DAGRS: Directed Antigonists to Cancer Cell Growth Signals

Abstract

The present invention describes a unique method of treating cancer with the administration of an improved DAGRS construct which functions as a humanized agent specifically targeting cancer cells in vivo. A specific DAGRS is described constructed of a humanized drug delivery biologic, carboxyl to an Apoptin fragment consisting of Apoptin's proline-rich SH3-binding fragment, a spacer, and a MAP kinase (MAPK) phosphorylation site, in replacement of the SH3-binding domain at HIV-1 TAT's amino terminus. Apoptin is a viral protein with incumbent immunogenicity and toxicity in humans. Improved DAGRS constructs are described that replace the viral VP3 peptide with human AKT peptide or derivative, all equivalently spaced 11 amino acids from the initial proline to the beginning of the MAPK phosphorylation site, through which technology the DAGRS is fully humanized. DAGRS provide for improved bioavailability, enhanced specific activity, and low toxicity for in vivo treatment of cancer. DAGRS are a superior method for targeting any oncogene with an inhibitory peptide.

An algorithm for humanization is described through which human functional equivalent(s) to viral product(s) are identified by alignment of peptides anchored at each end by matching functional motifs that are spaced equivalently distant in the two aligned peptides. The algorithm totally disregards the primary amino acid composition of the spacer, and as such separates from current computer algorithms that prioritize primary amino acid alignments. Accounting for spacing dictates that functional domains be oriented correctly in three dimensions. The invention taught here can be developed into computer algorithms for rapidly identifying these anchored alignments, and thereafter developing safe humanized drugs from disruptive viral activities. Computers once taught the basic rules for anchoring equivalents, can improve on the basic algorithm through artificial intelligence to expand drug development.

Claims

1. A method for treating cancer in a patient comprising administering a therapeutically effective amount of a DAGRS construct having at its amino cassette a signal transducing peptide (STP) able to inhibit activity of a specific oncogene, followed by a C-rich spacer, and further followed by a sequence enabling nuclear protein interactions and membrane translocations wherein the said administration causes a cessation of growth or regression of said cancer in said patient.

2. The DAGRS of claim 1 with its amino cassette comprising any peptide inhibiting the AKT or E2F oncogenes.

3. The AKT peptide of claim 2 (SEQ ID 8) derivatized for enhanced affinity to the Src oncogene.

4. The peptide of claim 1 inserted into a DAGRS cassette functioning to inhibit any oncogene.

5. The DAGRS construct of claim 1 consisting of an inhibitory peptide for AKT, E2F, CRK, or any oncogene, followed by a cysteine-rich spacer, followed by a nuclear translocation/interaction peptide.

6. The DAGRS of claim 1 with a 6 Cysteine spacer.

7. The DAGRS of claim 1 with a 6 Cysteine spacer derived from the defensin or wnt family of proteins.

8. The DAGRS of claim 1 with a spacer approximating 15 amino acids of any amino acid composition.

9. The DAGRS of claim 1 where the sequence enabling nuclear interactions and membrane translocations is the TAR/MTS sequences (aa 38-57, SEQ ID 1) of HIV or SIV.

10. The DAGRS of claim 1 where the sequence enabling nuclear interactions and membrane translocations is the sequence (aa 271-291, SEQ ID 3) of Atx-3.

11. The DAGRS of claim 1 with a penetrin sequence (SEQ ID 2) at its carboxyl terminus.

12. A method for removing toxicity from viral products (humanizing) by identifying human peptides with equivalent functional activity using an algorithm.

13. The algorithm of claim 12 that matches up functionally equivalent peptides between viral and human amino acid sequences.

14. The algorithm of claim 13 that matches functionally equivalent peptides by anchoring the alignment with identical motifs at its amino and carboxyl ends, and identifying identical spacing of the motifs, without regard to the primary sequence of the amino acids intervening between the two anchors.

15. The algorithm of claim 14 wherein Apoptin and AKT are aligned by an amino anchor of an SH3-binding motif compatible with Src oncogene interaction, and a carboxyl anchor of a MAP kinase phosphorylation site.

16. The algorithm of claim 14 further having a computer program to humanize viral activities.

17. The use of artificial intelligence to enhance the algorithm of claim 14.

18. The algorithm of claim 14 used to discover oncogene-inhibitory peptides, oncolytic drugs or oncoimmunologic drugs.

19. The use of the algorithm of claim 14 to develop drugs from humanized viral sequences for treating Alzheimer's disease, cardiac arrhythmias, fever, rheumatoid arthritis or other autoimmune diseases.

20. The use of the algorithm of claim 14 to develop drugs for treating human diseases.

21. The use of the algorithm of claim 14 used to develop compounds that alter the normal course of aging.

Description

DESCRIPTION OF THE FIGURES

[0011] FIG. 1: Schematic of DAGRS constructs. Illustrated are the 3 genetic components (tiles) of a DAGRS construct: 1) an NH.sub.2 terminal cassette encoding a signal transducing peptide (STP) designed to competitively inhibit an oncogene, a C-Rich spacer preferentially encoding 6 cysteine residues, that facilitates proper folding of the DAGRS, and a RK-rich membrane translocation sequence (MTS), SEQ ID 2) at the COOH terminus that is preceded by sequences interacting with cyclin (TAR, SEQ ID1, underlined) or other proteins that translocate from the cytoplasm to the nucleus. The entire third cassette could also be replaced by fully human sequences, such as amino acids 277 to 291 from Atx-3 that mediates interaction with human VCP with nuclear translocation of the complex. (Boeddrich et al. EMBO J 25, 1547, 2006.) Although modelled after the molecular design of Tat, either 0 or 1 of three DAGRS domains contain Tat sequences, permitting the approximation that DAGRS hold an overall homology to HIV Tat between 0-33%.

[0012] FIG. 2: Schematic showing the amino acid alignment of NH.sub.2 terminal sequences of SIV Tats with homology to transcription factors.

[0013] PRALINE program was used to generate the alignments.

[0014] FIG. 3: Schematic showing the amino acid alignment of NH.sub.2 terminal sequences of HIV and CPZ Tat containing a P-rich string with homology to SH3-binding domains.

[0015] FIG. 4: Monomer Tat transcriptional activation of the HIV ltr. A. Graph of induced luciferase activity. HeLa cells were transfected with an LTR luciferase reporter construct. 24 hours after transfection at a time when cells were approximately 75% confluent, cells were scrape-loaded with 2 g protein in the presence of 100 M chloroquine as described by Frankel (Frankel AD1, Pabo CO. Cell. 1988 Dec. 23; 55(6):1189-93.) After an additional 24 hours luciferase activity was measured and is recorded as relative activity compared to sham-transfected HeLa cells. The average of three independent experiments is shown. B. Western blot of recombinant Tat proteins synthesized in E. coli probed with polyclonal antibodies from mice receiving Tat immunotherapy, Monomeric Tat was isolated directly from cracked cells ((Lane 1), or Tat proteins were sequentially re-annealed to trimer (Lanes 2,3) by incubation with polyclonal antibody to aa 57-72 peptide (HIV1 SF2). Molecular weight in kilodaltons (MrKd). Trimeric Tat runs as an apparent 48 kd substrate and monomer as 16 kd; wherever monomer is present at high concentrations, cysteine-linked dimers are also observed (Lane 1).

[0016] FIG. 5: Bioavailability of Tat after membrane translocation. Peripheral blood mononuclear cells (PBMCs, 10.sup.6 cells/ml) were activated with phytohemagglutinin (PHA, 10 g/ml) for 48 hours. PBMCs were washed, re-suspended at 10.sup.7 cells/ml, and scrape-loaded with Tat genetically linked to Green Fluorescent Protein (Tat-GFP, 10 M). PBMCs were diluted back to 10.sup.6 cells/ml and cultured overnight (15 hours) in RPMI-10% FCS at which time they were harvested and assayed for green fluorescence.

[0017] FIG. 6: Compositions of Matter encoding oncogene-antagonizing peptides.

TABLE-US-00001 SEQID6 PKPPSKKRSCDPSEYR

[0018] DAGRS peptide derived from chicken anemia virus VP3

TABLE-US-00002 SEQID7 PPFKPQVTSETRYF

[0019] DAGRS peptide derived from the SH3-binding region of human AKT

TABLE-US-00003 SEQID8 PPKPPQVTSETDTRYF

[0020] DAGRS peptide derived from AKT modified to be right-handed as VP3 and to contain a canonical PPxPP Src SH3-binding site. (Kay, Williamson, and Sudol, FASEB J 14, 231, 2000).

TABLE-US-00004 SEQID9 HHHRLSH

[0021] DAGRS encoding the E2F promoter binding peptide as described by Bertino.

[0022] FIG. 7: Algorithm for Humanizing a viral peptide. in silico identification of the apoptotic determinant in CAV VP3 as a peptide homologous to the SH3-binding domain of AKT. The alignment is anchored by a P-rich SH3-binding region (Orange box) at its amino end, and anchored at its carboxyl end by an S/TxY (blue and green boxes) MAP kinase phosphorylation motif.

DETAILED DESCRIPTION OF THE INVENTION

[0023] DAGRS are targeted drugs aimed to control tumor growth, and prevent or resolve metastases, while avoiding many of the side effects associated with standard chemotherapy.

[0024] The present invention provides for improved oncogene-directed biologics which in its simplest realization locks a signal transducing peptide into an NH.sub.2 terminal cassette in a biologically active configuration protected from degradation, and links this sequence to a carboxyl KR-rich membrane translocation sequence (MTS, SEQ ID2). The construct is designed to facilitate bioavailability and stability of the oncogene-inhibitory peptide. The Tat-encoded membrane translocation sequence (SEQ ID2, penetrin) has been screened for safety in clinical trial (Voskens et al. Head Neck 34, 1734, 2012). Additionally, Tat contains sequences critical for its entering the nuclear transcriptome (TAR) and to its binding cyclin (SEQ ID1, underlined) that are a preferred realization of this invention (SEQ ID 1), because they are proposed to maintain all functionalities while conserving correct domain spacing within Tat. It is not known whether TAR (aa 38-47 within Tat) contributes to Tat toxicity, so another realization of this invention preferred for safety replaces Tat TAR/MTS with a fully human sequence studied to have similar functionalities as Tat. As an example, human Atx-3 mediates the translocation of human VCP to the nucleus: the peptide sequence responsible for these functionalities is illustrated (Atx-3 amino acids 277-291, SEQ ID 3). Noteworthy that like Tat SEQ ID3 encodes a short stretch of amino acids preceding its KR-rich MTS. A schematic of the DAGRS construct is illustrated in FIG. 1.

[0025] DAGRS use a molecular design evolved by the SIV/HIV Tat protein, but are humanized for safety. Overall, DAGRS composition of matter range between 0-33% identity to Tat. This is critical because HIV Tat is a toxic substance which precludes its use in clinical applications. Following the molecular design of SIV Tat (FIG. 2) and HIV/CPZ Tat (FIG. 3), DAGRS contain a signal transducing peptide (STP) at their NH.sub.2 terminus. The natural STP of the Tat design is removed, leaving behind a cassette for inserting a peptide theoretically capable of inhibiting any oncogene dependent on the sequence of the STP. An important embodiment of the present invention contemplates replacement of the Tat CRD ligand combining site with a neutral human genetic spacer of relatively similar composition, and in particular containing 6 C residues to facilitate proper folding of the biologic. Two examples illustrating this invention are the CRD (amino acids 41-60) from human -defensin 4 (SEQ ID 4) or the CRD from human wnt3 (SEQ ID 5), although any human CRD pairing 6 C is a preferred realization of this invention. Without modification, the CRD region, which is very autoreactive, could cause major toxicity. Therefore the present invention has redesigned (humanized) the region to provide for significantly less toxicity.

[0026] FIG. 2 shows an alignment of acidic transcription factor peptides (TFP) encoded at the NH.sub.2 terminus of SIV. The sequences are stapled on one side by the M initiator and move directly into a DE-rich (acidic transcription activator) segment. The SIV TFP are locked into configuration by a conserved P at their COOH end just before the start of the CRD, as illustrated in FIG. 2. FIG. 3 demonstrates that HIV-1, HIV-2, and CPZ carry a different class of STP at their NH.sub.2 terminus with characteristics of SH3-binding domains. In particular these three Tat STP initiate with a PxxP motif canonical for SH3-binding domains. As for SIV Tat, they are stapled at their COOH end by another P just prior to the C-rich domain (FIG. 3).

[0027] FIG. 4 shows the well-known property of monomeric Tat to enter into and influence cellular transcription. The TAR region (SEQ ID 1, underlined) and the MTS are critical components of this functionality. In particular, HeLa cells loaded with 2 g monomeric Tat protein transactivated an ltr-luciferase construct 85 fold above sham-loaded HeLa cells, or HeLa loaded with 2 g trimeric Tat, which is the biologically active form for oncoimmunotherapeutics. Tat provides the means to introduce the oncogene-inhibitory STP fragment at the site of action. FIG. 4 shows the activity of the monomer as a transcriptional regulator.

[0028] The present invention further improves bioavailability by combining the membrane translocation sequences of Tat with the targeted killing effect of Apoptin, or any STP. The invention is not interfered with by patent filings proposing to link Apoptin to Tat for improved bioavailability (US 20020176860, US 2008/0234466) because those inventors on the Tat-Apoptin patents acknowledge that native Tat is too toxic to be administered to humans (see Los et al., Apoptin, a tumor-selective killer, Biochem Biophys Acta. 1793, (2009) 1335-1342), and because the DAGRS sequences bear <33% identity to Tat. Translocation of Tat-GFP-monomer is shown in FIG. 5. Here, cells are incubated in 10 micromolar Tat-GFP monomer and fluorescently imaged.

[0029] FIG. 6 details specific DAGRS compositions of matter to be embedded into the STD (SEQ ID 6-9). In particular, SEQ ID 6 proposes a DAGRS with an unmodified 16 mer from the CAV VP3 (Apoptin) that contains the VP3 SH3-binding site and flanking carboxly amino acids. CAV VP3 (Apoptin), has been shown to specifically interact with AKT. Apoptin is known to kill most cancers using an AKT pathway, but Apoptin is not cytotoxic for normal cells. Prior to the present invention, nothing similar has been described that could function as an in vivo oncolytic without associated toxicity. SEQ ID 7 identifies a 16 mer homologue to the VP3 SH3-binding domain and carboxyl flanking sequences in human AKT, strongly supporting the proposal that VP3 functions as a competitive inhibitor to AKT activation. Further, polio oncolytic virus, now approved for treating recurrent glioblastoma cancers, appears to work, at least in part, through an AKT mechanism. The present invention proposes using the human AKT SH3-binding region (SEQ ID 7) as an alternative to SEQ ID 6 under the proposition that its fully human sequence will be better tolerated and less immunogenic in the clinical setting. A third DAGRS derivative (SEQ ID 8) aligns the paired prolines at the carboxyl terminus, as in VP3, but also retains the paired amino prolines, and in so doing creates a DAGRS with a canonical SH3-binding site for the src oncogene. Interaction between Src and the SH3-binding region of AKT is requisite for AKT activation (Jiang and Qiu, Journal of Biological Chemistry 278, 15789, 2003). SEQ ID8 describes a derivatization of AKT peptide that could give it higher affinity for Src than native human AKT. A further realization of the composition is extending 16 mer SEQ ID 6-8 with 4 or 5 COOH amino acids from their respective proteins (ie RVSEL for VP3), thereby engineering 20 mers with proposed carboxyl phosphorylation site anchors more distant from their P staples (FIG. 7), since the P staples are not present in either VP3 or AKT whole protein, and could be a source of steric hindrance.

[0030] Another embodiment of the present invention is a DAGRS with a transcription factor/protein activator region such as a peptide capable of binding to E2F promoter ((SEQ ID 9). This design bears analogy to SIV Tat in encoding an acidic region, while the AKT design bears analogy to HIV Tat in encoding an SH3-binding domain As for SEQ ID 6-8, it could be beneficial to distance E2F peptide (SEQ ID 9) by 4 or 5 amino acids from the COOH P staple.

[0031] FIG. 7 demonstrates the functional alignment between the viral VP3 SH3-binding domain, and human AKT SH3-binding domain, and establishes an algorithm generally useful for the alignment of viral tiles with human tiles (a humanization algorithm). In particular other than the alignment of the proline-rich SH3-binding domains (boxed orange) there is little or no homology (and none recognized by current standard protein alignment programs) until the sequences reach a tightly evolutionarily conserved S/TxY Mitogen Activated Protein kinase phosphorylation site (Mohanta et al Biological Procedures Online 17, 13, 2015) at their COOH end, with an identical spacing of 9 amino acids between P and S/T (boxed blue). Particularly insofar as AKT is known to require Y phosphorylation (by Src) for activation, a reasonable model is that in resting cells S/T is phosphorylated and sterically inhibiting Y (boxed green) phosphorylation carboxyl by 2 amino acids. Upon oncogenic transformation, which is known to induce phosphatases, S/T would become dephosphorylated and Y susceptible to AKT oncogenic phosphorylation. In either case, the VP3 cassette (SEQ ID 6) could function as a competitive inhibitor to AKT activation, as would be also expected for the Y phosphorylation sites of SEQ ID 7 and 8.

[0032] This is the first time that a functional viral domain has been matched up (humanized) to a human protein fragment, and in so doing describes a key humanization invention. The example of FIG. 7 can be generalized to an algorithm that identifies conserved functionalities among proteins (AKT and VP3 both influence G2 phase cell cycle transition and interact with identical proteins), aligns peptides from the two proteins through amino and carboxyl anchors with matched functional domains, eg an SH3-binding domain and a MAP kinase phosphorylation domain, and prioritizes equivalent spacing between the two functional domains, while at the same time totally ignoring the primary amino acid sequence of the spacer. The rationale supporting the algorithm is that correct amino acid spacing conserves functional interactions in three dimensions. The algorithm totally ignores the composition of amino acids intervening between the anchors, because the evolutionary distance between the species originally hosting the virus and humans is proposed to be too distant to conserve primary amino acid sequence of these non-essential residues. This is consistent with the vectors that transmit Zika virus and Ebola virus to humans, being respectively mosquitoes and bats. Many viral activities could be rendered safe and therapeutic via this algorithm converting viral components to human protein components.

[0033] Although the present invention has been described with reference to specific embodiments, workers skilled in the art will recognize that many variations may be made therefrom and it is to be understood and appreciated that the disclosures in accordance with the invention show only some preferred embodiments and advantages of the invention without departing from the broader scope and spirit of the invention. It is to be understood and appreciated that these discoveries in accordance with this invention are only those which are illustrated of the many additional potential applications that may be envisioned by one of ordinary skill in the art, and thus are not in any way intended to be limiting of the invention. Accordingly, other objects and advantages of the invention will be apparent to those skilled in the art from the detailed description together with the claims.

TABLE-US-00005 SEQID No Peptidesequence Source 1 FTRKGLGISYGRKKRRQRRR HIV 2 RKKRRQRRR HUMAN 3 TSEELRKRREAYFEK HUMAN 4 CLTKGGVCWGPCTGGFRQIGTCGLPRVRCC HUMAN 5 CRCVFHWCCYVSCQEC HUMAN 6 PKPPSKKRSCDPSEYR CHICKEN ANEMIA VIRUS 7 PPFKPQVTSETDTRYF HUMAN 8 PPKPPQVTSETDTRYF HUMAN 9 HHHRLSH HUMAN