Patent Application
20240016943
Incorporated by reference in its entirety herein is a computer-readable nucleotide sequence listing submitted concurrently herewith and identified as follows: One 281,989 Byte ASCII (Text) file named “767465_ST25” created on May 23, 2023.
Transcription factors (TFs) regulate cellular state by binding specific DNA promoter and enhancer sequences, thereby recruiting transcriptional machinery to activate or repress gene expression. DNA binding is carried out by modular domains that are shared by large families of transcription factors, and conserved across evolution. Aberrant TF activity is widely and unambiguously implicated in human disease. For example, many cancers are hallmarked by direct genetic alteration of TFs by amplification, deletion, translocation, or mutation. Cancers that do not harbor these direct alterations to TFs invariably rely on dysregulated upstream signaling pathways that ultimately impinge on TF function and gene expression programs. There is a need in the art for synthetic DNA binding domains (sDBDs), including those that are synthetic transcriptional regulators (STRs), including to treat or prevent cancer.
In aspects, the disclosure provides a polypeptide construct comprising (a) a first polypeptide comprising an amino acid sequence derived from a basic helix of a transcription factor protein that comprises a basic helix-loop-helix domain; and (b) a second polypeptide comprising an amino acid sequence derived from a helix that extends in the C-terminal direction from the end of the loop of a basic helix-loop-helix domain of a transcription factor protein that comprises a basic helix-loop-helix domain; wherein the first polypeptide and the second polypeptide are linked through an interpolypeptide covalent linkage.
In aspects, the disclosure provides a polypeptide construct comprising (a) the polypeptide construct as described above; (b) a third polypeptide comprising an amino acid sequence derived from a basic helix of a transcription factor protein that comprises a basic helix-loop-helix domain; and (c) a fourth polypeptide comprising an amino acid sequence derived from a helix that extends in the C-terminal direction from the end of the loop of a basic helix-loop-helix domain of a transcription factor protein that comprises a basic helix-loop-helix domain; wherein the third polypeptide and the fourth polypeptide are linked through an interpolypeptide covalent linkage.
In aspects, the disclosure provides pharmaceutical compositions and methods of treating disease using the polypeptide constructs and polypeptides as described herein.
Additional aspects of the disclosure are as described herein.
In aspects, the disclosure provides a polypeptide construct comprising (a) a first polypeptide comprising an amino acid sequence derived from a basic helix of a transcription factor protein that comprises a basic helix-loop-helix domain; and (b) a second polypeptide comprising an amino acid sequence derived from a helix that extends in the C-terminal direction from the end of the loop of a basic helix-loop-helix domain of a transcription factor protein that comprises a basic helix-loop-helix domain; wherein the first polypeptide and the second polypeptide are linked through an interpolypeptide covalent linkage.
In aspects of the disclosure, synthetic transcription factors bind to DNA with comparable affinity and specify when compared to native proteins. In aspects, synthetic transcription factors comprise a covalent helix cross-dimer, wherein two defined helices that comprise a DNA-binding helix (basic helix, B) and a structure-orienting zipper helix (Z), each derived from bHLH protein family proteins or derivatives thereof, are chemically connected, e.g., via intermolecular side chain-to-side chain linkers. Ligation positions on the helices for the intermolecular connection can be chosen for opposing helices of the tetrahelix bundle normally formed by two bHLH proteins that have bound to one another. In the case of synthetic DNA binding domains herein, the B-Z helices can be chosen from opposing monomers, and chemically linked such that they can self-assemble in a “sandwich-like” fashion to bind DNA. Therefore, the monomeric sDBDs described herein can be chemically and structurally defined but completely non-natural in structure. The fully synthetic di-helix monomer can dimerize with an additional synthetic transcription factor to form a tertiary structure that mimics the natural transcription factor DNA binding bHLH domain. Due to the cross-dimer linkage, synthetic transcription factors described herein may not form productive binding interactions with native bHLH domains. Synthesis of sDBDs derived from the bHLH transcription factors can be modular in nature.
The amino sequences of bHLH domains from 105 human proteins are identified in Tables 1A and 1B. Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) was used to perform a multiple sequence alignment and the aligned sequences are presented in Table 2. Approximately positions 1-29 represent the “B” helix, approximately positions 30-43 represent the loop, and approximately positions 44-60 represent the “Z” helix. To generate a synthetic transcription factor, a covalent chemical crosslink is formed between a “B” and “Z” helix derived from any bHLH domain. The chemical crosslink can be, e.g., between position 23 of the “B” helix and position 51 of the “Z” helix, or a different position that maintains the defined binding orientation of synthetic transcription factors. Altering the non-natural amino acid positions and helix-stabilization strategies can modulate the resulting STF's binding activity and proteolytic stability. N-terminal extension or truncation of amino acids to the “B” helix can be used to modulate DNA binding affinity and specificity and C-terminal amino acid extension or truncation to the “Z” helix can be used to modulate DNA binding affinity and specificity.
Thus, the basic helix of a protein is defined as the region of the protein amino acid sequence that aligns with the basic helices of the amino acid sequences as shown in Table 2. The zipper helix of a protein is defined as the region of the protein amino acid sequence that aligns with the zipper helices of the amino acid sequences as shown in Table 2. Such alignment can be achieved using an alignment program, such as, e.g., Clustal Omega, and performing a global alignment of a new protein sequence against the sequences as shown in Table 2 or the full length amino acid sequences of the proteins listed in Table 2.
The alignment can be enhanced using principles taken from the alignments of the sequences of Table 2. Based on the alignments shown in Table 2, “consensus” sequences emerge, wherein the basic helix can have the amino acid sequence of
wherein the representations of the symbols are found below in Table 3.
Some variations among sequences are possible, and there is a 90% likelihood that the basic helix can have a sequence of
an 80% likelihood that the basic helix can have a sequence of
a 70% likelihood that the basic helix can have a sequence of
The zipper helix can have the amino acid sequence of
a 90% likelihood that the zipper helix can have a sequence of
an 80% likelihood that the zipper helix can have a sequence of
a 70% likelihood that the zipper helix can have a sequence of
The sequences of Table 2 can be used without adding the new sequences to the list of sequences in Table 2, where the consensus criteria are maintained for each new sequence, as the criteria are given above. As additional alignments are performed with new sequences, the new sequences can be added to those sequences in Table 2 to update the list of sequences and the consensus criteria. As understood by those in the art, the consensus criteria may evolve with the addition of any new sequences.
In aspects, the basic helix of the first polypeptide comprises the amino acid sequence extending 36 residues in the N-terminal direction from the start of the loop of the basic helix-loop-helix domain. In aspects, the second polypeptide comprises the amino acid sequence extending 31 residues in the C-terminal direction from the end of the loop of the basic helix-loop-helix domain. In aspects, the second polypeptide comprises a leucine zipper helix.
In aspects, the amino acid sequence of the first polypeptide comprises a set of two non-natural amino acids, wherein the non-natural amino acids are the same or different, wherein each of the non-natural amino acids includes a moiety, wherein the moieties are capable of undergoing a reaction to form an intrapolypeptide covalent cross-link with each other, wherein when formed the covalent cross-link is internal to the first polypeptide. In aspects, the amino acid sequence of the second polypeptide comprises a set of two non-natural amino acids, wherein the non-natural amino acids are the same or different, wherein each of the non-natural amino acids includes a moiety, wherein the moieties are capable of undergoing a reaction to form an intrapolypeptide covalent cross-link with each other, wherein when formed the covalent cross-link is internal to the second polypeptide.
As used herein, “covalent cross-link is internal to the polypeptide” and the like means that the cross-link starts at a residue within the polypeptide chain and ends at a residue within the same polypeptide chain.
In aspects of the disclosure, a polypeptide according to the disclosure can include one or more non-natural amino acids. A first non-natural amino acid can be cross-linked to a second non-natural amino acid that is substituted or inserted at a position in the polypeptide which is four residues away. The relative positions of the first and second non-natural amino acids in this stapled polypeptide are designated as (i, i+4). In aspects of the disclosure, the first non-natural amino acid can be cross-linked to a second non-natural amino acid located seven residues away (i, i+7) in the polypeptide. In aspects of the disclosure, the first non-natural amino acid can be cross-linked to a second non-natural amino acid located three residues away (i, i+3) in the polypeptide.
In aspects, each set of non-natural amino acids of the first and second polypeptides are capable of undergoing a Diels-Alder reaction, a Huisgen reaction, or an olefin metathesis reaction.
In aspects, in the first or second polypeptides, one non-natural amino acid within a set is XaaA1 and the other non-natural amino acid within the set is XaaB1
In the aspects of the disclosure, halo includes any halogen, e.g., F, Cl, Br, I.
As used herein, unless otherwise specified, the term “alkyl” means a saturated straight chain or branched non-cyclic hydrocarbon having an indicated number of carbon atoms (e.g., C1-C20, C1-C10, C1-C4, C1-C6, etc.). An alky group may have 1, 2, 3, 4, 5, 6, 7, 8, or more carbons. Representative saturated straight chain alkyls include -methyl, -ethyl, -n-propyl, -n-butyl, -n-pentyl, -n-hexyl, -n-heptyl, -n-octyl, -n-nonyl and -n-decyl; while representative saturated branched alkyls include -isopropyl, -sec-butyl, -isobutyl, -tert-butyl, -isopentyl, 2-methylbutyl, 3-methylbutyl, 2-methylpentyl, 3-methylpentyl, 4-methylpentyl, 2-methylhexyl, 3-methylhexyl, 4-methylhexyl, 5-methylhexyl, 2,3-dimethylbutyl, 2,3-dimethylpentyl, 2,4-dimethylpentyl, 2,3-dimethylhexyl, 2,4-dimethylhexyl, 2,5-dimethylhexyl, 2,2-dimethylpentyl, 2,2-dimethylhexyl, 3,3-dimtheylpentyl, 3,3-dimethylhexyl, 4,4-dimethylhexyl, 2-ethylpentyl, 3-ethylpentyl, 2-ethylhexyl, 3-ethylhexyl, 4-ethylhexyl, 2-methyl-2-ethylpentyl, 2-methyl-3-ethylpentyl, 2-methyl-4-ethylpentyl, 2-methyl-2-ethylhexyl, 2-methyl-3-ethylhexyl, 2-methyl-4-ethylhexyl, 2,2-diethylpentyl, 3,3-diethylhexyl, 2,2-diethylhexyl, 3,3-diethylhexyl and the like. “Alkenyl” means an unsaturated straight chain or branched non-cyclic hydrocarbon having an indicated number of carbon atoms (e.g., C1-C20, C1-C10, C1-C4, C1-C6, etc.), where at least one carbon-carbon bond is a double bond. An alkenyl group may have 1, 2, 3, 4, 5, 6, 7, 8, or more carbons. “Alkynyl” means an unsaturated straight chain or branched non-cyclic hydrocarbon having an indicated number of carbon atoms (e.g., C1-C20, C1-C10, C1-C4, C1-C6, etc.), where at least one carbon-carbon bond is a triple bond. An alkynyl group may have 1, 2, 3, 4, 5, 6, 7, 8, or more carbons. As understood in the art, “alkylene,” “alkenylene,” and “alkynylene” are the bivalent radical forms of alkyl, alkenyl, and alkynyl, respectively.
The term “cycloalkyl,” as used herein, means a cyclic alkyl moiety containing from, for example, 3 to 6 carbon atoms, preferably from 5 to 6 carbon atoms. Examples of such moieties include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like. “Cycloalkylalkyl” is a cycloalkyl as defined above substituted with an alkyl as defined above.
The term “heterocyclyl” means a cycloalkyl moiety having one or more heteroatoms selected from nitrogen, sulfur, and/or oxygen. Preferably, a heterocyclyl is a 5 or 6-membered monocyclic ring and contains one, two, or three heteroatoms selected from nitrogen, oxygen, and/or sulfur. The heterocyclyl can be attached to the parent structure through a carbon atom or through any heteroatom of the heterocyclyl that results in a stable structure. Examples of such heterocyclic rings are pyrrolinyl, pyranyl, piperidyl, tetrahydrofuranyl, tetrahydrothiopheneyl, and morpholinyl. “Heterocyclylalkyl” is a heterocyclyl as defined above substituted with an alkyl as defined above.
As used herein, unless otherwise specified, the term “alkylamino” means —NH(alkyl) or —N(alkyl)(alkyl), wherein alkyl is defined above. As used herein, unless otherwise specified, the term “cycloalkylamino” means —NH(cycloalkyl) or —N(cycloalkyl)(cycloalkyl), wherein cycloalkyl is defined above.
The term “aryl” refers to an unsubstituted or substituted aromatic carbocyclic moiety, as commonly understood in the art, and includes monocyclic and polycyclic aromatics such as, for example, phenyl, biphenyl, naphthyl, anthracenyl, pyrenyl, and the like. An aryl moiety generally contains from, for example, 6 to 30 carbon atoms, preferably from 6 to 18 carbon atoms, more preferably from 6 to 14 carbon atoms and most preferably from 6 to 10 carbon atoms. It is understood that the term aryl includes carbocyclic moieties that are planar and comprise 4n+2 π electrons, according to Hückel's Rule, wherein n=1, 2, or 3. “Arylalkyl” means an aryl as defined above substituted with an alkyl as defined above.
The term “heteroaryl” refers to aromatic 4, 5, or 6 membered monocyclic groups, 9 or 10 membered bicyclic groups, and 11 to 14 membered tricyclic aryl groups having one or more heteroatoms (O, S, or N). Each ring of the heteroaryl group containing a heteroatom can contain one or two oxygen or sulfur atoms and/or from one to four nitrogen atoms provided that the total number of heteroatoms in each ring is four or less and each ring has at least one carbon atom. The nitrogen and sulfur atoms may optionally be oxidized, and the nitrogen atoms may optionally be quaternized. Illustrative examples of heteroaryl groups are pyridinyl, pyridazinyl, pyrimidyl, pyrazinyl, triazinyl, pyrrolyl, pyrazolyl, imidazolyl, (1,2,3)- and (1,2,4)-triazolyl, pyrazinyl, pyrimidinyl, tetrazolyl, furyl, thiophenyl, isothiazolyl, thiazolyl, isoxazolyl, oxadiazolyl, oxazolyl, pyrrolo[2,3-c]pyridinyl, pyrrolo[3,2-c]pyridinyl, pyrrolo[2,3-b]pyridinyl, pyrrolo[3,2-b]pyridinyl, pyrrolo[3,2-d]pyrimidinyl, and pyrrolo[2,3-d]pyrimidinyl. “Heteroarylalkyl” is a heteroaryl as defined above substituted with an alkyl as defined above.
Whenever a range of the number of atoms in a structure is indicated (e.g., a C1-C8, C1-C6, C1-C4, or C1-C3 alkyl, haloalkyl, alkylamino, alkenyl, etc.), it is specifically contemplated that any sub-range or individual number of carbon atoms falling within the indicated range also can be used. Thus, for instance, the recitation of a range of 1-8 carbon atoms (e.g., C1-C8), 1-6 carbon atoms (e.g., C1-C6), 1-4 carbon atoms (e.g., C1-C4), 1-3 carbon atoms (e.g., C1-C3), or 2-8 carbon atoms (e.g., C2-C8) as used with respect to any chemical group (e.g., alkyl, haloalkyl, alkylamino, alkenyl, etc.) referenced herein encompasses and specifically describes 1, 2, 3, 4, 5, 6, 7, or 8 carbon atoms, as appropriate, as well as any sub-range thereof (e.g., 1-2 carbon atoms, 1-3 carbon atoms, 1-4 carbon atoms, 1-5 carbon atoms, 1-6 carbon atoms, 1-7 carbon atoms, 1-8 carbon atoms, 2-3 carbon atoms, 2-4 carbon atoms, 2-5 carbon atoms, 2-6 carbon atoms, 2-7 carbon atoms, 2-8 carbon atoms, 3-4 carbon atoms, 3-5 carbon atoms, 3-6 carbon atoms, 3-7 carbon atoms, 3-8 carbon atoms, 4-5 carbon atoms, 4-6 carbon atoms, 4-7 carbon atoms, 4-8 carbon atoms, 5-6 carbon atoms, 5-7 carbon atoms, 5-8 carbon atoms, 6-7 carbon atoms, or 6-8 carbon atoms, as appropriate).
In aspects, the non-natural amino acids of the first or second polypeptide are capable of forming together a thioether, ether, amide, amine, triazole, or carbon-carbon double bond or a Diels-Alder adduct after reaction. In aspects, the non-natural amino acids are independently selected from (S)-2-(4′-pentenyl)alanine (S5), (R)-2-(2′-propenyl)alanine (R3), and (R)-2-(7′-octenyl)alanine (R8). In aspects, the non-natural amino acids have undergone reaction to form the intrapolypeptide covalent cross-link with each other.
In aspects of the disclosure, the cross-link of the polypeptide is formed from the amino acid at position i within the polypeptide and another amino acid at position i+4 within the polypeptide, and the amino acid at position i is (S)-2-(4′-pentenyl)alanine (S5) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the polypeptide and another amino acid at position i+3 within the polypeptide, and the amino acid at position i is (R)-2-(4′-pentenyl)alanine (R5) or (R)-2-(2′-propenyl)alanine (R3) and the amino acid at position i+3 is S5; or formed from the amino acid at position i within the polypeptide and another amino acid at position i+7 within the polypeptide, and the amino acid at position i is (R)-2-(7′-octenyl)alanine (R8) and the amino acid at position i+7 is S5.
In aspects of the disclosure, (a) the cross-link of the first polypeptide is formed from the amino acid at position i within the first polypeptide and another amino acid at position i+4 within the first polypeptide, and the amino acid at position i is (S)-2-(4′-pentenyl)alanine (S5) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the first polypeptide and another amino acid at position i+3 within the first polypeptide, and the amino acid at position i is (R)-2-(4′-pentenyl)alanine (R5) or (R)-2-(2′-propenyl)alanine (R3) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the first polypeptide and another amino acid at position i+7 within the first polypeptide, and the amino acid at position i is (R)-2-(7′-octenyl)alanine (R8) and the amino acid at position i+7 is S5; and (b) the cross-link of the second polypeptide is formed from the amino acid at position i within the second polypeptide and another amino acid at position i+4 within the second polypeptide, and the amino acid at position i is (S)-2-(4′-pentenyl)alanine (S5) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the second polypeptide and another amino acid at position i+3 within the second polypeptide, and the amino acid at position i is (R)-2-(4′-pentenyl)alanine (R5) or (R)-2-(2′-propenyl)alanine (R3) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the second polypeptide and another amino acid at position i+7 within the second polypeptide, and the amino acid at position i is (R)-2-(7′-octenyl)alanine (R8) and the amino acid at position i+7 is S5.
In aspects of the disclosure, a reside other than XaaA1 or XaaB1 within the first polypeptide and a residue other than XaaA1 and XaaB1 within the second polypeptide are covalently linked, forming a ligated construct. In aspects, the linkage involves butyrlmaleimide (ButMal), glyclmaleimde (Glymal), or bismaleimidohexane:
In aspects, the covalent linkage results in an adduct that forms from a Diels-Alder reaction, an olefin metathesis reaction, copper-catalyzed azide-alkyne click chemistry, cystine formation via oxidation of two cysteine residues, crosslink formation via alkylation of one or more cysteine residues, thiol-ene chemistry, or a lactam bridge formation between N- or C-termini and/or residue side chain(s). In aspects, at least one of the residues is a non-natural amino acid or an amino acid derivative. In aspects, the reactive functional groups are each independently bound to an amino acid side chain, amino acid amino group, amino acid carboxy group, or amino acid α-carbon. In aspects, the adduct is bound to a side chain, amine group, carboxy group, or α-carbon of one amino acid and to a side chain, amine group, carboxy group, or α-carbon of a different amino acid within the same polypeptide to provide a cyclic structure. In aspects, the macrocyclic polypeptide is formed in which one reactive functional group includes a diene and a different reactive functional group includes a dienophile. The complementary diene and dienophile pair can react to form a macrocyclic peptide through an intramolecular Diels-Alder reaction. The reactive functional groups may each independently be conjugated to a terminal amino acid or an internal amino acid. In aspects, the adduct is formed from a reaction between a hexadiene group and a maleimide group, a maleimide group and a furan group, a cyclopentadiene group and another cyclopentadiene group, a cyclopentadiene group and a maleimide group, or a cyclopentadiene group and an aliphatic olefin (for example, an aliphatic olefin used as a peptide staple). In aspects, the adduct is one of the Diels-Alder adducts:
In aspects of the disclosure, exemplary positions of residues that can be covalently linked are shown in
In aspects, the disclosure provides a polypeptide construct comprising (a) a polypeptide construct as described above; (b) a third polypeptide comprising an amino acid sequence derived from a basic helix of a transcription factor protein that comprises a basic helix-loop-helix domain; and (c) a fourth polypeptide comprising an amino acid sequence derived from a helix that extends in the C-terminal direction from the end of the loop of a basic helix-loop-helix domain of a transcription factor protein that comprises a basic helix-loop-helix domain; wherein the third polypeptide and the fourth polypeptide are linked through an interpolypeptide covalent linkage.
In aspects, the basic helix of the third polypeptide comprises the amino acid sequence extending 36 residues in the N-terminal direction from the start of the loop of the basic helix-loop-helix domain. In aspects, the fourth polypeptide comprises the amino acid sequence extending 31 residues in the C-terminal direction from the end of the loop of the basic helix-loop-helix domain. In aspects, the fourth polypeptide comprises a leucine zipper helix.
In aspects, the amino acid sequence of the third polypeptide comprises a set of two non-natural amino acids, wherein the non-natural amino acids are the same or different, wherein each of the non-natural amino acids includes a moiety, wherein the moieties are capable of undergoing a reaction to form an intrapolypeptide covalent cross-link with each other, wherein when formed the covalent cross-link is internal to the third polypeptide. In aspects, the amino acid sequence of the fourth polypeptide comprises a set of two non-natural amino acids, wherein the non-natural amino acids are the same or different, wherein each of the non-natural amino acids includes a moiety, wherein the moieties are capable of undergoing a reaction to form an intrapolypeptide covalent cross-link with each other, wherein when formed the covalent cross-link is internal to the fourth polypeptide.
In aspects, each set of non-natural amino acids of the third and fourth polypeptides are capable of undergoing a Diels-Alder reaction, a Huisgen reaction, or an olefin metathesis reaction.
In aspects, in the third or fourth polypeptides, one non-natural amino acid within a set is XaaA1 and the other non-natural amino acid within the set is XaaB1
In aspects, the non-natural amino acids of the third or fourth polypeptide are capable of forming together a thioether, ether, amide, amine, triazole, or carbon-carbon double bond or a Diels-Alder adduct after reaction. In aspects, the non-natural amino acids are independently selected from (S)-2-(4′-pentenyl)alanine (S5), (R)-2-(2′-propenyl)alanine (R3), and (R)-2-(7′-octenyl)alanine (R8). In aspects, the non-natural amino acids have undergone reaction to form the intrapolypeptide covalent cross-link with each other.
In aspects of the disclosure, the cross-link of the polypeptide is formed from the amino acid at position i within the polypeptide and another amino acid at position i+4 within the polypeptide, and the amino acid at position i is (S)-2-(4′-pentenyl)alanine (S5) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the polypeptide and another amino acid at position i+3 within the polypeptide, and the amino acid at position i is (R)-2-(4′-pentenyl)alanine (R5) or (R)-2-(2′-propenyl)alanine (R3) and the amino acid at position i+3 is S5; or formed from the amino acid at position i within the polypeptide and another amino acid at position i+7 within the polypeptide, and the amino acid at position i is (R)-2-(7′-octenyl)alanine (R8) and the amino acid at position i+7 is S5.
In aspects of the disclosure, (a) the cross-link of the third polypeptide is formed from the amino acid at position i within the third polypeptide and another amino acid at position i+4 within the third polypeptide, and the amino acid at position i is (S)-2-(4′-pentenyl)alanine (S5) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the third polypeptide and another amino acid at position i+3 within the third polypeptide, and the amino acid at position i is (R)-2-(4′-pentenyl)alanine (R5) or (R)-2-(2′-propenyl)alanine (R3) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the third polypeptide and another amino acid at position i+7 within the third polypeptide, and the amino acid at position i is (R)-2-(7′-octenyl)alanine (R8) and the amino acid at position i+7 is S5; and (b) the cross-link of the fourth polypeptide is formed from the amino acid at position i within the fourth polypeptide and another amino acid at position i+4 within the fourth polypeptide, and the amino acid at position i is (S)-2-(4′-pentenyl)alanine (S5) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the fourth polypeptide and another amino acid at position i+3 within the fourth polypeptide, and the amino acid at position i is (R)-2-(4′-pentenyl)alanine (R5) or (R)-2-(2′-propenyl)alanine (R3) and the amino acid at position i+4 is S5; or formed from the amino acid at position i within the fourth polypeptide and another amino acid at position i+7 within the fourth polypeptide, and the amino acid at position i is (R)-2-(7′-octenyl)alanine (R8) and the amino acid at position i+7 is S5.
In aspects of the disclosure, a reside other than XaaA1 or XaaB1 within the third polypeptide and a residue other than XaaA1 and XaaB1 within the fourth polypeptide are covalently linked, forming a ligated construct. In aspects, the linkage involves butyrlmaleimide (ButMal), glyclmaleimde (Glymal), or bismaleimidohexane. In aspects, the covalent linkage results in an adduct that forms from a Diels-Alder reaction, an olefin metathesis reaction, copper-catalyzed azide-alkyne click chemistry, cystine formation via oxidation of two cysteine residues, crosslink formation via alkylation of one or more cysteine residues, thiol-ene chemistry, or a lactam bridge formation between N- or C-termini and/or residue side chain(s). In aspects, at least one of the residues is a non-natural amino acid or an amino acid derivative. In aspects, the reactive functional groups are each independently bound to an amino acid side chain, amino acid amino group, amino acid carboxy group, or amino acid α-carbon. In aspects, the adduct is bound to a side chain, amine group, carboxy group, or α-carbon of one amino acid and to a side chain, amine group, carboxy group, or α-carbon of a different amino acid within the same polypeptide to provide a cyclic structure. In aspects, the macrocyclic polypeptide is formed in which one reactive functional group includes a diene and a different reactive functional group includes a dienophile. The complementary diene and dienophile pair can react to form a macrocyclic peptide through an intramolecular Diels-Alder reaction. The reactive functional groups may each independently be conjugated to a terminal amino acid or an internal amino acid. In aspects, the adduct is formed from a reaction between a hexadiene group and a maleimide group, a maleimide group and a furan group, a cyclopentadiene group and another cyclopentadiene group, a cyclopentadiene group and a maleimide group, or a cyclopentadiene group and an aliphatic olefin (for example, an aliphatic olefin used as a peptide staple). In aspects, the adduct is one of the Diels-Alder adducts:
In aspects of the disclosure, exemplary positions of residues that can be covalently linked are shown in
In aspects, the second polypeptide and the fourth polypeptide are linked through an interpolypeptide covalent linkage, creating what is referred to herein as a helical tetramer. In aspects, the interpolypeptide linkage is between the C-terminal amino acid of the second polypeptide and the C-terminal amino acid of the fourth polypeptide. In aspects, the interpolypeptide covalent linkage between the second polypeptide and the fourth polypeptide is a maleimide-thiol adduct. In aspects, any suitable helical dimer described herein may be covalently linked to any other suitable helical dimer described herein to create a helical tetramer.
In aspects of the disclosure, a reside other than XaaA1 or XaaB1 within the second polypeptide and a residue other than XaaA1 and XaaB1 within the fourth polypeptide are covalently linked, forming a ligated construct. In aspects, the linkage involves butyrlmaleimide (ButMal), glyclmaleimde (Glymal), or bismaleimidohexane. In aspects, the covalent linkage results in an adduct that forms from a Diels-Alder reaction, an olefin metathesis reaction, copper-catalyzed azide-alkyne click chemistry, cystine formation via oxidation of two cysteine residues, crosslink formation via alkylation of one or more cysteine residues, thiol-ene chemistry, or a lactam bridge formation between N- or C-termini and/or residue side chain(s). In aspects, at least one of the residues is a non-natural amino acid or an amino acid derivative. In aspects, the reactive functional groups are each independently bound to an amino acid side chain, amino acid amino group, amino acid carboxy group, or amino acid α-carbon. In aspects, the adduct is bound to a side chain, amine group, carboxy group, or α-carbon of one amino acid and to a side chain, amine group, carboxy group, or α-carbon of a different amino acid within the same polypeptide to provide a cyclic structure. In aspects, the macrocyclic polypeptide is formed in which one reactive functional group includes a diene and a different reactive functional group includes a dienophile. The complementary diene and dienophile pair can react to form a macrocyclic peptide through an intramolecular Diels-Alder reaction. The reactive functional groups may each independently be conjugated to a terminal amino acid or an internal amino acid. In aspects, the adduct is formed from a reaction between a hexadiene group and a maleimide group, a maleimide group and a furan group, a cyclopentadiene group and another cyclopentadiene group, a cyclopentadiene group and a maleimide group, or a cyclopentadiene group and an aliphatic olefin (for example, an aliphatic olefin used as a peptide staple). In aspects, the adduct is one of the Diels-Alder adducts:
In aspects, one residue is cysteine or a cysteine derivative and the other residue is lysine or a lysine derivative. In aspects, the cysteine and/or lysine are derivatized to form a diene or a dienophile. In aspects, the interpolypeptide covalent linkage between the second polypeptide and the fourth polypeptide is a maleimide-thiol adduct.
In aspects, the N-terminus or the C-terminus of the first, second, third, or fourth polypeptide is capped. In aspects of the disclosure, the N-terminus is capped and the cap is acetyl or the C-terminus is capped and the cap is —NH2. Exemplary N-terminal caps include:
In aspects, the polypeptide construct binds to duplex DNA comprising the sequence of 5′-CANNTG-3′, wherein each N is independently any one of A, C, G, or T. In aspects, the DNA comprises the sequence of 5′-CACGTG-3′, 5′-CAGCTG-3′, 5′-CATATG-3′, 5′-CGTACG-3′, or 5′-CGCGCG-3′.
In aspects, the disclosure provides a polypeptide construct comprising (a) a first polypeptide comprising an amino acid sequence derived from a basic helix as listed in Table 2; and (b) a second polypeptide comprising an amino acid sequence derived from a helix as listed in Table 2; wherein the first polypeptide and the second polypeptide are linked through an interpolypeptide covalent linkage.
In aspects, the disclosure provides a polypeptide comprising the sequence of any of the polypetides described herein. In aspects, the disclosure provides a polypeptide comprising the sequence of any one of:
The polypeptides may be synthesized using any suitable method. The Example below provides suitable methods. Also, for example, the process may include synthesis, ring closing metathesis (RCM) and capping for a single helix and partial synthesis, RCM, hydrogenation, synthesis, RCM, and capping for two helices. In aspects of the disclosure, the side chains of non-natural amino acids, wherein each non-natural amino acid includes a moiety, wherein each moiety is capable of undergoing a reaction with a moiety of one other of the non-natural amino acids to form a covalent cross-link, can be covalently linked (e.g., R3 to S5, S5 to S5, R5 to S5, or R8 to S5) in the presence of a catalyst to produce the “staple” of the polypeptide. Methods of synthesis that may be used are described in Bird et al., Methods in Enzymology, 446: 369-386 (2008), incorporated by reference herein, and Shim et al., Chem. Biol. Drug Des., 82: 635-642 (2013), incorporated by reference herein. Specifically, methods of making hydrocarbon stapled polypeptides are known in the art and have been described (see, e.g., the Examples and Verdine et al., “Stapled Peptides for Intracellular Drug Targets” in Methods in Enzymology, 503: 3-23 (2012), which is incorporated by reference herein).
In aspects of the disclosure, the polypeptides can be synthesized as shown in
In aspects of the disclosure, one or more peptide bonds may be replaced by a different bond that may increase the stability of the polypeptide. Peptide bonds can be replaced by: a retro-inverso bond (C(O)—NH); a reduced amide bond (NH—CH2); a thiomethylene bond (S—CH2 or CH2—S); an oxomethylene bond (O—CH2 or CH2—O); an ethylene bond (CH2—CH2); a thioamide bond (C(S)—NH); a trans-olefin bond (CH═CH); a fluoro substituted trans-olefin bond (CF═CH); a ketomethylene bond (C(O)—CHR) or CHR—C(O) wherein R is H or CH3; and a fluoro-ketomethylene bond (C(O)—CFR or CFR—C(O) wherein R is H or F or CH3.
Amino acids of the polypeptides may be substituted using amino acid substitutions. Such substitutions may be conservative substitutions. Conservative amino acid substitutions are known in the art, and include amino acid substitutions in which one amino acid having certain physical and/or chemical properties is exchanged for another amino acid that has the same or similar chemical or physical properties. For instance, the conservative amino acid substitution can be an acidic/negatively charged polar amino acid substituted for another acidic/negatively charged polar amino acid (e.g., Asp or Glu), an amino acid with a nonpolar side chain substituted for another amino acid with a nonpolar side chain (e.g., Ala, Val, Ile, Leu, Met, Phe, Pro, Trp, Cys, Val, etc.), a basic/positively charged polar amino acid substituted for another basic/positively charged polar amino acid (e.g., Lys, His, Arg, etc.), an uncharged amino acid with a polar side chain substituted for another uncharged amino acid with a polar side chain (e.g., Gly, Asn, Gln, Ser, Thr, Tyr, etc.), an amino acid with a beta-branched side-chain substituted for another amino acid with a beta-branched side-chain (e.g., Ile, Thr, and Val), an amino acid with an aromatic side-chain substituted for another amino acid with an aromatic side chain (e.g., His, Phe, Trp, and Tyr), etc. Also, substitution of amino acids may be accomplished using amino acids having high helical propensity, such as α-aminoisobutyric acid (Aib). Substitutions that do not impact DNA binding are preferable.
The polypeptides can be any suitable length of amino acids. For example, any of the inventive sequences can have an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more amino acids on either the N-terminus or C-terminus or both.
Any of the polypeptides may be isolated. Any of the polypeptides may be purified. By “isolated” is meant the removal of a substance (e.g., a polypeptide) from its natural environment. By “purified” is meant that a given substance (e.g., a polypeptide), whether one that has been removed from nature (e.g., a protein enzymatically cleaved into polypeptides) or synthesized (e.g., by polypeptide synthesis), has been increased in purity, wherein “purity” is a relative term, not “absolute purity.” It is to be understood, however, that polypeptides may be formulated with diluents or adjuvants and still for practical purposes be isolated. For example, polypeptides can be mixed with an acceptable carrier or diluent when used for introduction into cells.
The polypeptides described herein may be provided in the form of a salt, e.g., a pharmaceutically acceptable salt. Suitable pharmaceutically acceptable acid addition salts, for example, include those derived from mineral acids, such as hydrochloric, hydrobromic, phosphoric, metaphosphoric, nitric, and sulphuric acids, and organic acids, such as tartaric, acetic, citric, malic, lactic, fumaric, benzoic, glycolic, gluconic, succinic, and arylsulphonic acids, for example, p-toluenesulphonic acid.
In aspects of the disclosure, the disclosure provides a pharmaceutical composition comprising a therapeutically effective amount of a polypeptide or a polypeptide composition described herein and a pharmaceutically acceptable excipient.
In aspects, the disclosure provides a pharmaceutical composition comprising a therapeutically effective amount of a polypeptide construct or a polypeptide described herein or and a pharmaceutically acceptable excipient. Thus, one or more polypeptides described herein can be administered alone or in a composition (e.g., formulated in a pharmaceutically acceptable composition). Such a composition comprises a carrier (e.g., a pharmaceutically acceptable carrier), such as those known in the art. A pharmaceutically acceptable carrier (or excipient) preferably is chemically inert to the polypeptide and has few or no detrimental side effects or toxicity under the conditions of use. The choice of carrier is determined, in part, by the particular method used to administer the composition.
Carrier formulations suitable for parenteral, oral, nasal (and otherwise inhaled), topical, and other administrations can be found in Remington's Pharmaceutical Sciences 17th ed., Mack Publishing Co., Easton, PA (2000), which is incorporated by reference herein. Requirements for effective pharmaceutical carriers in parenteral and injectable compositions are well known to those of ordinary skill in the art. See, e.g., Pharmaceutics and Pharmacy Practice, J. B. Lippincott Co., Philadelphia, Pa., Banker and Chalmers, eds., pages 238-250 (1982), and ASHP Handbook on Injectable Drugs, Toissel, 4th ed., pages 622-630 (1986). Accordingly, there is a wide variety of suitable formulations of the composition.
The composition can contain suitable buffering agents, including, for example, acetate buffer, citrate buffer, borate buffer, or a phosphate buffer. The pharmaceutical composition also, optionally, can contain suitable preservatives, such as benzalkonium chloride, chlorobutanol, parabens, and thimerosal.
The composition can be presented in unit dosage form and can be prepared by any suitable method, many of which are well known in the art of pharmacy. Such methods include the step of bringing the polypeptide into association with a carrier that constitutes one or more accessory ingredients. In general, the composition is prepared by uniformly and intimately bringing the polypeptide into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product.
The composition can be administered using any suitable method including, but not limited to parenteral, oral, nasal (or otherwise inhaled), and topical administration. Delivery systems useful in the context of the disclosure include time-released, delayed-release, and sustained-release delivery systems.
A composition suitable for parenteral administration conveniently comprises a sterile aqueous preparation of the polypeptide, which may be isotonic with the blood of the recipient. This aqueous preparation can be formulated according to known methods using suitable dispersing or wetting agents and suspending agents.
Sterile powders for sterile injectable solutions can be prepared by vacuum drying and/or freeze-drying to yield a powder of the polypeptide, optionally, in association with a filler or diluent.
A composition suitable for oral administration can be formulated in discrete units such as capsules, cachets, tablets, or lozenges, each containing a predetermined amount of the polypeptide as a powder or granules. A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared by compressing in a suitable machine, with the polypeptide being in a free-flowing form, such as a powder or granules, which optionally is mixed with a binder, disintegrant, lubricant, inert diluent, surface polypeptide, or discharging agent. Molded tablets comprised of a mixture of the polypeptide with a suitable carrier may be made by molding in a suitable machine.
Liquid dosage forms for oral and parenteral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active polypeptide, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. In aspects of the disclosure for parenteral administration, the proteins, polypeptides, and polypeptides of the disclosure are mixed with solubilizing agents such a Cremophor, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, or any combination thereof.
Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution, and 1,3-butanediol. In addition, sterile, fixed oils can be employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.
The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
Topical formulations comprise at least one polypeptide dissolved or suspended in one or more media, such as mineral oil, petroleum, polyhydroxy alcohols, or other bases used for topical pharmaceutical formulations. Transdermal formulations may be prepared by incorporating the polypeptide in a thixotropic or gelatinous carrier such as a cellulosic medium, e.g., methyl cellulose or hydroxyethyl cellulose, with the resulting formulation then being packed in a transdermal device adapted to be secured in dermal contact with the skin of a wearer.
The amount (e.g., therapeutically effective amount) of polypeptide suitable for administration depends on the specific polypeptide used and the particular route of administration. In aspects of the disclosure, for example, polypeptide can be administered in a dose of about 0.5 ng to about 900 ng (e.g., about 1 ng, 25 ng, 50 ng, 100, ng, 200 ng, 300 ng, 400 ng, 500, ng, 600 ng, 700 ng, 800 ng, or any range bounded by any two of the aforementioned values), in a dose of about 1 μg to about 900 μg (e.g., about 1 μg, 2 μg, 5 μg, 10 μg, 15 μg, 20 μg, 25 μg, 30 μg, 40 μg, 50 μg, 60 μg, 70 μg, 80 μg, 90 μg, 100 μg, 200 μg, 300 μg, 400 μg, 500, μg, 600 μg, 700 μg, 800 μg, or any range bounded by any two of the aforementioned values), or in a dose of about 1 mg to about 200 mg (e.g., about 1 mg, 2 mg, 5 mg, 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 40 mg, 50 mg, 60 mg, 70 mg, 80 mg, 90 mg, 100 mg, 125 mg, 150 mg, 175 mg, or any range bounded by any two of the aforementioned values) per kilogram body weight of the subject. Several doses can be provided over a period of days or weeks.
In aspects, the disclosure provides a method of treating disease in a subject in need thereof comprising administering to the subject a therapeutically effective amount of a polypeptide construct or a polypeptide described herein, or a pharmaceutical composition described herein.
The terms “treat,” “treating,” “treatment,” “therapeutically effective,” “inhibit,” etc. used herein do not necessarily imply 100% or complete treatment/inhibition/reduction. Rather, there are varying degrees, which one of ordinary skill in the art recognizes as having a potential benefit or therapeutic effect. In this respect, the polypeptides and methods can provide any amount of any level of treatment/inhibition/reduction. Furthermore, the treatment provided by the inventive method can include the treatment of one or more conditions or symptoms of the disease being treated.
The terms “co-administering,” “co-administration” and “co-administered” used herein refer to the administration of an polypeptide described herein and one or more additional therapeutic agents sufficiently close in time to (i) enhance the effectiveness of the polypeptide or the one or more additional therapeutic agents and/or (ii) reduce an undesirable side effect of the polypeptide or the one or more additional therapeutic agents. In this regard, the polypeptide can be administered first, and the one or more additional therapeutic agents can be administered second, or vice versa. Alternatively, the polypeptide and the one or more additional therapeutic agents can be co-administered simultaneously.
The term “subject” is used herein to refer to human or animal subjects (e.g., mammals).
In aspects of the disclosure, the disclosure provides a method of treating disease in a subject in need thereof comprising administering to the subject a therapeutically effective amount of a polypeptide, a polypeptide composition, or a pharmaceutical composition described herein.
The following includes certain aspects of the disclosure.
wherein
It shall be noted that the preceding are merely examples of aspects. Other exemplary aspects are apparent from the entirety of the description herein. It will also be understood by one of ordinary skill in the art that each of these aspects may be used in various combinations with the other aspects provided herein.
The following examples further illustrate the disclosure but, of course, should not be construed as in any way limiting its scope.
This example demonstrates helical dimers, in accordance with aspects of the disclosure.
HeLa cells were purchased from ATCC (Manassas, VA, USA). HCT116 cells were purchased from BPS Biosciences (San Diego, CA, USA). HeLa and P493-6 cells were cultured in RPMI-1640 with 10% FBS and 1% penicillin/streptomycin. HCT116 cells were cultured in McCoy's 5A medium with 10% FBS and 1% penicillin/streptomycin. All cell culture was performed under 37° C. with 5% CO2.
A Symphony X automated peptide synthesizer was used to prepare linear peptides on Rink amide MBHA resin. Fmoc-based solid phase chemistry, ring closing metathesis, and N-terminal modifications were carried out as previously described (Kim et al., Nature Protocols, 6: 761-771 (2011); Mitra et al., Nat. Commun., 8: 660 (2017); each of which is incorporated by reference herein). Lysine residues bearing monomethoxy trityl (Mmt) side chain protecting groups were incorporated at cross-linking positions of basic helices. On-resin Mmt deprotection was carried out for 5×2 min consecutive cycles of 1% TFA/DCM solution mixed by N2 bubbling. Deprotected lysine residues were functionalized with maleimide by 2 hr treatment with a 0.1 M solution of 2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)acetic acid (Mal-Gly-OH) (5 eq), HCTU (4.8 eq), and DIPEA (10 eq.) in DMF, with the exception STR69, which was connected with an aminobutyric acid maleimide interhelix linker. Crude peptides cleaved from resin were purified on a Waters preparatory HPLC system using an Xbridge Prep C18 5 μm OBN (19.5×150 mm) column; solvent A (0.1% TFA in H2O); solvent B (MeOH); and a 10-min method with the following gradient (flowrate 30 mL/min): 35% B over 1 min; 35-85% B over 7 min; 95% B over 1 min; 35% B over 1 min. STR monomer ligation was performed in 50 mM sodium phosphate buffer pH 7.2+25% ACN as follows: a purified basic sequence bearing a maleimide (0.5 mL, 0.5 mM) and a purified zipper sequence with a free thiol (0.5 mL, 0.5 mM) were combined in a microcentrifuge tube and mixed by rotation for 2 hrs at room temperature. The reaction mixture was diluted into 3 mL of 50% ACN/H2O+0.1% TFA and the ligated STR was purified using the same HPLC method as for individual monomers. STR purity and molecular weight were confirmed by LC-MS using an Agilent system equipped with a Phenomonex C18, 5 μm (5.0×50 mm) column; solvent A (95:5:0.1 H2O/ACN/TFA) and solvent B (95:5:0.1 ACN/H2O/TFA); 0.5 ml min flowrate, 0-2 min (0% B), 2-16 min (0-75% B), 16.5-18.5 min (100% B), 19 min (0% B). STR concentrations were quantified using 280 nm absorbance readings and compounds were stored as lyophilized powder or DMSO stocks.
For direct DNA binding experiments, STRs were serial diluted (3-fold increments) at 2× concentration in 20 μL of 1× binding buffer (20 mM HEPES pH 8.0, 150 mM NaCl, 5% glycerol, 1 mM EDTA, 2 mM MgCl2, 0.5 mg/mL BSA, 1 mM DTT, 0.05% NP-40). 20 μL of 10 nM IRD700-labeled E-box probe in 1× binding buffer was added and samples were incubated for 30 min at RT followed by 15 min at 4° C. 3.5 μL of each reaction was loaded on a 6% acrylamide, 0.5× TBE gel equilibrated to 4° C. Higher affinity compounds (e.g., STR116 and STR118) were run at 10-fold lower concentration of compound and 0.5 nM final concentration of IRD-labeled oligo. Electrophoresis was carried out for 60 min at 110 V and 4° C. with 0.5× TBE+1 mM MgCl2 running buffer. Gels were pre-run at 110 V for 60 min prior to sample loading. For specificity experiments, 25 nM STR116, 10 nM STR118, or 5 nM MAX, and 5 nM labeled E-box probe were incubated with 0, 5, 25, 125, or 625 nM unlabeled competitor oligo for 30 min at RT in binding buffer. For protein competition experiments, 1 nM TRD-Ebox oligo was added to a mixture of STR (0-1 mM) and 30 nM protein (MAX or MYC:MAX) and incubated for 30 minutes at room temperature in binding buffer. For DNA probe specificity experiments B-Z (100 nM), STR69 (1 μM), and STR640 (125 nM) and MAX (10 nM) were incubated with 1 nM IRD-labeled oligo and 0.01 mg/ml salmon sperm DNA for 30 minutes at RT in binding buffer. All samples were equilibrated to 4° C. for 15 minutes before loading onto 6% gel. Gels were imaged using an Odyssey Li-COR. ImageJ was used to quantify band intensity and fraction bound DNA was calculated by dividing band intensity of bound DNA by the band intensity of the free DNA from a vehicle treated lane. A four-parameter dose-response curve fit to a plot of normalized fraction bound DNA vs. log B-Z concentration yields an IC50 which was reported as the apparent KD. The sequences of STR116, STR118, STR69, and STR640 are shown in Table 4.
Human MYC (residues 356-434) and MAX (residues 22-102) proteins was expressed with a N-terminal hexahistidine tag in Escherichia coli strain BL21(DE3) using a pET28c vector. Transformed bacteria was grown at 37° C. and induced with 0.5 mM isopropyl-β-D-thiogalactoside (IPTG) at an A600=0.8. Cells were pelleted 14 h after induction and lysed in lysis buffer (100 mM NaH2PO4, 10 mM Tris, 300 mM NaCl, 8 M urea, 10 mM imidazole, pH 8.0) with Complete EDTA-free Protease Inhibitor (Roche) by sonication. The lysate was centrifuged to clear insoluble matter before loading onto Ni-NTA resin (Qiagen). After being washed once with lysis buffer and three times with wash buffer (50 mM NaH2PO4, 300 mM NaCl, 8 M urea, 20 mM imidazole, pH 8.0), column-bound protein was eluted using elution buffer (50 mM NaH2PO4, 300 mM NaCl, 8 M urea, 250 mM imidazole, pH 8.0), dialyzed into desired buffer and further concentrated by centrifugation using a 3-kDa exclusion filter. The protein concentration was determined using A280 measurements and MAX protein was mixed with MYC at 1:1 ratio or used in homodimeric form.
Lyophilized STR samples were resuspended in 20 mM phosphate buffer pH 7.4 and diluted to 10 μM. Circular dichroism spectra were obtained on a Jasco J-170 using a 0.1 cm quartz cuvette with the following settings: wavelength, 260-180 nm; data pitch, 1.0 nm; scan rate, 50 nm min−1; accumulations, 3; temperature, 25-85° C. with 6° C. increments. Means-Movement smoothing at the lowest setting was applied to the recorded data.
Each STR, 30 μM, was dissolved in 330 μL of 20 mM phosphate buffer pH 7.4 in a microcentrifuge tube and heated to 37° C. on a tabletop shaker (500 rpm). 30 μL of the reaction mixture was added to 60 uL of quenching solution (ACN+3% formic acid with 500 nM fmoc-lysine-OH internal standard) for 0 s timepoint sample. Thermo-Pierce MS-Grade Trypsin was added to a final concentration of 0.5 μg/ml and additional 30 μL aliquots were quenched at indicated timepoints. Quenched samples were cooled to 4° C. and centrifuged at 20,000×G for 3 min. Sample injections were analyzed by LC-MS using an Agilent system equipped with a Phenomonex C18 5 μm (5.0×50 mm) column; solvent A (95:5:0.1 H2O/ACN/TFA) and solvent B (95:5:0.1 ACN/H2O/TFA); 0.5 ml min−1 flowrate, 0-2 min (5% B), 2-8.8 min (5-95% B), 9-11 min (95% B), 11.1 min (5% B). Intact STR was calculated by normalizing the background subtracted integrated area under the curve for the EIC of (M+4H)/4, ±0.5 mass units, where M is mass and H is hydrogen ion, to the integrated area under the curve for the A280 peak of the internal standard. Fraction intact STR was calculated by dividing the intact STR by the normalized STR signal in the initial 0 s sample. GraphPad Prism was used to plot fraction intact STR vs time, and the proteolytic half-life was derived using a non-linear one-phase decay with the plateau constant set equal to zero.
HeLa cells were grown to 90% confluency in a 6 cm plate and the media was collected. 10 μM STR was resuspended in 0.5 mL of the conditioned media and incubated with gentle shaking at 37° C. At 0, 24 and 48 hrs., treatment media (2 μL) was diluted into 48 μL of 1× EMSA binding buffer containing 5 nM E-box probe. DNA binding was measured using an electrophoretic mobility shift assay. Fraction bound to E-box probe was calculated by dividing the band intensity of bound DNA by the sum of the bound DNA+free DNA.
Approximately 5,000 HeLa cells were seeded in a 96-well plate. The following day an equal volume of media containing 2× compound or DMSO vehicle were added to experimental wells and the plate was incubated for the indicated time of experiment. A 2× volume of lysis buffer was added to additional wells 45 minutes prior to the final time-point and LDH activity in treatment medium was measured using the Pierce LDH Cytotoxicity Assay Kit according to manufacturer protocol (Thermo Scientific #88953), or cell viability was measured by using the CellTiter-Glo Cell Viability Assay (Promega #G9241). Approximately 1,000 P493-6 cells were seeded into a 96-well plate and an equal volume of 2× compound, DMSO vehicle in media, or 0.2 mg/ml tetracycline was added. Media was exchanged and cells were retreated at indicated timepoints. Cell viability was measured by using the CellTiter-Glo Cell Viability Assay (Promega #G9241) at the indicated timepoints. P493-6 cells were cultured for 72 Hrs with 0.1 mg/mL tetracycline to prepare ‘MYC-OFF’ phenotype.
HeLa cells were seeded in the 12-well chamber slide with 2500 cells per well (Ibidi, #81201). Cells at 70-80% confluency were treated either with DMSO as the negative control or 5 μM FITC-labeled STR for indicated duration. Cells were washed with phosphate buffer saline (PBS) for five consecutive times, fixed by 4% formaldehyde in PBS at room temperature for 10 mins, and then washed twice with PBS. The rubber frame was then removed and slide was dried in the dark at room temperature, covered with cover glass (Fisher, #12-545 M), mounted with 5 mL In Situ Mounting Medium with DAPI (Sigma, DUO82040), and sealed with nail polish. Leica Stellaris 8 Laser Scanning Confocal with an HC PL APO CS2 40× oil objective was used to image a single focal plane to accurately detect the DAPI and FITC signal location using HyD detectors. Identical microscope acquisition parameters were set and used within experiments. Post-acquisition processing was performed using ImageJ software (NIH). The workflow was as follows: open all channels for each field of view; designate a color for each channel; adjust brightness/contrast for all channels (applying the same levels for all conditions within and between experiments to allow for direct comparison); merge the channels together; adjust the image unit from pixel to micrometer; export the processed TIFF files for quantification. For quantitative analysis, nuclear boundaries were identified manually using the DAPI image. Then the “ROI Manager” tool in ImageJ was exploited to add all the cell outlines as a collection and overlay with the FITC channel to measure per-cell nuclear fluorescence intensity. Typical quantitative comparisons were made using data from three or more independent fields of view per independent biological replicate condition.
Approximately 0.1×106 HeLa cells were seeded in each well of a 12-well plate. Cells were treated for 12 hours with 1 μM B-Z-FITC, 1 μM STR116-FITC, or 1 μM STR118-FITC. After the indicated treatment time, media was aspirated, cells were washed with PBS (2×1 mL) and treated with 0.25% trypsin (0.25 mL) for 5 min at 37° C. The trypsin was quenched with the addition of 1 mL of media and the detached cells were transferred to a microcentrifuge tube and centrifuged at 500× g for 4 min. The media was aspirated, 20 μL of RIPA buffer (50 mM Tris, pH 7.4, 150 mM NaCl, 0.25% deoxycholate, 1% NP-40, 1 mM EDTA)+Complete EDTA-free Protease Inhibitor (Roche) was added and cells were incubated in RIPA buffer for 10 min on ice. After lysis, 6.6 μL of 4× SDS loading buffer was added, samples were heated to 95° C. for 10 minutes, cooled to RT and analyzed by SDS-PAGE using a tris-glycine buffer system with an 18% acrylamide gel.
P493-6 cells were treated with DMSO, 0.1 ug/mL tetracycline, 10 mM STR116, or 10 mM STR118 for 48 Hours. Harvested cells were lysed in RIPA buffer and protein concentration was determined using the Pierce BCA Protein Assay Kit (Thermo Scientific, Cat. no. 23225). Samples were loaded at equal protein concentration, separated by SDS-PAGE, and transferred to nitrocellulose membranes (Amersham, Cat. no. 10600001). Membranes were incubated with rabbit anti-C-Myc (1:1000, Cat. no. 18583, Cell Signaling Technology), mouse anti-CCNB1 (1:1000, Cat. no. 4135, Cell Signaling Technology), rabbit anti-β-Actin (1:4000, Cat. no. 4970, Cell Signaling Technology) and rabbit anti-LDHA (1:4000, Cat. no. 3582, Cell Signaling Technology). After washing, membranes were stained with IRDye-conjugated secondary antibodies (IRDye 680LT Goat anti-mouse 1:10000, Cat. no. 926-68020, and IRDye 800CW Donkey anti-Rabbit 1:10000, Cat. no. 926-32213, Licor) and blots were visualized by LI-COR.
Myc Reporter (Luc)—HCT116 cells were purchased from BPS Biosciences, Inc., San Diego (Cat. #: 60520). The assay was performed using the manufacturer procedure. 25,000 cells/well were seeded into a 96-well plate. The following day, the media was removed, and cells were treated in triplicate with the indicated treatment using Assay Medium 7B: Opti-MEM (Life Technologies #31985-062)+0.5% FBS+1% non-essential amino acids+1 mM sodium pyruvate+1% penicillin/streptomycin and a final concentration of 0.5% DMSO. Treated cells were incubated for 24 hours and luciferase activity was measured using the ONE-Step™ Luciferase Assay System (BPS Cat. #60690) and percent luciferase activity was calculated as directed in the manufacturer protocol.
MYC ChIP: HeLa cells were seeded in 200-mm dishes. After reaching 70% confluence, cells were crosslinked with 1% formaldehyde, fragmented by sonication, and incubated with c-Myc antibody (N-262, scbt) or IgG (ab171870, abcam) overnight. The mixture was then immunoprecipitated with protein A beads (Genescript, pre-treated with 1% BSA for 1 hour) for 1 hour. Immunoprecipitated complexes were successively washed with Low Salt Wash Buffer I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 150 mM NaCl, pH 8.0), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 500 mM NaCl, pH 8.0), and LiCl Wash Buffer (250 mM LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0). All washes were performed at RT for 8 min on a rotator. The complexes were eluted with 1% SDS at 30° C. for 15 min, and then incubated at 65° C. overnight to reverse crosslink protein-DNA complexes. After decrosslinking, DNA was purified using QIAQuick PCR Purification Kit (Qiagen) according to the manufacturer's instructions.
P493-6 cells (1.5×107) were treated with 10 mM P-BioSTR118 and incubated at 37° C. for 24 hours. Treatment media was aspirated to remove extracellular photo probe and cells were resuspend in 15 mL of RPMI, transferred to a 15 cm plate and irradiated over ice for 10 min (365 nm, Spectrolinker XL-1500a, Spectroline). After irradiation, media was removed, and cells were washed with 10 mL cold PBS. DNA was fragmented by sonication and an aliquot of input DNA was reserved. The remaining sample (˜900 uL) was diluted into binding and washing buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl [2×]) and equally divided between Dynabeads MyOne Streptavidin C1 (ThermoFisher Scientific, Cat. No. 65001) that were prepared with or without biotin blocking (200 mM biotin in binding and washing buffer, 2×10 min pretreatment). Biotinylated DNA enrichment was performed for 30 minutes at RT by rotation and samples were washed with binding and washing buffer (4×4 min.). Biotinylated DNA was dissociated from beads by adding 100 mL of 0.1% SDS and heating for 7 min at 95 C. Eluted and input DNA was purified using QIAQuick PCR Purification Kit (Qiagen) according to the manufacturer's instructions.
qPCR
ChIP DNA from both experiments was quantified in triplicate using quantitative PCR on a LightCycler 480 (Roche). The sequences of the qPCR primers are listed in Table 5.
Enrichment plots for each target gene show percent input relative to non-enriched input DNA.
Purified peptide B-Z was dissolved in 50 mM HEPES pH 6.0, 200 mM NaCl and 10 mM MgCl2 to yield a 200 μM solution. To this solution, 16-mer oligonucleotides (2.5 mM) containing E-box site in duplex buffer (100 mM potassium acetate, 30 mM HEPES, pH 7.5, Integrated DNA technologies, Lot #11-05-01-12) were added to make the final concentration of oligonucleotides 100 μM. Co-crystals were generated using hanging drop vapor diffusion where 1 μL of complex solution was mixed with 1 μL well solution. Clear rectangular crystals emerged in 50 mM Tris pH 7.0, 30% 2-Methyl-2,4-pentanediol, 50 mM NaCl and 10 mM MgCl2. Diffraction data was collected at the Advanced Photon Source, Argonne National Laboratories, Argonne, Illinois, at the SBC 19-BM beamline (0.97 Å). Data were indexed, scaled and merged using HKL-300016 (Minor et al., Acta Crystallogr D Biol Crystallogr, 62: 859-866 (2006), incorporated by reference herein). Molecular replacement was performed in Phenix using PDB: 1HLO as the search model with ligand removed (Adams et al., Acta Crystallogr D Biol Crystallogr, 66: 213-221 (2010), incorporated by reference herein). The model was refined using iterative rounds of Phenix Refine and manual inspection with Coot (Emsley et al., Acta Crystallogr D Biol Crystallogr, 66: 486-501 (2010), incorporated by reference herein). Ligand constraints for interhelix were generated using Elbow. Final deposited structure will be released for open access in the Protein Data Bank (Accession: 7RCU). All x-ray crystal structure images were generated using Pymol. Data collection and refinement statistics are reported in Table 6.
The core DNA-binding domain of basic helix-loop-helix (bHLH) TFs such as MYC and MAX, contain a leucine zipper helix connected to a basic DNA-binding helix through a flexible loop (
A model basic-zipper, cross-dimer STR derived from MAX was synthesized, and specific DNA binding was quantified using electrophoretic mobility shift assays (EMSA, or gel-shift) with either a consensus E-box oligonucleotide (targeted by MYC and MAX) or a control oligonucleotide containing the unrelated AP1 consensus binding site. It was found that a basic-zipper helix hybrid (B-Z) potently bound E-box containing DNA with an apparent KD of 16 nM and showed no stable binding to the control AP1 oligonucleotide. By contrast, it was found that neither the complete B-helix, nor a suitable hydrocarbon ‘stapled’ version (B1) showed any appreciable binding to E-box DNA. This observation runs contrary to reports in the literature that unmodified or ‘stapled’ basic domain helices alone can specifically bind DNA, at least for MAX.
Based on these results, a modular route was devised to synthesize STRs that contained both secondary and tertiary domain stabilization elements. Among the possible strategies to achieve this, a route was elected in which zipper and basic helix peptides were synthesized containing bis-alkylated, terminal olefin containing ‘S5’ amino acids for side-chain ‘stapling’ by ring-closing metathesis (
To identify MAX-STR structure-function relationships, a focused medicinal chemistry campaign was undertaken around the ‘B-Z’ progenitor. Two parallel libraries of basic and zipper helices with promising stapling positions, peptide lengths and modifications for stability (e.g., structural and metabolic;
Using these SAR determinants as a guide, a library of MAX-STRs was synthesized that contained stabilizing modifications in both helices, and several lead compounds for further study were identified. These included B1-Z2, which was based on and had a similar binding affinity to the original unmodified B-Z scaffold. Two additional leads, STR116 and STR118, encompassed changes predicted to preserve or improve binding and augment metabolic stability, as discussed below. STR118 exhibited very high affinity for E-box DNA (KD=3 nM), which is on par with measurements and reported affinities for full-length MYC/MAX and MAX/MAX. Competitive EMSA experiments demonstrated that STR116, STR118 and MAX protein binding could be effectively competed with excess unlabeled E-box oligonucleotide (
Next tested was whether STRs were capable of competing with DNA binding by recombinant MAX/MAX and MYC/MAX. Competition EMSAs at saturating concentrations of MAX showed minimal competition by the unmodified B-Z molecule, nor the stabilized progenitor B1-Z2. STR118 caused dose-dependent inhibition of both MAX/MAX and MYC/MAX bound E-box DNA complexes accompanied by the formation of the stable STR-E-box DNA complex with IC50 values of 61 nM and 170 nM, respectively. In line with its lower affinity, STR116 inhibited MAX/MAX and MYC/MAX DNA binding with IC50 values of 400 nM and 1.0 μM, respectively. STR116 and B-Z have similar equilibrium dissociation constants, suggesting that kinetic factors may play a role in effective competition for DNA binding. These data confirm that lead STRs can directly inhibit MYC/MAX and MAX/MAX DNA binding through the formation of a dominant-negative STR-DNA complex.
Beyond promoting potent and specific DNA binding, synthetic stabilization of secondary and tertiary elements should augment the structural, and therefore pharmacologic, stability of STRs. This effect has been demonstrated with diverse side chain macrocyclization of α-helical, loop and β-sheet peptides, resulting in molecules with demonstrated activity in cells, animal models and more recently in humans. Circular dichroism (CD) spectroscopy of the non-stapled B-Z progenitor confirmed that it is largely unstructured in solution. By contrast, spectra of all STRs showed strong absorbance minima at 208 and 222 nm, consistent with a predominantly α-helical structure. Temperature-dependent CD of STR118 confirmed that the structure templated by inter- and intramolecular stabilizing elements is highly thermally stable, with retention of helicity even at 85° C. Indeed, an aliquot of STR118 heated to 95° C. and then cooled showed identical binding activity compared to an aliquot kept at room temperature, reinforcing the hybrid properties of these fully synthetic ‘biologic’ structures.
To ascertain how this structural stability impacts biological activity, a series of experiments were performed aimed at quantifying the chemical and proteolytic sensitivity of wild-type and stabilized MAX-STRs. To start, a kinetic trypsin stability assay was employed which can be very active against arginine- and lysine-rich DNA binding domains. The full-length MAX bHLH domain, which is structurally analogous to Omomyc and related polypeptide mimics of natural bHLH domains, was immediately degraded and exhibited a half-life of 20 seconds in this assay. Likewise, the wild-type B-Z molecule was rapidly proteolyzed at several positions, as measured by LC-MS. Introduction of hydrocarbon staples clearly protected internal and adjacent cleavage sites in stabilized molecules like B1-Z2. Targeted helix-stabilizing substitutions, such as aminoisobutyric acid (Aib) or synonymous mutations not recognized by trypsin were introduced near those sites to further reduced proteolytic sensitivity, but typically led to losses in binding affinity (e.g., B5-Z4). Both STR116 and -118 embodied a combination of stabilizing modifications balanced with retained or improved binding affinity and exhibited significantly increased half-lives (>10-fold) relative to natural bHLH protein structures like MAX. To complement trypsin stability assays, MAX-STRs were incubated in conditioned media and assessed their functional integrity (e.g., retained capacity for DNA binding) over time by EMSA. The unmodified (B-Z) and stabilized (B1-Z2) showed >50% loss of activity within the first day. Consistent with higher stability in CD and trypsin assays, both STR118 and STR116 exhibited increased stability in conditioned media. Together, these data confirm that vigilant introduction of local and global stabilizing modifications can produce STRs with potent DNA-binding activity, hyperstable structures and improved pharmacologic features such as protease resistance (
Stabilized peptides and cell-penetrating proteins interact with and enter cells via different mechanisms compared to many cell-permeable small molecules. Attributes such as secondary structure, charge, hydrophobicity, solubility and proteolytic stability have been shown to be important for productive cellular uptake and sub-cellular distribution for different classes of stabilized peptides. To determine whether STRs were capable of penetrating cells, first synthesized were fluorescein isothiocyanate (FITC) labeled versions of lead compounds, and imaged cells incubated with each molecule by confocal fluorescence microscopy. Cellular uptake of all molecules was observed, however the intensity and sub-cellular localization showed distinct patterns. The unmodified B-Z compound demonstrated weak uptake and punctate distribution relative to its stabilized counterparts STR116 and STR118. STR118 and -116 were present in cells at much higher levels and showed significant distribution in the cytosol and nucleus of cells (
To confirm that intact MAX-STRs are present inside of cells—and at what relative concentrations—the intracellular contents of cells were extracted after treatment with each compound for visualization of the intact molecules by gel electrophoresis. Full-length FITC-STR116 and FITC-STR118 were observed in cells after 12 hrs at much higher concentrations relative to the unstructured B-Z progenitor. These combined data confirmed that MAX-STRs can penetrate cells and access intracellular compartments intact, and that differences in uptake and sub-cellular distribution likely stem from collective differences in proteolytic stability and target binding activities.
The combined biochemical and pharmacologic properties of optimized compounds suggested they should be capable of directly binding E-box sites within cells. Chromatin immunoprecipitation (ChIP) studies have validated the association of MYC and MAX proteins with specific E-box promoters and enhancers in numerous cell lines. Guided by these datasets, ChIP-qPCR assays were used to directly interrogate STR engagement with relevant target genes in cells. MYC- and MAX-dependent ChIP-qPCR confirmed that both proteins associated with several previously validated, E-box containing genes in P493-6 B-cells, including RPL37, MRPS15, TOR1A and FBXW8 (
To assess whether optimized MAX-STRs can inhibit MYC-dependent function in cells, the MYC-responsive P493-6 cancer cell line was utilized. P493-6 cells grown in the absence of tetracycline constitutively express MYC (‘MYC-ON’), however, cells treated with tetracycline (‘MYC-OFF’) have low levels of MYC protein and severely reduced proliferation in cell culture (
The biophysical and biochemical structure activity relationships elucidated here strongly suggest that STRs assemble and recognize E-box DNA in a manner similar to full length bHLH TFs like MYC and MAX. To directly confirm this hypothesis, the progenitor STR, B-Z, was crystallized with a 16-mer oligonucleotide containing a central 5′-CACGTG-3′ target sequence. A screen of crystallization conditions yielded reproducible rod-like crystals, permitting the 2.7 Å structure to be solved by X-ray diffraction followed by molecular replacement using a published structure of the MAX/MAX ternary complex with E-box DNA (PDB ID: 1HLO; Table 6 and methods) (Brownlie et al., Structure, 5: 509-520 (1997), incorporated by reference herein). The asymmetric unit cell consisted of four B-Z dimers, each bound to a single duplex DNA, with crystal contacts observed between inter-unit tetrahelix bundles and single base pair overhangs of adjacent oligonucleotide duplexes. The zipper and basic sequences in each B-Z monomer were completely α-helical and connected by a well-ordered glycyl-maleimide-cysteine adduct on the back face of each helix. The interhelix crosslink was closely packed by surrounding residues on each helix, effectively locking the B and Z helices into a defined register relative to one another. As predicted by the cross-dimer design, each B-Z monomer forms a ‘sandwich-like’ homodimer to form a tetrahelix bundle and orient the basic helices for sequence specific DNA binding. The interface formed between the pseudo-symmetric homodimer buries approximately 1590 Å2 and is mediated by extensive contacts between residues in both the B and Z helices. Anchoring this interface is an extensive hydrophobic core in the tetrahelix interior formed by bIIe39, bLys40, bPhe43, bLeu46, bArg47, bVal50, bPro51, zArg60, zIle63, zLeu64, zAla67, zThr68, zTyr70, zIle71, zNle74 and zArg75, where ‘b’ and ‘z’ refer to the basic and zipper helix numbering from the parent MAX protein. Supporting this core is an additional layer of solvent exposed hydrophobic and polar contacts that contribute to the intermolecular tertiary and quaternary structure, including close packing between zTyr70 and zNle74 with bVal50 and bPro51.
Like full-length MYC and MAX, the B-Z dimer binds the E-box target DNA with each monomer interacting with half of the 5′-CACGTG-3′ recognition sequence. Each basic helix makes numerous contacts to the phosphodiester backbone of DNA, as well as four sequence-specific contacts deep in the major groove. Backbone contacts are made by residues throughout the entire basic helix and encompass a 12-nucleotide span surrounding the E-box. These contacts include a bHis27-PO4 contact three nucleotides outside of the E-box, and bArg25, bAsn29, bArg33, bArg36, bLys40, zSer59 and zArg60 all make contacts to phosphodiester positions within the core E-box sequence (
Programming Alternative DNA Recognition with Modular STR Designs.
MAX homodimers exhibit sequence specificity for the E-Box sequence, whereas many of the 107 known human bHLH transcription factors bind distinct NCANNTGN motifs (where ‘N’ is any nucleotide). Given the near identical structural alignment of the DNA-binding region of MAX and a MAX-STR in crystal structures, next determined was if unique sequence-specific binding preferences could be programmed into novel STRs through incorporation of the aligned primary sequences of alternate bHLH proteins (
This study established design, synthesis, and structure activity relationships for a novel class of synthetic transcription factor mimetics derived from MAX. These non-natural, ‘cross-dimer’ STRs recapitulate the cooperative association of DNA binding domains, as found in hundreds of known transcription factors, however their hybrid architecture suggests they should not interfere with protein-protein interactions between endogenous bHLH proteins.
A modular, convergent synthetic route was developed that enabled introduction of multiple non-natural stabilizing elements and in the process identified the necessary structural features required for high affinity and specific DNA recognition. Basic helices alone, whether containing internal stabilizing elements or synthetically dimerized, lack significant DNA recognition capacity. Preorganization of the proximal basic-zipper helix register is sufficient to drive formation of the tetrahelix core above the basic helices, which ultimately permits high affinity and sequence-specific DNA binding. Notably, observed was comparable specificity, but not increased affinity, of several stapled STRs (e.g., B1-Z2 & B 11-Z6) relative to the non-stapled progenitor B-Z. As these molecules are considerably more helical and thermally stable than B-Z, these data support published models of disordered-to-ordered search and binding by the basic helices as being integral to forming tight, specific complexes with DNA. Preorganization of the individual helices may result in a thermodynamic trade-off between avoiding the energetic cost of folding to bind the major groove versus the restrictions on subtle conformational adjustments for optimal binding, which may be more accessible to non-stapled versions. STRs based on the minimal B-Z core were incapable of competing with MYC/MAX or MAX/MAX for E-box DNA binding. Optimized derivatives of this scaffold, including STR116 and STR118, were potent competitors with the full-length MYC/MAX and MAX/MAX complexes. This finding suggests that kinetic factors may be important determinants of effective competition, as STR116 and B-Z have identical KD values for E-box binding, but only the former effectively competed for DNA binding.
In addition to improved biochemical properties, it was found that activity-guided stabilization of tertiary and secondary elements led to significant increases in structural and proteolytic stability of several STRs. Targeted modification at and around sites of proteolysis within these molecules correlated with protection from proteolysis, however these changes had to be balanced with preservation of DNA binding. The net result of this enhanced stability for optimized molecules like STR116 and STR118, at least as explored here, was enhanced protease resistance, cellular penetration, DNA binding activity and activity in cellular models. The studies also confirmed that DNA binding domains comprised of canonical amino acids alone, such as MAX and by analogs like Omomyc and other engineered proteins, are largely unstructured and highly sensitive to proteases. As such, they are likely to suffer significant degradation inside and outside of cells if used as chemical probes and therapeutics. More generally, the data support the notion that modular synthesis of secondary and tertiary domain epitopes can be used to generate pharmacologically active mimetics, such as those targeting DNA in this study, and likely other proteins and biomolecules in the future.
Molecules with improved stability and biochemical properties, such as STR116 and STR118, are cell permeable and can specifically engage E-box target genes in live cells. Treatment of B cells with STR116, which is the more stable and cell permeable of the two, results in decreased expression of known MYC target genes and antiproliferative activity only in the context of oncogenic MYC-signaling in P493-6 B cells.
The biochemical and structural findings also support the notion that the self-associating, cross-dimer STR architecture mimics full-length TF protein structure and function, and therefore should be applicable to other bHLH TFs. The platform was applied to efficiently construct STRs derived from OLIG2 and TFAP4, two bHLH-TFs that are implicated in cancer pathogenesis. The resulting molecules, STR64 and STR69, display differentiated sequence specific DNA binding from their MAX-derived B-Z ancestor and represent potential antagonists of their respective transcription factors. These findings confirm that the general approach described herein forms a basis for methodical development of sequence specific synthetic transcriptional regulators for the study and pharmacologic targeting of gene expression regulated by diverse transcription factors.
This example further demonstrates helical dimers, in accordance with aspects of the disclosure.
This example further demonstrates helical dimers and helical tetramers, in accordance with aspects of the disclosure.
The following peptides in Table 10 have been synthesized. They have the core B-Z sequence with appended amino acid sequences from other transcription factors (MAX [isoforms 1 and 2], MAD, AND MYC).
The following peptides in Table 11 also have been synthesized. The zipper helix is extended. ZL1 is a natural variant for MAX protein, whereas ZM3 and ZM4 are designer sequences. Z6 is an extension of the Z4 sequence.
Results are provided in the tables below with respect to experiments performed using polypeptides of the Examples. Tables 12 and 13 present binding data with regard to helical dimers (a first polypeptide covalently bound to a second polypeptide as described herein) that come together to from tetrahelical structures when bound and helical tetramers (a first polypeptide covalently bound to a second polypeptide, a third polypeptide covalently bound to a fourth polypeptide, and the second polypeptide covalently bound to the fourth polypeptide).
Helical tetramers of STR116 (STR116T) and STR118 (STR118T) were tested in a luciferase assay, with the results shown in
Results are provided in the tables below with respect to experiments performed using polypeptides of the Examples.
This example further demonstrates aspects of the disclosure.
The sequences of Table 19 incorporate point mutations derived from homologous bHLH proteins of Table 20. The bHLH proteins have different DNA specificity. Substituting amino acids from the DNA binding groove is contemplated to alter sDBD specificity.
This example further demonstrates helical dimers, in accordance with aspects of the disclosure.
Additional sequences are provided in Table 21 below.
Certain sequences were made and tested together for binding to an E-box probe. The Kd values are shown in Table 22.
B11-Z70 and B11-Z80 have strategic substitutions to increase solubility and are soluble in RPMI media+10% FBS at concentrations >75 μM.
This example further demonstrates aspects of the disclosure.
HCT116 cells expressing a c-myc responsive luciferase reporter were treated with increasing concentrations of STR1180 for 24 hours and the activity of the reporter gene was measured (
The sequence of STR1180 is shown in Table 23.
All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.
The use of the terms “a” and “an” and “the” and “at least one” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The use of the term “at least one” followed by a list of one or more items (for example, “at least one of A and B”) is to be construed to mean one item selected from the listed items (A or B) or any combination of two or more of the listed items (A and B), unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
Preferred aspects of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred aspects may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.
This patent application is a U.S. National Phase of International Patent Application No. PCT/US2021/060808, filed Nov. 24, 2021, which claims the benefit of co-pending U.S. Provisional Patent Application No. 63/117,710, filed Nov. 24, 2020, each of which is incorporated by reference in its entirety herein.
This invention was made with government support under DP2GM128199-01 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/060808 | 11/24/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63117710 | Nov 2020 | US |
