Patent Grant
10993983
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. The ASCII copy, created on Feb. 11, 2019, is named 167774_010404_US_SL.txt and is 30,864 bytes in size.
In the last two decades, early-stage drug discovery has expanded to include targets outside the traditionally druggable classes of enzymes and cell surface receptors. Classically “undruggable” protein-protein interactions can make viable drug targets, but often have large interaction surfaces that are difficult for small molecules to bind with high affinity. Peptides are an attractive option for targeting protein-protein interactions, as they are intermediate in size between small molecules and large biologics and offer many advantages over both. Peptides are synthetically tractable, they can be optimized to high affinity and selectivity, and they often have good safety and tolerability profiles in animals and humans. However, short peptides are often poorly structured in aqueous solution, which can limit their affinity for their targets. One of the largest limitations of peptide drugs is poor membrane penetration, making delivery to intracellular targets difficult. Therefore, a need exists for peptides having effective cell penetration.
Macroautophagy (hereafter referred to as autophagy) is a coordinated process by which eukaryotic cells recycle material, including bulk cytosol, damaged organelles, protein aggregates, and invading organisms. It is an evolutionarily conserved pathway in all eukaryotes and is fundamental for cellular survival and development. Autophagy is initiated in the cytosol, where cellular or foreign material becomes engulfed by a double-membrane vesicle called the autophagosome (
The molecular pathways that control autophagy are an intense area of current study. Some of the upstream signaling events that trigger autophagy, such as mTOR inhibition and Akt activation, have been elucidated. However, the molecular mechanisms of cargo recognition, autophagosome initiation, remodeling of the double membrane, autophagosome trafficking, and lysosomal fusion are just starting to be revealed. The protein Beclin 1 is a master regulator of autophagy. When autophagy is triggered, Beclin 1 forms a large multiprotein complex with a class III phosphatidylinositol 3-kinase, and this complex nucleates autophagosomes. Beclin 1 interacts with several known positive and negative regulators of autophagy, including Bcl-2/Bcl-xL, AMBRA1, Rubicon, DAPK, AKT, EGFR, MAPAPK2/3, Golgi-Associated Plant Pathogenesis-Related protein 1 (GAPR-1), and HIV-Nef, highlighting its critical role in the control of autophagy initiation.
Impaired autophagy is a hallmark of diverse human diseases. Protein aggregation, a common feature of many neurodegenerative disorders including Alzheimer's, Parkinson's, and Huntington's, has been linked to reduced initiation of autophagy and impaired fusion of autophagosomes to lysosomes. Down-regulation of autophagy, including decreased expression of Beclin 1, has also been implicated in tumorigenesis. Mutations or polymorphisms in several different autophagy genes have also been linked to familial neurodegenerative disorders, muscular diseases, inflammatory bowel disease and other autoimmune and/or inflammatory disorders, and enhanced susceptibility to certain infectious diseases. Loss-of-function studies in mice and other model organisms demonstrate a crucial role for the autophagy pathway in protein and organelle quality control, metabolism, innate and adaptive immunity, protection against aging and a wide range of diseases. Since impaired autophagy is prominent in the pathogenesis and pathology of so many conditions, pharmacological activation of autophagy has been proposed as a promising avenue for new treatments. As proof-of-principle for this concept, tissue-specific autophagy gene delivery in liver, muscle, brain or lung improves hepatic insulin resistance/diabetes, lysosomal storage disorders, muscular dystrophy, neurodegenerative diseases, and cystic fibrosis in mouse models. However, such gene therapy approaches are not readily translatable to patients. While many existing FDA-approved drugs enhance autophagy, they have pleiotropic effects and it is not known whether their clinical benefits are mediated by autophagy. Thus, potent and selective molecules are highly sought after to test autophagy activation as a therapeutic mode for these and other conditions.
To date, one of the most potent, selective inducers of autophagy is the peptide Tat-Beclin 1, which was derived from the sequence of Beclin 1 (
Thus, a need exists for the development of new autophagy inducing compounds and compositions.
Provided herein are cyclic peptides and small-molecule mimics that are cell penetrating, and methods of using the same to induce cellular autophagy in vitro and in vivo. In some embodiments, the cyclic peptide is a compound selected from Formulae I, II, ilia, Mb, and Mc:
wherein:
R1 is selected from
H) H2N—,
I) MeC(O)—, and
J) c(FΦRRRRE) (SEQ ID NO: 14);
R2 is —C(O)2NH2,
Z is selected from:
X1 is selected from C, D, G, T, V and W,
X2 is selected from C, C, F, H, L, N, W, and Y,
X3 is selected from A, D, N, and W,
X4 is selected from A, I, S and T,
X5 is selected from A, C, C, F, H, and T,
X6 is selected from C, C, F, H, and W,
X7 is selected from A, D, E, H, I, and T,
X8 is selected from A, F, I, L, M, R, V, W, and Y,
X9 is selected from A, F, H, N, and W,
X10 is selected from A, C, C, D, H, R, W, and Y, and
X11 is selected from D, E, and V;
X1-X11 are all in the L configuration, except for C which is in the D configuration;
m is 0 or 1, and
n is 0 or 1,
or a pharmaceutically acceptable salt thereof.
In some embodiments, R1 is
In other embodiments, R1 is
In some embodiments, R1 is H2N—.
In some embodiments, Z is
In some embodiments, Z is
In some embodiments, Z is
In other embodiments, Z is
In some embodiments, X2 is C and X6 is C. In some embodiments, X2 is C and X6 is C. In other embodiments, X2 is C and X5 is C. In some embodiments, X1-X10 is VCNATCHIWH (SEQ ID NO: 1), and m is 1. In some embodiments, X1-X10 is VCNATCHIWH (SEQ ID NO: 2), and m is 1. In some embodiments, X1-X10 is VCNATCHIWH (SEQ ID NO: 9), and m is 1. In some embodiments, X1-X10 is VCNATCHIWR (SEQ ID NO: 3), and m is 1. In some embodiments, X1-X10 is VWNATCHIWC (SEQ ID NO: 4), and m is 1. In some embodiments, X1-X10 is VWNATFHIWHD (SEQ ID NO: 5), m is 1 and n is 1. In some embodiments, X1-X10 is VWNATCHIWC (SEQ ID NO: 11), and m is 1.
In some embodiments, the compound is Formula I. In some embodiments, R1 is A and Z is selected from MP and OP. In some embodiments, R1 is H2N and Z is selected from MP. In other embodiments, R1 is MeC(O) and Z is selected from MP. In still other embodiments, R1 is c(FΦRRRRE) (SEQ ID NO: 14) and Z is selected from MP.
In some embodiments, the compound is Formula II. In some embodiments, R1 is A and Z is selected from PP, MP and OP. In some embodiments, Z is OP.
In other embodiments, the compound is Formula Ma. In some embodiments, R1 is A. In some embodiments, R1 is H2N. In other embodiments, R1 is c(FΦRRRRE) (SEQ ID NO: 14). In some embodiments, the compound is Formula IIIb. In some embodiments, R1 is A. In some embodiments, the compound is Formula IIIc. In some embodiments, R1 is C.
Disclosed herein are compounds, and pharmaceutically acceptable salts thereof, that include those of Formula I, II, Ma, and Mb such as:
In a further aspect, provided herein is a modified peptide, or pharmaceutically acceptable salt thereof, comprising a linker of formula VI covalently bonded at two amino acids (e.g., at the alpha-carbon), Xa and Xb of formula VII:
wherein:
a is an integer selected from 1-7, inclusive;
b is an integer selected from 4-10, inclusive;
Xa and Xb are 3, 4, or 7 amino acid residues apart;
the alpha-carbon on Xa and/or Xb optionally contains a methyl group substitution;
p and q are each independently an integer selected from 2, 3, and 4;
R1 is selected from
H) H2N—,
I) MeC(O)—, and
J) c(FΦRRRRE) (SEQ ID NO: 14);
R2 is —C(O)2NH2;
X1 is selected from C, D, G, T, V, and W,
X2 is selected from C, C, F, H, L, N, W, and Y,
X3 is selected from A, D, N, and W,
X4 is selected from A, I, S, and T,
X5 is selected from A, C, C, F, H, and T,
X6 is selected from C, C, F, H, and W,
X7 is selected from A, D, E, H, I, and T,
X8 is selected from A, F, I, L, M, R, V, W, and Y,
X9 is selected from A, F, H, N, and W,
X10 is selected from A, C, C, D, H, R, W, and Y, and
X11 is selected from D, E, and V;
X1-X11 are all in the L configuration, except for C which is in the D configuration;
m is 0 or 1; and
n is 0 or 1.
In another aspect, provided herein are methods of inducing autophagy in a cell, the method comprising contacting the cell with an effective amount of a peptide as disclosed herein. Also provided herein are methods of treating a disease or condition having impaired autophagy, including but not limited to neurodegenerative disorders, cancers, muscular diseases, inflammatory bowel disease, autoimmune and/or inflammatory disorders, infectious diseases (e.g., infection with intracellular pathogens such as virus or bacteria), metabolic disorders, innate and adaptive immune disorders, aging, hepatic insulin resistance/diabetes, lysosomal storage disorders, muscular dystrophy, and cystic fibrosis. The methods can include administering to a subject in need thereof an effective amount of a peptide as disclosed herein. In some embodiments, the subject is a mammal, such as a human, feline, canine, bovine, avian, or rodent.
Pharmaceutical compositions are also provided herein, comprising any peptide disclosed herein, as well as kits that comprise such peptide.
In addition to modified peptides, small-molecule helix mimics are also provided, such as those disclosed in Okuyama et al., Nature Methods 4, 153-159 (2007); Whitby and Boger, Acc Chem Res 2012, 45, 1698; Arkin et al., Chemistry & Biology 2014, 21(9): 1102-1114; Lanning and Fletcher, Biology 2015, 4, 540-555; Hoggard et al., J. Am. Chem. Soc., 2015, 137 (38), pp 12249-12260; Wang et al., RSC Adv., 2016, 6, 61599; and Groβ et al., Front. Bioeng. Biotechnol., 2016, dx.doi.org/10.3389/fbioe.2015.00211; all of which are incorporated herein by reference in their entirety.
Provided herein are cell penetrating cyclic peptide, small-molecule mimics and methods of using such peptides and small-molecule mimics to induce cellular autophagy in vitro and in vivo.
In some aspects, disclosed herein are the design, synthesis and application of intrinsically cell-penetrant peptides derived from Tat-Beclin 1. Truncation and optimization of Tat-Beclin 1 produced a smaller, Tat-linked tool compound with greater potency. Then, a new, structure-independent stapling strategy is used to constrain the peptide into a stable structure that promotes activity and cell penetration. This strategy produced DD5-o, an autophagy-inducing peptide of only ten residues. DD5-o induces autophagy in vitro and in vivo as potently as Tat-Beclin 1, but DD5-o lacks Tat and has minimal overall charge at neutral pH. The solution structure of DD5-o was solved and, surprisingly, a helical conformation stabilized by a new type of (i, i+3) staple was revealed. Since Beclin 1 and its immediate effectors are all oriented towards the cytosol, the cytosolic penetration of this new class of stapled peptides was measured. Most cell penetration assays require labelling with a fluorescent dye, and often cannot distinguish between endosomal and cytosolic localization. A new assay that quantitatively measures cytosolic delivery of an exogenously added peptide was developed and described in detail in U.S. Provisional Application No. 62/424,955, filed Nov. 21, 2016, and corresponding to U.S. Pat. No. 10,620,214, which is incorporated herein by reference in its entirety. This straightforward assay demonstrates the intrinsically cell-penetrant nature of DD5-o, and will be generally applicable for quantitative measurement of cytosolic penetration of nearly any exogenously added molecule.
Thus, the cyclic/stapled peptides disclosed herein (such as DD5-o and derivatives) can present real lead for pre-clinical and clinical development. Furthermore, the DD5-o pharmacophore can be used to design and/or screen for small-molecule drugs. For example, the NMR structure of stapled peptide provides 3D search queries that can be used to search (e.g., in silico) small molecule databases to find matches, or to design small molecules with similar properties. Additionally, based on the helical confirmation of DD5-o, small-molecule helix mimics can also be designed, such as those disclosed in Whitby and Boger, Acc Chem Res 2012, 45, 1698, incorporated herein by reference in its entirety.
Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art of the present disclosure. The following references provide one of skill with a general definition of many of the terms used in this disclosure: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them below, unless specified otherwise.
By “agent” is meant a substance selected from a protein, a peptide, an antibody, a nucleic acid molecule, or fragments thereof, and an organic, organometallic or inorganic compound, each of which can be present as free of other substances. An agent also includes compositions, such as formulations, complexes, composites, matrices and the like, that contain one or more of these substances. An agent can be the active compound or constituent in a therapeutic setting.
By “ameliorate” or “modulate” is meant to decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease or a chemical reaction.
By “amino acid” or “residue” is meant a free compound or unit in a peptide or protein that has the general structure H2N—C(RaRb)—COOH or —HN—C(RaRb)—CO—. Ra and Rb can be selected, for example, from the carbon substituents found in the 20 natural amino acids and those unnatural ones known in the art. Amino acids can be in either the L or S (natural) or D or R (unnatural) stereochemical configuration using the optical rotation D/L system of nomenclature or the Cahn-Ingold-Prelog R/S system.
By “cell penetrating” as applied to a peptide is meant that the peptide is capable of crossing the cell membrane whether by endocytosis, passively permeable and/or some other mechanism.
In this disclosure, “comprises,” “comprising,” “containing” and “having” and the like can have the meaning ascribed to them in U.S. Patent law and can mean “includes,” “including,” and the like; “consisting essentially of” or “consists essentially” likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.
As used herein, the term “detect” refers to identifying the presence, absence or amount of the analyte to be detected. One of ordinary skill in the art readily appreciates that measurement methods inherently possess a limit(s) to its lowest and highest levels of detection. Thus, an indication of not detected as used herein is not to be construed to mean the analyte is not present at all. It is simply not present between the upper or lower limits of the detection method.
By “disease” is meant any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. In one embodiment, the disease is a condition having impaired autophagy, including but not limited to neurodegenerative disorders, cancers, muscular diseases, inflammatory bowel disease, autoimmune and/or inflammatory disorders, infectious diseases (e.g., infection with intracellular pathogens such as virus or bacteria), metabolic disorders, innate and adaptive immune disorders, aging, hepatic insulin resistance/diabetes, lysosomal storage disorders, muscular dystrophy, and cystic fibrosis.
“Enantiomers” are a pair of stereoisomers that are non-superimposable mirror images of each other. A mixture of a pair of enantiomers in any proportion can be known as a “racemic” mixture. The term “(±)” is used to designate a racemic mixture where appropriate. “Diastereoisomers” are stereoisomers that have at least two asymmetric atoms, but which are not mirror-images of each other. The absolute stereochemistry is specified according to the Cahn-Ingold-Prelog R-S system. When a compound is an enantiomer, the stereochemistry at each chiral carbon can be specified by either R or S. Resolved compounds whose absolute configuration is unknown can be designated (+) or (−) depending on the direction (dextro- or levorotatory) which they rotate plane polarized light at the wavelength of the sodium D line. Certain of the compounds described herein contain one or more asymmetric centers and can thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that can be defined, in terms of absolute stereochemistry at each asymmetric atom, as (R)- or (S)-. The present chemical entities, pharmaceutical compositions and methods are meant to include all such possible isomers, including racemic mixtures, optically substantially pure forms and intermediate mixtures. Optically active (R)- and (S)-isomers can be prepared, for example, using chiral synthons or chiral reagents, or resolved using conventional techniques.
Another system used to describe enantiomers is based on how a compound rotates plane-polarized light. “D” means the light is rotated to the right, while “L” means the light is rotated to the left. These designations do not necessarily correlate with absolute stereochemistry. For example, an S-enantiomer of one compound may be a D or L configuration, which is determined experimentally. For the natural amino acids, a correlation has been made where S-configurations correspond to L designation, while unnatural R-configurations correspond to D designations. As used herein, an underlined amino acid indicates the stereochemistry is the unnatural R and D configuration, where non-underlined residues are the natural S and L configuration.
An isomer/enantiomer can, in some embodiments, be provided substantially free of the corresponding enantiomer, and can also be referred to as “optically enriched,” “enantiomerically enriched,” “enantiomerically pure” and “non-racemic,” as used interchangeably herein. These terms refer to compositions in which the percent by weight of one enantiomer is greater than the amount of that one enantiomer in a control mixture of the racemic composition (e.g., greater than 1:1 by weight). For example, an enantiomerically enriched preparation of the S enantiomer means a preparation of the compound having greater than about 50% by weight of the S enantiomer relative to the R enantiomer, such as at least about 75% by weight, further such as at least about 80% by weight. In some embodiments, the enrichment can be much greater than about 80% by weight, providing a “substantially enantiomerically enriched,” “substantially enantiomerically pure” or a “substantially non-racemic” preparation, which refers to preparations of compositions which have at least about 85% by weight of one enantiomer relative to other enantiomer, such as at least about 90% by weight, and further such as at least about 95% by weight. In certain embodiments, the compound provided herein is made up of at least about 90% by weight of one enantiomer. In other embodiments, the compound is made up of at least about 95%, about 98%, or about 99% by weight of one enantiomer.
In some embodiments, the compound is a racemic mixture of (S)- and (R)-isomers. In other embodiments, provided herein is a mixture of compounds wherein individual compounds of the mixture exist predominately in an (S)- or (R)-isomeric configuration. For example, the compound mixture has an (S)-enantiomeric excess of greater than about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99%, about 99.5%, or more. In other embodiments, the compound mixture has an (S)-enantiomeric excess of greater than about 55% to about 99.5%, greater than about 60% to about 99.5%, greater than about 65% to about 99.5%, greater than about 70% to about 99.5%, greater than about 75% to about 99.5%, greater than about 80% to about 99.5%, greater than about 85% to about 99.5%, greater than about 90% to about 99.5%, greater than about 95% to about 99.5%, greater than about 96% to about 99.5%, greater than about 97% to about 99.5%, greater than about 98% to greater than about 99.5%, greater than about 99% to about 99.5%, or more. In other embodiments, the compound mixture has an (R)-enantiomeric purity of greater than about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99%, about 99.5% or more. In some other embodiments, the compound mixture has an (R)-enantiomeric excess of greater than about 55% to about 99.5%, greater than about 60% to about 99.5%, greater than about 65% to about 99.5%, greater than about 70% to about 99.5%, greater than about 75% to about 99.5%, greater than about 80% to about 99.5%, greater than about 85% to about 99.5%, greater than about 90% to about 99.5%, greater than about 95% to about 99.5%, greater than about 96% to about 99.5%, greater than about 97% to about 99.5%, greater than about 98% to greater than about 99.5%, greater than about 99% to about 99.5% or more.
In other embodiments, the compound mixture contains identical chemical entities except for their stereochemical orientations, namely (S)- or (R)-isomers. For example, if a compound disclosed herein has a —CH(R)— unit, and R is not hydrogen, then the —CH(R)— is in an (S)- or (R)-stereochemical orientation for each of the identical chemical entities. In some embodiments, the mixture of identical chemical entities is a racemic mixture of (S)- and (R)-isomers. In another embodiment, the mixture of the identical chemical entities (except for their stereochemical orientations), contain predominately (S)-isomers or predominately (R)-isomers. For example, the (S)-isomers in the mixture of identical chemical entities are present at about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99%, about 99.5%, or more, relative to the (R)-isomers. In some embodiments, the (S)-isomers in the mixture of identical chemical entities are present at an (S)-enantiomeric excess of greater than about 55% to about 99.5%, greater than about 60% to about 99.5%, greater than about 65% to about 99.5%, greater than about 70% to about 99.5%, greater than about 75% to about 99.5%, greater than about 80% to about 99.5%, greater than about 85% to about 99.5%, greater than about 90% to about 99.5%, greater than about 95% to about 99.5%, greater than about 96% to about 99.5%, greater than about 97% to about 99.5%, greater than about 98% to greater than about 99.5%, greater than about 99% to about 99.5% or more.
In another embodiment, the (R)-isomers in the mixture of identical chemical entities (except for their stereochemical orientations), are present at about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99%, about 99.5%, or more, relative to the (S)-isomers. In some embodiments, the (R)-isomers in the mixture of identical chemical entities (except for their stereochemical orientations), are present at a (R)-enantiomeric excess greater than about 55% to about 99.5%, greater than about 60% to about 99.5%, greater than about 65% to about 99.5%, greater than about 70% to about 99.5%, greater than about 75% to about 99.5%, greater than about 80% to about 99.5%, greater than about 85% to about 99.5%, greater than about 90% to about 99.5%, greater than about 95% to about 99.5%, greater than about 96% to about 99.5%, greater than about 97% to about 99.5%, greater than about 98% to greater than about 99.5%, greater than about 99% to about 99.5%, or more.
Enantiomers can be isolated from racemic mixtures by any method known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC), the formation and crystallization of chiral salts, or prepared by asymmetric syntheses. See, for example, Enantiomers, Racemates and Resolutions (Jacques, Ed., Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Stereochemistry of Carbon Compounds (E. L. Eliel, Ed., McGraw-Hill, N Y, 1962); and Tables of Resolving Agents and Optical Resolutions p. 268 (E. L. ElM, Ed., Univ. of Notre Dame Press, Notre Dame, Ind. 1972).
Optical isomers can be obtained by resolution of the racemic mixtures according to conventional processes, e.g., by formation of diastereoisomeric salts, by treatment with an optically active acid or base. Examples of appropriate acids are tartaric, diacetyltartaric, dibenzoyltartaric, ditoluoyltartaric, and camphorsulfonic acid. The separation of the mixture of diastereoisomers by crystallization followed by liberation of the optically active bases from these salts affords separation of the isomers. Another method involves synthesis of covalent diastereoisomeric molecules by reacting disclosed compounds with an optically pure acid in an activated form or an optically pure isocyanate. The synthesized diastereoisomers can be separated by conventional means such as chromatography, distillation, crystallization or sublimation, and then hydrolyzed to deliver the enantiomerically enriched compound. Optically active compounds can also be obtained by using active starting materials. In some embodiments, these isomers can be in the form of a free acid, a free base, an ester or a salt.
By “effective amount” is meant the amount of an active agent required to ameliorate the symptoms of a disease relative to an untreated subject. In some cases, the effective amount is sufficient to palliate, ameliorate, stabilize, reverse or slow the progression of a disease or condition having impaired autophagy, including but not limited to neurodegenerative disorders, cancers, muscular diseases, inflammatory bowel disease, autoimmune and/or inflammatory disorders, infectious diseases (e.g., infection with intracellular pathogens such as virus or bacteria), metabolic disorders, innate and adaptive immune disorders, aging, hepatic insulin resistance/diabetes, lysosomal storage disorders, muscular dystrophy, and cystic fibrosis. The amount can be sufficient to effect a beneficial or desired clinical result. The effective amount of active agent(s) disclosed herein for therapeutic treatment of a disease varies depending upon a number of factors, including, but not limited to, the manner of administration, the age, body weight, and general health of the subject. A therapeutically effective amount can be administered in one or more doses. The attending physician or veterinarian can decide the appropriate amount and dosage regimen.
By “inducing” is meant to cause a chemical reaction to occur where the reagents may or may not react without the inducing agent. For example, inducing phosphorylation of a protein can involve activating a kinase and bringing it into proximity with another protein such that a residue in that protein can undergo addition of a phosphate group.
As used herein, the term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of subjects without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al. describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences (1977) 66:1-19. Pharmaceutically acceptable salts of the compounds provided herein include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, besylate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecyl sulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. In some embodiments, organic acids from which salts can be derived include, for example, acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, lactic acid, trifluoracetic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like.
The salts can be prepared in situ during the isolation and purification of the disclosed compounds, or separately, such as by reacting the free base or free acid of the compound with a suitable base or acid, respectively. Pharmaceutically acceptable salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(C1-4alkyl)4 salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, iron, zinc, copper, manganese, aluminum, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate and aryl sulfonate. Organic bases from which salts can be derived include, for example, primary, secondary, and tertiary amines, substituted amines, including naturally occurring substituted amines, cyclic amines, basic ion exchange resins, and the like, such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine. In some embodiments, the pharmaceutically acceptable base addition salt is chosen from ammonium, potassium, sodium, calcium, and magnesium salts.
By “reference” is meant a standard or control condition.
The term “subject,” “patient” or “individual” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g., infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult)) and/or other primates (e.g., cynomolgus monkeys, rhesus monkeys); mammals, including commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs; and/or birds, including commercially relevant birds such as chickens, ducks, geese, quail, and/or turkeys.
Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive. Unless specifically stated or obvious from context, as used herein, the terms “a”, “an”, and “the” are understood to be singular or plural.
Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.
The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
Any compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.
Peptide Therapeutics
Peptides are synthetically tractable, they can be optimized to high affinity and selectivity, and they often have good safety and tolerability profiles in animals and humans. Nevertheless, the clinical utility of conventional peptides has been limited by a number of factors. Short peptides are often poorly structured in aqueous solution, which can limit their affinity for their targets. One of the largest limitations of peptide drugs is poor membrane permeability, making delivery to intracellular targets difficult.
One solution to the inherent limitations of peptides is macrocyclization, which is typically applied as a structure-promoting conformational constraint. Several chemistries are available that capitalize on the reactivity of cysteine residues. For example, thioether ligation was used to link a cysteine to a bromoacetylated ornithine, yielding an alternative to lactam bridge formation. Another effective result is that these cyclic peptides are generally more stable to proteolytic degradation. In some cases, cyclic peptides have increased cytosolic penetration compared to linear peptides.
Linear peptides, such as Tat-beclin-1, have been identified as inducing autophagy, a cellular lysosomal degradation pathway that defends again infection, neurodegenerative disorders, cancer and ageing. Tat-beclin-1 was identified using an epitope of the HIV-1 virulence factor Nef. This peptide has been demonstrated to bind the autophagy inhibitor GAPR-1, which negatively regulates autophagy. Other studies indicated Tat-beclin-1 decreases protein aggregates and soluble protein concentrations. Given the need in the art for more targeted and pharmacologically available therapeutics, Tat-beclin-1 is an attractive target for development of constrained peptides through macrocyclization.
Previous work on helical peptides has demonstrated the major benefits of macrocyclization for promoting peptide structure and function, but applying cyclic constraints to non-helical structures has not been as straightforward. While the results from screening large, unbiased libraries of cyclic peptides clearly indicate that this is a valuable chemical space for protein inhibitors, rational design of small, non-helical cyclic peptides is still largely trial-and-error. Therefore, the present disclosure provides, inter alia, the design and execution of synthetic cyclic peptides with the targeted approach to a molecule with increased properties for inducing autophagy.
Autophagy-Inducing Cyclic Peptides
Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. Tat-beclin, derived from a region of the autophagy protein, beclin 1, which binds human immunodeficiency virus (HIV)-1 Nef, is a potent inducer of autophagy, and interacts with a negative regulator of autophagy, GAPR-1 (also called GLIPR2). Beclin 1, an essential autophagy protein in the class III phosphatidylinositol-3-OH kinase (PI(3)K) complex, is involved in autophagic vesicle nucleation, and interacts with the HIV-1 virulence factor, Nef. Investigating this interaction led to the identification of Tat-beclin-1, an HIV-1 Tat protein transduction domain (YGRKKRRQRRR; SEQ ID NO: 20) attached via a diglycine linker to 18 amino acids derived from amino acids 267-284 of beclin 1 (Shoji-Kawata et al., Nature 484:201-206, 2013, US App. Pub. No. US2015/0359840; each incorporated herein by reference in its entirety). Tat-beclin-1 decreases the accumulation of polyglutamine expansion protein aggregates and the replication of several pathogens (including HIV-1) in vitro, and reduces mortality in mice infected with chikungunya or West Nile virus.
While Tat-beclin-1 has demonstrated good activity in affecting autophagy pathways and functions, it is a linear peptide susceptible to degradation and requires the Tat poly-cationic sequence for cellular permeability. Linear peptides can often fluctuate between multiple 3-dimensional orientations at any given time, such that the needed conformation to interact with the target protein may only be accessed sporadically. To gain conformer control and design, peptides can be cyclized through a wide variety of linkers. Structure-activity relationship (SAR) studies often enlarge to synthesizing hundreds of variants of a molecule to narrow in on essential features for potency, which requires significant time and resources. However, rational design can focus attention to key molecular components in a more efficient and directed fashion. The rational design approach is greatly assisted by starting with a peptide epitope derived from a known protein binding partner. Ideally, this epitope accounts for a majority of the binding energy of the interaction by comprising the most important “hot spot” residues. Cyclization of peptides, for example, translates these epitopes to effective inhibitory peptides requires replacing the entire protein tertiary structure with a synthetic linker that stabilizes the epitope's highest-affinity 3D structure.
To date, computational methods for the prediction of cyclic peptide structure have not advanced to a stage where it is possible to predict the lowest-energy structural ensemble for a given cyclic peptide. This makes it impossible to predictively design specific cross-links to stabilize a desired loop structure within a cyclic peptide. Selection of the proper linker chemistry, length and positioning can only be done in a traditional SAR process. One way to accelerate this process is to introduce diverse conformational constraints at a late stage of synthesis. Described herein is an efficient method for late-stage conformational diversification of peptide epitopes using thiol bis-alkylation chemistry. This allows for rapid preparation and screening of many conformations of a given loop using a panel of linkers, experimentally searching for the highest-affinity conformation.
Thiol linkers produced by linking cysteine residues can provide stable linkers with increased conformational rigidity. Thiol bis-alkylation has rapid kinetics and broad sequence tolerance. Late-stage conformational diversification is introduced by including two thiol-containing amino acids at positions known to be non-essential for target binding. Utilizing thiol bis-alkylation chemistry, peptides can be cross-linked using a wide variety of different linkers by incubating them in solution with a variety of dibromomethyl aryl compounds (See,
Beginning with Tat-beclin-1, a set of analogs were synthesized having the Tat sequence at the N-terminus, followed by two glycine residues before the beclin-1 peptide sequence. These Tat peptides T1-T46 are linear peptides where one or two amino acids were varied at a time (shown in bold in Table 2 below) to determine which were important for potency, which alterations decreased potency, or which had little effect compared to Tat-beclin-1 itself.
Another assessment of the beclin-1 peptide activity was performed using an alanine scan shown in
The understandings gained from SAR studies with Tat-beclin-1 analogs informed the design of a series of cyclic peptides using bis-thiol linkers. The Tat sequence was removed from most analogs and replaced with an N-terminal carbonyl cap. Without wishing to be bound by theory, the cyclic nature of the peptides is believed to contribute to successful cell penetration as born out in the Examples below. Exemplary linkers are given in
Disclosed herein, in some embodiments, are compounds of Formulae I, II, IIIa, Mb, and IIIc:
wherein:
R1 is selected from
H) H2N—,
I) MeC(O)—, and
J) c(FΦRRRRE) (SEQ ID NO: 14);
R2 is —C(O)2NH2;
Z is selected from:
X1 is selected from C, D, G, T, V and W,
X2 is selected from C, C, F, H, L, N, W, and Y,
X3 is selected from A, D, N, and W,
X4 is selected from A, I, S and T,
X5 is selected from A, C, C, F, H, and T,
X6 is selected from C, C, F, H, and W,
X7 is selected from A, D, E, H, I, and T,
X8 is selected from A, F, I, L, M, R, V, W, and Y,
X9 is selected from A, F, H, N, and W,
X10 is selected from A, C, C, D, H, R, W, and Y, and
X11 is selected from D, E, and V;
X1-X11 are all in the L configuration, except for C which is in the D configuration;
m is 0 or 1, and
n is 0 or 1;
or a pharmaceutically acceptable salt thereof.
In some embodiments, R1 is
In other embodiments, R1 is
In some embodiments, R1 is H2N—.
In some embodiments, Z is
In some embodiments, Z is
In some embodiments, Z is
In other embodiments, Z is
In some embodiments, X2 is C and X6 is C. In some embodiments, X2 is C and X6 is C. In other embodiments, X2 is C and X5 is C. In some embodiments, X1-X10 is VCNATCHIWH (SEQ ID NO: 1), and m is 1. In some embodiments, X1-X10 is VCNATCHIWH (SEQ ID NO: 2), and m is 1. In some embodiments, X1-X10 is VCNATCHIWH (SEQ ID NO: 9), and m is 1. In some embodiments, X1-X10 is VCNATCHIWR (SEQ ID NO: 3), and m is 1. In some embodiments, X1-X10 is VWNATCHIWC (SEQ ID NO: 4), and m is 1. In some embodiments, X1-X10 is VWNATFHIWHD (SEQ ID NO: 5), m is 1 and n is 1. In some embodiments, X1-X10 is VWNATCHIWC (SEQ ID NO: 11), and m is 1.
In some embodiments, the compound is Formula I. In some embodiments, R1 is A and Z is selected from MP and OP. In some embodiments, R1 is H2N and Z is selected from MP. In other embodiments, R1 is MeC(O) and Z is selected from MP. In still other embodiments, R1 is c(FΦRRRRE) (SEQ ID NO: 14) and Z is selected from MP.
In some embodiments, the compound is Formula II. In some embodiments, R1 is A and Z is selected from PP, MP and OP. In some embodiments, Z is OP.
In other embodiments, the compound is Formula IIIa. In some embodiments, R1 is A. In some embodiments, R1 is H2N. In other embodiments, R1 is c(FΦRRRRE) (SEQ ID NO: 14). In some embodiments, the compound is Formula Mb. In some embodiments, R1 is A. In some embodiments, the compound is Formula Inc. In some embodiments, R1 is C.
Disclosed herein are compounds, and pharmaceutically acceptable salts thereof, that include those of Formula I, II, Ilia, and IIIb, such as:
Compounds of Tables 1 and 12 are also exemplary embodiments of the present disclosure.
Disclosed herein, in certain embodiments, are compounds of Formulae IV and V:
or a pharmaceutically salt thereof, where variables R1, R2 and X1-X10 are as described above.
In certain embodiments, disclosed herein are modified peptides, or pharmaceutically acceptable salt thereof, comprising a linker of formula VI covalently bonded at two amino acids (e.g., at the alpha-carbon), Xa and Xb of formula VII:
wherein:
a is an integer selected from 1-7, inclusive;
b is an integer selected from 4-10, inclusive;
Xa and Xb are 3, 4, or 7 amino acid residues apart;
the alpha-carbon on Xa and/or Xb optionally contains a methyl group substitution;
p and q are each independently an integer selected from 2, 3, and 4;
R1 is selected from
H) H2N—,
I) MeC(O)—, and
J) c(FΦRRRRE) (SEQ ID NO: 14);
R2 is —C(O)2NH2;
X1 is selected from C, D, G, T, V, and W,
X2 is selected from C, C, F, H, L, N, W, and Y,
X3 is selected from A, D, N, and W,
X4 is selected from A, I, S, and T,
X5 is selected from A, C, C, F, H, and T,
X6 is selected from C, C, F, H, and W,
X7 is selected from A, D, E, H, I, and T,
X8 is selected from A, F, I, L, M, R, V, W, and Y,
X9 is selected from A, F, H, N, and W,
X10 is selected from A, C, C, D, H, R, W, and Y, and
X11 is selected from D, E, and V;
X1-X11 are all in the L configuration, except for C which is in the D configuration;
m is 0 or 1; and
n is 0 or 1.
As described herein below, the autophagy activity of cyclic peptides is assayed using routine methods known in the art, including but not limited to LC3 or p62/actin immunoblots, cell based quantitation of LC3-GFP puncta as measured, or by any other method known in the art.
Compounds 1, 2, and 3 induced autophagy at 50-100 μM. Most often, the 10-mer peptide sequences, such as those of Compound, showed greater activity compared to peptide that were truncated at X1 or X10. The position of the dithiol linker at X2 and X6 in Formula I and X2 and X5 in Formula II both provided useful cyclic peptides for inducing autophagy.
Small-Molecule Helix Mimics
Based on the helical confirmation of DD5-o, small-molecule helix mimics can also be designed, such as those disclosed in Okuyama et al., Nature Methods 4, 153-159 (2007); Whitby and Boger, Acc Chem Res 2012, 45, 1698; Arkin et al., Chemistry & Biology 2014, 21(9): 1102-1114; Lanning and Fletcher, Biology 2015, 4, 540-555; Hoggard et al., J. Am. Chem. Soc., 2015, 137 (38), pp 12249-12260; Wang et al., RSC Adv., 2016, 6, 61599; and Groβ et al., Front. Bioeng. Biotechnol., 2016, dx.doi.org/10.3389/fbioe.2015.00211; all of which are incorporated herein by reference in their entirety.
Pharmaceutical Compositions
Cyclic peptides disclosed herein are cell penetrating and can be used to induce autophagy in a cell in need thereof (e.g., a cell infected with a bacteria or virus). The compositions disclosed herein (e.g., cyclic peptides) are useful for treating a disease or condition having impaired autophagy, including but not limited to neurodegenerative disorders, cancers, muscular diseases, inflammatory bowel disease, autoimmune and/or inflammatory disorders, infectious diseases (e.g., infection with intracellular pathogens such as virus or bacteria), metabolic disorders, innate and adaptive immune disorders, aging, hepatic insulin resistance/diabetes, lysosomal storage disorders, muscular dystrophy, and cystic fibrosis. The compositions can be administered in a pharmaceutically acceptable excipient, such as water, saline, aqueous dextrose, glycerol, or ethanol. The compositions can also contain other medicinal agents, pharmaceutical agents, adjuvants, carriers, and auxiliary substances such as wetting or emulsifying agents, and pH buffering agents. Standard texts, such as Remington: The Science and Practice of Pharmacy, 17th edition, Mack Publishing Company, incorporated herein by reference, can be consulted to prepare suitable compositions and formulations for administration, without undue experimentation. Suitable dosages can also be based upon the text and documents cited herein. A determination of the appropriate dosages is within the skill of one in the art given the parameters herein.
As a rule, the dosage for in vivo therapeutics or diagnostics will vary. Several factors are typically taken into account when determining an appropriate dosage. These factors include age, sex and weight of the patient, the condition being treated, the severity of the condition and the form of the compound being administered.
The dosage of the cyclic peptide compositions can vary from about 0.01 mg/m2 to about 500 mg/m2, such as about 0.1 mg/m2 to about 200 mg/m2, further such as about 0.1 mg/m2 to about 10 mg/m2. Alternatively, the dosages of the cyclic peptide compositions can vary from about 0.01 mg/kg per day to about 1000 mg/kg per day. It is expected that doses ranging from about 50 to about 2000 mg/kg will be suitable. In various embodiments, a dosage ranging from about 0.5 to about 100 mg/kg of body weight is useful; or any dosage range in which the low end of the range is any amount between 0.1 mg/kg/day and 90 mg/kg/day and the upper end of the range is any amount between 1 mg/kg/day and 100 mg/kg/day (e.g., 0.5 mg/kg/day and 5 mg/kg/day, 25 mg/kg/day and 75 mg/kg/day).
Administrations can be conducted infrequently, or on a regular daily or weekly basis until a desired, measurable parameter is detected, such as diminution of disease symptoms. Administration can then be diminished, such as to a biweekly or monthly basis, as appropriate.
Compositions disclosed herein are administered by a mode appropriate for the form of composition. Available routes of administration include subcutaneous, intramuscular, intraperitoneal, intradermal, oral, intranasal, intrapulmonary (i.e., by aerosol), intravenously, intramuscularly, subcutaneously, intracavity, intrathecally or transdermally, alone or in combination with other agents.
Compositions for oral, intranasal, or topical administration can be supplied in solid, semi-solid or liquid forms, including tablets, capsules, powders, liquids, and suspensions. Compositions for injection can be supplied as liquid solutions or suspensions, as emulsions, or as solid forms suitable for dissolution or suspension in liquid prior to injection. For administration via the respiratory tract, a suitable composition is one that provides a solid, powder, or liquid aerosol when used with an appropriate aerosolizer device. Although not required, compositions can be supplied in unit dosage form suitable for administration of a precise amount. Also contemplated herein are slow release or sustained release forms, whereby a relatively consistent level of the active compound are provided over an extended period.
Another method of administration is intralesionally, for instance by direct injection directly into a site in need of autophagy. Alternatively, the cyclic peptide or related compound is administered systemically.
Other delivery systems can include time release, delayed release or sustained release delivery systems. Such systems can avoid repeated administrations of disclosed compositions, increasing convenience to the subject and the physician. Many types of release delivery systems are available and known to those of ordinary skill in the art. They include polymer base systems such as polylactides (U.S. Pat. No. 3,773,919; European Patent No. 58,481), poly(lactide-glycolide), copolyoxalates, polycaprolactones, polyesteramides, polyorthoesters, polyhydroxybutyric acids, such as poly-D-(−)-3-hydroxybutyric acid (European Patent No. 133, 988), copolymers of L-glutamic acid and gamma-ethyl-L-glutamate (Sidman, K. R. et al., Biopolymers 22: 547-556), poly (2-hydroxyethyl methacrylate) or ethylene vinyl acetate (Langer, R. et al., J. Biomed. Mater. Res. 15:267-277; Langer, R. Chem. Tech. 12:98-105), and polyanhydrides.
Other examples of sustained-release compositions include semi-permeable polymer matrices in the form of shaped articles, e.g., films, or microcapsules. Delivery systems also include non-polymer systems that are: lipids including sterols such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono- di- and tri-glycerides; hydrogel release systems such as biologically-derived bioresorbable hydrogel (i.e., chitin hydrogels or chitosan hydrogels); sylastic systems; peptide based systems; wax coatings; compressed tablets using conventional binders and excipients; partially fused implants; and the like. Specific examples include, but are not limited to: (a) erosional systems in which the agent is contained in a form within a matrix such as those described in U.S. Pat. Nos. 4,452,775, 4,667,014, 4,748,034 and 5,239,660 and (b) diffusional systems in which an active component permeates at a controlled rate from a polymer such as described in U.S. Pat. Nos. 3,832,253, and 3,854,480.
Analogs
Analogs can differ from the cyclic peptides provided herein by alterations in primary sequence. Amino acids and analogs are well known in the art. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. One substitution is to change the absolute configuration of the amino acid, from L to D or D to L. Amino acids include naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, for example, hydroxyproline, gamma-carboxyglutamate, O-phosphoserine, and phosphothreonine. Other analogs can have a serine amino acid substituted for another thiol containing amino acid, such as homocysteine and penicillamine, as shown in
Chemical modifications include, but are not limited to, substituting alternative R groups and varying the degree of saturation at specific carbon atoms of a reference peptide. Such cyclic peptide analogs are relatively resistant to in vivo degradation, resulting in a more prolonged therapeutic effect upon administration. Assays for measuring functional activity include, but are not limited to, those described in the Examples below.
In some embodiments, the cyclic peptides contain a chemical tag that aids in isolation and/or identification. Such tags are well known in the art, such as biotin and fluorescent tags such as fluorescein and rhodamine. Peptides substituted with an alkyne can be reacted with azido-substituted tags to provide a triazole linker via “click chemistry”. The same triazole linker can be obtained with an azido substituted peptide and alkynyl-substituted tag.
Also included are methods where the peptides contain an affinity tag. An “affinity tag” is any moiety used for the purification of a protein to which it is fixed. Virtually any affinity tag known in the art may be used in these methods, including, but not limited to, calmodulin-binding peptide (CBP), glutathione-S-transferase (GST), 6×His (SEQ ID NO: 15), Maltose Binding Protein (MBP), Green Fluorescent Protein (GFP), biotin, Strep II, and FLAG. A “detectable amino acid sequence” is a composition that when linked with the protein molecule of interest renders the latter detectable, via any means, including spectroscopic, photochemical (e.g., luciferase, GFP), biochemical, immunochemical, or chemical means. For example, useful labels include radioactive isotopes, magnetic beads, metallic beads, colloidal particles, fluorescent dyes, electron-dense reagents, enzymes (e.g., horseradish peroxidase, alkaline phosphatase), biotin, digoxigenin, or haptens.
In some embodiments, the linker can be any chemical group that is covalently bonded to two different amino acids in the peptide. The linker could be an alkene (as produced by ring-closing metathesis described in Walensky and Bird, J. Med. Chem., 2014, 57 (15), pp 6275-6288 and Walensky et al., Science 305(56891:1466-1470, both incorporated herein by reference in their entirety), alkane (as produced by hydrogenation of an alkene linker), a benzyl thioether (as describe herein), an alkyl thioether (Wang and Chou, Angew. Chem. Int. Ed., 2015, 54, 10931-10934, incorporated herein by reference in its entirety), a disulfide bond, a lactam (as illustrated in Quartararo, Wu and Kritzer, ChemBioChem 13, 1490-1496 (2012), incorporated herein by reference in its entirety), a lactone, a triazole (as produced by the well-known “click” reaction, described in, e.g., Kolb et al., Angew. Chem. Int. Ed. Engl. 40 (11): 2004-2021 and Rostovtsev et al., Angew. Chem. Int. Ed. Engl. 41 (14): 2596-9, both incorporated herein by reference in their entirety), or any other suitable chemical group known to those skilled in the relevant art.
For example, a helix-stabilizing linker that is covalently bonded to two different amino acids in the peptide can be used to stabilize alpha-helical structure. The linker can be an alkene having formula VI below, wherein p and q are each an integer selected from 2, 3, and 4. The alkene linker can be produced by ring-closing metathesis described in Walensky and Bird, J. Med. Chem., 2014, 57 (15), pp 6275-6288 and Walensky et al., Science 305(5689):1466-1470. In this case, the peptide can have an alkene-containing linker between amino acids Xa (a is an integer selected from 1-7, inclusive) and Xb (b is an integer selected from 4-10, inclusive), wherein Xa and Xb are 3, 4, or 7 amino acid residues apart such that distance between Xa and Xb and the length of the linker permit formation of a stable helix. For each amino acid that is used to form the alkene-containing linker, one can independently vary the side-chain length, the presence or absence of a methyl group on the backbone alpha-carbon, and the stereochemistry of the alpha-carbon, in order to produce the optimal helical geometry for target binding.
In some embodiments, formula VI linker can be used to staple a peptide having the following sequence, wherein variables m, n, R1, R2 and X1-X10 are as described above:
Exemplary stapled peptides having alkene helix-stabilizing linker are shown below, as compared to DD5-o.
The above peptides are examples only. It should be noted that the linker can be stapled at, for example, positions 1 and 4, 1 and 5, 3 and 6, 3 and 7, 4 and 7, 4 and 8, 5 and 8, 5 and 9, 6 and 9, 6 and 10, and 7 and 10.
Therapy
Cyclic peptides disclosed herein are cell penetrating, and provide for the induction of autophagy in a cell contacted with the peptide. Autophagy functions in metazoans in cellular and tissue homeostasis, physiology, development, and protection against disease, and abnormalities in autophagy may contribute to many different pathophysiological conditions. Thus, strategies that augment autophagy may prevent or treat human disease including, but not limited to, neurodegeneration, steatohepatitis, and cancer. Induction of autophagy is also known to be useful to reduce the replication of several pathogens, including but not limited to viruses and bacteria.
Accordingly, provided herein are methods of enhancing or inducing autophagy in persons in need of enhanced autophagy. Also provided herein are methods of treating diseases and pathologies where the upregulation of autophagy is therapeutically beneficial, including neurodegenerative disorders, cancers, muscular diseases, inflammatory bowel disease, autoimmune and/or inflammatory disorders, infectious diseases (e.g., infection with intracellular pathogens such as virus or bacteria), metabolic disorders, innate and adaptive immune disorders, aging, hepatic insulin resistance/diabetes, lysosomal storage disorders, muscular dystrophy, and cystic fibrosis. In some embodiments, the disease can be infections with intracellular pathogens, neurodegenerative diseases (such as Alzheimer's, Parkinson's, and Huntington's disease), cancers, cardiomyopathy, and aging. For example, one method of treating bacterial or viral infections or symptoms thereof, neurodegenerative diseases, cancers, cardiomyopathy, steatohepatitis, and/or aging can comprise administering a therapeutically effective amount of a pharmaceutical composition comprising a compound of the formulae disclosed herein to a subject in need thereof (e.g., a mammal such as a human).
The methods herein include administering to the subject (including a subject identified as in need of such treatment) an effective amount of a compound described herein, or a composition described herein to produce such effect. Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g. opinion) or objective (e.g. measurable by a test or diagnostic method).
Therapeutic methods (which include prophylactic treatment) in general comprise administration of a therapeutically effective amount of the compounds herein, such as a compound of the formulae herein to a subject (e.g., animal, human) in need thereof, including a mammal, such as a human. Such treatment will be suitably administered to subjects, such as humans, suffering from, having, susceptible to, or at risk for a disease, disorder, or symptom thereof. Determination of those subjects “at risk” can be made by any objective or subjective determination by a diagnostic test or opinion of a subject or health care provider (e.g., genetic test, enzyme or protein marker, Marker (as defined herein), family history, and the like). The compounds herein may be also used in the treatment of any other disorders in which a need for the induction of autophagy may be implicated.
One embodiment provides a method of monitoring treatment progress. The method includes the step of determining a level of diagnostic marker (Marker) (e.g., any target delineated herein modulated by a compound herein, a protein or indicator thereof, etc.) or diagnostic measurement (e.g., screen, assay) in a subject suffering from or susceptible to a disorder or symptoms thereof associated with neurodegenerative disorders, cancers, muscular diseases, inflammatory bowel disease, autoimmune and/or inflammatory disorders, infectious diseases (e.g., infection with intracellular pathogens such as virus or bacteria), metabolic disorders, innate and adaptive immune disorders, aging, hepatic insulin resistance/diabetes, lysosomal storage disorders, muscular dystrophy, and cystic fibrosis, in which the subject has been administered a therapeutic amount of a compound herein sufficient to treat the disease or symptoms thereof. The level of Marker determined in the method can be compared to known levels of Marker in either healthy normal controls or in other afflicted patients to establish the subject's disease status. In some embodiments, a second level of Marker in the subject is determined at a time point later than the determination of the first level, and the two levels are compared to monitor the course of disease or the efficacy of the therapy. In certain embodiments, a pre-treatment level of Marker in the subject is determined prior to beginning treatment; this pre-treatment level of Marker can then be compared to the level of Marker in the subject after the treatment commences, to determine the efficacy of the treatment.
The practice of the presently disclosed molecules, compounds, and methods employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry, immunology and chemistry, which are well within the purview of the skilled artisan. Such techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, second edition (Sambrook, 1989); “Oligonucleotide Synthesis” (Gait, 1984); “Animal Cell Culture” (Freshney, 1987); “Methods in Enzymology” “Handbook of Experimental Immunology” (Weir, 1996); “Gene Transfer Vectors for Mammalian Cells” (Miller and Calos, 1987); “Current Protocols in Molecular Biology” (Ausubel, 1987); “PCR: The Polymerase Chain Reaction”, (Mullis, 1994); “Current Protocols in Immunology” (Coligan, 1991). These techniques are applicable to the production of the chimeric small molecules as provided herein, and, as such, may be considered in making and practicing the disclosed embodiments. The following examples are put forth so as to provide those of ordinary skill in the art with a description of how to make and use the disclosed assay, screening, and therapeutic methods, and are not intended to limit the scope of the recited claims.
From the foregoing description, it will be apparent that variations and modifications may be made to the procedures described herein to adopt it to various usages and conditions. Such embodiments are also within the scope of the following claims.
All patents and publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent and publication was specifically and individually indicated to be incorporated by reference.
The synthesis of Tat-containing linear peptides was performed as described in Shoji-Kawata 2013:
L-amino acid peptides were synthesized by the University of Texas Southwestern Medical Center (UTSW) Protein Chemistry Technology Core and purified to 0.95% by HPLC (confirmed by mass spectrometry). The Tat-beclin 1 peptide sequence, YGRKKRRQRRRGGTNVFNATFEIWHDGEFGT (SEQ ID NO: 8), consisted of 11 amino acids from the Tat PTD at the N terminus, a GG linker to increase flexibility, and at the C terminus, 18 amino acids derived from beclin 1 267-284 containing three substitutions, including H275E, S279D, Q281E. Wild-type Tat-beclin 1 peptide consisted of the Tat PTD, a GG linker, and 18 amino acids derived from the natural beclin 1 sequence (267-284) (YGRKKRRQRRRGGTNVFNATFHIWHSGQFGT; SEQ ID NO: 25). Control peptide, Tatscrambled, consisted of the Tat protein transduction domain, a GG linker, and a scrambled version of the C-terminal 18 amino acids from Tat-beclin 1 (YGRKKRRQRRRGGVGNDFFINHETTGFATEW; SEQ ID NO: 26). For experiments comparing Tat-beclin 1 and Tat-scrambled, peptides were dissolved in PBS(2), whereas in the experiment comparing Tat-beclin 1 and wild-type Tat-beclin 1, peptides were dissolved in H2O. Peptides were stored at 280 uC. For peptide treatment, cells were washed with PBS(2) and treated with peptides (10-50 mM, 1-4 h) dissolved in OPTI-MEM (Gibco) acidified with 0.15% (v/v) 6N HCl. For treatment of primary human MDMs, cells were washed with PBS and pre-treated with peptides (0.5-5 mM, 24 h) in 500 ml macrophage-SFM (serum-free media) (Gibco) before infection with HIV-1. D-amino acid peptides were synthesized at the HHMI Mass Spectrometry Laboratory at UC-Berkeley. The retro-inverso Tat-beclin 1 D-amino acid sequence was RRRQRRKKRGYGGTGFEGDHWIEFTANFVNT (SEQ ID NO: 27). Peptides were synthesized by solid-phase methodology on Wang resin of 0.44 meq g21 substitution using an ABI 431A synthesizer. Appropriate N-FMOC amino acid derivatives were coupled via dicyclohexylcarbodiimide activation in dichloromethane/N-methylpyrrolidone using user-devised extended activation, coupling and piperidine deprotection cycles. Dried resin-peptide was deprotected in reagent K 4 h at room temperature. Peptide was extracted with warm acetonitrile/water, lyophilized, and purified by RPLC. Crude peptide purity was roughly 75%; after purification, 95%. D-amino acid peptides were dissolved in H2O and stored at 280 uC until use. Peptide purity was assessed by FTICR mass spectrometry.
Standard fluorenylmethoxycarbonyl (Fmoc) solid-phase peptide synthesis (SPPS) was used to synthesize the linear precursor peptides. For an amidated C-terminus we used Rink Amide Resin (100-200 mesh) with a loading of 0.3-0.6 mmol/g. In order to produce a panel of cross-linked peptides, we began with the synthesis of one parent linear peptide at a scale of 50-100 μmoles. Peptides were synthesized by hand or using an automated synthesizer. After synthesizing the linear sequence, the N-terminus was capped or left as a free amine, and the peptide was cleaved off the resin. The peptide was precipitated using cold ether in order to separate it from protecting groups and cleavage reagents. The linear peptide was either purified using reverse-phase high performance liquid chromatography (RP-HPLC) or directly used in thiol bis-alkylation reactions. The linear peptide was divided into multiple reaction vessels, and reacted with different linkers in a 50:50 mixture of acetonitrile (CH3CN) and water buffered at pH 8.0. The reaction was typically complete within 1 hour at room temperature. After bis-alkylation, solvents were be concentrated by lyophilizing the reaction and resuspending in a smaller volume of CH3CN/H2O. The reaction mixture was purified by RP-HPLC to obtain the final cyclic product. An abbreviated procedure is provided below:
Peptides were synthesized on Rink Amide resin (0.53 mmol/g) using standard Fmoc chemistry. For each coupling 5 eq. of Fmoc-amino acid, 5 eq. of 2-(7-aza-1H-benzo-triazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate (HATU), 5 eq. of 1-hydroxy-7-azabenzotriazole (HOAt), and 13 eq. of diisopropylethylamine (DIPEA) were dissolved in N,N-Dimethylformamide (DMF) and added to the resin. The reaction was allowed to proceed for 30 mins. For the N-terminal caps double coupling was required. For HaloTag-peptides, HaloTag-COOH (kindly obtained from the Chenoweth Lab at University of Pennsylvania) was appended to the N-terminus by reacting 3 eq. with 3 eq. benzotriazol-1-yl-oxytripyrrolidino phosphonium hexafluorophosphate (PyBOP), 3 eq. 1-hydroxybenzotriazole (HOBt), and 6 eq. DIPEA for 1 hour at room temperature. The peptides were globally deprotected and cleaved off the resin by treatment with 94:2.5:2.5:1 (v/v) TFA/ethanedithiol/water/triisipropylsilane for 3 hour. The peptides were triturated in cold diethyl ether and washed two times. The crude pellet was then dissolved in 50:50 acetonitrile/water, and after confirming the identity of the peptide by MALDI-TOF mass spectrometry, was subjected to bis-alkylation conditions as previously shown.52 All peptides were purified by reserved-phase HPLC on a C8 preparative column. Purity of the final product was confirmed on a C18 analytical column.
The autophagy-inducing peptide Tat-Beclin 1 (
Once we narrowed down the necessary sequence to just eleven residues, we next sought to render the peptide intrinsically cell-penetrant. Our laboratory and others have shown that conformationally constraining peptides can increase potency, metabolic stability and cell penetration.45-48 Many successful strategies have employed side-chain-to-side-chain covalent cross-linking, or “stapling.” Current stapling approaches include ring-closing olefin metathesis, lactam formation, oxime linkages, and click chemistry,49 but the low-yielding nature of many macrocyclization reactions can limit the throughput and conformational diversity available to these strategies.50 Moreover, the Beclin 1-derived sequence had no evidence of defined secondary structure from structural or modeling data, so it was not possible to predict which stapled conformations would yield peptides with increased potency. We therefore devised a structure-independent stapling strategy (
Stapled peptides were tested in phenotypic assays in HeLa cells, using the accepted measurements of p62 degradation and LC3-II conversion to assess autophagy induction.44 Removing Tat and capping the N-terminus (peptide pa-11mer; sequence in Table 1) produced a peptide that did not increase autophagic activity (
Our unique synthesis and screening strategy provided ample evidence that the activity of the stapled peptides was dependent on conformation. For instance, the ortho-xylene cross-linked DD5-o was active, whereas isomers of DD5-o that were cross-linked with meta- and para-xylene linkers (DD5-m and DD5-p) were not. This suggested that activity required not just the cyclic nature of the peptide, but the specific shape conferred by the ortho-xylene linker. Similarly, the meta-xylene cross-linked DD6-m was capable of inducing autophagy, while ortho- and para-xylene variants were not (
The activity of DD5-o was also dependent on the N-terminal cap. DD5-o was capped with 4-pentynoic acid, but when analogs with free or acetylated N-termini were tested, we observed no activity (
An alanine scan was also performed on DD5-o to determine which residues are important for autophagy-inducing activity. Substituting Vail, Phe6, or Ile8 with Ala led to complete loss of activity (
Autophagy was measured in an additional assay to confirm the results obtained from immunoblotting, and to confirm that Tat-11mer and DD5-o truly induced autophagic flux (rather than blocking autophagosome maturation or lysosomal function). HeLa cells stably expressing GFP-LC3 were treated with peptide for 3 hours in serum-free media, and the number of GFP-LC3 puncta per cell were counted using fluorescence microscopy.10 These experiments were also performed in the presence of bafilomycin A1 (Baf A1), which prevents the fusion of autophagosomes with lysosomes by inhibiting vacuolar ATPase (
Immunoblot Assays.
Cells were treated with peptide in OPTI-MEM (Thermo Scientific) acidified with 0.15% (v/v) 6N HCl for 3 hour. Cells were rinsed with Dulbecco's phosphate buffered saline (PBS) and lysed in lysis buffer (20 mM HEPES, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, protease inhibitor cocktail (Roche) on ice for 1 hour. Cell lysates were centrifuged at 16,000 g for 10 min at 4° C. and analyzed by SDS-PAGE and transferred to PVDF membranes. The membranes were blocked 5% non-fat dry milk (NFDM) in PBST (PBS+0.05% Tween-20) for 1 hour, then incubated overnight at 4° C. with primary antibody in 5% NFDM in PBST. The blots were washed with PBST and incubated with HRP-conjugated secondary antibodies diluted in 5% NFDM in PBST for 1 hour at room temperature. Membranes were washed with PBST and visualized with SuperSignal West Pico Chemiluminescent Substrate (Thermo Scientific). Semi-quantitative results were obtained by noting the lowest concentration at which both p62 degradation and LC3-I to LC3-II conversion were observed.
Despite its micromolar potency, the Tat-Beclin 1 peptide has been shown to be effective in several animal models of human disease. To show whether Tat-11mer and DD5-o have similar in vivo activity, we tested their ability to induce autophagy in GFP-LC3 transgenic mice59 as described.10 Peptides were delivered via intraperitoneal injection, and after 6 hours, muscle tissue was collected. GFP-LC3 puncta were imaged in thin sections and counted by an observer blinded to experimental condition (
Along with proteasomal degradation, autophagy is the major pathway by which aggregated proteins are removed from the cytoplasm. Increasing autophagy leads to the reduction of accumulated and aggregated protein, reversing a characteristic feature of polyglutamine disorders such as Huntington's disease (HD).60 We thus tested whether our peptides would help clear protein aggregates from HeLa cells expressing a polyglutamine-expanded huntingtin exon 1 (htt103Q fused to CFP for imaging) from a doxycycline-repressible promoter.10, 60 In this model of protein aggregation, autophagy has been shown to clear small aggregates, but not large (>1 μm) aggregates.61 Treatment with 20 μM Tat-Beclin 1 previously was shown to decrease the number of small, but not large, htt103Q aggregates, consistent with autophagy-mediated protein turnover.10 We found that treatment with 20 μM DD5-o or 10 μM Tat-11mer led to a significant decrease in the percentage of cells that have small aggregates, and in the number of small aggregates observed per cell (
GFP-LC3 In Vitro and In Vivo Experiments.
HeLa/GFP-LC3 cells generated as previously shown,10 treated with peptides for 3 hour as described above. Cells were fixed with 2% paraformaldehyde (PFA) in PBS, GFP-LC3 puncta per cell were counted, and quantified as described.86 To measure autophagy in mouse tissues, 6-week-old GFP-LC3 transgenic mice59 (2 males and 2 females per experimental group) were injected i.p. with Tat-Beclin 1 (20 mg/kg), Tat-11mer (15 mg/kg), D-(Tat-11mer) (15 mg/kg), D-(Tat-11mer)_S (15 mg/kg), DD5-o (15, 30 mg/kg). After 6 h, mice were sacrificed and fixed by perfusion with 4% PFA in PBS. Tissues were fixed in 4% PFA overnight, 15% sucrose for 4 hours, and 30% sucrose overnight before frozen sections were prepared and used for fluorescence microscopy analysis as described.16 GFP-LC3 puncta were quantified per 2500 μm2 of tissue. Animal experiments were approved by the UTSW Institutional Animal Care Use Committee and performed in accordance with institutional guidelines.
Htt Aggregate Assay.
HeLa-htt103Q cells were cultured as described previously.60 For the Htt103Q aggregate assay, cells were fixed with 2% PFA in PBS and CFP-positive aggregates <1 μm were counted via fluorescence microscopy by an observer blinded to experimental condition.
Tat peptides have the following structure: YGRKKRRQRRRGG (SEQ ID NO: 16)-Sequence. In Table 2, bold amino acids show the mutation of WT (Tat-beclin-1). The N-terminus was capped with an acetyl group while the C terminus was capped with a —C(O)—NH2 group. The activity reported is a summation of results from both the p62 degradation assay and the LC3 marker assay. The activity is recorded as follows:
−=activity not reported
0=decreased vs. WT
+=similar to WT
++=modest increase vs. WT
+++=significant increase vs. WT
CFNATFEIWHD
TFNATFEIWHD
DFNATFEIWHD
GFNATFEIWHD
WNATFHIWHD
WNATFHIW
WNATFHI
WNATFHIW
From the data above,
Compounds 1-10 were evaluated using the assays described in Examples 4 and 5. Activity for each compound was measured in the p62 degradation assay and the LC3 marker assay as described herein. The activity at each concentration of peptide is given as, for example, (0/+) where 0 would be the p62/actin assay activity and + would be the LC3 assay activity. In some assays, the negative control was an inactive Tat-Beclin mutant, which does not induce autophagy. The results are shown in Tables 2-7 below.
C
C
C
C
C
The in vitro and in vivo data suggested that the stapled peptides required a specific 3D conformation. However, it was unclear what this conformation might be. The crystal structure of the ECD of Beclin 1 is composed of three consecutive and symmetrical β-sheet-α-helix autophagy-specific (BARA) motifs.62 Published data have highlighted the importance of the ECD in the architecture of the autophagy initiation complex, though its role is not fully understood.63, 64 The sequence of the ECD corresponding to the autophagy-inducing peptides is at the edge of the region that was crystallized, and shows no regular secondary structure (
We used 2D-NMR spectroscopy to determine the structure of DD5-o in methanol (
NMR spectra were processed in Bruker Topspin software and imported into CcpNMR Analysis v2.4.2 for assignments and to generate distance constraints. A total of 114 NOEs were compiled, including 12 medium- and long-range NOEs. Three phi dihedral angle constraints, derived from JNH-CαH coupling constants, were also compiled. These were used as constraints in simulated annealing experiments using CNS Solve version 1.3. Simulated annealing involved a high-temperature annealing stage of 1000 steps, followed by two slow-cooling stages, each 1000 steps, which was then followed by a 10 cycles of 200 steps of energy minimization. Structure calculations were iterated until the distance and dihedral violations were completely resolved. A total of 25-lowest energy structures with no NOE and dihedral angle violation greater than 0.1 Å and 5°, respectively, were then selected for further analysis.
The 1D proton spectrum was well-resolved with excellent dispersion among the amide protons (
1H chemical shifts for DD5-o at 289 K in CD3OH.
Molecular dynamics (MD) simulations were performed with the Gromacs 4.6.7 engine in conjunction with the CHARMM22 force field with CMAP correction. The parameters for the D-Cys residue and the o-xyl linker were determined based on chemical similarity to already-defined atom types (see
The production simulation was performed in the NPT (isothermal-isobaric) ensemble at 300K/1 bar. The temperature was controlled using the Nosé-Hoover thermostat with a coupling constant of 1.0 ps. To alleviate the “hot-solvent/cold-solute” artifact, two separate thermostats were applied to both the peptide and the solvent molecules. The pressure of the system was maintained using an isotropic Berendsen barostat, with a coupling time of 2.0 ps and a compressibility of 4.5×10−5 bar−1. All bonds were constrained with the LINCS algorithm to enable the use of a 2 fs time step with the leap-frog algorithm. The non-bonded interactions (Lennard-Jones and Columbic) were truncated at 8 Å. Long-range Columbic interactions beyond the cut-off distance were treated using the Particle Mesh Ewald (PME) summation method. A long-range analytic dispersion correction was applied to both the energy and pressure to account for the truncation of Lennard-Jones interactions. The production simulation was performed for 100 ns. In the production simulation, the C-terminal residues underwent side-chain reorganization and formed a related (slightly more α-helical) structure in water. Once formed, the structure was relatively stable during the rest of the simulation. This behavior was observed in three independent runs, which each started from different initial velocities (
DD5-o has similar activity as Tat-Beclin 1, but is roughly one-third the size and does not require a polycationic transducing sequence. Extensive biological data support that these autophagy-inducing peptides act at the stage of autophagy initiation, during which a large Beclin 1-mediated complex must assemble in order to nucleate autophagosome formation.10, 63 Since this complex is associated with the cytoplasmic surfaces of the endoplasmic reticulum and other organelles, it was critical to verify that DD5-o reaches the cytosol and to quantify the relative extent of cytosolic delivery without interference from endosomally trapped peptide.48, 65-67 Due to the small size and relative hydrophobicity of the peptide, and due to the sensitivity of the SAR, we wanted to avoid using large perturbing tags such as fluorescent dyes. For these reasons, we developed a novel cell penetration assay to quantify the cytosolic delivery of DD5-o. The assay, called Chloroalkane Penetration Assay (CAPA), is inexpensive, quantitative, high-throughput, does not require labelling with large aromatic dyes, and can be adapted for measuring access to any cellular compartment (
The Chloroalkane Penetration Assay is described in detail in U.S. Provisional Application No. 62/424,955, filed Nov. 21, 2016, and corresponding to U.S. Pat. No. 10,620,214, which is incorporated herein by reference in its entirety. Briefly, this assay uses a cell line that stably expresses a cytosolically-oriented protein as a fusion with GFP and Haloenzyme. Haloenzyme is a modified bacterial chloroalkane dehydrogenase that covalently labels itself with the small, otherwise inert Haloligand functional group.68-70 If an exogenously added molecule bearing the Haloligand (a small chloroalkane) reaches the cytosol, it reacts exclusively with the Haloenzyme and blocks its active site. Following this incubation period, the amount of unreacted Haloenzyme was measured by chasing with a Haloligand-bearing dye (here, Htag-TAMRA). The relative amount of red cellular fluorescence after this chase was then quantified by flow cytometry. The red signal reports directly on the amount of free Haloenzyme, which is inversely proportional to the degree to which the added molecule accessed the cytoplasm during the incubation period. We evaluated CAPA with HTag-cTMP, a small molecule previously used as a tool for cytosolic protein localization.71 As quantitated by flow cytometry, we observed inhibition of the HTag-TAMRA signal when cells were pre-incubated with HTag-cTMP, and this inhibition was dose-dependent with respect to amount of the HTag-cTMP used in the pre-incubation step. Fluorescence microscopy confirmed that the HTag-TAMRA colocalized with the cytosolically oriented GFP-Haloenzyme, and that pre-incubation with HTag-cTMP suppressed up to 90% of the HTag-TAMRA signal (
Chloroalkane Penetration Assay.
HaLo-GFP-Mito+mCherry-DHFR HeLa cells were obtained from the Chenoweth Lab.71 Cells were cultured using DMEM+10% FBS+1% Pen/Strep+1 μg/mL puromycin. For experiments, cells were seeded in a 24-well plate the day before at 1.0×105 cells/well. Cells were rinsed 1× with PBS, then treated with peptides in acidified Opti-MEM (0.15% 6N HCl) for 4 hour. Media was aspirated and cells were washed for 30 min with phenol red-free DMEM+10% FBS+1% pen/strep. Cells were chased with 5 μM HTag-TAMRA (Promega) in phenol red-free DMEM+10% FBS+1% pen/strep for 30 min. Cells were washed for 15 min with phenol red-free DMEM+10% FBS+1% pen/strep. Cells were rinsed 1× with PBS, then trypsinized and transferred to eppys. Cells were pelleted and washed with PBS 2×. Cell pellet was resuspended in 250 μL of PBS and 200 μL were transferred to 96-well plate for flow cytometry analysis. Data was gated for live cells measuring 10,000 cells per sample. Mean fluorescence intensity was obtained in the Yellow channel for HTag-TAMRA, and data was normalized. Background yellow fluorescence was observed both by flow cytometry and microscopy due to the constituent expression of mCherry-DHFR, but the signal observed for HTag-TAMRA-treated cells was 10-fold higher than background.
Additional peptide compounds (Table 12) are assayed for inducing autophagy in a p62 degradation assay and an LC3 marker assay as described above.
Structures of the peptides in Table 12 are shown below.
As shown in
First reported in 2013, the autophagy-inducing peptide Tat-Beclin 1 has become a critical tool for exploring the therapeutic potential of autophagy activation.10 Here, we describe two new autophagy-inducing peptides based on Beclin 1-derived sequences. The first, Tat-11mer, has up to 4-fold greater potency than the original peptide, and the second, DD5-o, has nearly equal potency but does not require a large polycationic sequence for cell penetration. Extensive SAR revealed conserved residues among these Beclin 1-derived sequences, suggesting that they operate via the same mechanism. Notably, the conserved residue Trp2 in Tat-11mer is replaced by a cross-linked D-Cys in DD5-o, suggesting that the hydrophobic staple may functionally replace this part of the conserved Beclin 1-derived sequence. Going forward, these two compounds serve different applications. Tat-11mer is the more potent in vitro tool, while DD5-o is more promising for the development of peptide and small-molecule therapeutics.
DD5-o was developed using a novel stapling strategy that scans different structures by varying several aspects of staple position, length, and stereochemistry. Similar chemistry has been applied to phage display libraries and to the design of protein-protein interaction inhibitors, and can incorporate further diversity using alternative linkers or artificial thiol-containing amino acids.52, 56, 72, 73 Here, we used this approach to convert a 10-mer peptide into a cell-penetrant stapled peptide with activity in vitro and in vivo. Previous work had shown that, in the context of a sequence with high helical propensity, bis-alkylation of L-cysteines at (i, i+4) positions using the meta-xylene linker will stabilize α-helical structure.74 This matches the staple in DD6-m (
To directly measure cell penetration of DD5-o, we developed a novel, quantitative assay that can determine cytosolic localization using the small Haloligand as a chemical tag. The most common method currently used to judge cell penetration is to monitor the uptake of dye-labeled molecules by microscopy or flow cytometry. This method has difficulty distinguishing material that is trapped in endosomes from material in the cytosol, and it is prone to additional artifacts including leakage of peptide after fixation79, 80 and light-induced redistribution from endosomes to the cytoplasm.81 Several groups have developed alternative assays, including dye-mediated assays that produce signals based on changing chemical environment,82, 83 transcriptional readouts using dexamethasone-tagged peptides,84 and fluorescence correlation spectroscopy (FCS) for localizing signals in femtoliter volumes within the cell.85 The Chloroalkane Penetration Assay does not require large, hydrophobic dyes, just a small chloroalkane tag. Because the HeLa cells stably express Haloenzyme fused to a cytosolically-oriented protein domain, any signal dependent on the Haloenzyme reports exclusively on cytoplasmic access of the Haloligand-bearing molecule. When the Haloligand-bearing molecule of interest enters the cell, it covalently reacts with cytoplasmic Haloenzyme and blocks subsequent reaction with the Haloligand-bearing dye in the next step. Control experiments revealed that up to 90% of the overall signal could be suppressed by pre-incubation with a cell-penetrant, Haloligand-conjugated small molecule. The remaining 10% is likely due to Haloenzyme expressed during the subsequent dye incubation and wash steps. The signal was measured using a benchtop flow cytometer. Other readouts are feasible, but flow cytometry provided high-quality, quantitative data in an inexpensive and high-throughput format.
CAPA allowed direct assessment of the dose-dependence of cell penetration for DD5-o. Importantly, this dose dependence closely matches the dose-dependence of autophagy induction. These data imply that potency is currently limited by cell penetration, and that improving cell penetration will improve overall activity. The ability to quantitate cell penetration in a high-throughput manner will greatly accelerate development of these and other potential peptide therapeutics. In fact, the CAPA method can be directly applied to any chemically tractable molecule, including small molecules, peptides, proteins, nucleic acids, antibodies, viral particles, and nanoparticles. Because the Haloenzyme is genetically introduced, it can be directed to any cellular compartment, enabling specific relative quantitation of access to any compartment or organelle. We also anticipate that this method will be directly applicable to whole-organism pharmacokinetics, enabling direct assessment of molecule distribution and subcellular compartmentalization throughout an entire organism.
Finally, the cumulative SAR of all the Beclin 1-derived peptides, the structure of DD5-o, and the activity of retro inverso variants of Tat-Beclin 1 and Tat-11mer provide multiple independent lines of evidence that Beclin 1-derived peptides are most active in helical conformations. This finding contrasts with the published structure of the Beclin 1 ECD and current models of Beclin 1 complexes. The importance of helical structure for Beclin 1-derived peptides raises new questions about the structure and function of the BARA domain of Beclin 1. Further studies on Beclin 1 will be necessary to determine whether this domain assumes a helical structure in its relevant multiprotein complexes, or whether it converts to a helical structure when binding autophagy-regulating Beclin 1 modulators. We expect these and other Beclin 1-derived peptides will continue to reveal molecular details of autophagy induction and regulation, and will continue to serve as potent tools and potential lead compounds for examining the effects of autophagy induction on human disease.
All publications, patents and patent applications cited herein are incorporated by reference herein in their entirety for all purposes to the same extent as if each individual publication or patent application were specifically indicated to be so incorporated by reference.
This application is the U.S. national phase application, pursuant to 35 U.S.C. § 371, of PCT International Application Serial No.: PCT/US2017/022974, filed Mar. 17, 2017, designating the United States and published in English, which claims priority to and the benefit of the following U.S. Provisional Application No. 62/310,448, filed Mar. 18, 2016 and 62/424,934, filed Nov. 21, 2016, the disclosure of which applications are incorporated herein by reference in their entirety.
This invention was made with government support under contract number U19AI109725 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2017/022974 | 3/17/2017 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2017/161274 | 9/21/2017 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 20150133633 | Rushala et al. | May 2015 | A1 |
| 20150359840 | Levine et al. | Dec 2015 | A1 |
| Entry |
|---|
| Chan, et al., “Modification of N-Terminal alpha-Amino Groups of Peptides and Proteins Using Ketenes,” J. Am. Chem. Soc., vol. 134, pp. 2589-2598 (2012). |
| International Search Report and Written Opinion for Corresponding PCT/US2017/022974, dated Aug. 25, 2017 (9 pages). |
| Number | Date | Country | |
|---|---|---|---|
| 20190382443 A1 | Dec 2019 | US |
| Number | Date | Country | |
|---|---|---|---|
| 62310448 | Mar 2016 | US | |
| 62424934 | Nov 2016 | US |
