Patent Application
20230250134
A computer readable form of the Sequence Listing is filed with this application by electronic submission and is incorporated into this application by reference in its entirety. The Sequence Listing is contained in the file created on May 25, 2021, having the file name “20-1074-WO_SeqList_ST25” and is 1,112 kb in size.
SARS-COV-2 infection is thought to often start in the nose, with virus replicating there for several before spreading to the broader respiratory system. Delivery of a high concentration of a viral inhibitor into the nose and into the respiratory system generally could therefore potentially provide prophylactic protection, and therapeutic efficacy early in infection, and could be particularly useful for health care workers and others coming into frequent contact with infected individuals.
In a first aspect the disclosure provides polypeptides comprising an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:1-17, 19-21, 23-34 and 100-101, wherein the polypeptide binds to SARS-COV-2 Spike glycoprotein receptor binding domain (RBD). In one embodiment, amino acid substitutions relative to the reference polypeptide amino acid sequence are selected from the exemplary amino acid substitutions provided in Table 1. In another embodiment, interface residues are identical to those in the reference polypeptide or are conservatively substituted relative to interface residues in the reference polypeptide. In a further embodiment the polypeptides comprise two or more copies of the amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-101. In one embodiment, the polypeptide comprises the formula Z1-Z2-Z3, wherein:
Z1 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-164;
Z2 comprises an optional amino acid linker; and
Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-164;
wherein Z1 and Z3 may be identical or different.
In another embodiment, the polypeptides comprises the formula B1-B2-Z1-Z2-Z3-B3-B4, wherein:
Z1, Z2, and Z3 are as defined;
B2 and B3 comprise optional amino acid linkers; and one or both of B1 and B4 independently comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-164, wherein one of B1 and B4 may be absent.
In one embodiment, the polypeptides comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:47-60, 193-355 and 454-588, and a genus selected from those recited in the right hand column of Table 8 wherein genus positions X1, X2, X3, and X4 may be present or absent, and when present may be any sequence of 1 or more amino acids.
In another embodiment, the polypeptide comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 356-453 and 595-692, and a genus selected from those recited in the middle column of Table 9 wherein genus positions X1, X2, X3, and X4 may be present or absent, and when present may be any sequence of 1 or more amino acids.
In a further embodiment, the polypeptide comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 65-96, wherein in embodiments where a secretion signal is present (MARAWIFFLLCLAGRALA; SEQ ID NO:63) it can be replaced with any other secretion signal.
In other aspects, the disclosure provides nucleic acids encoding the polypeptide of the disclosure, expression vectors comprising the nucleic acids operatively linked to a promoter, host cell comprising a polypeptide, nucleic acid, and/or expression vector of the disclosure, oligomers of the polypeptides of the disclosure, compositions comprising 2, 3, 4, or more copies of the polypeptide any embodiment of the disclosure attached to a support, including but not limited to a polypeptide particle support, and pharmaceutical compositions, comprising a polypeptide, nucleic acid, expression vector, host cell, oligomer, and/or composition of the disclosure, and a pharmaceutically acceptable carrier.
In another aspect, the disclosure provides methods for treating or limiting development of a severe acute respiratory syndrome (SARS) coronavirus infection (including SARS-Co-V and SARS-COV-2), comprising administering to a subject in need thereof an amount of the polypeptide, the nucleic acid, the expression vector, the host cell, the oligomer, the composition, and/or the pharmaceutical composition of the disclosure, effective to treat or limit development of the infection.
All references cited are herein incorporated by reference in their entirety. Within this application, unless otherwise stated, the techniques utilized may be found in any of several well-known references such as: Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), “Guide to Protein Purification” in Methods in Enzymology (M. P. Deutshcer, ed., (1990) Academic Press, Inc.); PCR Protocols: A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, Calif.), Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.), Gene Transfer and Expression Protocols, pp. 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.).
As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise.
As used herein, the amino acid residues are abbreviated as follows: alanine (Ala; A), asparagine (Asn; N), aspartic acid (Asp; D), arginine (Arg; R), cysteine (Cys; C), glutamic acid (Glu; E), glutamine (Gln; Q), glycine (Gly; G), histidine (His; H), isoleucine (Ile; I), leucine (Leu; L), lysine (Lys; K), methionine (Met; M), phenylalanine (Phe; F), proline (Pro; P), serine (Ser; S), threonine (Thr; T), tryptophan (Trp; W), tyrosine (Tyr; Y), and valine (Val; V).
In all embodiments of polypeptides disclosed herein, an N-terminal methionine residue is optional (i.e.: may be present or absent).
All embodiments of any aspect of the disclosure can be used in combination, unless the context clearly dictates otherwise.
Unless the context clearly requires otherwise, throughout the description and the claims, the words ‘comprise’, ‘comprising’, and the like are to be construed in an inclusive sense as opposed to an exclusive or exhaustive sense; that is to say, in the sense of “including, but not limited to”. Words using the singular or plural number also include the plural and singular number, respectively. Additionally, the words “herein,” “above,” and “below” and words of similar import, when used in this application, shall refer to this application as a whole and not to any particular portions of the application.
In a first aspect, the disclosure provides polypeptides comprising an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-101, wherein the polypeptide binds to SARS-COV-2 Spike glycoprotein receptor binding domain (RBD).
As detailed in the examples that follows, the polypeptides bind with high affinity to the SARS-COV-2 Spike glycoprotein receptor binding domain (RBD).
In all of embodiments herein, the percent identity requirement does not include any additional functional domain that may be incorporated in the polypeptide. In one embodiment, 1, 2, or 3 amino acids may be deleted from the N and/or C terminus.
The polypeptides have been subjected to extensive mutational analysis as described in the examples that follow, permitting determination of allowable substitutions at each residue within the polypeptide. Exemplary substitutions are as shown in Table 1 (The number denotes the residue number, and the letters denote the single letter amino acids that can be present at that residue). Thus, in one embodiment, amino acid substitutions relative to the reference polypeptide amino acid sequence (i.e.: one of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-101) are selected from the exemplary amino acid substitutions provided in Table 1.
The residue numbers of the interface residues which are within 8A to the RBD target are listed in Table 2 for the various design types. In another embodiment, amino acid residues at the interface residues listed in Table 2 are either identical at that residue to the reference sequence, or may be substituted by a conservative amino acid substitution. Such conservative amino acid substitutions involve replacing a residue by a residue having similar physiochemical characteristics, e.g., substituting one aliphatic residue for another (such as Ile, Val, Leu, or Ala for one another), or substitution of one polar residue for another (such as between Lys and Arg; Glu and Asp; or Gln and Asn). Other such conservative substitutions, e.g., substitutions of entire regions having similar hydrophobicity characteristics, are known. Amino acids can be grouped according to similarities in the properties of their side chains (in A. L. Lehninger, in Biochemistry, second ed., pp. 73-75, Worth Publishers, New York (1975)): (1) non-polar: Ala (A), Val (V), Leu (L), Ile (I), Pro (P), Phe (F), Trp (W), Met (M); (2) uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), Gln (Q); (3) acidic: Asp (D), Glu (E); (4) basic: Lys (K), Arg (R), His (H). Alternatively, naturally occurring residues can be divided into groups based on common side-chain properties: (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln; (3) 35 acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro; (6) aromatic: Trp, Tyr, Phe. Non-conservative substitutions will entail exchanging a member of one of these classes for another class. Particular conservative substitutions include, for example; Ala into Gly or into Ser; Arg into Lys; Asn into Gln or into His; Asp into Glu; Cys into Ser; Gln into Asn; Glu into Asp; Gly into Ala or into Pro; His into Asn or into Gln; Ile into Leu or into Val; Leu into Ile or into Val; Lys into Arg, into Gln or into Glu; Met into Leu, into Tyr or into Ile; Phe into Met, into Leu or into Tyr; Ser into Thr; Thr into Ser; Trp into Tyr; Tyr into Trp; and/or Phe into Val, into Ile or into Leu.
In one embodiment, amino acid residues at the interface residues listed in Table 2 are identical at that residue to the reference sequence.
In another embodiment, the polypeptide comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:1-10, 13-17, 19-21, 33-34, and 100-101.
In one embodiment, the polypeptides comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:1-10 and 102-136 (see Table 3).
The polypeptides may contain a substantial number of mutations while retaining binding activity, as detailed in the examples that follow. In one embodiment, the polypeptide comprises an amino acid substitution relative to the amino acid sequence of SEQ ID NO:1 at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all 18 residues selected from the group consisting of 2, 4, 5, 14, 15, 17, 18, 27, 28, 32, 37, 38, 39, 41, 42, 49, 52, and 55. In another embodiment, the substitutions are selected from the substitutions listed in Table 4, either individually (i.e.: any single mutation listed in the Table) or in combinations in a given row.
In another embodiment, the polypeptides comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 13-17, 19-21 and 137-163 (see Table 5).
The polypeptides may contain a substantial number of mutations while retaining binding activity, as detailed in the examples that follow. In one embodiment, the polypeptide comprises an amino acid substitution relative to the amino acid sequence of SEQ ID NO:13 at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or all 20 residues selected from the group consisting 2, 6, 8, 9, 13, 14, 19, 22, 25, 26, 28, 29, 34, 35, 37, 40, 43, 45, 49, and 62. In another embodiment, the substitutions are selected from the substitutions listed in Table 6, either individually or in combinations in a given row.
In a further embodiment, the polypeptides comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:33-34 and 100-101 and 164 (see Table 7). 5
In one embodiment, the polypeptide comprises an amino acid substitution relative to the amino acid sequence of SEQ ID NO: 101 at or both residues selected from the group consisting 63 and 75. In a further embodiment, the substitutions comprise R63A and/or K75T.
In all embodiments disclosed herein, the polypeptides may comprise one or more additional functional groups or residues as deemed appropriate for an intended use. In one embodiment, the polypeptides may further comprise one or more added cysteine residues at the N-terminus and/or C-terminus. In another embodiment, the polypeptides may further comprise an N-linked glycosylation site (i.e.: NX(S/T), where X is any amino acid).
In another embodiment, the polypeptides may comprise two or more (i.e.: 2, 3, 4, 5, or more) copies of the amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-101. In this embodiment, 2 or more of the binders are linked. In one embodiment, the two or more copies of the polypeptide are all identical; in another embodiment, the two or more copies of the polypeptide are not all identical. In any of these embodiments, the two or more copies of the polypeptide may be separated by amino acid linker sequences, though such linkers are not required. The amino acid linkers may be of any length and amino acid composition as suitable for an intended purpose. In one embodiment, the amino acid linkers are independently between 2-100 or 3-100 amino acids in length.
In another embodiment, the amino acid linker sequences comprise Gly-Ser rich (at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% Gly-Ser residues) amino acid linkers. In a further embodiment, the Gly-Ser rich linkers comprise an amino acid sequence selected from the group consisting of GG and SEQ ID NOs:35-46 and 165-171
In another embodiment, the amino acid linker sequences may comprise Pro-rich (at least 15%, 20%, 25%, or greater Pro residues) amino acid linkers. Non-limiting and exemplary embodiments may comprise an amino acid sequence selected from the group consisting of SEQ ID NOs:97-98 and 172-176.
In further non-limiting embodiments, the amino acid linkers may comprise the amino acid sequence selected from the group consisting of SEQ ID NOS: 99 and 177-178.
In one embodiment, the polypeptide comprises the formula Z1-Z2-Z3, wherein:
Z1 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-164;
Z2 comprises an optional amino acid linker; and
Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-164;
wherein Z1 and Z3 may be identical or different. In one embodiment, Z1 and Z3 are identical; in another embodiment Z1 and Z3 are different. In embodiments where Z1 and Z3 differ, each may be a variant of a given starting monomer (ex: Z1 comprises the amino acid sequence of SEQ ID NO:1 (LCB1), and Z3 comprises the amino acid sequence of SEQ ID NO: 102-136. Any such combination of the monomers disclosed herein may be used. It will further be understood that the polypeptides may comprise 2, 3, 4, 5, or more monomers of any embodiment disclosed herein. In embodiments where there are 3 or more monomers, all 3 monomers may be identical; 2 monomers may be identical and one may differ, or all 3 monomers may be different.
In one embodiment employing LCB1 and variants thereof, Z1 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-10 and 102-136; and
Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-10 and 102-136.
In another embodiment employing LCB3 and variants thereof,
Z1 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 13-17, 19-21 and 137-163; and
Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 13-17, 19-21 and 137-163.
In another embodiment employing AHB and variants thereof,
Z1 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 33-34, 100-101, and 164; and
Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 33-34, 100-101, and 164.
In one embodiment, one of Z1 and Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-10 and 102-136; and
the other of Z1 and Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 13-17, 19-21 and 137-163.
In another embodiment, one of Z1 and Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-10 and 102-136; and
the other of Z1 and Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 33-34, 100-100, and 164.
In a further embodiment, one of Z1 and Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting SEQ ID NOS: 13-17, 19-21 and 137-163; and
the other of Z1 and Z3 comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 33-34, 100-100, and 164.
In another embodiment of any of the other embodiments disclosed herein, the polypeptide comprises at least 3 monomers (i.e.: 3, 4, 5, or more). In one such embodiment, the polypeptide comprises the formula B1-B2-Z1-Z2-Z3-B3-B4, wherein:
Z1, Z2, and Z3 are as defined above;
B2 and B3 comprise optional amino acid linkers; and
one or both of B1 and B4 independently comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: SEQ ID NOS: 1-17, 19-21, 23-34 and 100-164, wherein one of B1 and B4 may be absent. In one embodiment, one of B1 and B4 is absent. In another embodiment, both B1 and B4 are present. In one embodiment, B1 and B4 independently comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-17, 19-21, 23-34 and 100-164. In this embodiment, B1 and B4 may be identical or may be different. In one embodiment, B1 when present and B4 when present, are identical to one or both of Z1 and Z3. In another embodiment, B1 when present and B4 when present, are not identical to either of Z1 and Z3.
In one embodiment, B1 when present, and B4 when present, independently comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-10, 13-17, 19-21, 33-34, 100-101, and 102-164.
In another embodiment, B1 when present, and B4 when present, independently comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-10 and 102-136.
In a further embodiment, B1 when present, and B4 when present, independently comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 13-17, 19-21 and 137-163.
In a still further embodiment, B1 when present, and B4 when present, independently comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 33-34, 100-101, and 164.
In various embodiments when both B1 and B4 are present,
In various non-limiting embodiments, the polypeptides comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS:47-60, 193-355, and 454-588 and a genus selected from those recited in the right hand column of Table 8 wherein genus positions X1, X2, X3, and X4 may be present or absent, and when present may be any sequence of 1 or more amino acids. In all embodiments, any N-terminal methionine residues may be present or absent in the polypeptide. In one embodiment, any N-terminal methionine residues are absent in the polypeptide.
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVERGGSGGSDKEWILQKIYEIMRLLDELGH
AEASMRVSDLIYEFMKKGDERLLEEAERLLEEVER
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVERGGSGGSGSGGSGDKEWILQKIYEIMRL
LDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVER
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVERGGGSGGGSSGGSGGSSGGGSGGGSDKE
WILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVER
DKENILQKIYEIMKTLDOLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERGGGGSGGGGSGGGGSGGGGSGGGGSGG
MKQGDERLLEEAERLLEEVER
DKENILQKIYEIMKTLDQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERAGSGGSGGSGGSPVPSTPPTPSPSTPP
MKQGDERLLEEAERLLEEVER
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLSGGGGSGGGGSGGGGSGGGG
HVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLS
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLSAGSGGSGGSGGSPVPSTPP
HVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLS
DKENILQKIYEIMKTLDQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERGGGGSGGGGSGGGGSGGGGSGGGGSGG
ATKAYKNKDRQKLEKVVEELKELLERLLS
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLSGGGGSGGGGSGGGGSGGGG
VSDLIYEFMKOGDERLLEEAERLLEEVER
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLSGGSGGSGGSGDKENILQKI
YEIMKTLDQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVER
DKENILQKIYEIMKTLDQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERAGSGGSGGSGGSPVPSTPPTPSPSTPP
ATKAYKNKDRQKLEKVVEELKELLERLLS
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLSAGSGGSGGSGGSPVPSTPP
VSDLIYEFMKQGDERLLEEAERLLEEVER
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVERGGSGSSGGSGSGSGDKEWILQKIYEIM
RLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVERGGSGSSGGSGSGSGDKEWILQKIYEIMRLLDELGHAEASM
RVSDLIYEFMKKGDERLLEEAERLLEEVERGGSGSSGGSGSGSGDKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKG
DERLLEEAERLLEEVERGGSGSSGGSGSGSGDKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLE
In some embodiments, the polypeptides comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of a genus selected from those recited in the middle column of Table 8. In these embodiments, X1, X2, X3 (when recited in the genus), and X4 (when recited in the genus) may be present or absent, and when present may be any sequence of 1 or more amino acids. By way of example, the genus in the middle column, first row of sequences in Table 8 is X1-(SEQ ID NO:4)-X2-(SEQ ID NO:4). In this embodiment, X2 may be present or absent and, when present, may (for example) comprise an amino acid linker of any suitable length and amino acid composition as deemed appropriate. X1 may be present or absent, and when present may comprise any amino acid residue or residues as deemed appropriate, including but not limited to a leader sequence, a detectable tag, a purification tag, etc.
In another example, the genus in the middle column, last row of sequences in Table 8 is X1-(SEQ ID NO: 155)-X2-(SEQ ID NO: 164)-X3-(SEQ ID NO: 135)-X4. In this embodiment, X2 and X3 may be present or absent and, when present, may (for example) comprise an amino acid linker of any suitable length and amino acid composition as deemed appropriate. X1 and X4 may be present or absent, and when present may comprise any amino acid residue or residues as deemed appropriate, including but not limited to a leader sequence, a detectable tag, a purification tag, secretion signal etc.
In some embodiments, the optional domain that is present between monomer domains is present and may comprise an amino acid linker. Under this embodiment, (a) in the first example above X2 would be present and comprise an amino acid linker of any appropriate length and amino acid composition, and X1 may be present or absent; and (b) in the second example above one or both of X2 and X3 would be present and comprise an amino acid linker of any appropriate length and amino acid composition, and X1 and X4 may independently be present or absent.
In any embodiment or combination of embodiments of the polypeptides disclosed herein, the polypeptide may further comprise one or more additional functional peptide domain. Any such additional functional peptide domain may be used as appropriate for an intended purpose. In various non-limiting embodiments, the additional functional peptide domain may comprise, for example, a targeting domain, a detectable domain, a scaffold domain, a secretion signal, an Fc domain, or a further therapeutic peptide domain. In one embodiment, the additional functional domain comprises an Fc domain, including but not limited to an Fc domain comprising an amino acid sequence comprising the amino acid sequence of SEQ ID NO:64.
In another embodiment, the added functional domain may comprise an oligomerization domain. Any oligomerization domain may be used as suitable to generate an oligomer as suitable for an intended purpose. In one non-limiting embodiment, the oligomerization domain may comprise a homotrimerization domain. Exemplary oligomerization domains may comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:179-189 and 589-594.
In one embodiment, the polypeptide comprises an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS 356-453 and 595-692 and a genus selected from those recited in the right hand column of Table 9 wherein genus positions X1, X2, X3, and X4 may be present or absent, and when present may be any sequence of 1 or more amino acids. In all embodiments, any N-terminal methionine residues may be present or absent in the polypeptide. In one embodiment, any N-terminal methionine residues are absent in the polypeptide.
In some embodiments, the polypeptides comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of a genus selected from those recited in the middle column of Table 9. In these embodiments, X1, X2, X3 (when recited in the genus), and X4 (when recited in the genus) may be present or absent, and when present may be any sequence of 1 or more amino acids, as described above for embodiments listed in Table 8. In some embodiments, the optional domain that is present between monomer domains is present and may comprise an amino acid linker, as described above for embodiments listed in Table 8.
In another embodiment, the polypeptides comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to an amino acid sequence comprising the amino acid sequence selected from the group consisting of SEQ ID NOS:693 to 701, wherein any N-terminal methionine residue may be absent or present, and wherein residues in parentheses may be present or absent (preferably absent) and are not considered in determining percent identity. In one embodiment, the N-terminal methionine residue is absent and the optional residues are absent.
The polypeptide of any embodiment or combination of embodiments described here may further be linked to a stabilization domain to promote increased residency time upon administration to a subject. Any suitable stabilization domain may be used for an intended purpose. Exemplary stabilization domains include, but are not limited to, polyethylene glycol (PEG), albumin, hydroxyethyl starch (HES), conformationally disordered polypeptide sequence composed of the amino acids Pro, Ala, and/or Ser (‘PASylation’), and/or a mucin diffusivity polypeptide composed of amino acids Lys and Ala, with or without Glu. Non-limiting embodiments of such mucin diffusivity polypeptides include, but are not limited to:
Exemplary polypeptides of these embodiments may, for example, comprise an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS: 65-96, wherein in embodiments where a secretion signal is present (MARAWIFFLLCLAGRALA; SEQ ID NO:63) it can be replaced with any other secretion signal.
DKENILQKIYEIMKTLEQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERGGAKAKAKAKAKAKAKAKAKAK SEQ
MARAWIFFLLCLAGRALA
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVERGSGSEPKSS
MARAWIFFLLCLAGRALA
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVERGGSGSGGSG
MARAWIFFLLCLAGRALAEPKSSDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVD
MARAWIFFLLCLAGRALA
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKKGDERLLEEAERLLEEVERGGSGSGGSG
MARAWIFFLLCLAGRALA
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKQGDERLLEEAERLLEEVERGSGSEPKSS
MARAWIFFLLCLAGRALA
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKQGDERLLEEAERLLEEVERGGSGSGGSG
MARAWIFFLLCLAGRALAEPKSSDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVD
MARAWIFFLLCLAGRALA
DKEWILQKIYEIMRLLDELGHAEASMRVSDLIYEFMKQGDERLLEEAERLLEEVERGGSGSGGSG
MARAWIFFLLCLAGRALA
DKENILQKIYEIMKTLDQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERGGSGSGGSG
MARAWIFFLLCLAGRALA
DKENILQKIYEIMKTLDQLGHAEASMNVSDLIYEFMKQGDERLLEEAERLLEEVERGGSGSGGSG
MARAWIFFLLCLAGRALA
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLSG
MARAWIFFLLCLAGRALA
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFENATKAYKNKDRQKLEKVVEELKELLERLLSG
MARAWIFFLLCLAGRALA
DKENILQKIYEIMKTLDQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERAGSGGSGGS
MARAWIFFLLCLAGRALA
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLSA
MARAWIFFLLCLAGRALADKENILQKIYEIMKTLDQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERGGGSGGGGS
MARAWIFFLLCLAGRALA
NDDELHMQMTDLVYEALHFAKDEEIQKHVFQLFEKATKAYKNKDRQKLEKVVEELKELLERLLSG
MARAWIFFLLCLAGRALA
DKENILQKIYEIMKTLEQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERGGSGSGGSG
MARAWIFFLLCLAGRALA
DKENILQKIYEIMKTLEQLGHAEASMNVSDLIYEFMKQGDERLLEEAERLLEEVERGGSGSGGSG
MARAWIFFLLCLAGRALA
DKENILQKIYEIMKTLEQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERAGSGGSGGS
MARAWIFFLLCLAGRALA
DKENILQKIYEIMKTLEQLGHAEASMQVSDLIYEFMKQGDERLLEEAERLLEEVERGGGSGGGGS
MARAWIFFLLCLAGRALADKENVLQKIYEIMKELERLGHAEASMQVSDLIYEFMKTKDENL
MARAWIFFLLCLAGRALANIDELLMQVTDLIYEALHFAKDEEFQKHAFQLFEKATKAYKNK
MARAWIFFLLCLAGRALANIDELLMQVTLDIYEALHFAKDEEFQKHAFQLFEKATKAYKNK
MARAWIFFLLCLAGRALAELEEQVMHVLDQVSELAHELLHKLTGEELERAAYFNWWATEMM
MARAWIFFLLCLAGRALANIDELLMQVTDLIYEALHFAKDEEFQKHAFQLFEKATKAYKNK
MARAWIFFLLCLAGRALANIDELLMQVTDLIYEALHFAKDEEFQKHAFQLFEKATKAYKNK
MARAWIFFLLCLAGRALANIDELLMQVTDLIYEALHFAKDEEFQKHAFQLFEKATKAYKNK
MARAWIFFLLCLAGRALANIDELLMQVTDLIYEALHFAKDEEFQKHAFQLFEKATKAYKNK
MARAWIFFLLCLAGRALANIDELLMQVTDLIYEALHFAKDEEFQKHAFQLFEKATKAYKNK
The disclosure further provides oligomers of the polypeptide of any embodiment or combination of embodiments herein. In one embodiment, the oligomers are oligomers of polypeptides disclosed herein that comprise oligomerization domains. In one embodiment, the oligomer comprises a trimer, including but not limited to a homotrimer.
In another embodiment, the disclosure provides compositions, comprising 2, 3, 4, or more copies of the polypeptide of any embodiment or combination of embodiments herein attached to a support, including but not limited to a polypeptide particle support, such as a nanoparticle or virus like particle.
As disclosed herein, the polypeptides bind to the SARS-COV-2 Spike glycoprotein, and thus are useful (for example), as therapeutics to treat SARS-COV-2 infection. In one embodiment, the polypeptides bind to the SARS-COV-2 Spike glycoprotein with an affinity of at least 10 nM, measured as described in the attached examples.
In another aspect, the disclosure provides nucleic acids encoding a polypeptide of the disclosure. The nucleic acid sequence may comprise RNA (such as mRNA) or DNA. Such nucleic acid sequences may comprise additional sequences useful for promoting expression and/or purification of the encoded protein, including but not limited to polyA sequences, modified Kozak sequences, and sequences encoding epitope tags, export signals, and secretory signals, nuclear localization signals, and plasma membrane localization signals. It will be apparent to those of skill in the art, based on the teachings herein, what nucleic acid sequences will encode the proteins of the invention.
In another aspect, the disclosure provides expression vectors comprising the nucleic acid of any embodiment or combination of embodiments of the disclosure operatively linked to a suitable control sequence. “Expression vector” includes vectors that operatively link a nucleic acid coding region or gene to any control sequences capable of effecting expression of the gene product. “Control sequences” operably linked to the nucleic acid sequences of the disclosure are nucleic acid sequences capable of effecting the expression of the nucleic acid molecules. The control sequences need not be contiguous with the nucleic acid sequences, so long as they function to direct the expression thereof. Thus, for example, intervening untranslated yet transcribed sequences can be present between a promoter sequence and the nucleic acid sequences and the promoter sequence can still be considered “operably linked” to the coding sequence. Other such control sequences include, but are not limited to, polyadenylation signals, termination signals, and ribosome binding sites. Such expression vectors can be of any type known in the art, including but not limited to plasmid and viral-based expression vectors. The control sequence used to drive expression of the disclosed nucleic acid sequences in a mammalian system may be constitutive (driven by any of a variety of promoters, including but not limited to, CMV, SV40, RSV, actin, EF) or inducible (driven by any of a number of inducible promoters including, but not limited to, tetracycline, ecdysone, steroid-responsive).
In one aspect, the present disclosure provides cells comprising the polypeptide, the composition, the nucleic acid, and/or the expression vector of any embodiment or combination of embodiments of the disclosure, wherein the cells can be either prokaryotic or eukaryotic, such as mammalian cells. In one embodiment the cells may be transiently or stably transfected with the nucleic acids or expression vectors of the disclosure. Such transfection of expression vectors into prokaryotic and eukaryotic cells can be accomplished via any technique known in the art. A method of producing a polypeptide according to the invention is an additional part of the invention. The method comprises the steps of (a) culturing a host according to this aspect of the invention under conditions conducive to the expression of the polypeptide, and (b) optionally, recovering the expressed polypeptide. In other embodiments, the polypeptides may be produced via any other suitable technique, including but not limited to using cell-free protein synthesis (or in vitro transcription and translation).
In another aspect, the disclosure provides pharmaceutical compositions/vaccines comprising
(a) the polypeptide, the nucleic acid, the expression vector, and/or the host cell of any embodiment or combination of embodiments herein; and
(b) a pharmaceutically acceptable carrier.
The compositions may further comprise (a) a lyoprotectant; (b) a surfactant; (c) a bulking agent; (d) a tonicity adjusting agent; (e) a stabilizer; (f) a preservative and/or (g) a buffer. In some embodiments, the buffer in the pharmaceutical composition is a Tris buffer, a histidine buffer, a phosphate buffer, a citrate buffer or an acetate buffer. The composition may also include a lyoprotectant, e.g. sucrose, sorbitol or trehalose. In certain embodiments, the composition includes a preservative e.g. benzalkonium chloride, benzethonium, chlorohexidine, phenol, m-cresol, benzyl alcohol, methylparaben, propylparaben, chlorobutanol, o-cresol, p-cresol, chlorocresol, phenylmercuric nitrate, thimerosal, benzoic acid, and various mixtures thereof. In other embodiments, the composition includes a bulking agent, like glycine. In yet other embodiments, the composition includes a surfactant e.g., polysorbate-20, polysorbate-40, polysorbate-60, polysorbate-65, polysorbate-80 polysorbate-85, poloxamer-188, sorbitan monolaurate, sorbitan monopalmitate, sorbitan monostearate, sorbitan monooleate, sorbitan trilaurate, sorbitan tristearate, sorbitan trioleaste, or a combination thereof. The composition may also include a tonicity adjusting agent, e.g., a compound that renders the formulation substantially isotonic or isoosmotic with human blood. Exemplary tonicity adjusting agents include sucrose, sorbitol, glycine, methionine, mannitol, dextrose, inositol, sodium chloride, arginine and arginine hydrochloride. In other embodiments, the composition additionally includes a stabilizer, e.g., a molecule which substantially prevents or reduces chemical and/or physical instability of the nanostructure, in lyophilized or liquid form. Exemplary stabilizers include sucrose, sorbitol, glycine, inositol, sodium chloride, methionine, arginine, and arginine hydrochloride.
The polypeptide, the nucleic acid, the expression vector, and/or the host cell may be the sole active agent in the composition, or the composition may further comprise one or more other agents suitable for an intended use.
In a further aspect, the disclosure provides methods for treating a severe acute respiratory syndrome (SARS) coronavirus infection (including SARS-Co-V and SARS-COV-2), comprising administering to a subject in need thereof an amount of the polypeptide, the nucleic acid, the expression vector, the host cell, the oligomer, the composition, and/or the pharmaceutical composition of any of the preceding claims, effective to treat the infection. In one embodiment, the SARS coronavirus comprises SARS-COV-2.
In another aspect, the disclosure provides methods for limiting development of a severe acute respiratory syndrome (SARS) coronavirus infection (including SARS-Co-V and SARS-COV-2), comprising administering to a subject in need thereof an amount of the polypeptide, the nucleic acid, the expression vector, the host cell, the oligomer, the composition, and/or the pharmaceutical composition of any of the preceding claims, effective to treat the infection. In one embodiment, the SARS coronavirus comprises SARS-COV-2.
The polypeptide, the nucleic acid, the expression vector, the host cell, and/or the pharmaceutical composition may be administered via any suitable administrative route as deemed appropriate by attending medical personnel. In one embodiment, the polypeptide, the nucleic acid, the expression vector, the host cell, the oligomer, the composition, and/or the pharmaceutical composition is administered intra-nasally. In another embodiment, the polypeptide, the nucleic acid, the expression vector, the host cell, the oligomer, the composition, and/or the pharmaceutical composition is administered systemically.
When the method comprises treating a SARS coronavirus infection, the one or more polypeptides, nucleic acids, expression vectors, host cells, and/or pharmaceutical compositions are administered to a subject that has already been diagnosed as having a SARS coronavirus infection. As used herein, “treat” or “treating” means accomplishing one or more of the following: (a) reducing severity of symptoms of the infection in the subject; (b) limiting increase in symptoms in the subject; (c) increasing survival; (d) decreasing the duration of symptoms; (e) limiting or preventing development of symptoms; and (f) decreasing the need for hospitalization and/or the length of hospitalization for treating the infection.
When the method comprises limiting development of SARS coronavirus infection, the one or more polypeptides, nucleic acids, expression vectors, host cells, and/or pharmaceutical compositions are administered prophylactically to a subject that is not known to have a SARS coronavirus infection, but may be at risk of such an infection. As used herein, “limiting” means to limit development of a SARS coronavirus infection in subjects at risk of such infection, which may be any subject.
The subject may be any subject, such as a human subject
Exemplary symptoms of SARS-COV-2 infection include, but are not limited to, fever, fatigue, cough, shortness of breath, chest pressure and/or pain, loss or diminution of the sense of smell, loss or diminution of the sense of taste, and respiratory issues including but not limited to pneumonia, bronchitis, severe acute respiratory syndrome (SARS), and upper and lower respiratory tract infections.
As used herein, an “effective amount” refers to an amount of the composition that is effective for treating and/or limiting SARS-COV-2 infection. The polypeptide, composition, nucleic acid, or composition of any embodiment herein are typically formulated as a pharmaceutical composition, such as those disclosed above, and can be administered via any suitable route, including orally, parentally, by inhalation spray, rectally, or topically in dosage unit formulations containing conventional pharmaceutically acceptable carriers, adjuvants, and vehicles. The term parenteral as used herein includes, subcutaneous, intravenous, intra-arterial, intramuscular, intrasternal, intratendinous, intraspinal, intracranial, intrathoracic, infusion techniques or intraperitoneally. Polypeptide compositions may also be administered via microspheres, liposomes, immune-stimulating complexes (ISCOMs), or other microparticulate delivery systems or sustained release formulations introduced into suitable tissues (such as blood). Dosage regimens can be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). A suitable dosage range may, for instance, be 0.1 μg/kg-100 mg/kg body weight of the polypeptide or nanoparticle thereof. The composition can be delivered in a single bolus, or may be administered more than once (e.g., 2, 3, 4, 5, or more times) as determined by attending medical personnel.
The disclosure also provides methods for designing polypeptides that bind to the receptor binding site (RBD) of SARS-Cov-2, wherein the methods comprise steps as described in the examples that follow. Such methods may comprise the steps of polypeptide design (as described in any embodiment or combination of embodiments in the examples), cell-free synthesis, and evaluation for SARS-Cov-2 RBD binding using any suitable technique.
Effective therapeutics for SARS-COV-2 are needed. We sought to use computational protein design to generate high affinity binders to the receptor binding site (RBD) of SARS-Cov-2 that block the interaction with the Ace2 receptor required for cell entry. We generated small protein scaffolds with shape complementary to the Ace2 binding site on the RBD using two strategies: first, scaffolds were built around the helix in Ace2 that makes the majority of the interactions with the RBD, and second, diverse de novo designed scaffolds less than 65 residues in length were docked against this region. In both cases, the scaffold residues at the RBD interface were then optimized for high affinity binding and those in the remainder of the protein, for folding to the target structure and stability. The 50,000 designs predicted to bind most strongly to the virus were encoded in large oligonucleotide arrays, and screened using yeast surface display for binding to the RBD with fluorescence activated cell sorting; deep sequencing of the population before and after sorting identified hundreds of designs that bind the target. The binding modes of the highest affinity (most enriched by sorting) binders were confirmed by high resolution sequence mapping, and the affinities were further increased by combining 1-4 beneficial substitutions. Eight of the optimized designs with different binding sites surrounding the Ace2 interface on the RBD, and completely different sequences, were found to express at high levels in E coli, and to bind the RBD with Kd's ranging from 100 pM to 10 nM. The designs blocked infection of vero-6 cells by live virus with IC50's ranging from 10 nM to 20 pM. The polypeptides are thus useful, for example, in both intra-nasal and systemic SARS-COV-2 therapeutics, and, more generally, our results demonstrate the power of computational protein design for rapidly generating potential therapeutic candidates against pandemic threats.
SARS-COV-2 infection is thought to often start in the nose, with virus replicating there for several before spreading to the broader respiratory system. Delivery of a high concentration of a viral inhibitor into the nose and into the respiratory system generally could therefore potentially provide prophylactic protection, and therapeutic efficacy early in infection, and could be particularly useful for health care workers and others coming into frequent contact with infected individuals. A number of monoclonal antibodies are in development as systemic SARS-COV-2 therapeutics, but these compounds are not ideal for intranasal delivery as antibodies are large and often not extremely stable molecules, and the density of binding sites is low (two per 150 Kd antibody); the Fc domain provides little added benefit. More desirable would be protein inhibitory with the very high affinity for the virus of the monoclonals, but with higher stability and very much smaller size to maximize the density of inhibitory domains and enable direct delivery into the respiratory system through nebulization.
We set out to de novo design high affinity binders to the RBD that compete with Ace2 binding. We explored two strategies: first we attempted to scaffold the alpha helix in Ace2 that makes the majority of the interactions with the RBD in a small designed protein that makes additional interactions with the RBD to attain higher affinity, and second, we sought to design binders completely from scratch that do not incorporate any known binding interaction with the RBD. An advantage of the second approach is that the range of possibilities for design is much larger, and so potentially higher affinity binding modes can be identified. For the first approach, we used the Rosetta™ blue print builder to generate small proteins which incorporate the Ace2 helix and for the second approach, RIF docking and design using large miniprotein libraries. The designs interact with distinct regions of the RBD surface surrounding the Ace2 binding sites (
To determine whether the designs binding the RBD through the designed interfaces, site saturation libraries in which every residue in each design was substituted with each of the 20 amino acids one at a time were constructed, and subjected to FACS sorting for RBD binding. Deep sequencing showed that the binding interface residues and protein core residues were conserved in many of the designs for which such site saturation libraries (SSM's) were constructed (SSMs were used to define allowable positions for amino acid changes in Table 1). For most of the designs, a small number of substitutions were enriched in the FACS sorting, suggesting they increase binding affinity for RBD. For the highest affinity of the approach 1 designs, and 8 of the approach 2 designs, combinatorial libraries incorporating these substitutions were constructed and again screened for binding with FACS; because of the very high binding affinity the concentrations used in the sorting were as low as 20 pM. Each library converged on a small number of closely related sequences, and for each design, one of the optimized variants was expressed in E. coli and purified.
The binding of the 8 optimized designs with different binding modes to RBD (
We investigated the ability of the designs to block infection of human cells by live virus. 100 FFU of SARS-COV-2 was added to 2.5-3×104 vero cells in the presence of varying amounts of the designed binders. Details are provided in the legend to
Details on specific designs are provided in Table 10.
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
E. coli
The designed binders have several advantages over antibodies as potential therapeutics. Together, they span a range of binding modes, and in combination viral escape would be quite unlikely. The retention of activity after extended time at elevated temperatures suggests they would not require a cold chain. The designs are 20 fold smaller than a full antibody molecule, and hence in an equal mass have 20 fold more potential neutralizing sites, increasing the potential efficacy of a locally administered drug. The cost of goods and the ability to scale to very high production should be lower for the much simpler miniproteins, which unlike antibodies, do not require expression in mammalian cells for proper folding. The small size and high stability should make them amenable to direct delivery into the respiratory system by nebulization. Immunogenicity is a potential problem with any foreign molecule, but for previously characterized small de novo designed proteins little or no immune response has been observed, perhaps because the high solubility and stability together with the small size makes presentation on dendritic cells less likely.
Ultrapotent Miniproteins Targeting the Receptor-Binding Domain Protect Against SARS-CoV-2 Infection and Disease
Despite the introduction of public health measures and spike protein-based vaccines to mitigate the COVID-19 pandemic, SARS-COV-2 infections and deaths continue to rise. Here, we investigated the capacity of modified versions of one lead binder, LCB1, to protect against SARS-COV-2-mediated lung disease in human ACE2-expressing transgenic mice. Systemic administration of LCB1-Fc reduced viral burden, diminished immune cell infiltration and inflammation, and completely prevented lung disease and pathology. A single intranasal dose of LCB1v1.3 reduced SARS-COV-2 infection in the lung even when given as many as five days before or two days after virus inoculation. Importantly, LCB1v1.3 protected in vivo against a historical strain (WA1/2020), an emerging B.1.1.7 strain, and a strain encoding key E484K and N501Y spike protein substitutions. These data support the use of LCB1v1.3 for prevention or treatment of SARS-COV-2 infection.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2), the cause of the Coronavirus Disease 2019 (COVID-19) pandemic, has resulted in global disease, suffering, and economic hardship. Despite implementation of public health measures, SARS-COV-2 transmission persists principally through human-to-human spread (Day, 2020; Li et al., 2020; Stand1 et al., 2020). SARS-COV-2-induced clinical manifestations range from asymptomatic infection to severe pneumonia, multi-organ failure, and death. Although the underlying mechanisms that dictate disease severity are poorly understood, the immunocompromised, the elderly, and those with specific comorbidities (e.g., history of cardiovascular disease, diabetes, or obesity) are at increased risk for poor outcome (Zhou et al., 2020).
Here, using a stringent model of SARS-COV-2 disease pathogenesis in human ACE2 (hACE2)-expressing transgenic mice (Golden et al., 2020; Winkler et al., 2020a), we evaluated the efficacy in vivo of exemplary miniprotein binder, LCB1. For our in vivo experiments, we evaluated two versions of LCB1: (a) an Fc-modified bivalent form, LCB1-hIgG-Fc9 (LCB1-Fc) that should extend half-life in vivo and engage effector arms of the immune system; and (b) a further optimized, monomeric form of LCB1 lacking an Fc domain, LCB1v1.3. Intraperitoneal administration of LCB1-Fc at one day pre- or post SARS-CoV-2 exposure conferred substantial protection including an absence of weight loss, reductions in viral burden approaching the limit of detection, and inhibition of lung inflammation and pathology. Intranasal delivery of LCB1v1.3 conferred protection as many as five days before or two days after SARS-COV-2 inoculation. Dosing experiments revealed that LCB1v1.3 retained efficacy at pharmacologically attainable concentrations and was weakly immunogenic. Most importantly, LCB1v1.3 protected animals against the currently emerging B.1.1.7 United Kingdom variant and a SARS-COV-2 strain encoding key spike substitutions E484K and N501Y present in both the South Africa (B.1.351) and Brazil (B.1.1.248) variants of concern. Overall, these studies establish LCB1-Fc and LCB1v1.3 as possible treatments to prevent or mitigate SARS-COV-2 disease.
Results
LCB1v1.3 prophylaxis limits viral burden and clinical disease. We modified LCB1 to generate two versions for in vivo testing: (a) we introduced polar mutations into LCB1 to increase expression yield and solubility without altering RBD binding (LCB1v1.3) and (b) we modified LCB1 by fusing it to a human IgG1 Fc domain (LCB1-Fc) to enhance bioavailability. LCB1v1.3 and LCB1-Fc bound avidly to a single RBD within the S trimer (
To determine the protective potential of these miniproteins against SARS-COV-2, we utilized K18 human hACE2-expressing transgenic mice, which develop severe lung infection and disease after intranasal inoculation of SARS-COV-2 (Golden et al., 2020; Winkler et al., 2020a). In prophylaxis studies, a single 250 μg (10 mg/kg) dose of LCB1-Fc administered by intraperitoneal injection (i.p.) one day prior to intranasal (i.n.) inoculation with 103 PFU of SARS-COV-2 WA1/2020 prevented weight loss compared to animals given a control protein (influenza A virus hemagglutinin minibinder) designed using similar computational methods (
Diffuse alveolar damage, inflammation, and pneumonia are manifestations of COVID-19 lung disease, culminating in respiratory failure and a requirement for mechanical ventilation (Johnson et al., 2020; Kordzadeh-Kermani et al., 2020). We evaluated the capacity of LCB1-Fc to prevent the compromised lung function seen after SARS-COV-2 infection of K18-hACE2 mice (Winkler et al., 2020a). At 7 dpi, mechanical ventilation tests of lung biomechanics in animals treated with LCB1-Fc showed no difference from naïve animals (
Post-exposure therapy with anti-RBD binders reduces viral burden. To evaluate its efficacy in a post-exposure setting, we administered LCB1-Fc by i.p. injection at 1 dpi. Therapy with LCB1-Fc prevented weight loss (
We next tested the efficacy of LCB1v1.3 as an i.n.-delivered post-exposure therapy. I.n. delivery, might enable self-administration of an anti-SARS-CoV-2 biological drug. Indeed, miniprotein inhibitors against influenza virus have shown efficacy as a nasal mist (Chevalier et al., 2017). For these studies, we used LCB1v1.3 because it can bind an increased number of RBD molecules for a given mass dose, resulting in increased neutralization activity (
Intranasal delivery of LCB1v1.3 confers protection against SARS-CoV-2 when administered up to 5 days before infection. We next evaluated the durability of LCB1v1.3 administered via i.n. prophylaxis. At 5 days, 3 days, 1 day, or 6 hours prior to inoculation with 103 PFU of SARS-COV-2, K18-hACE2 transgenic mice received a single 50 μg i.n. dose of LCB1v1.3 or the control binder. At 4 or 7 dpi, viral burden in tissues was determined by RT-qPCR. As expected, protection by LCB1v1.3 was better when administered closer to the time of SARS-COV-2 exposure, as reflected by greater reductions in viral load and weight loss (
We tested a range of i.n. doses LCB1v1.3 for efficacy (
LCB1v1.3 is weakly immunogenic and retains protective activity after repeated dosing. We treated K18-hACE2 transgenic mice with 50 μg of control binder or LCB1v1.3 every three days for a total of 18 days (
LCB1v1.3 protects against emerging SARS-COV-2 variants. We evaluated the activity of LCB1v1.3 against a B.1.1.7 isolate containing deletions at 69-70 and 144-145, and substitutions at N501Y, A570D, D614G, and P681H, and against a recombinant WA1/2020 strain containing key substitutions present in the B.1.351 and B.1.248 variant strains at residues E484K, N501Y, and D614G (Xie et al., 2021a). Although the neutralizing activity of LCB1v1.3 against the B.1.1.7 and E484K/N501Y/D614G strains was approximately 45 to 50-fold lower than for the WA1/2020 strain, the EC50 values still were ˜800 pM and 667 pM, respectively (
Here, using the stringent K18-hACE2 mouse model of SARS-COV-2 pathogenesis, we show that LCB1-Fc prevented SARS-COV-2 infection and disease when administered one day before or after virus inoculation. Lung biomechanics of mice treated with LCB1-Fc mirrored those of naïve animals in all parameters tested.
We also evaluated the efficacy of LCB1v1.3, an optimized, monomeric form of LCB1 without an Fc domain. A single i.n. dose of LCB1v1.3 reduced viral burden when administered as many as five days before or two days after SARS-COV-2 infection. Our i.n. delivery approach is unique. I.n. therapy of SARS-COV-2 has been reported only with type I interferon in a hamster model of disease (Hoagland et al., 2021) and efficacy was limited. The K18-hACE2 mouse model recapitulates several aspects of severe COVID-19, including lung inflammation and reduced pulmonary function (Golden et al., 2020; Winkler et al., 2020a). Since K18-hACE2 mice are highly vulnerable to infection, the therapeutic window of treatment is limited (Winkler et al., 2020b) and for our miniproteins, might only curb viral infection. Importantly, our data demonstrate that LCB1v1.3 binder treatment before or after infection limited immune cell infiltration and lung inflammation, which prevented tissue damage and compromise of respiratory function. As part of our proof-of-principle studies for a nasal prophylaxis, we observed little immunogenicity of LCB1v1.3, suggesting that repeated dosing may be possible.
Although several antibody-based therapies demonstrate promise against SARS-COV-2, and a few have been granted EUA status, viral evolution could jeopardize these interventions as evidenced by the emerging variants in the United Kingdom (B.1.1.7), South Africa (B.1.351), Brazil (B.1.248), and elsewhere. Indeed, we and others have observed that many monoclonal and polyclonal antibodies showed reduced neutralization activity against several of these variant strains (Chen et al., 2021; Wang et al., 2021a; Wang et al., 2021b; Wibmer et al., 2021; Xie et al., 2021b). In comparison, LCB1v1.3 showed efficacy against historical (WA1/2020) and emerging (B.1.1.7 and E484K/N501Y/D614G) SARS-COV-2 strains. Based on the cryo-EM structure of the parent LCB1 binder in complex with SARS-CoV-2 RBD (Cao et al., 2020), only the N501Y mutation is expected to affect binding. While we observed a decrease in the neutralizing activity of LCB1v1.3 against the emerging variants, EC 50 values were still less than 800 pM, suggesting substantial potency was retained.
Compared to other potential SARS-COV-2 antibody-based treatments, miniproteins have several benefits: (a) due to their smaller size, they can bind each protomer of a single trimeric spike, resulting in greater potency for a given dose; (b) they can be manufactured cost-effectively; and (c) they can be mixed using linker proteins to generate multimerized constructs that limit resistance.
Experimental Model and Subject Details
Cells and viruses. Vero E6 (CRL-1586, American Type Culture Collection (ATCC), Vero CCL81 (ATCC), Vero-furin (Mukherjee et al., 2016), and Vero-hACE2-TMPRSS2 (a gift of A. Creanga and B. Graham, NIH) were cultured at 37° C. in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES pH 7.3, 1 mM sodium pyruvate, 1× non-essential amino acids, and 100 U/ml of penicillin-streptomycin. Additionally, Vero-hACE2-TMPRSS2 cells were cultured in the presence of 5 μg/mL puromycin. The WA1/202 (2019n-CoV/USA_WA1/2020) isolate of SARS-COV-2 was obtained from the US Centers for Disease Control (CDC). The B.1.1.7 and WA1/2020 E484K/N501Y/D614G viruses have been described previously (Chen et al., 2021; Xie et al., 2021a). Infectious stocks were propagated by inoculating Vero CCL81 or Vero-hACE2-TMPRSS2 cells. Supernatant was collected, aliquoted, and stored at −80° C. All work with infectious SARS-COV-2 was performed in Institutional Biosafety Committee-approved BSL3 and A-BSL3 facilities at Washington University School of Medicine using positive pressure air respirators and protective equipment.
Mouse experiments. Animal studies were carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocols were approved by the Institutional Animal Care and Use Committee at the Washington University School of Medicine (assurance number A3381-01).
Virus inoculations were performed under anesthesia that was induced and maintained with ketamine hydrochloride and xylazine, and all efforts were made to minimize animal suffering.
Heterozygous K18-hACE c57BL/6J mice (strain: 2B6·Cg-Tg(K18-ACE2)2Prlmn/J) were obtained from The Jackson Laboratory. Animals were housed in groups and fed standard chow diets. Mice of different ages and both sexes were administered 103 PFU of SARS-COV-2 via intranasal administration.
Miniprotein production. LCB1-Fc was synthesized and cloned by GenScript into pCMVR plasmid, with kanamycin resistance. Plasmids were transformed into the NEB 5-alpha strain of E. coli (New England Biolabs) to recover DNA for transient transfection into Expi293F mammalian cells. Expi293F cells were grown in suspension using Expi293F expression medium (Life Technologies) at 33° C., 70% humidity, and 8% CO2 rotating at 150 rpm. The cultures were transfected using PEI-MAX (Polyscience) with cells grown to a density of 3×106 cells per mL and cultivated for 3 days. Supernatants were clarified by centrifugation (5 min at 4000×g, addition of PDADMAC solution to a final concentration of 0.0375% (Sigma Aldrich, #409014), and a second spin (5 min at 4000×g). Clarified supernatants were purified using a MabSelect PrismA™ 2.6×5 cm column (Cytiva) on an AKTA Avant150 FPLC (Cytiva). Bound protein was washed with five column volumes of 20 mM NaPO4 and 150 mM NaCl pH 7.2, then five column volumes of 20 mM NaPO4 and 1 M NaCl pH 7.4, and eluted with three column volumes of 100 mM glycine at pH 3.0. The eluate was neutralized with 2 M Tris base to a final concentration of 50 mM. SDS-PAGE was used to assess protein purity. The protein was passed through a 0.22 μm filter and stored at 4° C. until use.
LCB1v1.3 with polar mutations (4N, 14K, 15T, 17E, 18Q, 27Q, 38Q) relative to the original LCB1 was cloned into a pet29b vector. LCB1v1.3 was expressed in Lemo21(DE3) (NEB) in terrific broth media and grown in 2 L baffled shake flasks. Bacteria were propagated at 37° C. to an O.D.600 of ˜0.8, and then induced with 1 mM IPTG. Expression temperature was reduced to 18° C., and the cells were shaken for ˜16 h. The cells were harvested and lysed using heat treatment and incubated at 80° C. for 10 min with stirring. Lysates were clarified by centrifugation at 24,000×g for 30 min and applied to a 2.6×10 cm Ni Sepharose™ 6 FF column (Cytiva) for purification by IMAC on an AKTA Avant150 FPLC system (Cytiva). Proteins were eluted over a linear gradient of 30 mM to 500 mM imidazole in a buffer of 50 mM Tris pH 8.0 and 500 mM NaCl. Peak fractions were pooled, concentrated in 10 kDa MWCO centrifugal filters (Millipore), sterile filtered (0.22 μm) and applied to either a Superdex™ 200 Increase 10/300, or HiLoad S200 pg GL SEC column (Cytiva) using 50 mM phosphate pH 7.4, 150 mM NaCl buffer. After size exclusion chromatography, bacterial-derived components were tested to confirm low levels of endotoxin.
Biolayer interferometry. Biolayer interferometry data were collected using an Octet™ RED96 (ForteBio) and processed using the instrument's integrated software. Briefly, biotinylated RBD (Acro Biosystems) was loaded onto streptavidin-coated biosensors (SA ForteBio) at 20 nM in binding buffer (10 mM HEPES (pH 7.4), 150 mM NaCl, 3 mM EDTA, 0.05% surfactant P20, and 0.5% non-fat dry milk) for 360 s. Analyte proteins (LCB1v1.3 or LCB1-Fc) were diluted from concentrated stocks into binding buffer. After baseline measurement in the binding buffer alone, the binding kinetics were monitored by dipping the biosensors in wells containing the target protein at the indicated concentration (association step) for 3,600 s and then dipping the sensors back into baseline/buffer (dissociation) for 7,200 s.
Plaque assay. Vero-furin cells (Mukherjee et al., 2016) were seeded at a density of 2.5×105 cells per well in flat-bottom 12-well tissue culture plates. The following day, medium was removed and replaced with 200 μL of 10-fold serial dilutions of the material to be titrated, diluted in DMEM+2% FBS, and plates incubated at 37° C. with rocking at regular intervals. One hour later, 1 mL of methylcellulose overlay was added. Plates were incubated at 37° C. for 72 h, then fixed with 4% paraformaldehyde (final concentration) in PBS for 20 min. Fixed cell monolayers were stained with 0.05% (w/v) crystal violet in 20% methanol and washed twice with distilled, deionized water.
Measurement of viral burden. Tissues were weighed and homogenized with zirconia beads in a MagNA Lyser™ instrument (Roche Life Science) in 1,000 μL of DMEM media supplemented with 2% heat-inactivated FBS. Tissue homogenates were clarified by centrifugation at 10,000 rpm for 5 min and stored at −80° C. RNA was extracted using the MagMax mirVana™ Total RNA isolation kit (Thermo Scientific) on a Kingfisher Flex extraction robot (Thermo Scientific). RNA was reverse transcribed and amplified using the TaqMan™ RNA-to-CT 1-Step Kit (ThermoFisher). Reverse transcription was carried out at 48° C. for 15 min followed by 2 min at 95° C. Amplification was accomplished over 50 cycles as follows: 95° C. for 15 s and 60° C. for 1 min. Copies of SARS-COV-2 N gene RNA in samples were determined using a previously published assay (Case et al., 2020; Hassan et al., 2020). Briefly, a TaqMan™ assay was designed to target a highly conserved region of the N gene (Forward primer: ATGCTGCAATCGTGCTACAA (SEQ ID NO: 190); Reverse primer: GACTGCCGCCTCTGCTC (SEQ ID NO: 191); Probe: /56-FAM/TCAAGGAAC/ZEN/AACATTGCCAA/3IABKFQ/) (SEQ ID NO: 192). This region was included in an RNA standard to allow for copy number determination down to 10 copies per reaction. The reaction mixture contained final concentrations of primers and probe of 500 and 100 nM, respectively.
Cytokine and chemokine mRNA measurements. RNA was isolated from lung homogenates as described above. cDNA was synthesized from DNAse-treated RNA using the High-Capacity cDNA Reverse Transcription kit (Thermo Scientific) with the addition of RNase inhibitor following the manufacturer's protocol. Cytokine and chemokine expression was determined using TaqMan™ Fast Universal PCR master mix (Thermo Scientific) with commercial primers/probe sets specific for IFN-g (IDT: Mm.PT.58.41769240), IL-6 (Mm.PT.58.10005566), IL-1b (Mm.PT.58.41616450), Tnfa (Mm.PT.58.12575861), CXCL10 (Mm.PT.58.43575827), CCL2 (Mm.PT.58.42151692), CCL5 (Mm.PT.58.43548565), CXCL11(Mm.PT.58.10773148.g), Ifnb (Mm.PT.58.30132453.g), CXCLI (Mm.PT.58.42076891) and results were normalized to GAPDH (Mm.PT.39a.1) levels. Fold change was determined using the 2−ΔΔCt method comparing treated mice to naïve controls.
Lung Pathology. Animals were euthanized before harvest and fixation of tissues. The left lung was first tied off at the left main bronchus and collected for viral RNA analysis. The right lung was inflated with approximately 1.2 mL of 10% neutral buffered formalin using a 3-mL syringe and catheter inserted into the trachea. Tissues were embedded in paraffin, and sections were stained with hematoxylin and eosin. Slides were scanned using a Hamamatsu NanoZoomer™ slide scanning system, and images were viewed using NDP view software (ver.1.2.46).
Respiratory mechanics. Mice were anesthetized with ketamine/xylazine (100 mg/kg and 10 mg/kg, i.p., respectively). The trachea was isolated via dissection of the neck area and cannulated using an 18-gauge blunt metal cannula (typical resistance of 0.18 cmH2O·s/mL), which was secured in place with a nylon suture. The mouse then was connected to the flexiVent™ computer-controlled piston ventilator (SCIREQ Inc.) via the cannula, which was attached to the FX adaptor Y-tubing. Mechanical ventilation was initiated, and mice were given an additional 100 mg/kg of ketamine and 0.1 mg/mouse of the paralytic pancuronium bromide via intraperitoneal route to prevent breathing against the ventilator and during measurements. Mice were ventilated using default settings for mice, which consisted in a positive end expiratory pressure at 3 cm H2O, a 10 mL/kg tidal volume (Vt), a respiratory rate at 150 breaths per minute (bpm), and a fraction of inspired oxygen (FiO2) of 0.21 (i.e., room air). Respiratory mechanics were assessed using the forced oscillation technique, as previously described (McGovern et al., 2013), using the latest version of the flexiVent™ operating software (flexiWare v8.1.3). Pressure-volume loops and measurements of inspiratory capacity also were performed.
Neutralization assay. Serial dilutions of binder proteins were incubated with 102 focus-forming units (FFU) of SARS-COV-2 for 1 h at 37° C. Binder-virus complexes were added to Vero E6 (WA1/2020) or Vero-hACE2-TMPRSS2 (B.1.1.7 and WA1/2020 E484K/N501Y/D614G) cell monolayers in 96-well plates and incubated at 37° C. for 1 h. Subsequently, cells were overlaid with 1% (w/v) methylcellulose in MEM supplemented with 2% FBS. Plates were harvested 24-30 h later by removing overlays and fixed with 4% PFA in PBS for 20 min at room temperature. Plates were washed and sequentially incubated with an oligoclonal pool of SARS2-2, SARS2-11, SARS2-16, SARS2-31, SARS2-38, SARS2-57, and SARS2-71 anti-spike protein antibodies (Zhou et al., 2021) and HRP-conjugated goat anti-mouse IgG in PBS supplemented with 0.1% saponin and 0.1% bovine serum albumin. SARS-COV-2-infected cell foci were visualized using TrueBlue™ peroxidase substrate (KPL) and quantitated on an ImmunoSpot™ microanalyzer (Cellular Technologies). Data were processed using Prism™ S software (GraphPad Prism™ 8.0).
ELISA. C-terminal biotinylated LCB1.1v3 was immobilized on streptavidin-coated plates (RayBiotech #7C-SCP-1) at 2.5 μg/mL in 100 μL total volume per well and incubated at 4° C. overnight. Plates were washed with wash buffer (TBS+0.1% (w/v) BSA+0.05% (v/v) Tween20) and blocked with 200 μL/well blocking buffer (TBS+2% (w/v) BSA+0.05% (v/v) Tween20) for 1 h at room temperature. Plates were rinsed with wash buffer using 200 μL/well, and 100 μL of 1:100 diluted sera samples in blocking buffer were added to respective wells. For a positive control, Fc-RBD was serially diluted 1:5 starting at 240 ng/ml in 100 μL of blocking buffer. All samples were incubated for 1 h at room temperature. Plates were washed using 200 μL/well of wash buffer. For the serum samples, HRP-conjugated horse anti-mouse IgG antibody (Vector Laboratories #PI-2000-1) was diluted 1:200 in blocking buffer, and 100 μL was incubated in each well at room temperature for 30 min. For the positive control, HRP-conjugated mouse anti-human IgG antibody (Invitrogen #05-4220) was diluted 1:500 in blocking buffer, and 100 μL was incubated in each well at room temperature for 30 min. Plates were rinsed with wash buffer, and 100 μL of TMB (SeraCare) was added to each well for 2 min. The reaction was quenched by adding 100 μL of 1N HCl. Optical densities were determined at 450 nm on a Synergy Neo21M plate reader (BioTek Instruments).
Quantification and Statistical Analysis
Statistical significance was assigned when P values were <0.05 using Prism™ Version 8 (GraphPad). Tests, number of animals, median values, and statistical comparison groups are indicated in each of the Figure legends. Analysis of weight change was determined by two-way ANOVA. Changes in functional parameters or immune parameters were compared to control binder-treated animals and analyzed by one-way ANOVA with multiple comparisons tests. Statistical analyses of viral burden between two groups were determined by Mann-Whitney test.
Multivalent Designs
Escape variants of SARS-COV-2 are threatening to considerably prolong the COVID-19 pandemic. Here we develop multivalent minibinders as potential prophylactic and therapeutic agents to address this problem. We designed multivalent minibinders containing three copies of a minibinder (self-assembled homotrimer), or three linked distinct minibinders (multi-domain fusion) targeting different sites, geometrically matched to the spike trimer and optimized their composition using a rapid cell-free expression and evaluation workflow. The optimized designs have greatly slowed dissociation rates from the SARS-COV-2-S-glycoprotein with complex half-lives of more than two weeks. Cryo-EM of the structures reveal that both homotrimer and fusion minibinder constructs can engage all three RBDs on a single spike protein. The top trimeric and fusion candidates neutralize the wild-type SARS-CoV-2 virus in addition to the B.1.1.7, B.1.351, B.1.1.28 variants of concern with IC50s in the low pM range. Additionally, the top homotrimer candidate provided prophylactic protection in a human ACE2-expressing transgenic mice against the same variant strains. Our approach highlights the utility of computational protein design coupled to rapid experimental prototyping to design potent multivalent inhibitors that can broadly neutralize widely circulating variants of concern.
We sought to develop multivalent versions of our computationally designed miniproteins that block the SARS-COV-2 receptor binding domain (RBD) interaction with its host receptor ACE2. In principle, the small size of the designed minibinders enables simultaneous engagement of multiple RBDs within a single spike protein trimer. We hypothesized that this multivalent binding would lead to ultra-high affinity inhibitors that are more resistant to escape mutations than their monomeric counterparts. The resulting avidity from these multivalent interactions could ameliorate the effects of mutations that would escape individual domains. Additionally, single proteins containing domains targeting multiple distinct epitopes or containing different sets of contacts with the target epitope could further increase the robustness of the designs to mutational escape. Starting with the LCB1, AHB2, and LCB3 minibinders (hereafter referred to as M1, M2, and M3 respectively; Table 11) and their known binding modes we pursued two parallel strategies for designing multivalent inhibitors, self-assembled homotrimers and multi-domain fusions.
To enable rapid prototyping of the designed proteins, we developed a cell-free DNA assembly and protein expression workflow enabling a greatly shortened design-build-test cycle better matched to the urgency of a pandemic. The workflow combines a cell-free DNA assembly step utilizing Gibson assembly followed by PCR to generate linear expression templates that are used to drive cell-free protein synthesis (CFPS). The developed workflow allows us to translate synthetic DNA to purified protein in as little as 6 hours, is easily scaled to high-throughput formats (e.g., 96- or 384-well plates), and is amenable to automated liquid handling. Furthermore, we coupled this cell-free workflow to an AlphaLISA protein-protein interaction (PPI) competition assay to enable comparison of dissociation rates of the designed proteins against either the monomeric RBD or the trimeric hexapro SARS-COV-2-S-glycoprotein (S6P). Because multivalency largely only impacts the dissociation rate constant of the interaction, we reasoned that an in-solution off-rate screen would enable us to distinguish mono- from multi-valent binding. The resulting workflow can evaluate hundreds of candidate multivalent proteins per week.
Design and validation of multivalent binders
In the first strategy, we designed self-assembling trimeric versions of the M1, M2, and M3 miniproteins geometrically matched to the three RBDs in the spike trimer (hereafter referred to as H[binding domain #]-[homotrimer #]; for example, H1-1 represents a homotrimer of M1 with homotrimerization domain 1, Table 11). We designed, expressed, and evaluated more than one hundred different proteins containing various homotrimerization domains and linker lengths using our cell-free expression and multivalency screen workflow. We identified versions of each homotrimer that showed slow dissociation rates potentially indicating multivalent binding (
In the second strategy, we generated two- and three-domain fusions of the M1, M2 and M3 binding domains separated by flexible linkers (hereafter referred to as F[binding domain #s]-[linker]; for example, F231-P12 represents a fusion of M2 to M3 to M1 all separated by a PAS12 linker, Table 11). We evaluated a range of linker lengths chosen to span the distances between the termini of the domains when bound to the “open” and “closed” states of the RBD. We again expressed and evaluated more than one hundred different designs varying binding domain connectivity and linker length to optimize multivalency. Several identified two- and three-domain fusions show slow dissociation rates comparable to the homo-trimeric constructs described above (
The best candidates from each strategy showed little to no dissociation after 14 days of with competitor, with further measurements being limited by the stability of S6P. From these data we estimate the complex has a dissociation rate constant of slower than 1 ×10−7 s−1. To our knowledge, these are the slowest measured dissociation rate constant for a synthetic protein-protein interactions ever reported.
We next used single particle cryo-electron microscopy (cryo-EM) to characterize the complex between S6P and the top candidate minibinders constructs (
Multivalent Minibinders Neutralize Widely Circulating SARS-CoV-2 Variants
We next sought to determine ability of the multivalent constructs to neutralize SARS-CoV-2 variants. We screened the off rate of the best multivalent minibinders against a panel of mutant spike proteins (
We additionally evaluated the potency of these proteins via neutralization assays against both a SARS-COV-2 HIV pseudovirus in addition to authentic SARS-COV-2 isolates (
Multivalent Minibinders Resist Viral Escape
In addition to evaluating the top candidate's ability to neutralize currently circulating SARS-COV-2 mutants, we also tested the ability of the inhibitors to resist escape viral escape (
H2-0 Provides Prophylactic Protection in Human ACE2-Expressing Transgenic Mice
To determine the ability of our multivalent minibinders to protect in an in vivo model, we evaluated them as a pre-exposure prophylactic treatment in human ACE2-expressing transgenic mice (
We anticipate that the cell-free protein expression and evaluation workflow will find utility in many different applications where the evaluation of individual protein variants is the limiting process step. In addition, our developed multivalency screen will accelerate the ability of researchers to develop multivalent protein therapeutics.
The designed protein constructs could have a number of advantages over monoclonal antibodies for preventing and treating COVID-19 infection. 1) direct administration into respiratory system, 2) low cost of goods and amenability to very large-scale production, 3) high stability and lack of need for cold chain, and 4) very broad resistance to escape mutants in single compounds. More generally, designed high affinity multivalent minibinders could provide a powerful platform for combating viral pandemics.
This application claims priority to U.S. Provisional Patent Application Serial Nos. 63/051,474 filed Jul. 14, 2020 and 63/067,593 filed Aug. 19, 2020, each incorporated by reference herein in its entirety.
This invention was made with government support under Grant No. FA8750-17-C-0219, awarded by the Defense Advanced Research Projects Agency and Grant Nos. HHSN272201700059C and R01 GM120553, awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/034069 | 5/25/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63067593 | Aug 2020 | US | |
| 63051474 | Jul 2020 | US |
