which contain one or more sequences of the base sequence N.sup.1N.sup.2C GN.sup.3N.sup.4, wherein N.sup.1N.sup.2 is an element from the GT, GG, GA, AT or AA group, N.sup.3N.sup.4 is an element from the CT or TT group, as well as C deoxycytosine, G deoxyguanosine, A deoxyadenosine and T deoxythymidine, are used in combination with chemicals or molecules able to bind T-cell regulator of the immune system for immunostimulation in humans or higher animals.
(30) The deoxyribonucleic acid molecules relating to the instant disclosure may have a length of up to 200 nucleotides. In particular, sequences with a length between 48 and 116 nucleotide are intended.
(31) The dumbbell-shaped non-coding sequences of deoxyribonucleic acid molecules may comprise the base sequence N.sup.1N.sup.2CGN.sup.3N.sup.4 is their single-stranded regions.
(32) The immunostimulation may take place in vitro or in vivo.
(33) The instant disclosure provides also linear open-chained DNA sequence comprising at least one CpG motif and at least one nucleotide in L-conformation. Due to the partial/complete L-conformation, the DNA sequence has no 5′- or 3′-ends that are accessible to exonucleases. In case that the construct has on one end of a double strand a single stranded-loop, the end is also protected against degradation. Thereby, the ODNs are in total protected against cellular degradation without having the need to use a phosphorothioate backbone, which has been shown to be toxic. In addition, the ODNs only consist of a minimum number of nucleotides, which makes them small and thereby easy to transfect into cells.
(34) The non-coding sequence of ddeoxyribonucleic acids comprising at least one sequence motif N.sup.1N.sup.2CGN.sup.3N.sup.4 can be single-stranded or partially or completely double-stranded. This includes base-pairing within the same molecule (intramolecular) or within different molecules (intermolecular) or any combination thereof. It is also possible that the construct comprises at least one unpaired, single-stranded region. As a further embodiment, hairpin structures are included. Due to the partial or complete L-conformation, a longer half-life of the construct is ensured as nucleotides in L-conformation are not subject to degradation.
(35) It is also within the scope of the instant disclosure that at least two molecules, which are single-stranded or partially or completely double-stranded can ligate to each other to form multimeric constructs. These multimeric constructs thus incorporate at least as many CpG motifs as ligation partners, tightly packed within one molecule, and are therefore expected to elicit also a considerable immune response as part of the combination with T-cell regulators. The resulting single-stranded or partially or completely double-stranded multimeric constructs can either be covalently closed comprising nucleotides in L-conformation within the molecule or open multimeric constructs comprising nucleotides in L-conformation at the 5′- and/or the 3′-end for protection against cellular degradation.
(36) The disclosure further comprises chemical modifications of at least one nucleotide in the non-coding sequence of deoxyribonucleic acids comprising at least one sequence motif N.sup.1N.sup.2CGN.sup.3N.sup.4 with a functional group selected from the group comprising carboxyl, amine, amide, aldimine, ketal, acetal, ester, ether, disulfide, thiol and aldehyde groups. This allows coupling of the DNA construct to a compound selected from the group comprising peptides, proteins, carbohydrates, antibodies, synthetic molecules, polymers, micro projectiles, metal particles or a solid phase by, for example, adsorption, covalent or ionic bonding.
(37) The modification can be specifically selected for the respective purpose. The construct can thus be used, for example, to shuttle other molecules to the specific cell responding to the CpG motif/s incorporated. In addition, it is possible by such modifications to couple the construct to micro projectiles, which can be used to transfer the construct into the cell. The construct can also be coupled to a solid phase, e. g. a microtiter plate.
(38) Experiments described below were performed to investigate the influence of combining non-coding sequences of deoxyribonucleic acids with T-cell regulators. The experiments were conducted using dumbbell-shaped comprising the sequence motif N.sup.1N.sup.2CGN.sup.3N.sup.4, linear open-chained non-coding sequence of deoxyribonucleic acids comprising N.sup.1N.sup.2CGN.sup.3N.sup.4, wherein those constructs comprise nucleotides in L-conformation to prevent them from degradation. In addition, the effect of combining T-cell regulators with a non-coding sequence of deoxyribonucleic acids comprising N.sup.1N.sup.2CGN.sup.3N.sup.4 and twice the sequence of SEQ ID NO:4 were be investigated. T-cell regulators antibodies binding to PD1, PD-L1, OX40, LAG-3, TIM3 and CD137(4-1BB) were used in a mouse model with injected human tumors. The effect on therapy after a growth phase is described in more detail below on growth of tumors in comparison to control groups.
(39) The experiments compare dosage regimen with simultaneous, alternating or successive application of the components of the combination of the instant disclosure. In addition to the qualitative application of the compounds it was investigated whether reduced amounts of T-cell regulator are necessary for achieving comparable or even better results in applying the checkpoint inhibitor without a non-coding DNA sequence comprising a N.sup.1N.sup.2CGN.sup.3N.sup.4 sequence motif.
(40) The in vitro analysis of the combinatory potential of TLR9 agonists with molecules binding to T-cell regulators comprises the use of in vitro cell culture system of human PBMC for evaluation of their T cells responses after stimulation. Stimulation of PBMC will be achieved with a mixture of immunogenic peptides from CMV, EBV, influenza and tetanus-toxin in the presence of antibodies against immunological T-cell regulators (e.g. PD-1, PD-L1, etc.) and TLR9 agonists (i.e. SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:10, SEQ ID NO:6).
(41) The quantification of cytokines (IL-2 and IFN-gamma) in cell culture supernatants was determined. Although this in vitro cell culture system cannot mirror the complex interactions of immune cells in vivo, it provides evidences for an advantage of the combination of those TLR9 agonists.
DETAILED DESCRIPTION OF THE FIGURES
(42) The combination of SEQ ID NO:5 with anti-PD-1 showed a surprisingly vastly increased anti-tumor effect compared to either anti-PD-1 or SEQ ID NO:5 monotherapy in a mouse A20 tumor model.
(43) Tumor growth was surprisingly nearly completely inhibited by the combination of SEQ ID NO:5 and PD-1 (
(44) The synergistic combinatory effect of SEQ ID NO:5 with anti-PD-1 shown in
(45) Furthermore, in a mouse CT26 tumor model, the surprising beneficial effects of the combination therapy of anti-PD-L1 and SEQ ID NO:5 was also clearly superior to the either SEQ ID NO:5 or anti-PD-L1 monotherapy. Tumor growth was reduced (
(46) The combinatorial effect of applying SEQ ID NO:6 having the loop sequence TCATCGTCGTTTTGTCGTTTTGTCGTTCTT was also investigated.
(47) SEQ ID NO:6 was administered together with anti-PD-1 in a mouse CT26 tumor model. This combination surprisingly profoundly augmented the anti-tumor effect compared to the monotherapy with the single agents, SEQ ID NO:6 or anti-PD-1 (
(48) The results shown in
(49) Oligos comprising nucleotides in L-conformation were used in further studies. Those oligos comprise L-nucleotides at indicated positions. DNA molecules were used with the core sequence [yTCATTxCGTGACGTGACGTTCzv] (y=2 to 8 G, protected with 1 to 3 L-deoxyribose or not; x=3 to 4 A; z=2 to 6 T protected with 1 to 3 L-deoxyribose; v=A, G, C, T).
(50) These L-nucleotide comprising molecules showed increased immune modulatory and anti-tumor properties when combined with checkpoint inhibitors. For instance, combination of SEQ ID NO:7 (GGGGTCATT AAAACGTGACGTGACGTTCTTTTT, L-deoxyribose containing bases underlined) with anti-CTLA-4 in a mouse CT26 tumor model resulted in a surprisingly efficient decreased tumor growth compared to SEQ ID NO:7 or anti-CTLA-4 monotherapy (
(51) The combination of SEQ ID NO:7 with anti-PD-L1 also showed a moderately increased anti-tumor effect compared to that of the single compounds SEQ ID NO:7 or anti-PD-L1 in the mouse CT26 tumor model (
(52) In in vitro studies the benefit of the combination of anti-PD-1 with SEQ ID NO:7, SEQ ID NO:8 (GGGGGGGGTCATTAAAACGTGACGTGACGTTCTTTTT, L-deoxyribose containing bases underlined), and SEQ ID NO:9 (GGGGTCATTAAACGTGACGTGA CGTTCTTTTT, L-deoxyribose containing bases underlined) was observed regarding IFN-gamma secretion from PBMC stimulated with antigenic peptides (
(53) In another series of experiments DNA molecules with the core sequence [yTCATTxCGTTCTTCGGGGCGTTCzv] (y=2 to 8 G, protected with 1 to 3 L-deoxyribose or not; x=3 to 4 A; z=2 to 6 T protected with 1 to 3 L-deoxyribose; v=A, G, C, T) were used.
(54) The combinatory effect regarding immunomodulation and anti-tumor effect was established for this group as well. As example for this group, SEQ ID NO:10 (GGGGTCATTAAACGTTCTTCGGGG CGTTCTTTTT, L-deoxyribose containing bases underlined) was used to investigate the combination with anti-PD-1.
(55) The combination resulted in a profound reduction of the tumor growth in a mouse CT26 tumor model (
(56) In addition, a combination of SEQ ID NO:10 with anti-CTLA-4 lead to a decreased tumor growth in mouse CT26 tumor model compared to treatment with the single agents, SEQ ID NO:10 or anti-CTLA-4 (
(57) Furthermore, a combination of SEQ ID NO:10 and anti-PD-1 was evaluated in in vitro PBMC stimulation studies and showed an increased effect regarding IFN-gamma secretion compared to SEQ ID NO:10 or anti-PD-1 alone (
(58) In a further experiment, a DNA molecule with a core sequence [yTCATTxTCGTCGTTTTGTCGTTTTGTCGzv] (y=2 to 8 G, protected with 1 to 3 L-deoxyribose or not; x=3 to 4 A; z=2 to 6 T protected with 1 to 3 L-deoxyribose; v=A, G, C, T) was used in experiments.
(59) SEQ ID NO:11 (GGGGTCATTAAATCGTCGTTTTGTCGTTTTGTCGTTTTT, L-deoxyribose containing bases underlined) was used as example for this group. When SEQ ID NO:11 was combined with anti-PD-1 in vitro in PBMC studies,—IFN-gamma secretion surprisingly significantly increased showing an improvement compared to SEQ ID NO:11 or anti-PD-1 alone (
(60) Finally, a DNA molecules with the core sequence [yACGATCGTCwT] (y=2 to 8 G, protected with 1 to 3 L-deoxyribose or not; w=4 to 12 G protected with 1 to 3 L-deoxyribose) was used for testing effects of combinatorial application.
(61) An example for this group is SEQ ID NO:12 (GGGGGACGATCGTCGGGGGGT, L-deoxyribose containing bases underlined). In in vitro stimulation studies with human PBMC its combination with anti-PD-1 was evaluated leading to a significantly augmented immune response compared to the single compounds (
(62) Taking the above described experimental settings into account and a weight of a mouse of about 20 g, the amounts of DNA to be applied lies in a range of about 12.5 mg/kg weight, so that it seems to be feasible that maximal 15 mg/kg will be necessary for obtaining the shown surprising results.
(63) Anti-PD-1 antibody has been applied with 10 mg/kg weight so that the application of maximal 15 mg/kg weight also seems to be necessary for obtaining the shown surprising results.