Patent Application
20240408194
The contents of the electronic sequence listing (112624.01366.xml; Size: (7,003 bytes; and Date of Creation: Oct. 14, 2022) is herein incorporated by reference in its entirety.
The present disclosure generally relates to DNA-peptide hybrid nanostructures. In some embodiments, the DNA-peptide hybrid molecules specifically bind to a target of interest and act as carriers for immunogenic molecules.
Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has rapidly spread across the globe and infected more than 200 million individuals. SARS-Cov-2 causes coronavirus disease 2019 (Covid-19), which manifests as a mild respiratory illness in most infected individuals but can lead to acute respiratory distress syndrome and death in a significant percentage of cases. SARS-CoV-2 is also a member of the coronavirus family, which carries the largest genome among single-stranded RNA viruses that mutate frequently.
There are now reports of multiple variants emerging around the world as the duration of the SARS-COV-2 pandemic extends, such as Alpha (B1.1.7) from the UK, Beta (B1.351) from South Africa, Gamma (P1) from Brazil, and Delta (B1.617.2) from India, among others. These lineages are each characterized by numerous mutations in the spike protein, raising concerns that they are not affected by neutralizing monoclonal and vaccine-induced antibodies. As of August 2021, COVID-19 has caused over 4 million deaths and continues to place a heavy burden on healthcare systems. Hence, the development of a safe and effective vaccine that can prevent SARS-CoV-2 variant infection and transmission has rapidly become a top priority. It was recently shown that a two-component protein-based nanoparticle vaccine that displays multiple copies of the SARS-COV-2 spike protein and receptor-binding domain (RBD) induces potent neutralizing antibody responses in mice, rabbits, and cynomolgus macaques and protects the animal against a high-dose challenge, resulting in strongly reduced viral infection. Subunit vaccines are among the safest and most widely used vaccines and have been highly effective against a variety of infectious diseases, such as hepatitis B, HPV, tetanus, etc. DNA has emerged as an exceptional molecular building block for functional molecules assemble due to its predictable conformation and high programmability which allow assembling protein-DNA shape design and easy modification.
In some embodiments, compositions for eliciting an immune response against SARS-CoV-2 are provided. In some embodiments, the compositions comprise: a DNA nanocarrier linked to (1) a SARS-COV-2 specific binding peptide (SBP), and (2) a SARS-COV-2 spike protein or antigenic fragment thereof. In some embodiments, the DNA nanocarrier is selected from the group consisting of: an icosahedron, a three-helix bundle, four-helix bundle, a six-helix bundle, a triangular DNA origami structure, a tetrahedral wireframe cage, a block-like origami cuboid, reconfigurable tweezers, double crossover tiles, branched three-way junctions, and a three-legged stool. In some embodiments, the DNA nanocarrier comprises at least one of a three-helix bundle or a four-helix bundle linked to three SARS-COV-2 specific binding peptides (SBP). In some embodiments, the composition comprises a DNA icosahedron comprising 12 four-helix bundles, or 12 three-helix bundles, each linked to three SBPs. In some embodiments, the SARS-COV-2 spike proteins are not identical. In some embodiments, the spike proteins comprise the spike protein from a SARS-COV-2 variant, such as but not limed to the SARS-COV-2 alpha, beta, gamma, or delta variants. In some embodiments, the compositions further comprise an adjuvant. In some embodiments, the adjuvant is selected from the group consisting of aluminum containing compounds, CpG nucleotides, monophosphoryl lipid A (MPL), oil in water emulsion of squalene, and extracts of Quillaja saponaria. In some embodiments, the adjuvant comprises CpG nucleotides.
In another aspect of the current disclosure, methods of eliciting an immune response against SARS-COV-2 spike protein are provided. In some embodiments, the method comprises administering a composition comprising a DNA nanocarrier linked to (1) a SARS-COV-2 specific peptide, and (2) a SARS-COV-2 spike protein or an antigenic fragment thereof. In some embodiments, the DNA nanocarrier is selected from the group consisting of: an icosahedron, a three-helix bundle, four-helix bundle, a six-helix bundle, a triangular DNA origami structure, a tetrahedral wireframe cage, a block-like origami cuboid, reconfigurable tweezers, double crossover tiles, branched three-way junctions, and a three-legged stool. In some embodiments, the DNA nanocarrier comprises at least one of a three helix bundle or a four-helix bundle linked to three SARS-COV-2 specific binding proteins (SBPs). In some embodiments, the composition comprises a DNA icosahedron comprising 12 four-helix bundles, or 12 three-helix bundles, each linked to three SBPs. In some embodiments, the SARS-COV-2 spike protein is bound to one or more of the SBPs. In some embodiments, the SARS-COV-2 spike proteins are not identical. In some embodiments, the spike proteins comprise the spike protein from a SARS-COV-2 variant, such as but not limited to the SARS-COV-2 alpha, beta, gamma, or delta variants. In some embodiments, the composition further comprises an adjuvant. In some embodiments, the adjuvant is selected from the group consisting of aluminum containing compounds, CpG nucleotides, monophosphoryl lipid A (MPL), oil in water emulsion of squalene, and extracts of Quillaja saponaria. In some embodiments, the adjuvant is CpG nucleotides. In some embodiments, administration of the composition elicits an immune response to more than one variant strain of SARS-COV-2.
DNA origami is a powerful nanomaterial for biomedical applications due in part to its capacity for programmable, site-specific functionalization. Recent studies suggest that SARS-Cov-2-specific neutralizing antibody (Nab) titers are an important immune correlate of protection (1). Inventors disclose herein two kinds of in vitro self-assembling DNA origami-SARS-COV-2 receptor binding domain (RBD) nanoparticles, allowing for controlled DNA origami and RBD nanoparticle formation. Inventors further disclose protein-DNA origami nanoparticle subunit vaccines multivalently displaying the SARS-Cov-2 RBD, which can elicit potent and protective Ab response in mice, with neutralizing titers.
In one aspect of the current disclosure, DNA-protein hybrid molecules are provided. DNA nanostructures may be prepared by methods using one or more oligonucleotides. For example, such nanostructures may be assembled based on the concept of base-pairing. While no specific sequence is required, the sequence of each oligonucleotide must be partially complementary to certain other oligonucleotides to enable hybridization of all strands or sequences within a single oligonucleotide to enable hybridization and assembly of the nanostructure. For example, in some embodiments, the DNA nanostructure is a DNA icosahedron frame wire origami nanostructure, self-assembled from one single-stranded DNA molecule. In some embodiments, the DNA nanostructure is designed to have all or a portion of the oligonucleotide sequence to be complementary to all or a portion of a ssDNA oligonucleotide. In some embodiments, the oligonucleotide sequence can comprise DNA, protein-DNA/peptide-DNA, Ni-NTA-DNA, or combinations thereof. In some embodiments, the oligonucleotide is 5′-modified with a thio-comprising nucleotide. In some embodiments, the thio-comprising nucleotide or cystine-comprising protein or peptide is further reacted with a cross linker. In some embodiments, the cross linker is sulfo-SMCC (sulfosuccinimiidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate) (Thermofisher cat. 22322). In some embodiments, the cross linker is SPDP (sucinimidyl) 6-93′-(2-pyridyldithio) propionamido) hexanoate) (ThermoFisher Cat. No. 21650). In some embodiments, the sequence of the oligonucleotide sequence which is complementary to all or a portion of a ssDNA is selected from the following loading oligonucleotide sequences:
In one aspect of the current disclosure, DNA-peptide hybrid molecules are provided. In some embodiments, the DNA-peptide hybrid molecules comprise a DNA nanostructure chemically linked to one or more target-specific binding peptides, wherein the one or more target-specific binding peptides are specific for SARS-COV-2, or an immunogenic variant thereof. Also disclosed herein are methods and compositions comprising the DNA-peptide hybrid molecules, for therapeutic and/or prophylactic use.
In some embodiments, the crosslinker can further be reacted with an agent. In some aspects, the agent is amine-comprising nucleotide, protein (e.g. RBD of SARS-Cov-2 spike protein) or NTA (Nα,Nα-bis(carboxymethyl)-L-lysine) comprising a lysine. The amine on the nucleotide or lysine can react with the amino-reactive cross linker to form a loading oligonucleotide-functionalized agent. In some embodiments, the oligonucleotide-functionalized agent is hybridized to a portion of the ssDNA.
In some embodiments, the DNA nanostructure can include the use of “staple strands.” The DNA nanostructure can self-assemble with the staple strands. As used herein, the term “staples strands” refers to short single-stranded oligonucleotides of about 20-40 nucleotides in length, for example, 20, 21, 22, 25, 30, 35, or 40 nucleotides in length, wherein one end of the staple strand hybridizes with a region of the scaffold strand, thereby “stapling” the two regions of the scaffold strand together.
The assembly of such DNA framewire origami may be based on base-pairing principles or other non-canonical binding interactions. For example, regions of complementary within a single DNA molecule or between multiple DNA molecules may be used for assembly. Persons of ordinary skill in the art will readily understand and appreciate that the optimal sequence for any given DNA nanostructure will depend on the selected shape, size, nucleic acid content, and selected use of such DNA structure. In some embodiments, wherein the nanostructure comprises more than one ssDNA molecule (e.g. two or more oligonucleotides/polynucleotides), each ssDNA molecule may have a region that is complementary to a region on another ssDNA molecule to enable hybridization of the strands and assembly of the nanostructure. In some embodiments, wherein the nanostructure consists of a single ssDNA, region within the molecule may be complementary to complementary to certain other regions within the molecule to enable hybridization and assembly of the nanostructure. DNA nanostructure produced in accordance with the present disclosure are typically nanometer-scale structure (e.g., assembled from more than ten nanometer-scale or micrometer-scale structure). In some embodiments, a DNA nanostructure described herein has a length scale of about 10-500 nm. In some embodiments, a DNA nanostructure (icosahedron) described herein has a length scale of about 1 micrometer or about 2 micrometers.
In some embodiments, the DNA nanostructure comprise, consists essentially of multiple ssDNA molecules (e.g., more than one oligonucleotide/polynucleotide strands, such as two or more ssDNA molecules). In some embodiments, the icosahedron DNA nanostructure comprises two or more ssDNA molecules, which are capable of self-assembling into a nanostructure. In some embodiments, the icosahedron DNA nanostructure is assembled from two or more ssDNA molecules through paranemic cohesion crossovers. Thus, in some embodiments, the DNA nanostructure comprises two or more the LCB1-DNA molecules, wherein the LCB1-DNA molecules self-assemble to form at least one paranemic cohesion crossover.
In some embodiments, the DNA nanostructure comprise, consists essentially of multiple ssDNA molecules (e.g., more than one oligonucleotide/polynucleotide strands, such as two or more ssDNA molecules). In some embodiments, the icosahedron DNA nanostructure comprises two or more ssDNA molecules, which are capable of self-assembling into a nanostructure. In some embodiments, the icosahedron DNA nanostructure is assembled from two or more ssDNA molecules through paranemic cohesion crossovers. Thus, in some embodiments, the DNA nanostructure comprises two or more of the NTA-DNA molecules, wherein the LCB1-DNA molecules self-assemble to form at least one paranemic cohesion crossover.
In some embodiments, the DNA nanostructure comprises, consists essentially of multiple ssDNA molecules (e.g., more than one oligonucleotide/polynucleotide strands, such as two or more ssDNA molecules). In some embodiments, the icosahedron DNA nanostructure comprises two or more ssDNA molecules, which are capable of self-assembling into a nanostructure. In some embodiments, the icosahedron DNA nanostructure is assembled from two or more ssDNA molecules through paranemic cohesion crossovers. Thus, in some embodiments, the DNA nanostructure comprises two or more the RBD-DNA molecules, wherein the LCB1-DNA molecules self-assemble to form a at least one paranemic cohesion crossover.
The length of each DNA strand is variable and depends on, for example, the type of nanostructure to be formed. In some embodiments, the DNA nanostructure is comprised of multiple oligonucleotide strands. In some embodiments, the oligonucleotide or DNA strand is about 15 nucleotides (nt) in length to about 150,000 nt in length, about 15 to about 7500 nt in length, about 1500 to about 2500 nt in length, or between any of the aforementioned nucleotide lengths. In some embodiments, the at least one ssDNA molecule is about 10 nt in length to about 4000 nt in length.
In some embodiments, the DNA is synthesized de novo using chemical or biological methods. The DNA can be chemically synthesized in a step-wise manner. In some embodiments, the DNA can be synthesized using the cyanoethyl phosphoramidite method. These chemistries can be performed by a variety of automated oligonucleotide synthesizers available in the market.
In some embodiments, about 95% of the DNA nanostructure is double stranded and about 5% of the DNA nanodevice is single stranded.
In certain embodiments, the DNA nanocarrier comprises icosahedron origami nanostructure.
In some embodiments, the DNA nanocarrier comprises a nucleic acid sequence about 1500 to about 2500 nucleotides in length.
In some embodiments, the LCB1-DNA describe herein comprise one modified DNA, crosslinker, and LCB1 protein, which are chemically conjugated as one molecule. In some embodiments, the modified nucleic acid is a modified nucleotide. In some embodiments, the modified ribonucleoside can be selected from NA-incorporated from, in part, 5-Aminoallyluridine-5′-Triphosphate (Trilink, N-1062),
In some embodiments, amino acid sequence modification are introduced by making a codon nucleotides changes to DNA encoding the protein (including LCB1, RBD protein) described herein. Such modifications include, for example, insertion of an extra cysteine codon into the sequence. The insertion can be made, provided that the final product possesses the desired characteristics. The amino acid alterations may be introduced in the LCB1 or RBD substrate sequence at the time that sequence is synthesized or cloned.
Amino acid sequence (cysteine) insertions include amino-, thio, or carboxyl-terminal fusions ranging in length from one residue to protein containing a hundred or more residues and intrasequence insertion of single amino acid residues. For example, a terminal insertion includes an LCB1 protein with a C-terminal cysteine residue.
In some embodiments, modifications in the biological properties of the protein described herein are accomplished by selecting substitution that differ significantly in their effect on maintaining a) the structure of the protein backbone is the area of the substitution, for example, as a sheet or helical conformation. b) the charge or hydrophobicity of the protein at the target site, or c) the bulk of the side chain.
Nucleic acid molecules encoding amino acid sequence variants of the antibody are prepared by a variety of methods known in the art. These methods include, but are not limited to, isolation from a natural source (in the case of naturally occurring amino acid sequence variants) or preparation by oligonucleotide-mediated (or site-directed) mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlier prepared variant or a non-variant version of the antibody. LCB1 protein can be expression in E. coli, and purified by fast protein liquid chromatography (FPLC).
In some embodiments, the cross linker (SMCC) will react with amine-modified DNA oligonucleotide, purified by high-performance liquid chromatography (HPLC). The LCB1 protein will be reduced by DTT or TCEP, and wash 3 times. The LCB1-reduced thio-group will be conjugated with SMCC-DNA modified oligonucleotide. The LCB1-SMCC-DNA will be purified by FPLC.
DNA origami-based nanostructure affords high specificity and efficiency for self-assembly multivalent LCB1 or RBD proteins for subunit vaccine. In some embodiments, this invention functions as a subunit protein-DNA vaccine to elicit neutralizing antibodies to produce protection from SARS-Cov-2 variants of concern.
As shown in
In a further aspect of the current disclosure, icosahedron DNA origami (
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of skill in the art to which the invention pertains. All definitions, as defined and used herein, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and/or ordinary meanings of the defined terms.
The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.”
A range includes each individual member. Thus, for example, a group having 1-3 members refers to groups having 1, 2, or 3 members.
It should also be understood that, unless clearly indicated to the contrary, in any methods claimed herein that include more than one step or act, the order of the steps or acts of the method is not necessarily limited to the order in which the steps or acts of the method are recited.
The modal verb “may” refers to the preferred use or selection of one or more options or choices among the several described embodiments or features contained within the same. Where no options or choices are disclosed regarding a particular embodiment or feature contained in the same, the modal verb “may” refers to an affirmative act regarding how to make or use an aspect of a described embodiment or feature contained in the same, or a definitive decision to use a specific skill regarding a described embodiment or feature contained in the same. In this latter context, the modal verb “may” has the same meaning and connotation as the auxiliary verb “can.”
In the claims, as well as in the specification above, all transitional phrases such as “comprising,” “including,” “carrying,” “having,” “containing,” “involving,” “holding,” “composed of,” and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases “consisting of” and “consisting essentially of” shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.
As used herein, “about,” “approximately,” “substantially,” and “significantly” will be understood by persons of ordinary skill in the art and will vary to some extent on the context in which they are used. If there are uses of the term which are not clear to persons of ordinary skill in the art given the context in which it is used, “about” and “approximately” will mean up to plus or minus 10% of the particular term and “substantially” and “significantly” will mean more than plus or minus 10% of the particular term.
As used herein, the term “nanostructure” is a defined structure having at least one dimension (e.g., length, width, thickness) in the nanoscale range (approximately 1 nanometer (nm) to 100 nm).
The term “DNA nanostructure”, as used herein, refers to a nanostructure at least partially composed of DNA assembled in a defined structure and having at least one dimension (e.g., length, width, thickness) in the nanoscale range (approximately 1 nm to 100 nm). By way of example, but not by way of limitation, in some embodiments, a DNA nanostructure comprises an icosahedron, a three-helix bundle, a four-helix bundle, a six-helix bundle, a triangular DNA origami structure, a tetrahedral wireframe cage, a block-like origami cuboid, reconfigurable tweezers, double crossover tiles, branched three-way junctions, and a three-legged stool. In some embodiments, a DNA nanostructure comprises a nucleic acid handle. In some embodiments, the handle is single stranded.
As used herein, “DNA-peptide hybrid molecule” refers to a molecule comprising a DNA molecule chemically linked to a peptide molecule thereby generating a DNA-peptide hybrid molecule. In some embodiments, the DNA-peptide linkage is achieved using an orthogonal chemical reaction. In some embodiments, the chemical linkage is a reversible chemical linkage. In some embodiments, the DNA molecule comprises a DNA nanostructure. In some embodiments, a DNA-peptide hybrid molecule comprises a DNA nanocarrier.
As used herein, the term “DNA nanocarrier” refers to a DNA nanostructure that is capable of carrying or otherwise acting as a delivery agent for a therapeutic molecule which is, in some embodiments, chemically linked to the DNA nanocarrier. In some embodiments, the chemical linkage is reversible. In some embodiments, the DNA nanocarrier acts as a molecule to facilitate efficient delivery of a therapeutic agent, such as an antigen, to a host wherein the antigen is configured on the DNA nanostructure to elicit an immune response from the host. Thus, in some embodiments, a DNA nanocarrier comprises a DNA-peptide hybrid molecule. In some embodiments, the DNA acts as a structural element. In some embodiments, the DNA nanostructure can also serve as a scaffold for the formation of multivalent vaccine.
As used herein, “adjuvant” refers to a compound or composition which further increases the immune response against an antigen. By way of example, but not by way of limitation, adjuvants for use in the compositions and methods of the current disclosure include: aluminum containing compounds, CpG nucleotides, monophosphoryl lipid A (MPL), oil in water emulsion of squalene, and extracts of Quillaja saponaria. In some embodiments, CpG oligonucleotides contain unmethylated CpG dinucleotides in particular sequence contexts (CpG motifs). These CpG motifs are present at a 20-fold greater frequency in bacterial DNA, which can be recognized by Toll-like receptor 9 (TLR9) leading to strong immunostimulatory effects as an immune adjuvant to enhance the immunogenicity of antigens in vivo. In some embodiments, the icosahedron DNA origami is used to assemble multiple CpG oligonucleotides on the edge of the icosahedron, and then self-assemble the RBD-DNA origami nanoparticle subunit vaccine, for example, according to the schematic in
As used herein, “LCB1” refers to a protein with the sequence DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVER (SEQ ID NO: 2). More information surrounding the properties and the use of LCB1 can be found in the publication Cao L et al. Science. Vl. 370, No. 6515 pp. 426-431, 2020, incorporated by reference herein in its entirety. In some embodiments, LCB1 is chemically linked to a DNA nanostructure. In some embodiments, more than one LCB1 molecule is chemically linked to one DNA nanostructure.
The phrases “% sequence identity,” “percent identity,” or “% identity” refer to the percentage of amino acid residue matches between at least two amino acid sequences aligned using a standardized algorithm. Methods of amino acid sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail below, generally preserve the charge and hydrophobicity at the site of substitution, thus preserving the structure (and therefore function) of the polypeptide. Percent identity for amino acid sequences may be determined as understood in the art. (See, e.g., U.S. Pat. No. 7,396,664, which is incorporated herein by reference in its entirety). A suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST), which is available from several sources, including the NCBI, Bethesda, Md., at its website. The BLAST software suite includes various sequence analysis programs including “blastp,” that is used to align a known amino acid sequence with other amino acids sequences from a variety of databases.
The terms “protein,” “peptide,” and “polypeptide” are used interchangeably herein and refer to a polymer of amino acid residues linked together by peptide (amide) bonds. The terms refer to a protein, peptide, or polypeptide of any size, structure, or function. Typically, a protein, peptide, or polypeptide will be at least three amino acids long. A protein, peptide, or polypeptide may refer to an individual protein or a collection of proteins. One or more of the amino acids in a protein, peptide, or polypeptide may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation, functionalization, or other modification, etc. A protein, peptide, or polypeptide may also be a single molecule or may be a multi-molecular complex. A protein, peptide, or polypeptide may be just a fragment of a naturally occurring protein or peptide. A protein, peptide, or polypeptide may be naturally occurring, recombinant, or synthetic, or any combination thereof. A protein may comprise different domains, for example, a nucleic acid binding domain and a nucleic acid cleavage domain. In some embodiments, a protein comprises a proteinaceous part, e.g., an amino acid sequence constituting a nucleic acid binding domain.
Nucleic acids, proteins, and/or other compositions described herein may be purified. As used herein, “purified” means separate from the majority of other compounds or entities, and encompasses partially purified or substantially purified. Purity may be denoted by a weight by weight measure and may be determined using a variety of analytical techniques such as but not limited to mass spectrometry, HPLC, etc.
Polypeptide sequence identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured.
The terms “nucleic acid” and “nucleic acid molecule,” as used herein, refer to a compound comprising a nucleobase and an acidic moiety, e.g., a nucleoside, a nucleotide, or a polymer of nucleotides. Nucleic acids generally refer to polymers comprising nucleotides or nucleotide analogs joined together through backbone linkages such as but not limited to phosphodiester bonds. Nucleic acids include deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) such as messenger RNA (mRNA), transfer RNA (tRNA), etc. Typically, polymeric nucleic acids, e.g., nucleic acid molecules comprising three or more nucleotides are linear molecules, in which adjacent nucleotides are linked to each other via a phosphodiester linkage. In some embodiments, “nucleic acid” refers to individual nucleic acid residues (e.g. nucleotides and/or nucleosides). In some embodiments, “nucleic acid” refers to an oligonucleotide chain comprising three or more individual nucleotide residues. As used herein, the terms “oligonucleotide” and “polynucleotide” can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least three nucleotides). In some embodiments, “nucleic acid” encompasses RNA as well as single and/or double-stranded DNA. Nucleic acids may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid, chromosome, chromatid, or other naturally occurring nucleic acid molecule. On the other hand, a nucleic acid molecule may be a non-naturally occurring molecule, e.g., a recombinant DNA or RNA, an artificial chromosome, an engineered genome, or fragment thereof, or a synthetic DNA, RNA, DNA/RNA hybrid, or include non-naturally occurring nucleotides or nucleosides. Furthermore, the terms “nucleic acid,” “DNA,” “RNA,” and/or similar terms include nucleic acid analogs, i.e. analogs having other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc. Where appropriate, e.g., in the case of chemically synthesized molecules, nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications. A nucleic acid sequence is presented in the 5′ to 3′ direction unless otherwise indicated. In some embodiments, a nucleic acid is or comprises natural nucleosides (e.g. adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, O(6)-methylguanine, and 2-thiocytidine); chemically modified bases; biologically modified bases (e.g., methylated bases); intercalated bases; modified sugars (e.g., 2′-fluororibose, ribose, 2′-deoxyribose, arabinose, and hexose); and/or modified phosphate groups (e.g., phosphorothioates and 5′-N-phosphoramidite linkages).
The term “nucleic acid handle”, as used herein, is a nucleic acid attached to or intended for attachment to a polypeptide and having at least some nucleic acid bases available for hybridization to complementary nucleic acid strands of a nucleic acid mold or other structure. Nucleic acid handles may include single-stranded DNA, double-stranded DNA with at least a portion of single-stranded DNA, RNA, aptamers, and peptide nucleic acids (PNAs), or combinations thereof.
The phrase “DNA origami nanostructure” as used herein refers to a nanostructure composed of DNA folded into a precise two- or three-dimensional shape. A DNA origami nanostructure as described herein may function as a DNA mold.
As used herein, “orthogonal chemical reactions” refers to different chemical reactions that occur selectively and in high yield in the presence of other functional groups. Exemplary orthogonal reactions include, but are not limited to, click chemistry (“click reaction”), maleimide chemistry, disulfide formation, oxime formation between an aminooxy group and a ketone/aldehyde, tetrazine/trans-cyclooctene conjugation, enzymatic ligations (e.g., transglutaminase), copper-catalyzed click reactions, and tyrosine oxidation reactions. Various other reactions may include those described in Stephanopoulos, N., “Hybrid Nanostructures from the Self-Assembly of Proteins and DNA”, Chem. 6, pp. 364-405, 2020, incorporated herein by reference. In some embodiments, such reactions are used to link one or more polypeptides to a DNA nanostructure.
As used herein, the term “click reaction” refers to the reaction of an azide group with an alkyne group to form a 5-membered heteroatom ring.
As used herein, “target-specific binding peptide” is a polypeptide molecule that is able to bind to another protein, peptide, or other molecule of interest. Target-specific binding peptides may be chemically linked, for example, to DNA nanostructures or DNA nanocarriers. In some embodiments, more than one target-specific binding peptides are linked to a single DNA nanostructure or nanocarrier. In some embodiments, linking more than one target-specific binding peptides to one DNA nanostructure increases the affinity of the DNA nanostructure-peptide hybrid compared to the target-specific binding protein alone. In some embodiments, the peptide LCB1 is a target-specific binding peptide. As used herein, “target-specific” refers to the property of a molecule having a high affinity for another molecule. In some embodiments, target specific molecules may have a Kd or dissociation constant of less than 1 micromolar, or preferably less than 5 nanomolar with a target molecule. In some embodiments target-specific binding peptides are SARS-COV-2 binding peptides.
As used herein, “SARS-COV-2 binding peptide” or “SBP” refers to a peptide that is capable of binding specifically with SARS-COV-2. In some embodiments, the SBP binds to the surface glycoprotein of SARS-COV-2 and, in some embodiments, the SBP has a KD of less than 1 micromolar for SARS-COV-2 surface glycoprotein. In some embodiments, the SBP has a KD of less than 5 nanomolar for surface glycoprotein of SARS-COV-2. An exemplary, non-limiting SBP comprises LCB1.
As used herein, “photocleavable linkage” is a chemical link between two or more molecules that can be cleaved upon exposure to light of a given wavelength or energy. A photocleavable linkage comprises an exemplary reversible chemical linkage. In some embodiments, o-nitrobenzyl ester moieties are installed into the DNA backbone of a DNA-peptide hybrid molecule such that, upon exposure to 350 nm ultraviolet (UV) light, the chemical linkages in the DNA molecule are cleaved. In some embodiments, placement of the cleavable linkages is selected such that the cleavage separates the DNA portion of the molecule from the peptide portion of the molecule. Therefore, in the context of a DNA-peptide hybrid molecule, wherein the peptide portion of the molecule binds specifically to a target molecule, the cleavage of the o-nitrobenzyl ester moieties in the DNA portion of the molecule upon exposure to 350 nm UV light effectively separates the target-binding, i.e., peptide portion of the molecule, from the rest of the molecule.
As used herein, “binding affinity” or “affinity” is the strength of the binding interaction between a single molecule and its ligand or binding partner.
As used herein, “binding avidity”, “avidity”, or “functional affinity” is the strength of binding between a molecule comprising multiple target-binding sites and the target molecule. In some embodiments, the DNA-peptide hybrid molecules of the present disclosure comprise multiple target-specific peptides bound to a single DNA nanostructure. Therefore, the avidity of the DNA-peptide hybrid molecule is the strength of the binding of the complete structure of the molecule including the multiple target-specific binding peptides to the target molecule.
As used herein, “immunoglobulin Fc domain” or “Fc domain” refers to the fragment crystallizable domain or the tail region of an antibody that interacts with cell surface receptors called Fc receptors and some proteins of the complement system. This property allows antibodies to activate the immune system. In IgG, IgA and IgD antibody isotypes, the Fc region is composed of two identical protein fragments, derived from the second and third constant domains of the antibody's two heavy chains; IgM and IgE Fc regions contain three heavy chain constant domains (CH domains 2-4) in each polypeptide chain. In some embodiments, the DNA-peptide hybrid molecules of the present disclosure comprise an immunoglobulin Fc domain. In some embodiments, the type of Fc domain selected is designed such that the appropriate immune response is instigated by the Fc domain selected. For example, the properties of the Fc domains are known in the art and include the ability to promote antibody directed cellular cytotoxicity (ADCC). As used herein, “antibody directed cellular cytotoxicity” or “ADCC” refers to lysis of target cells coated with antibody by effector cells with cytolytic activity and specific immunoglobulin receptors called Fc receptors, including NK cells, macrophages, and granulocytes.
As used herein, “nanobody” refers to a single monomeric variable antibody domain, also known as single-domain antibodies (sdAbs) that are able to bind selectively to a specific antigen.
As used herein, “antigen” refers to a molecule that is capable of stimulating the immune system of a subject.
As used herein, “paratope” refers to region of an antibody that binds to the antigen-binding site (epitope) of the target molecule.
In some embodiments, the DNA-peptide hybrid molecules of the present disclosure which, in some embodiments, are designed to bind to a target molecule, can be “sized” or “tuned” to match the distance and/or arrangement of the binding domains in the target molecule. Put another way, if, for example, the target molecule contains two target-binding domains for which the DNA-hybrid molecule is designed to bind, that are 5 nm apart, the DNA nanostructure may be sized or tuned such that the target-specific binding peptides, when attached to the DNA nanostructure, are located about 5 nm apart in a conformation that enables favorable access of the target-specific binding peptides to the target-binding domains. Thus, without being limited by any theory or mechanism, this tunable property of the compositions of the current disclosure is thought to enable rational design of DNA nanostructures that takes advantage of the property of avidity of multiple binding domains binding to a single target molecule. In essence, being able to be tuned increases the functional affinity of the DNA-hybrid molecule to its target molecule when compared to the affinity of a similar molecule that does not present the target-specific binding peptides in a conformation that allows them to be accessible to the target binding regions of the target molecule.
In a second aspect of the current disclosure, methods of treatment are provided. In some embodiments, the method comprises administering a DNA-peptide hybrid molecule comprising a DNA nanostructure chemically linked to one or more target-specific binding peptides, wherein the one or more target-specific binding peptides are specific for a molecule associated with a disease or disorder in an amount sufficient to treat the disease or disorder.
As used herein, “infectious disease” refers to diseases caused by pathogenic microorganisms including, for example, bacteria, fungi, viruses and eukaryotic parasites. In some embodiments, the infectious disease is coronavirus disease discovered in 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV-2).
As used herein, “autoimmune disease” refers to a disease or disorder wherein a subject's immune system attacks normal cells and tissues in the subject.
As used herein, “cancer” refers to a large group of cell proliferative disorders caused by an uncontrolled division of abnormal cells.
As used herein, “psychiatric disease or disorder” refers to wide variety of behavioral or mental patterns that cause significant distress or impairment of personal functioning in affected subjects. Psychiatric diseases or disorders are caused by abnormal functioning of the central nervous system.
As used herein, “environmental exposure” refers to contact with chemical, biological, or physical substances found in air, water, food, or soil that may have a harmful effect on a person's health.
As used herein, the terms “treating” or “to treat” each mean to alleviate symptoms, eliminate the causation of resultant symptoms either on a temporary or permanent basis, and/or to prevent or slow the appearance or to reverse the progression or severity of resultant symptoms of the named disease or disorder. As such, the methods disclosed herein encompass both therapeutic and prophylactic administration.
As used herein the term “effective amount” refers to the amount or dose of the compound, upon single or multiple dose administration to the subject, which provides the desired effect in the subject under diagnosis or treatment. The disclosed methods may include administering an effective amount of the disclosed compounds (e.g., as present in a pharmaceutical composition) for treating a disease or disorder associated with the target molecule to which the disclosed compositions are targeted.
An effective amount can be readily determined by the attending diagnostician, as one skilled in the art, by the use of known techniques and by observing results obtained under analogous circumstances. In determining the effective amount or dose of compound administered, a number of factors can be considered by the attending diagnostician, such as: the species of the subject; its size, age, and general health; the degree of involvement or the severity of the disease or disorder involved; the response of the individual subject; the particular compound administered; the mode of administration; the bioavailability characteristics of the preparation administered; the dose regimen selected; the use of concomitant medication; and other relevant circumstances.
A typical daily dose may contain from about 0.01 mg/kg to about 100 mg/kg (such as from about 0.05 mg/kg to about 50 mg/kg and/or from about 0.1 mg/kg to about 25 mg/kg) of each compound used in the present method of treatment.
Compositions can be formulated in a unit dosage form, each dosage containing from about 1 to about 500 mg of each compound individually or in a single unit dosage form, such as from about 5 to about 300 mg, from about 10 to about 100 mg, and/or about 25 mg. The term “unit dosage form” refers to a physically discrete unit suitable as unitary dosages for a patient, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect, in association with a suitable pharmaceutical carrier, diluent, or excipient.
Oral administration is an illustrative route of administering the compounds employed in the compositions and methods disclosed herein. Other illustrative routes of administration include transdermal, percutaneous, intravenous, intramuscular, intranasal, buccal, intrathecal, intracerebral, or intrarectal routes. The route of administration may be varied in any way, limited by the physical properties of the compounds being employed and the convenience of the subject and the caregiver.
As one skilled in the art will appreciate, suitable formulations include those that are suitable for more than one route of administration. For example, the formulation can be one that is suitable for both intrathecal and intracerebral administration. Alternatively, suitable formulations include those that are suitable for only one route of administration as well as those that are suitable for one or more routes of administration, but not suitable for one or more other routes of administration. For example, the formulation can be one that is suitable for oral, transdermal, percutaneous, intravenous, intramuscular, intranasal, buccal, and/or intrathecal administration but not suitable for intracerebral administration.
The inert ingredients and manner of formulation of the pharmaceutical compositions are conventional. The usual methods of formulation used in pharmaceutical science may be used here. All of the usual types of compositions may be used, including tablets, chewable tablets, capsules, solutions, parenteral solutions, intranasal sprays or powders, troches, suppositories, transdermal patches, and suspensions. In general, compositions contain from about 0.5% to about 50% of the compound in total, depending on the desired doses and the type of composition to be used. The amount of the compound, however, is best defined as the “effective amount”, that is, the amount of the compound which provides the desired dose to the patient in need of such treatment. The activity of the compounds employed in the compositions and methods disclosed herein are not believed to depend greatly on the nature of the composition, and, therefore, the compositions can be chosen and formulated primarily or solely for convenience and economy.
Capsules are prepared by mixing the compound with a suitable diluent and filling the proper amount of the mixture in capsules. The usual diluents include inert powdered substances (such as starches), powdered cellulose (especially crystalline and microcrystalline cellulose), sugars (such as fructose, mannitol and sucrose), grain flours, and similar edible powders.
Tablets are prepared by direct compression, by wet granulation, or by dry granulation. Their formulations usually incorporate diluents, binders, lubricants, and disintegrators (in addition to the compounds). Typical diluents include, for example, various types of starch, lactose, mannitol, kaolin, calcium phosphate or sulfate, inorganic salts (such as sodium chloride), and powdered sugar. Powdered cellulose derivatives can also be used. Typical tablet binders include substances such as starch, gelatin, and sugars (e.g., lactose, fructose, glucose, and the like). Natural and synthetic gums can also be used, including acacia, alginates, methylcellulose, polyvinylpyrrolidine, and the like. Polyethylene glycol, ethylcellulose, and waxes can also serve as binders.
Tablets can be coated with sugar, e.g., as a flavor enhancer and sealant. The compounds also may be formulated as chewable tablets, by using large amounts of pleasant-tasting substances, such as mannitol, in the formulation. Instantly dissolving tablet-like formulations can also be employed, for example, to assure that the patient consumes the dosage form and to avoid the difficulty that some patients experience in swallowing solid objects.
A lubricant can be used in the tablet formulation to prevent the tablet and punches from sticking in the die. The lubricant can be chosen from such slippery solids as talc, magnesium and calcium stearate, stearic acid, and hydrogenated vegetable oils.
Tablets can also contain disintegrators. Disintegrators are substances that swell when wetted to break up the tablet and release the compound. They include starches, clays, celluloses, algins, and gums. As further illustration, corn and potato starches, methylcellulose, agar, bentonite, wood cellulose, powdered natural sponge, cation-exchange resins, alginic acid, guar gum, citrus pulp, sodium lauryl sulfate, and carboxymethylcellulose can be used.
Compositions can be formulated as enteric formulations, for example, to protect the active ingredient from the strongly acid contents of the stomach. Such formulations can be created by coating a solid dosage form with a film of a polymer which is insoluble in acid environments and soluble in basic environments. Illustrative films include cellulose acetate phthalate, polyvinyl acetate phthalate, hydroxypropyl methylcellulose phthalate, and hydroxypropyl methylcellulose acetate succinate.
Transdermal patches can also be used to deliver the compounds. Transdermal patches can include a resinous composition in which the compound will dissolve or partially dissolve; and a film which protects the composition, and which holds the resinous composition in contact with the skin. Other, more complicated patch compositions can also be used, such as those having a membrane pierced with a plurality of pores through which the drugs are pumped by osmotic action.
As one skilled in the art will also appreciate, the formulation can be prepared with materials (e.g., actives excipients, carriers (such as cyclodextrins), diluents, etc.) having properties (e.g., purity) that render the formulation suitable for administration to humans. Alternatively, the formulation can be prepared with materials having purity and/or other properties that render the formulation suitable for administration to non-human subjects, but not suitable for administration to humans.
The compounds employed in the compositions and methods disclosed herein may be administered as pharmaceutical compositions and, therefore, pharmaceutical compositions incorporating the compounds are considered to be embodiments of the compositions disclosed herein. Such compositions may take any physical form which is pharmaceutically acceptable; illustratively, they can be orally administered pharmaceutical compositions. Such pharmaceutical compositions contain an effective amount of a disclosed compound, which effective amount is related to the daily dose of the compound to be administered. Each dosage unit may contain the daily dose of a given compound or each dosage unit may contain a fraction of the daily dose, such as one-half or one-third of the dose. The amount of each compound to be contained in each dosage unit can depend, in part, on the identity of the particular compound chosen for the therapy and other factors, such as the indication for which it is given. The pharmaceutical compositions disclosed herein may be formulated so as to provide quick, sustained, or delayed release of the active ingredient after administration to the patient by employing well known procedures.
As indicated above, pharmaceutically acceptable salts of the compounds are contemplated and also may be utilized in the disclosed methods. The term “pharmaceutically acceptable salt” as used herein, refers to salts of the compounds, which are substantially non-toxic to living organisms. Typical pharmaceutically acceptable salts include those salts prepared by reaction of the compounds as disclosed herein with a pharmaceutically acceptable mineral or organic acid or an organic or inorganic base. Such salts are known as acid addition and base addition salts. It will be appreciated by the skilled reader that most or all of the compounds as disclosed herein are capable of forming salts and that the salt forms of pharmaceuticals are commonly used, often because they are more readily crystallized and purified than are the free acids or bases.
The “alpha” variant of SARS-COV-2, or B.1.1.7 variant has the following mutations: 69-70del, N501Y, and P681H.
The “beta” variant of SARS-COV-2, or B.1.351 variant has the following mutations: K417N, E484K and N501Y.
The “gamma” variant of SARS-COV-2, or P.1 variant has the following mutations: K417T, E484K, and N501Y.
The “delta” variant of SARS-COV-2, or B.1.617.2 variant has the following mutations: L451R, T478K, and P681R.
While four variants are described above, additional variants, as they develop and are sequenced, may be used in the context of the present invention. Based on the present disclosure, the skilled artisan would understand how to make and use such variants.
1. A composition for eliciting an immune response against SARS-COV-2 including: a DNA nanocarrier linked to (1) a SARS-COV-2 specific binding peptide (SBP), and (2) a SARS-COV-2 spike protein or antigenic fragment thereof.
2. The composition of embodiment 1, wherein the DNA nanocarrier is selected from the group consisting of: an icosahedron, a three-helix bundle, a four-helix bundle, a six-helix bundle, a triangular DNA origami structure, a tetrahedral wireframe cage, a block-like origami cuboid, reconfigurable tweezers, double crossover tiles, branched three-way junctions, and a three-legged stool.
3. The composition of embodiments 1 or 2, wherein the DNA nanocarrier includes at least one four-helix bundle or at least one three-helix bundle linked to three SARS-CoV-2 specific binding peptides (SBP).
4. The composition of any of the preceding embodiments, wherein the composition includes a DNA icosahedron including 12 four-helix bundles, or 12 three-helix bundles, each linked to three SBPs.
6. The composition of any of the preceding embodiments, wherein the SARS-CoV-2 spike proteins are not identical.
7. The composition of embodiment 6, wherein the spike proteins include the spike protein from the SARS-COV-2 alpha, beta, gamma, or delta variants.
8. The composition of any of the preceding embodiments, further including an adjuvant.
9. The composition of embodiment 8, wherein the adjuvant is selected from the group consisting of aluminum containing compounds, CpG nucleotides, monophosphoryl lipid A (MPL), oil in water emulsion of squalene, and extracts of Quillaja saponaria.
10. The composition of embodiment 9, wherein the adjuvant includes CpG nucleotides.
11. A method of eliciting an immune response against SARS-COV-2 spike protein, the method including administering a composition including a DNA nanocarrier linked to (1) a SARS-COV-2 specific peptide, and (2) a SARS-COV-2 spike protein or antigenic fragment thereof.
12. The method of embodiment 11, wherein the DNA nanocarrier is selected from the group consisting of: an icosahedron, a three-helix bundle, a four-helix bundle, a six-helix bundle, a triangular DNA origami structure, a tetrahedral wireframe cage, a block-like origami cuboid, reconfigurable tweezers, double crossover tiles, branched three-way junctions, and a three-legged stool.
13. The method of embodiments 11 or 12, wherein the DNA nanocarrier includes at least one four-helix bundle or at least one three-helix bundle linked to three SARS-CoV-2 specific binding proteins (SBPs).
14. The method of any of embodiments 11-13, wherein the composition includes a DNA icosahedron including 12 four-helix bundles, or including 12 three-helix bundles each linked to three SBPs.
15. The method of any of embodiments 11-14, wherein the SARS-COV-2 spike protein is bound to one or more of the SBPs.
16. The method of any of embodiments 11-15, wherein the SARS-COV-2 spike proteins are not identical.
17. The method of embodiment 16, wherein the spike proteins include the spike protein from the SARS-COV-2 alpha, beta, gamma, or delta variants.
18. The method of any of embodiments 11-17, wherein the composition further includes an adjuvant.
19. The method of embodiment 18, wherein the adjuvant is selected from the group consisting of aluminum containing compounds, CpG nucleotides, monophosphoryl lipid A (MPL), oil in water emulsion of squalene, and extracts of Quillaja saponaria.
20. The method of embodiment 19, wherein the adjuvant is CpG nucleotides.
21. The method of any of embodiments 11-20, wherein administration of the composition elicits an immune response to more than one variant strain of SARS-COV-2.
Blocking protein-protein interactions is crucial for biological studies. The ability to block protein-protein interactions (PPIs) is crucial not just for therapeutic purposes—e.g. neutralizing antibodies for pathogenic threats like SARS-COV-2, or small molecule drugs for cancer therapy—but also for fundamental biological studies. Countless biological processes are mediated by protein-protein interactions, such as cell-cell interactions, signal transduction, cell-matrix interactions, immune system recognition, and many others, but it can be difficult to block these interactions with high affinity and specificity. Approaches like small molecule drugs, or peptides found through rational design or high-throughput evolutionary methods like phage, mRNA, or ribosome display are often hindered by lack of binding to the key protein-protein interface. Antibodies can block PPIs, but again must target a key interface (
Multivalent binding enhances affinity and expands target scope. One way to dramatically increase affinity for a target is by leveraging avidity: positioning multiple binding groups so that they can act cooperatively. Antibodies like IgG and IgM are intrinsically multivalent, although their geometry cannot be tuned to match the target. Extensive work in bionanotechnology has sought to rationally design multivalent binding agents for biomaterial applications. Most of these examples simply rely on a high density of the binding agents for activity, but a number of recent efforts have focused on matching the target size and valency with greater precision. For example, intrinsically symmetric assemblies can be targeted with designed homo-oligomeric binding agents. One report described a de novo designed homotrimeric protein grafted with a complementarity determining region (CDR) loop derived from a hemagglutinin (HA)-binding antibody could neutralize influenza with an IC50 in the picomolar range. Precisely matching the HA trimer geometry (namely the distance between monomers and the threefold rotational symmetry) was critical to the binding affinity. Using a similar design principle, another group reported a starshaped DNA nanostructure that positioned aptamers to match the distance and fivefold symmetry of the dengue virus coat proteins, resulting in potent binding and virus inhibition (EC50=2 nM). Once again, the ability to recapitulate the geometry of the capsid proteins with the aptamer was critical; structures that were too large or too small, or that had fewer or more than five ligands, did not bind as effectively. Furthermore, this example demonstrated the great potential of DNA as a programmable scaffold with controllable dimensions, relying on the precise valence and distances of the star-shaped scaffold to recapitulate the capsid protein symmetry.
The above examples, however, are restricted to homo-oligomeric targets like HA or viral capsids. Extending this paradigm to multiple different targets (either on a single protein or a protein complex) would dramatically expand the range of possible targets. Even simple DNA duplexes can be used as “molecular rulers” to position two binding groups, such as peptides or scFv molecules with a tunable distance to bind two separate sites on a target and enhance binding. In the latter example, two scFv fragments (either identical or different) could target HIV-1 virion spike proteins and improve virus neutralization by over 100-fold, whereas native IgG molecules were too large to effectively bind. Recent work also demonstrated that a DNA tile bearing two aptamer loops could be evolved to target non-overlapping sites of a target protein with femtomolar affinity, with the tile imparting the appropriate spacing to match the protein size. Here, inventors ask the question: can a DNA nanostructure be designed to position multiple protein binding groups with precise spatial control, but without the scaffold size limitations of antibodies or antibody mimetics? Such a general method that can position multiple (2-3) protein peptide-based ligands, on a size- and shape-programmable scaffold is still lacking. These nanoscale synthetic antibodies, hereinafter “DNA-peptide hybrid molecules,” will be designed and optimized/“evolved” in silico using coarse-grained molecular dynamics simulations, in a feedback loop with experimental results.
DNA nano-scaffolds possess several key advantages over other display methods. The use of DNA nanostructures—such as DNA origami, multi-helical bundles, branched tiles, wireframe cages, or single stranded “brick” assemblies—to display peptides or proteins in a multivalent fashion has certain key benefits over other scaffolds like proteins, polymers, or self-assembled nanoparticles/fibers. These advantages include: (1) Facile presentation of multiple polypeptides (either identical or different) with stoichiometric control and user-defined valency; (2) Control over the spacing of the peptides with ˜3-5 nm resolution; (3) User-defined size and shape of the ultimate structure to best match a target size (up to tens of nanometers); (4) Attachment of the final targeting assembly with other nanoscale carriers like liposomes or nanoparticles via DNA hybridization; (5) Potential for multivalent, or bi-/multi-specific structures by oligomerizing individual DNA-peptide hybrid molecules using DNA; (6) Steric blockage of protein-protein interactions due to their large size; (7) Demonstrated stability and functionality in vivo of either bare nanostructures or after stabilization using simple peptide coatings; (8) Large scale (˜$100/gram) production using recent breakthrough DNA production methods; (9) Dynamic assembly/disassembly of structures using light 18 or input displacement strands 19. (10) Ability to be shielded from the immune system, or to stimulate an immune response depending on the desired application. (11) Capacity for intracellular delivery and subcellular trafficking. (12) Potential to target assembled protein complexes by combining binders to distinct components of the complex on a DNA scaffold. Inventors also highlight that using a rigid DNA nanostructure (as opposed to a simple dsDNA molecular ruler) will enable enhanced binding due to lower entropic penalties, and the use of three or more binding peptides/proteins with precise display in 3D space.
One aspect of the disclosed technology is to use a DNA nano-scaffold to control the spatial orientation of multiple binding peptides or proteins, to create a highly specific synthetic blocking agent for protein-protein interactions. In antibodies, a large portion of the sequence is dedicated to positioning a few key CDR loops in the correct conformation; in Inventors work, inventors effectively decouple this structural component from the binding agents. Unlike antibodies, however, our structures will be designed to match the given target size and geometry. This will enable not only tighter binding (even if the individual peptides/proteins have only modest affinity), but also blocking of the target cell surface receptors due to the steric bulk provided by the scaffolding nanostructure. Crucially, this method enables peptides that bind to areas away from the targeted interface to be converted to a blocking function through the appended nanoscaffold. Because our approach can use both short, synthetic peptides and larger, folded proteins, it serves as a rapid way to quickly extend binding agents found from other approaches (e.g. phage/mRNA/yeast/ribosome display, de novo designed proteins, or novel nanobodies or scFv fragments) to multivalent scaffolds. In addition to using reported peptide/proteins and designing nanostructures to best bind a target, inventors will also find novel binding agents for fibrin/fibrinogen, and attach them to a DNA scaffold in a multivalent fashion. All of these approaches include seamless molecular integration of the protein/peptide groups with a DNA nanoscaffold, with control over the linker length and rigidity, so tailored protein-DNA bioconjugation will play a role in these studies.
Another aspect of the disclosed technology is the in silico screening and optimization of hybrid peptide/protein-DNA nanostructures. Aspects to consider when designing nanostructures of the present disclosure include, but are not limited to: (1) enough rigidity so that there is no entropic penalty to binding, yet (2) sufficient flexibility to tolerate thermal fluctuations and imperfections in the design. To tune these competing forces, inventors will develop the first integrated, coarse-grained model of protein-DNA nanostructures, where both molecules can be parameterized in a way that is accurate and computationally tractable. The model will in turn allow us to computationally screen multiple different DNA nanostructure designs, both in terms of geometry and strategic introduction of flexible/bulged sections, and to test the effect of peptide-DNA linker length and flexibility. Inventors employ computational models to best estimate pairwise distances between two binding agents whose binding site is unknown, and then use these distances as guidelines to design high-affinity blocking agents.
Currently, the major obstacle of in silico design in therapeutics are the system sizes and timescales involved in studying the binding pathways, as well as the correct parametrization of the models that predict binding interactions. As DNA nanostructures contain hundreds to several thousands of nucleotides, they are not amenable to atomistic-resolution computational studies that would sample their binding pathways to proteins. However, the coarse-grained approach allows for efficient sampling, making in silico evolutionary design possible by automatically generating and testing in simulation the binding of libraries of DNA nanostructures. Thus, this work will develop a new efficient design framework for automated evolutionary design, analysis and optimization of peptide/protein-DNA nanoscaffolds. Such a platform can greatly reduce experimental costs and speed-up development of high-affinity blocking DNA-peptide hybrid molecules. Although our work will develop and validate the system on the SARS-COV-2 spike protein and fibrinogen as model systems, the emphasis will be on a workflow that can be readily adapted to new targets and new binding agents.
Overview: The overall goal was to create a method for designing DNA nanostructures that can spatially display 2-3 binding ligands (primarily peptides and proteins, though aptamers can also be employed) that bind to different portions of a given protein target. Accomplishing this goal, however, includes accurate methods for computationally modeling the hybrid protein/peptide-DNA nanostructure, and “docking” it with the target without too great of an entropic cost. Inventors will describe an integrated computational-experimental pipeline, where coarse-grained simulation methods will be used to design an initial set of DNA-peptide hybrid molecules that can be experimentally tested for binding. The results of these experiments will be used to refine the models and generate a library in silico of slightly mutated nanostructures, the best-performing of which will be selected for future rounds of experimental characterization.
In a first aspect, inventors focus on a target for which multiple binding groups are known—the SARS-COV-2 spike protein receptor binding domain (RBD)—as a test bed in order to develop and benchmark the method. Inventors create DNA-peptide hybrid molecules with three identical binding groups that target the known ACE2 binding site of the RBD. Inventors then use one of these binding agents in conjunction with recently reported molecules that bind to a different region of the spike protein to develop hetero-bivalent structures. This process will involve novel chemical strategies for integrating the proteins/peptides with the DNA scaffold, optimizing the computational methods used, and testing DNA-peptide hybrid molecule “activity” by blocking the RBD interaction with the ACE2 receptor in a reversible fashion. In a second aspect, inventors use phage display to find several new nanobodies for fibrinogen, and then use these to discover heterobi- and tri-valent DNA-peptide hybrid molecules that bind to this target and block its activity in a stimulus-responsive, light-switchable fashion.
Develop DNA-peptide hybrid molecules for blocking the SARS-COV-2 spike protein. The COVID-19 pandemic has highlighted the need for high-affinity binding/blocking agents for viral threats like SARS-COV-2. As a result, there are a number of promising protein and peptide ligands for the spike trimer receptor binding domain (RBD), which is presented as a homotrimer with a known crystal structure on the capsid surface. Designing a DNA-peptide hybrid molecule that positions three identical proteins/peptides with a geometry and distances that match the RBD trimer will serve as an ideal test bed for both DNA nanostructure synthesis, but also to validate and optimize the theoretical model and computational pipeline. By the end of this aspect, inventors will have demonstrated that a DNA scaffold bearing three identical protein/peptide binding groups can serve as a high-affinity blocking agent for a virus.
Synthesize RBD-binding proteins and peptides and conjugate them to DNA. Several protein/peptides have been reported that target the SARS-COV-2 spike protein RBD and can neutralize virus association with the target ACE2 receptor. In particular, inventors explore three categories of such binders: (1) a de novo designed mini-binder proteins reported by Cao et al. and Linsky et al. that target RBD with IC50 values ranging from femtomolar to nanomolar; (2) several nanobodies that bind with nanomolar or better affinity; (3) short synthetic peptides that are highly tractable but tend to bind more weakly than proteins. Inventors highlight that one of the nanobodies inventors investigate was trimerized using a Gly-Ser linker and achieved femtomolar binding affinity and picomolar virus inhibition, despite using a flexible linkage and linear concatenation via genetic fusion. Thus, our nanostructure-scaffolded, size/geometry-matched approach may give even greater affinity by reducing the entropic penalties for rearrangement to the correct geometry.
All polypeptides will be conjugated to DNA one of two ways, both of which have been extensively used in PI Stephanopoulos's lab: (1) via a unique, mutagenically-introduced cysteine using a bifunctional linker (
Test RBD binding activity of peptides/proteins and DNA conjugates. To test the ability of the synthesized peptides/proteins to bind to the SARS-COV-2 RBD, inventors employ two methods: (1) an ELISA assay using the RBD and its targeting antibody; and (2) surface plasmon resonance (SPR), which was used in the characterization of most of the binding groups mentioned above, and enables greater insight into on- and off-rates of the binding molecules. Preliminary data: Inventors have probed the binding of our in-house expressed LCB1 to RBD using both ELISA and an SPR assay. The LCB1 protein was adsorbed to the surface, followed by exposure to varying concentrations of the monomeric spike RBD protein; the amount of RBD adhered was then probed with a primary antibody and a secondary antibody-HRP conjugate. The RBD protein did indeed bind to the LCB1, with a Kd in the 100-200 pM range, similar to reported values (
Inventors test the LCB1-DNA conjugate—and all the peptide/protein-DNA hybrids made in an analogous fashion—in the same manner, cognizant of the fact that the DNA handle could decrease the binding affinity. Although the attachment site for DNA has been engineered to be distant from the RBD-binding interface, it may be necessary to screen several attachment sites, as well as linker identities (e.g. alkyl, aryl, PEG) and lengths. Mutated peptide/protein molecules, where the binding interface residues are scrambled to abolish binding, will be used as controls. Inventors will use SPR to determine rates of binding (kon, koff), and thus the Kd values. All conjugates will be compared with the original (i.e. non-DNA-conjugated) binding groups as positive controls.
Design, synthesize, and characterize hetero-trivalent peptide/protein-DNA nanostructures. The ideal DNA nano-scaffold for hetero-trivalent presentation of the above peptide/protein-DNA conjugates is a structure that is reasonably rigid (to avoid entropic penalties in nanostructure reconfiguration), and roughly size-matched to the spike RBD trimer diameter (˜7-8 nm). Nanostructures scaffolds will be assembled using thermal annealing of the constituent strands, and purified using either spin filtration, gel excision, or anion exchange chromatography. Single-stranded DNA handles will be included for attachment of peptide/protein-DNA conjugates, and successful incorporation will be probed using gel shift assays and/or using fluorescently tagged peptides/proteins. Nanostructures with zero, one, and two handles for peptide/protein incorporation will be synthesized to probe the effect of not just binding group, but also valency; indeed, this straightforward tunability is an advantage of DNA nanoscaffolds. Preliminary data: A series of DNA nanostructures were designed and used, including (
For this work, inventors primarily focus on simpler DNA nanostructures (rather than full-size origami) in order to better match the protein size, and to improve the overall scalability of the final assemblies. Towards this end, inventors will test structures like four- and six-helix bundles (
Develop a computational model for simulating hybrid peptide/protein-DNA nanostructures. One bottleneck to developing the proposed DNA-peptide hybrid molecules is that no model exists for the design of hybrid polypeptide-DNA nanostructures (unlike for proteins where packages like Rosetta50 exist for modeling structure and designing novel binding groups). Accurately representing the 3D spatial display of multiple heterogeneous molecules on a DNA nanostructure would allow more accurate matching of the hybrid structure to the target. Such a model would also enable the in silico “mutagenesis” and screening of designs that best match the binding sites on the target in order to guide experimental realization. Preliminary data: The oxDNA tool, a coarse-grained model of DNA that reproduces mechanical, structural and thermodynamic properties of both single-stranded (ss) and double-stranded (ds) DNA will be used. The model has been used in a range of settings, from biophysical studies of DNA to probing the assembly of nanostructures and active nanodevices, usually with good agreement with existing experimental data. OxDNA can efficiently simulate nanostructures consisting of up to tens of thousands of nucleotides and captures timescales that correspond to tens of milliseconds in experiment51. Recently, an extension of the model was introduced: ANM-oxDNA, that uses the oxDNA model for DNA and also represents protein structures and short peptides using the anisotropic-network-model (ANM) to capture their basic dynamics and conformations. The model is able to reproduce the structure of protein-DNA hybrid structures previously realized in Stephanopoulos lab. Currently, the model does not predict de novo interactions between peptides and proteins, and the possible interactions have to be explicitly specified based on prior knowledge of the binding sites. The model can, however, very quickly sample nanostructure diffusion well as its binding trajectory to a protein. Our prior analysis has shown that the simulation can efficiently sample the possible conformations of a DNA nanostructure—and the regions that a multivalent binder can cover on a protein—within less than 1 GPU-hour for a protein and a nanostructure system consisting of several hundred residues in total.
Here, inventors implement an automated in-silico nanostructure mutation generation using our recently developed ox View design tool for nucleic acid nanotechnology, which was recently extended to also support protein structure representation. The initial design for a multivalent peptide/protein-DNA nanostructure can be either imported from other DNA nanotechnology design tools or created directly in ox View. Inventors will then implement an automated algorithm for introducing “mutations” to the structure design, which will include: changing the position for peptide/protein attachment, extending/shortening dsDNA and ssDNA segments in the nanostructure, and introducing bulges and junctions into the design (
Use the experimental and computational pipeline to optimize DNA-peptide hybrid molecule structures. Following synthesis of hetero-trivalent DNA-peptide hybrid molecules bearing LCB1 or other RBD-binding domains, inventors will probe their binding to a homotrimeric spike protein complex (SP3), and use the computational model to guide nanostructure refinement and testing. This trimerized spike protein is available from commercial suppliers, and inventors will rationally design a set of starting designs, approximately positioning the binding peptides to match the position of the ACE2 binding sites on the SP3 (
A key feature of multivalent binding is not just enhanced affinity, but a greatly decreased koff for binding, e.g. as seen by Strauch et al. for homotrivalent HA binding proteins. Inventors will probe the binding kinetics of DNA-peptide hybrid molecules by SPR, and compare to nanostructures bearing only one or two peptides/proteins, and mutated (non-binding) molecules. While our model will not be able to directly predict the binding affinity, it will still be possible to rank the structures based on the scoring function. Inventors will compare the experimentally-measured binding affinity with the ranking produced by the model, and seek to adapt the scoring function to match the experiments. Thus, rather than creating a funnel-like approach commonly used in computational design pipelines—where a set of binders is generated, from which only subset is then successfully verified in experiment—our work will create a feedback design loop, where the efficient but coarse model is improved through experimental measurements. At the same time, the model will allow us to effectively search design space and provide iteratively improved designs for experimental probing. As well as determining the affinity between DNA-peptide hybrid molecules and SP3, inventors will also probe the structure's ability to block the spike trimer association with the ACE2 receptor, as a proxy for inhibiting viral infection. In addition to traditional binding/blocking studies via SPR, inventors will also probe the DNA-peptide hybrid molecule binding via negative stain transmission electron microscopy (TEM) and atomic force microscopy (AFM). Both DNA nanostructures and bound proteins can be readily visualized using these methods, so they can be used to demonstrate not just binding, but also affinity (e.g. by counting structures with and without proteins). Results will be compared to free proteins/peptides, and homo-trimerized binding groups using flexible chemical or genetically expressed linkers.
Determine distances between RBD site and a separate binding site. Most targets of interests are not homo-oligomeric, so the approach outlined above will not be applicable. Thus, inventors will develop a DNA-peptide hybrid molecule that can position two different targeting groups—where one has a known and the other an unknown binding site on the target—with 3D precision in order to enhance the affinity. Once again, inventors will use the SARS-COV-2 spike protein as the target, because recently several nanobodies, a bispecific IgG mimetic, and an aptamer were reported that did not target the ACE2 binding domain on RBD. One nanobody in particular was shown to bind the N-terminal domain (NTD) of the spike protein, and did not compete with a separate nanobody that bound to the RBD. Inventors will use this NTD site as a test system to (1) develop new computational experimental method that will be able to de novo identify location of binding sites, and (2) create a DNA-peptide hybrid molecule that can position the two groups with spatial precision to match this experimentally-determined distance. Inventors will initially develop a computational-experimental pipeline to determine the location of the second binding site as if the NTD binding site was not known, allowing us to compare our unbiased results to the known location after the fact. The pipeline will generate a set of “nano-rulers,” consisting of the two binding groups linked by simple dsDNA linkers of known length. Inventors will annotate the possible binding sites using available peptides global docking tools that provide a list of approximately 4-10 candidate binding sites, featuring multiple false positives. Inventors will then use the computational platform to design a set of DNA scaffolds with the peptides attached at different distances. Thus, when one peptide (e.g. LCB1) is bound to the RBD, the second peptide on the scaffold covers different distances on the surface of the protein. The set of scaffolds will be designed to cover the respective possible binding distances between the known binding site and the candidate binding site. By comparing the experimental affinity measurements between the designed scaffolds, inventors will be able to select the scaffold that binds to both sites at the same time, and thus “identify” (i.e. confirm) the position on the second binding site (
Design and test hetero-bivalent DNA-peptide hybrid molecules to match the distances determined. Once the approximate distances and location have been determined for the two binding groups, inventors will design heterobivalent DNA-peptide hybrid molecules that recapitulate this distance and probe for both binding and blocking of the structure to the spike RBD monomer. Although the nanostructures discussed previously can be used, inventors will also explore simpler structure like rigid double-crossover (DX) tiles, where the binding groups can be positioned at multiple locations. The tile will provide added steric bulk for blocking the interaction with ACE2. Inventors will follow the same computational-experimental pipeline as presented previously, and compare the DNA-peptide hybrid molecules to binding groups dimerize using flexible linkers (either alkyl, PEG, or amino acid (via recombinant expression)).
Demonstrate stimulus-responsive “off” switch for DNA-peptide hybrid molecule binding. One key advantage of our approach for blocking protein function is that it can, in principle, be reversed by disassembling the nanostructure in a stimulus-responsive fashion. In particular, o-nitrobenzyl ester moieties can be installed into the DNA backbone, resulting in clean scission upon exposure to 350 nm UV light, an approached used by PI Stephanopoulos to install photocleavable functionality into a DNA nanomechanical device. Inventors will incorporate such a photocleavable moiety into the DNA handles attached to the binding groups from presented earlier, so upon UV illumination the entire scaffolding DNA nanostructure is released (
Expected outcomes, potential pitfalls, and alternative approaches: By the end of this work, inventors will have developed DNA nanostructures bearing: (1) three copies of an RBD-2 binding peptide/protein, or (2) two different binding groups for the spike protein. Inventors will have optimized the computational pipeline to in silico evolve these nanostructures by comparing their bound and unbound state, which is efficient enough to run freely diffusing simulations of the binding trajectory. Potential pitfalls and alternate solutions include the following. (1) Attachment of a DNA handle may compromise peptide binding. While inventors expect that folded proteins like LCB1 will not be greatly affected by DNA handle attachment, it is possible that shorter peptides may be more sensitive helix stabilizing residues or backbone (i, i+7) crosslinks, or use neutral peptide nucleic acid (PNA) handles instead of anionic DNA. (2) The simulations might incorrectly predict the affinity of the designed nanostructures. In that case, inventors will use the experimentally measured affinity to further update the scoring function that will be used in the simulation to assess the enthalpic contribution of binding to the protein surface. (3) The proteins used are too large to effectively position them in 3D space. It is possible that, especially for targeting two different spots on the spike monomer, using LCB1 and a nanobody (or two nanobodies) will be too sterically bulky. In this case, inventors will use cyclic peptides recapitulating the CDR3 loop from the nanobodies, as described in greater length previously. (4) The SARS-COV-2 spike protein is a poor target. If no successful hetero-bivalent DNA-peptide hybrid molecules against the spike protein are found—e.g. because distances determined previously are too small for a DNA nanostructure to effectively bind—inventors will instead turn to a different target: influenza hemagglutinin (HA). Indeed, trivalent protein scaffolds with grafted CDR loops have demonstrated high-affinity binding to this target3, so inventors will use the same loops as starting points for our design. Furthermore, a number of short peptides discovered from on-chip peptide arrays have been reported for HA. Inventors will carry out our “molecular ruler” method for these peptides to find combinations that span distances suitable to DNA nanostructures. Most of these peptides have only modest affinities (Kd˜low micromolar), so attachment to a scaffold could increase the affinity to/past the nanomolar regime, as demonstrated using chemical linkers.
Develop a photo-switchable blocking DNA-peptide hybrid molecule for fibrinogen. Rationale: If multiple binding agents are not readily available for a target, one or more must be discovered using selection methods like phage display. However, this approach poses the challenge that the binding sites for these new targeting groups are not known, and thus must be determined prior to incorporation into a scaffolding nanostructure (which will itself be tuned to best recapitulate these distances). Inventors will work to discover new binding peptides for fibrinogen, in order to block its assembly into fibrin clots. These peptides will not all bind in the same location, so the methods developed in previously will be employed to map their likely distances on the target, in order to design a heterobi- or tri-valent DNA-peptide hybrid molecule that can inactivate the protein-protein interactions. Inventors will also use the photocleavable approach described previously to “turn on” fibrin self-assembly by unblocking the structure. Although inventors will focus on fibrinogen as a proof of principle, inventors will have developed a pipeline for future targeting of any protein through a three-step process: (1) Identify a subset of binding nanobodies/peptides against the target; (2) Determine the pairwise distances for proteins/peptides that bind to nonoverlapping sites; and (3) Design a DNA-peptide hybrid molecule to effectively envelop the target, using the computational experimental approach outlined earlier.
Preliminary data: Phage display can be used to find novel targeting nanobodies against complex targets such as fibrin, in vitro cell culture models of reactive astrocytes, ex vivo tissue sections from small and large animal models of brain injury, and in vivo brain injury mouse models. However, the target nanobodies are often difficult to express recombinantly, leading to poor yields or aggregation. Thus, it was recently reported that cyclized peptides from the CDR3 loop of targeting nanobodies can be highly effective as targeting agents, while retaining a small size and ease of synthesis. This approach was termed the CDR3 Loop Assembly via Structured Peptide (“CLASP”) system (
Phage display against key fibrinogen polymerization domains to discover nanobody CDR3 loops. Inventors will leverage prior knowledge of the fibrin knob-pocket interactions that drive fibrin assembly and polymerization; specifically, inventors will use the short peptide sequence of GPRPXX (SEQ ID NO: 3) that recognizes hydrophobic pocket domains on the beta and gamma chains. Phage display with the aforementioned dAb phage library against fibrinogen in the presence of the GPRPXX (SEQ ID NO: 3) peptide (at millimolar concentrations to compensate for its modest Kd (5-10 μM) will be conducted to identify recognition domains outside of the pocket regions. Human fibrinogen will be immobilized on microbeads via EDC/NHS chemistry. Inventors will carry out biopanning with a naïve human dAb phage library, which will be produced and purified per protocol. Substrates will be incubated with dAb phage (100 μl of 1010-1012 CFU) for 1 hr. Non-specific binding phage will be removed via a series of rinses with PBS+0.1% Tween 20 (PBST). The target bound phage will then be eluted, collected, and amplified. Subsequent rounds will be repeated with an enriched population of eluted phage from the previous round. A minimum of three biopanning rounds will be completed, with a goal of obtaining 10-20 nanobodies that span a range of binding areas on the protein. To identify the CDR3 loop, inventors will carry out next generation sequencing (NGS) and bioinformatic analysis. The use of NGS provides a robust and high-throughput alternative to Sanger sequencing with extensive coverage, enabling an in-depth analysis on the eluted phage libraries. Here, amplified plasmid DNA from the eluted phage libraries will be prepared for Illumina MiSeq 2×250 sequencing. Paired end sequences will be stitched together using Fast Length Adjustment of SHort Reads (FLASH). HCDR3 sequences will be clustered using a hierarchical Levenshtein Distance algorithm with FASTApatmer Perl scripts. Each library will be searched for HCDR3 sequences that are enriched through the biopanning round using a combination of in-house R scripts and Galaxy modules. The top enriched dAb sequences will be selected based on the HCDR3 analysis and the following selection criteria: 1) unique to a distinct target, 2) not present in control phage library (amplified without biopanning), and 3) high frequency and enrichment observed round to round.
Synthesis of cyclic peptides and DNA conjugates. Following identification of nanobody-derived CDR3 loops that bind to fibrinogen, inventors will next synthesize cyclic version of these peptides by introducing terminal cysteine residues and bis-bromoacetamide linkers as described previously. The linkers will also incorporate linear alkynes for copper-catalyzed click coupling to azide DNA. Peptide-DNA conjugates will be purified and characterized as described in earlier, and individually tested for binding to fibrinogen by SPR (both cyclic peptides alone and DNA conjugates thereof).
Determination of pairwise distances for three-peptide sets. Inventors will next use the set of peptide-DNA conjugates to map out potential binding sites to fibrinogen, as outlined above. One of the peptides used will be the GPRPXX (SEQ ID NO: 3) sequence that binds to the pocket domains, and it will serve as a way to “pin” the possible distances covered by the other peptides. Following the experimental-simulation pipeline developed in a first aspect, inventors will use available global docking tools to annotate likely binding sites for the peptides identified to bind to fibrinogen in the phage display experiments (
Design and testing of hetero-trivalent DNA-peptide hybrid molecules. Inventors will use in silico iterative evolution framework developed in earlier to design candidate DNA nanostructures that position the peptides in 3D space. These structures will constrain GPRPXX (SEQ ID NO: 3) and, ideally, two additional CLASP peptides at the distances determined previously, and binding to fibrinogen will be probed using SPR as described in a first aspect. In addition, inventors will probe the functional blocking of fibrin polymerization by the nanobody, following proteolytic cleavage by thrombin, using a suite of fibrin polymerization assays. Specifically, inventors will assess polymerization dynamics (turbidity and thrombin clotting time), extent of clottable protein, and clot structure (confocal microscopy). Fibrin polymerization assay: Thrombin-initiated fibrin polymerization assays will be used to evaluate anticoagulant activity. For all assays, fibrin clots will be prepared with final concentrations of human fibrinogen at 1 mg/mL (plasminogen-, fibronectin-, von Willebrand Factor-depleted), human α-thrombin at 1 NIH U/mL (ERL), activated human factor XIII at 1 U/mL in a HEPES-buffered solution supplemented with calcium chloride. Prior to initiating polymerization, 50 μL of fibrinogen or fibrinogen+hetero-trivalent DNA-peptide hybrid molecules will be incubated at room temperature for 30 min in a transparent 96-well plate. Polymerization will be initiated by adding 50 μL of thrombin+FXIIIa to each well. Turbidity curves will be generated from absorbance measurements recorded every minute for 60 min at 350 nm. Post-assay analysis of turbidity curves will include the peak absorbance and thrombin clotting time. Percent clottable protein: Upon completing turbidity assays, the resulting fibrin clots will be removed, leaving behind the remaining soluble protein (i.e., the clot liquor). The soluble protein content in the clot liquor will be quantified using a Quant-iT protein assay (Invitrogen). Data will be assessed as percent clottable protein, the amount of initial protein minus soluble protein in the clot liquor all divided by the initial protein. Fibrin fiber structure: Confocal microscopy will be used to evaluate the fibrin fiber structure. Briefly, fibrin clots will be prepared as described above with addition of 5% fluorescently labeled fibrinogen. Upon initiating polymerization with thrombin and FXIIIa, 100 μL will be immediately transferred to a glass slide with 300 μm spacers and capped with a cover slide. Clots will be imaged 60 min after polymerization. Five random 10 μm zstack sections of each clot will be imaged with a Zeiss Laser Scanning Microscope. Image analysis and 3D projections will be performed with ZEN imaging software.
Reversible blocking of fibrin assembly. As outlined above, an advantage of our approach is the ability to cleave the nanostructure for the binding peptides/proteins using UV light. Given that some of the peptides discovered herein will bind to sites away from the key binding interface, it is likely that photo-removal of the DNA scaffold will restore binding even if the individual peptides remain bound. In particular, the weak (micromolar) affinity of GPRPXX (SEQ ID NO: 3) for the pocket suggests that upon nanostructure cleavage, this peptide will dissociate from the protein without the avidity effects of the other binding groups. Pre-blocked fibrin will be cleaved using thrombin as above, and then exposed to UV light to remove the DNA-peptide hybrid molecule. The kinetics of polymerization will be compared with unblocked controls, and the fibrin fibers examined.
Expected outcomes, potential pitfalls, and alternative approaches: Inventors will have developed a novel DNA-peptide hybrid molecule that positions up to 3 cyclic peptides derived from phage display to block fibrin assembly until activated using light. Potential pitfalls and alternate solutions include the following. (1) Phage display against the fully intact fibrinogen protein does not yield relevant CDR3 domains. If the CDR3 domains cannot block polymerization, inventors will use enzymatically or chemically cleaved fragments of fibrinogen to further refine/constrain the target to the pocket domain (i.e. fragment D). (2) Global docking tools are unable to give sufficient number of candidate binding sites and none of the designed nano-rulers can successfully identify the binding sites of the CD3 loops. In such case, inventors will design in silico a set multivalent nanostructure functionalized with CDR3 loops selected against chemically cleaved individual fragments of fibrinogen. Inventors will optimize the nanostructure so that its respective arms with attached CD3 loop are designed to cover the entire protein fragment against which the CDR3 loop was selected. (3) DNA conjugation perturbs cyclic peptide binding affinity. If the DNA handles reduce or abolish the CLASP peptide binding, inventors will explore constructs with varied linker lengths, or use PNA handles instead of DNA to avoid charge repulsion. It may also be necessary to append both ends of the peptide directly to the DNA backbone (using the structure to effectively cyclize it) in order to reduce flexibility in the system.
The two broad aspects of the disclosed technology outlined above rely on knowing individual binding proteins or peptides. A more powerful method, however, would be to directly select the bi- or tri-valent nanostructure, by creating a combinatorial library of all possible peptide/protein combinations on the scaffold. Inventors envision creating libraries of formed nanostructures with random combinations of peptides/proteins and selecting for the final assembly. For instance, peptide-RNA conjugates generated from mRNA display can be integrated into the scaffolds through a common poly(A) linker. However, the nanostructures used to scaffold these peptides/proteins will be tunable from the outset to match the rough size of the target, and a subsequent optimization of the scaffold could be performed to further enhance binding. Following selection of the best heterotrivalent nanostructure, the peptide identity can be deduced via sequencing of the appended mRNA handles. Finally, our approach can be used to block previously un-targetable proteins; by using any surface on the protein as a “handle” to help associate a nanostructure and block a key interface, inventors expand the space of targetable protein patches. The use of multiple binding sites to enhance affinity can also reduce mutational escape if any patch changes, and allow the combination of peptides, aptamers, and even small molecules on the scaffold.
There are now reports of multiple variants emerging around the world as the duration of the SARS-Cov-2 pandemic extends, such as Alpha (B1.1.7) from the UK, Beta (B1.351) from South Africa, Gamma (P1) from Brazil, and Delta (B1.617.2) from India, among others. These lineages are each characterized by numerous mutations in the spike protein, raising concerns that they are not affected by neutralizing monoclonal and vaccine-induced antibodies. As of August 2021, COVID-19 has caused over 4 million deaths and continues to place a heavy burden on healthcare systems. Hence, the development of a safe and effective vaccine that can prevent SARS-COV-2 variant infection and transmission has rapidly become a top priority. It was recently shown that a two-component protein-based nanoparticle vaccine that displays multiple copies of the SARS-COV-2 spike protein and receptor-binding domain (RBD) induces potent neutralizing antibody responses in mice, rabbits, and cynomolgus macaques and protects the animal against a high-dose challenge, resulting in strongly reduced viral infection4,5. Subunit vaccines are among the safest and most widely used vaccines and have been highly effective against a variety of infectious diseases, such as hepatitis B, HPV, tetanus, etc. DNA has emerged as an exceptional molecular building block for functional molecules assemble due to its predictable conformation and high programmability which allow assembling protein-DNA shape design and easy modification. Currently, the Baker lab showed that there is a de novo designed mini-binder protein called LCB1, which possesses high-affinity binding (KD˜1 nM) to the spike protein, but also displays no immunogenicity. Inventors have recently designed and constructed trivalent mini-binder using DNA nanostructure-directed assembly and it shows high affinity (KD˜1 pM) and high specificity against spike RBD (
Inventors have already designed and constructed the icosahedron DNA origami, and obtained strong preliminary data showing that the DNA directed trivalent mini-binder has high-affinity binding with the spike and variants. To overcome the multiple spike variants escaping the neutralization antibody in vaccinated people, inventors hypothesize that the variant spike and icosahedron DNA origami subunit vaccine, displaying 12 copies of different spike variants and 36 copies of different variant spike receptor-binding domain (RBD), could provide specific and highly efficient target spike variants for prevention against a SARS-Cov-2 virus variant infection.
Design and development of icosahedron DNA origami displaying multivalent SARS-Cov-2 spike variants nanoparticle, in vitro assembly, and characterization. An icosahedron DNA origami will be designed to carry three mini-binders and CpG DNA adjuvants as a multi-valent subunit vaccine for prevention against the SARS-COV-2 variants virus. 1) Trivalent mini-binders conjugated with a DNA sequence will be assembled on an icosahedron surface as a strong binding domain against spike variant proteins; 2) Icosahedral DNA origami is used as a framework to assemble spike variants and CpG adjuvants; 3) Different spike variants co-assemble on the icosahedron DNA origami via trivalent mini-binder to present SARS-COV-2 spike variant immunogen. Our preliminary data show that the mini-binder has a robust binding affinity up to picomolar for spike and variants. Inventors hypothesize that there are 12 copies of different spike trimer variants, which contain 36 copies of different variant spike receptor-binding domain (RBD), and they are displayed in a highly immunogenic array using an icosahedron DNA origami for protective immunity against SARS-COV-2 virus infection. To design the DNA origami and optimize the placement of adjuvants and presented mini-binders on the origami, inventors will use molecular simulations and our in-house design tools for protein-DNA hybrid nanostructure design.
In vivo test to evaluate the DNA origami based subunit vaccine in mouse and rabbit models. The DNA origami based subunit vaccine will be evaluated to measure the vaccine-elicited antibody responses against the SARS-COV-2 variant spike antigens and viruses. Inventors will also assess the neutralization of and protection against SARS-Cov-2 virus and vaccine-induced heterosubtypic antibody responses and protective immunity using the mouse and rabbit models.
Effective activation of antigen-specific B cells is a crucial factor for vaccine action. Multivalent presentation of immunogens is a well-established strategy for efficiently activating B cells. Antigen multimerization allows complete activation of low-affinity B cells. For example, proto-multimers, antigen-bound polymers displaying immunogen at high densities, and virus-like nanoparticles (NPs) have all been shown to initiate early B-cell signaling vigorously. In addition, antigen spatial arrangement, copy number, stiffness, and size of the affinity scaffold are also vital considerations driving early B cell activation and humoral immunity. Leveraging these key elements of vaccine design, DNA scaffold-based multivalent antigen presentation enables precise programmability of antigen spatial distance, copy number, and size. Precise functionalization of DNA scaffolds is typically achieved by post-assembly hybridization, in which ssDNA cantilevers on DNA nanostructures hybridize to complementary nucleic acid strands attached to the desired conjugate. This approach allows nucleic acid-modified proteins, peptides, lipids, and dyes to be conveniently and site-specifically linked in an orthogonal and sequence-programmable manner.
Herein, inventors designed SARS-COV-2 spike protein receptor binding domain (RBD)-functionalized DNA-VLPs as a novel SARS-COV-2 subunit vaccine. The RBD, a key antigen for eliciting neutralizing antibodies against SARS-COV-2, was assembled to the apex of an icosahedral DNA origami to form a virus-like nanoparticle displaying 36 proteins, as shown in
As shown in
Reaction conditions were optimized for the efficient high-density functionalization of DNA-VLPs, which were subsequently purified using dialysis. For the characterization of DNA-VLPs, gel electrophoresis, Nanoparticle tracking analysis, and Cryogenic electron microscopy (cryo-EM) were used to confirm their geometry, monodispersed, and structural rigidity. Gel electrophoresis results showed distinct bands of Ico-RBD compared to the unfunctionalized DNA origami (
Florescence Quantification of DNA-NP Coverage with Antigen
Next, to quantify the coverage of the protein on the DNA structure, the conjugation of RBD to DNA-NP was quantified using a fluorometer. RBD monomers were modified with AF647 dye as described above prior to passing through hybridization to DNA-NPs. RBD proteins were incubated with five molar equivalents of AF647 for two hr. and subsequently purified by dialysis. The AF647-labeled RBD proteins were subsequently assembled onto DNA nanostructures as previously described. Fluorescence calibration curves were first measured with free monomeric DNA-LCB-RBD by varying the antigen concentration using free monomers conjugated to the AF647 dye and subsequently used as a reference curve to determine the yield of conjugation to DNA-NPs. AF647-labeled RBD functionalized onto DNA-NPS was subsequently determined by gel electrophoresis, with AF647 channels and EB lanes showing corresponding bands indicating successful functionalization (
As the uptake of antigens by APCs (DCs and macrophages) is critical for antigen processing and cross-presentation, inventors first examined the internalization of DNA vaccine (icosahedron-protein complex) by macrophage cell line (RAW264.7). Confocal microscopy was used to quantify the uptake by RAW 264.7 cells after incubation with the DNA vaccine. The protein was labeled with Alex647 dye and then assembled on an icosahedron to form an icosahedron-protein complex (Ico-pr) and then incubated with RAW264.7 cells (
It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention. Thus, it should be understood that although the present invention has been illustrated by specific embodiments and optional features, modification and/or variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.
The present application claims priority to U.S. Provisional Patent Application No. 63/257,835, filed Oct. 20, 2021, the entire contents of which are hereby incorporated by reference.
This invention was made with government support under GM132931 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2022/078426 | 10/20/2022 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63257835 | Oct 2021 | US |
