Patent Grant
10342863
The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 15-016 Sequence Listing_ST25.txt. The text file is about 182 KB, was created on Mar. 22, 2018, and is being submitted electronically via EFS-Web.
Engineered and multimerized human immunodeficiency virus (HIV) envelope glycoproteins are described. The engineered envelope glycoproteins can be provided as multimerized heptamers. The engineered and multimerized envelope glycoproteins can be derived from glycoprotein 120 (gp120) and can used as an HIV vaccine.
Acquired Immunodeficiency Syndrome (AIDS) is characterized by immunosuppression that results in opportunistic infections and malignancies; wasting syndromes; and central nervous system degeneration. Destruction of CD4+ T-cells, which are critical to immune defense, is a major cause of the progressive immune dysfunction that is the hallmark of AIDS disease progression. The loss of CD4+ T cells seriously impairs the body's ability to fight most pathogens, but it has a particularly severe impact on the defenses against viruses, fungi, parasites and certain bacteria, including mycobacteria.
AIDS is caused by infection with human immunodeficiency virus (HIV). An infectious HIV particle includes two strands of RNA packaged within a viral protein core. The core is surrounded by a phospholipid bilayer envelope derived from a host cell membrane that also includes virally-encoded membrane proteins.
The HIV genome encodes several structural proteins and has the characteristic 5′-LTR-Gag-Pol-Env-LTR-3′ organization of the retrovirus family. The env gene encodes the viral envelope glycoprotein (Env) that is translated as a 160-kilodalton (kDa) precursor (gp160) and cleaved by a cellular protease to yield an external 120-kDa envelope glycoprotein (gp120) and a transmembrane 41-kDa envelope glycoprotein (gp41). These glycoproteins are required for HIV to infect cells.
HIV infection begins when gp120 on the viral particle binds to CD4 and chemokine receptors on the cell membrane of a subject's target immune system cells (e.g., CD4+ T-cells, macrophages and dendritic cells). The bound virus then fuses with the target cell and reverse transcribes its RNA genome. The resulting viral DNA integrates into the subject cell's genome and begins to produce new viral RNA, resulting in new viral proteins and virions. The virions leave the originally infected cell to then infect new cells. This process kills the originally infected cell.
HIV-1 broadly neutralizing antibodies (bNAbs) are antibodies capable of neutralizing HIV. HIV bNAbs target four major areas of the Env: (i) the membrane proximal external region of the gp41 subunit; (ii) the CD4 receptor-binding site (CD4-BS); (iii) two sites including both carbohydrate and amino acid moieties, one at the base of the “V3” and another on the “V1/V2” loops of the gp120 subunit; and (iv) regions spanning elements of both gp120 and gp41.
Based on their ontogenies and mode of recognition, the CD4-BS bNAbs are grouped into two major types: (i) heavy chain complementary determining region three (CDRH3)-dominated; and (ii) variable heavy (VH)-gene-restricted. Antibodies that make contact primarily through their CDRH3 regions are further subdivided into the CH103, HJ16, VRC13 and VRC16 classes while the VH-gene-restricted Abs include the VRC01- and the 8ANC131-class antibodies.
VRC01-class bNAbs protect non-human primates from experimental simian/human HIV (SHIV)-infection and humanized mice from HIV-1 infection. It was therefore thought that vaccine-elicited VRC01-class bNAbs would protect humans from HIV-1 infection. With the exception of llamas however, all efforts to elicit such antibodies by immunization in humans or wild type animals with recombinant Env (rEnv) have been unsuccessful.
One of the many important reasons for the lack of success is thought to be the inability of the Env proteins used as immunogens to engage B cell receptors (BCRs) that encode the germline (gl) of VRC01-class antibodies (e.g., “immature” or not fully developed Abs). Indeed maturation of these antibodies to full neutralizing Abs requires that they circumvent steric constraints on Env through extensive somatic hypermutation. For example, HIV-1 has evolved to avoid detection by gl B cells that give rise to VRC01-class bNAbs through development of specific N-linked glycosylation sites (NLGS) (for example, in Loop D and V5 of the gp120 subunit). As a consequence, recombinant Env proteins derived from diverse HIV-1 isolates are ineffective in binding to and stimulating B cells engineered to express the glBCR forms of VRC01-class bNAbs in vitro. Targeted disruption of conserved NLGS at position 276 in Loop D, and at positions 460 and 463 in V5 of the 426c clade C Env, however, permits binding and activation gl B cell lines expressing BCRS of two clonally-related VRC01-class bNAbs, VRC01 and NIH45-46 in vitro. These two BCRs represent a small subset of potential VRC01-class antibody progenitors. Thus, designing immunogens capable of recognizing a larger group of glVRC01-class BCRs should increase the chances of activating rare, naïve glVRC01-class B cells during human immunization.
Previous reports describe preparation of artificial gp120 proteins (in some instances called “engineered outer domain” or “eOD” proteins) for use as HIV vaccines. The previous reports also describe multimerizing the artificial gp120 proteins to enhance immunogenicity of the proteins, and more particularly, the VRC01 epitope of the proteins. It was envisioned that multimerized artificial gp120 proteins would stimulate gl B cells using multivalent avidity, and, further, that the addition of the larger particulate forms would mimic a virus-like symmetric presentation of epitopes, reduce immune responses to regions buried in the multimer, and enhance in vivo trafficking of the artificial gp120 proteins to lymph nodes.
These previous reports described eOD proteins that lack normally occurring loops. The eOD proteins were also multimerized as trimers, tetramers, and octamers using coiled-coil multimerization domains. From the trimers and tetramers, octamers, 24mers, 60mers, and 180mers were formed.
The present disclosure provides engineered and multimerized (e/m) human immunodeficiency virus (HIV) envelope glycoproteins (Env). The engineered Env can be provided as multimerized heptamers, dextramers or larger order -mers. The e/m Env can be derived from glycoprotein 120 (gp120) and can used as an HIV vaccine.
More particularly, the present disclosure provides specific gp120 modifications and multimerization strategies that expand the germline (gl) VRC01-class antibody-recognition potential of the Env. Importantly, B cells were inefficiently activated by soluble trimeric multimerization forms of disclosed engineered Env. Higher order multimeric forms, however, based on heptamers were effective, indicating usefulness as an HIV-1 vaccination. Of note, heptameric multimerized forms were produced using the C4b multimerization domain.
Particular embodiments of the e/m Env include the following mutations: N460D; N463D; S278R; G471S; V65C; S115C; removal of V1 and V2; V3 replacement with a flexible linker; and an N-terminal truncation. In particular embodiments, the e/m Env does not include a mutation at position 276. In particular embodiments, the e/m Env is multimerized with a C4b multimerization domain derived from chicken. In particular embodiments, the e/m Env is multimerized with a modified chicken heptamerization domain. In particular embodiments, the e/m Env includes all characteristics described in this paragraph.
Acquired Immunodeficiency Syndrome (AIDS) is characterized by immunosuppression that results in opportunistic infections and malignancies; wasting syndromes; and central nervous system degeneration. Destruction of CD4+ T-cells, which are critical to immune defense, is a major cause of the progressive immune dysfunction that is the hallmark of AIDS disease progression. The loss of CD4+ T cells seriously impairs the body's ability to fight most pathogens, but it has a particularly severe impact on the defenses against viruses, fungi, parasites and certain bacteria, including mycobacteria.
AIDS is caused by infection with human immunodeficiency virus (HIV). An infectious HIV particle includes two strands of RNA packaged within a viral protein core. The core is surrounded by a phospholipid bilayer envelope derived from a host cell membrane that also includes virally-encoded membrane proteins.
The HIV genome encodes several structural proteins and has the characteristic 5′-LTR-Gag-Pol-Env-LTR-3′ organization of the retrovirus family. The env gene encodes the viral envelope glycoprotein (Env) that is translated as a 160-kilodalton (kDa) precursor (gp160) and cleaved by a cellular protease to yield an external 120-kDa envelope glycoprotein (gp120) and a transmembrane 41-kDa envelope glycoprotein (gp41). These glycoproteins are required for HIV to infect cells.
Mature gp120 wildtype (wt) protein have about 500 amino acids in the primary sequence. gp120 is heavily N-glycosylated giving rise to an apparent molecular weight of 120 kD. The protein includes five conserved regions (C1-C5) and five regions of high variability (V1-V5). Exemplary sequences of wt gp120 proteins are found in GENBANK®, for example accession numbers AAB05604 (SEQ ID NO: 1) and AAD12142 (SEQ ID NO: 2). It is understood that there are numerous variations in the sequence of gp120 from what is given in these examples. Reference to residues and mutation positions herein refer to HXB2 numbering, unless clearly noted to the contrary.
HIV infection begins when gp120 on the viral particle binds to CD4 and chemokine receptors on the cell membrane of a subject's target immune system cells (e.g., CD4+ T-cells, macrophages and dendritic cells). The bound virus then fuses with the target cell and reverse transcribes its RNA genome. The resulting viral DNA integrates into the subject cell's genome and begins to produce new viral RNA, resulting in new viral proteins and virions. The virions leave the originally infected cell to then infect new cells. This process kills the originally infected cell.
HIV-1 broadly neutralizing antibodies (bNAbs) are antibodies capable of neutralizing HIV. HIV bNAbs target four major areas of the Env: (i) the membrane proximal external region of the gp41 subunit; (ii) the CD4 receptor-binding site (CD4-BS); (iii) two sites including both carbohydrate and amino acid moieties, one at the base of the “V3” and another on the “V1/V2” loops of the gp120 subunit; and (iv) regions spanning elements of both gp120 and gp41.
Based on their ontogenies and mode of recognition, the CD4-BS bNAbs are grouped into two major types: (i) heavy chain complementary determining region three (CDRH3)-dominated; and (ii) variable heavy (VH)-gene-restricted. Antibodies that make contact primarily through their CDRH3 regions are further subdivided into the CH103, HJ16, VRC13 and VRC16 classes while the VH-gene-restricted Abs include the VRC01- and the 8ANC131-class antibodies.
VRC01-class bNAbs protect non-human primates from experimental simian/human HIV (SHIV)-infection and humanized mice from HIV-1 infection. It was therefore thought that vaccine-elicited VRC01-class bNAbs would protect humans from HIV-1 infection. However, all efforts to elicit such antibodies by immunization in humans or wild type animals with recombinant Env (rEnv) have been unsuccessful.
One of the many important reasons for the lack of success is thought to be the inability of the Env proteins used as immunogens to engage B cell receptors (BCRs) that encode the germline (gl) of VRC01-class antibodies (e.g., “immature” or not fully developed Abs). Indeed maturation of these antibodies to full neutralizing Abs requires that they circumvent steric constraints on Env through extensive somatic hypermutation. For example, HIV-1 has evolved to avoid detection by gl B cells that give rise to VRC01-class bNAbs through development of specific N-linked glycosylation sites (NLGS) (for example, in Loop D and V5 of the gp120 subunit). As a consequence, recombinant Env proteins derived from diverse HIV-1 isolates are ineffective in binding to and stimulating B cells engineered to express the glBCR forms of VRC01-class bNAbs in vitro. Targeted disruption of conserved NLGS at position 276 in Loop D, and at positions 460 and 463 in V5 of the 426c clade C Env, however, permits binding and activation gl B cell lines expressing BCRS of two clonally-related VRC01-class bNAbs, VRC01 and NIH45-46 in vitro. These two BCRs represent a small subset of potential VRC01-class antibody progenitors. Thus, designing immunogens capable of recognizing a larger group of glVRC01-class BCRs should increase the chances of activating rare, naïve glVRC01-class B cells during human immunization.
Previous reports describe preparation of artificial gp120 proteins (in some instances called “engineered outer domain” or “eOD” proteins) for use as HIV vaccines. The previous reports also describe multimerizing the artificial gp120 proteins to enhance immunogenicity of the proteins, and more particularly, the VRC01 epitope of the proteins. It was envisioned that multimerized artificial gp120 proteins would stimulate gl B cells using multivalent avidity, and, further, that the addition of the larger particulate forms would mimic a virus-like symmetric presentation of epitopes, reduce immune responses to regions buried in the multimer, and enhance in vivo trafficking of the artificial gp120 proteins to lymph nodes.
These previous reports described eOD proteins that lack normally occurring loops. The eOD proteins were also multimerized as trimers, tetramers, and octamers using coiled-coil multimerization domains. From the trimers and tetramers, octamers, 24mers, 60mers, and 180mers were formed.
The present disclosure provides engineered and multimerized (e/m) human immunodeficiency virus (HIV) envelope glycoproteins (Env). The engineered Env can be provided as multimerized heptamers. The e/m Env glycoproteins can be derived from glycoprotein 120 (gp120) and can used as an HIV vaccine.
More particularly, the present disclosure provides specifically engineered gp120 sequences with particular multimerization strategies that expand the germline (gl) VRC01-class antibody-recognition potential of the Env. Importantly, B cells were inefficiently activated by soluble trimeric multimerization forms of the Env. Higher order multimeric forms, however, based on heptamers were effective, indicating usefulness as an HIV-1 vaccination. Of note, heptameric multimerized forms were produced using the C4b multimerization domain.
Particular embodiments of the e/m Env include the following mutations: N460D; N463D; S278R; G471S; V65C; S115C; removal of V1 and V2; V3 replacement with a flexible linker; and an N-terminal truncation. In particular embodiments, V1 refers to 131-152 and V2 refers to 161-196. In particular embodiments, removal of V1 and V2 loops includes removal of 123-196. In particular embodiments, V3 refers to 296-331. In particular embodiments, removal of V3 with a flexible linker replacement includes removal of 301-323 and replacement with GGSGSG (SEQ ID NO: 3). Particular embodiments exclude a mutation at position 276. Exclusion of a mutation at this position is unexpected because as previously stated, this position is an important NLGS site used by HIV to avoid B cell detection. Particular embodiments disclosed herein present the outer domain and the inner domain.
In addition to SEQ ID NO: 3, a number of flexible linkers can be used to replace V3. The linker sequence should not be significantly deleterious to the immunogenicity of the e/m Env, and may even be beneficial to immunogenicity. Particular exemplary linkers include flexible Gly-Ser linkers. Such linkers are known to those of skill in the art. One exemplary Gly-Ser linker includes Ac-Cys-Gly-Gly-Gly (SEQ ID NO: 122). Additional Gly-Ser linkers include GSTSGSGKPGSGEGSTKG (SEQ ID NO: 4) and SGRAHAG (SEQ ID NO: 5). Further examples include a linker that includes (Gly)n, where n=1 to 10 (e.g., n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; SEQ ID NO: 6); (Ser)n, where n=1 to 10 (e.g., n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; SEQ ID NO: 7), (Ala)n, where n=1 to 10 (e.g., n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; SEQ ID NO: 8), (Gly-Ser)n, where n=1 to 10 (e.g., n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; SEQ ID NO: 9), (Gly-Ser-Ser-Gly)n, where n=1 to 10 (e.g., n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; SEQ ID NO: 10), (Gly-Ser-Gly)n, where n=1 to 10 (e.g., n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; SEQ ID NO: 11), (Gly-Ser-Ser)n, where n=1 to 10 (e.g., n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; SEQ ID NO: 12), (Gly-Ala)n, where n=1 to 10 (e.g., n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; SEQ ID NO: 13), or any combination thereof.
An N-terminal truncation refers to a truncation at the N-terminal end of a naturally-occurring Env. In particular embodiments, the N-terminal truncation is before residue 49, 48, 47, 46, 45, 44, 43, 42, 41, 40 or 39. In particular embodiments, the N-terminal truncation is before residue 46, 45, 44, 43 or 42. In particular embodiments, the N-terminal truncation is before residue 44.
Particular embodiments include a C-terminal truncation. In particular embodiments, the C-terminal truncation is after residue 499, 498, 497, 496, 495, 494, 493, 492, 491, 490 or 389. In particular embodiments, the C-terminal truncation is after residue 496, 495, 494, 493 or 492. In particular embodiments, the C-terminal truncation is after residue 494.
In particular embodiments, the e/m Env is multimerized with a C4b multimerization domain. C4 binding protein (C4b) is the major inhibitor of the classical complement and lectin pathway. The complement system is a major part of innate immunity and is the first line of defense against invading microorganisms. Orchestrated by more than 60 proteins, its major task is to discriminate between host cells and pathogens and to initiate immune responses when necessary. It also recognizes necrotic or apoptotic cells. Hofmeyer et al., J Mol Biol. 2013 Apr. 26; 425(8):1302-17.
Full-length native C4b includes seven α-chains linked together by a multimerization (i.e., heptamerization) domain at the C-terminus of the α-chains. Blom et al., (2004) Mol Immunol 40: 1333-1346. One of the α-chains can be replaced by a β-chain in humans. The wild-type C4b multimerization domain is 57 amino acid residues in humans and 54 amino acid residues in mice. Forbes et al., PLoS One. 2012; 7(9): e44943. It contains an amphipathic α-helix region, which is necessary and sufficient for heptamerization, as well as two cysteine residues which stabilize the structure. Kask et al., (2002) Biochemistry 41: 9349-9357.
Immunization of mice with antigen and murine C4b can lead to the induction of auto-antibodies against murine C4b. Ogun et al., (2008) Infect Immun 76: 3817-3823. Ogun et al. tested the C4b α-chain multimerization domains from a variety of mammalian and avian species for adjuvant activity in mice without induction of auto-antibodies. All the C4b oligomerization domains tested formed soluble heptameric proteins, and induced higher antigen-specific antibody titers in mice than antigen alone or in Freund's adjuvant. The most immunogenic form, the C4b derived multimerization domain of IMX313, was a hybrid derived from the multimerization domains of the two chicken orthologues of the C4b α-chain. It was designed to minimize similarity to mammalian C4b α-chain domains and has less than 20% amino acid identity to human C4b. Ogun et al, (2008) Infect Immun 76: 3817-3823. This sequence particularly therefore minimizes the potential for auto-antibody induction in humans, and is a candidate “molecular adjuvant” for enhancement of vaccine-induced immune responses in humans. Forbes et al., PLoS One. 2012; 7(9): e44943.
In the recombinant protein vaccine studies by Ogun et al., however, the antibody titers induced against antigen when fused to different C4b α-chain multimerization domains varied significantly. Forbes et al. concluded that the C4b α-chain multimerization domain can effectively adjuvant antigen-specific T cell responses to some, but not all, antigens when fused to their C-termini and delivered by an adenoviral vectored vaccine. Forbes et al. hypothesized that the varying adjuvant activity observed with the C4b α-chain multimerization domain from different species when fused to an antigen could be due to the variable stability and strength of multimers formed.
The current disclosure provides that engineered gp120 antigens fused to C4b multimerization domains provide enhanced immune system responses (e.g., B cell responses) over engineered gp120 antigen alone and over trimeric engineered gp120 multimers. The current disclosure also provides that C4b multimerization of gp120 can induce stronger immune responses against gp120 antigens than other multimerization domains, such as coiled-coil domains.
The sequences of a number of C4b domain proteins are available in the art. These include human C4b multimerization domains as well as a number of homologues of human C4b multimerization domain available in the art. There are two types of homologues: orthologues and paralogues. Orthologues are defined as homologous genes in different organisms, i.e. the genes share a common ancestor coincident with the speciation event that generated them. Paralogues are defined as homologous genes in the same organism derived from a gene, chromosome or genome duplication, i.e. the common ancestor of the genes occurred since the last speciation event.
GenBank indicates mammalian C4b multimerization domain homologues in species including chimpanzees, rhesus monkeys, rabbits, rats, dogs, horses, mice, guinea pigs, pigs, chicken, and cattle. Further C4b multimerization domains may be identified by searching databases of DNA or protein sequences, using commonly available search programs such as BLAST.
Particular C4b multimerization domains that can be used include:
In particular embodiments, the C4b multimerization domain will be a multimerization domain which includes (i) glycine at position 12, (ii) alanine at position 28, (iii) leucines at positions 29, 34, 36, and/or 41; (iv) tyrosine at position 32; (v) lysine at position 33; and/or (vi) cysteine at positions 6 and 18. In particular embodiments, the C4b multimerization domain will be a multimerization domain which includes (i) glycine at position 12, (ii) alanine at position 28, (iii) leucines at positions 29, 34, 36, and 41; (iv) tyrosine at position 32; (v) lysine at position 33; and (vi) cysteine at positions 6 and 18.
C4b multimerization domains can include any of SEQ ID NOs: 14-46 with an N-terminal deletion of at least 1 consecutive amino acid residues (eg. at least 2, 3, 4, 5, 6, 7, 8, 9, 10 consecutive amino acid residues) in length. Additional embodiments can include a C-terminal deletion of at least 1 consecutive amino acid residues (eg. at least 2, 3, 4, 5, 6, 7, 8, 9, 10 consecutive amino acid residues) in length.
Particular C4b multimerization domain embodiments will retain or will be modified to include at least 1 of the following residues: A6; E11; A13; D21; C22; P25; A27; E28; L29; R30; T31; L32; L33; E34; 135; K37; L38; L40; E41; 142; Q43; K44; L45; E48; L49; or Q50. Further embodiments will retain or will be modified to include A6; E11; A13; D21; C22; P25; A27; E28; L29; R30; T31; L32; L33; E34; 135; K37; L38; L40; E41; 142; Q43; K44; L45; E48; L49; and Q50. Particular C4b multimerization domain embodiments will include the amino acid sequence “AELR”.
Particular embodiments can utilize a heptamerization domain such as:
Particular embodiments include e/m Env that differ from previously engineered Env based on (i) the precise selection of mutations and (ii) the particular multimerization strategy. When (i) and (ii) are combined, an exemplary e/m Env includes:
This e/m Env includes: the following mutations: N460D; N463D; S278R; G471S; V65C; S115C; removal of V1 and V2; V3 replacement with a flexible linker; an N-terminal truncation before 44, a C-terminal truncation after 494 and a C4b multimerization domain (see
The present disclosure also encompasses other engineered Env multimerized with a C4b binding protein multimerization domain. For example, the C4b multimerization strategy can be used with any engineered Env when C4b multimerization generates a statistically significantly increase in an immunization effect. A statistically significantly increase in an immunization effect can be confirmed by B cell activation as measured by calcium flux and/or by staining bone marrow cells for IgD and IgM to identify mature B cell populations. While C4b multimerization is preferred, in particular embodiments, dextrameric and ferritin-based multimerization can also be used. An exemplary ferritin fusion sequence includes, for example, PMID 26279189. In particular embodiments, a ferritin fusion sequence includes
Particular engineered gp120 sequences useful within the present disclosure also include those that (i) maintain high affinity for broadly neutralizing antibodies b12 and VRC01; (ii) bind with little or no detectable affinity to CD4 or non-neutralizing CD4bs antibodies such as b6, b13, F105, 15e, m14 or m18; (iii) lack the V3 loop and beta20/21 hairpin and are minimal in size (175 residues compared to 230 for wild-type outer domain); (iv) display no or low evidence of aggregation; (v) have N and C termini located distal from the CD4bs to allow coupling, by chemical or genetic means, to larger particles for the purpose of multimeric display; and/or (vi) may be expressed with a minimum of only two (2) glycans which may be useful for manipulating immune responses.
In particular embodiments, high affinity means that a binding domain associates with its target epitope with a dissociation constant (1(D) of 10−5 M or less, in one embodiment of from 10−5 M to 10−13 M, or in one embodiment of from 10−5 M to 10−10 M. In particular embodiments, high affinity means that a binding domain associates with its target epitope with a dissociation constant (1(D) of 10−7 M or less, or in one embodiment of from 10−7 M to 10−12 M, or in one embodiment of from 10−7 M to 10−15 M. In particular embodiments, high affinity means that a binding domain associates with its target epitope with an association constant presented in
In particular embodiments, little or no detectable affinity means that the binding domain associates with its target epitope with a dissociation constant (KD) of 10−4 M or more, in one embodiment of from 10−4 M to 1 M.
Exemplary engineered Env that can be multimerized with C4b, ferritin, and/or other heptamerization domains include:
Within these examples, SEQ ID NOs: 53-63 are advantageous for the elicitation of CD4-binding site (CD4bs)-directed broadly-neutralizing antibodies (bnAbs). SEQ ID NOs: 64-76 are advantageous for improving binding of mature VRC01. SEQ ID NOs: 77-109 are advantageous for improving binding to gl VRC01 and/or other VI-11-2 antibodies. SEQ ID NOs: 110-121 are involved in glycan masking.
As will be understood by one of ordinary skill in the art, all sequences disclosed herein and all combinations of resulting e/m Env can additionally include additional amino acid sequences to include further beneficial attributes. For example, sequences disclosed herein can include tag peptides which in some embodiments can provide an epitope to which an anti-tag antibody can selectively bind. The epitope tag generally can be placed at the amino- or carboxyl-terminus of the e/m Env. However, in some embodiments, an epitope tag can be placed within the amino acid sequence of an e/m Env. In some embodiments, an epitope tag can be used as a linker to join a g120 peptide to a C4b multimerization domain or another peptide or another type of molecule. In some embodiments a linker can be Ac-Cys-Gly-Gly-Gly (SEQ ID NO: 122). The presence of such epitope-tagged forms of e/m Env can be detected using an antibody against the epitope tag. Also, provision of the epitope tag enables the e/m Env to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag; this also can be useful for binding the e/m Env to a support for heterogeneous screening methods. Various tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags (e.g., GSHHHHHH (SEQ ID NO: 123); GTKHHHHHH (SEQ ID NO: 124)); the flu HA tag polypeptide and its antibody 12CA5 (Field et al., Mol. Cell. Biol., 8:2159-2165 (1988)); the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto (Evan et al., Molecular and Cellular Biology, 5:3610-3616 (1985)); and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody (Paborsky et al., Protein Engineering, 3(6):547-553 (1990)). Other tag polypeptides include the Flag-peptide (Hopp et al., BioTechnology, 6:1204-1210 (1988)); the KT3 epitope peptide (Martin et al., Science, 255:192-194 (1992)); tubulin epitope peptide (Skinner et al., J. Biol. Chem., 266:15163-15166 (1991)); and the T7 gene 10 protein peptide tag (Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA, 87:6393-6397 (1990)).
In particular embodiments, the e/m Env include an intervening linker between the engineered Env and C4b multimerization domains. In general, the amino acids within the linker sequences are not deleterious to the immunogenicity of the fusion, and may even be beneficial to immunogenicity. Alternatively, a e/m Env can lack linker sequences, but for the linker sequence that replaces the V3 loop. Particular embodiments can include flexible linkers described elsewhere herein. In particular embodiments, rigid linker sequences, such as proline-rich sequences may also be used.
e/m Env may additionally include additional domains such as additional antigen or antigenic fragment (e.g., 2, 3, 4, 6, 8, 10 additional antigens or antigenic fragments). Additional antigen(s) or antigenic fragments may be the same as the gp120 domain of a particular embodiment or may be different.
“Variants” include protein sequences having one or more amino acid additions, deletions, stop positions, or substitutions, as compared to a protein sequence disclosed elsewhere herein.
An amino acid substitution can be a conservative or a non-conservative substitution. Variants of protein sequence disclosed herein can include those having one or more conservative amino acid substitutions. A “conservative substitution” or “conservative amino acid substitution” involves a substitution found in one of the following conservative substitutions groups: Group 1: Alanine (Ala; A), Glycine (Gly; G), Serine (Ser; S), Threonine (Thr; T); Group 2: Aspartic acid (Asp; D), Glutamic acid (Glu; E); Group 3: Asparagine (Asn; N), Glutamine (Gln; Q); Group 4: Arginine (Arg; R), Lysine (Lys; K), Histidine (His; H); Group 5: Isoleucine (Ile; I), Leucine (Leu; L), Methionine (Met; M), Valine (Val; V); and Group 6: Phenylalanine (Phe; F), Tyrosine (Tyr; Y), Tryptophan (Trp; W).
Additionally, amino acids can be grouped into conservative substitution groups by similar function, chemical structure, or composition (e.g., acidic, basic, aliphatic, aromatic, or sulfur-containing). For example, an aliphatic grouping may include, for purposes of substitution, G, A, V, L, and I. Other groups including amino acids that are considered conservative substitutions for one another include: sulfur-containing: M and C; acidic: D, E, N, and Q; small aliphatic, nonpolar or slightly polar residues: A, S, T, P, and G; polar, negatively charged residues and their amides: D, N, E, and Q; polar, positively charged residues: H, R, and K; large aliphatic, nonpolar residues: M, L, I, V, and C; and large aromatic residues: F, Y, and W.
Non-conservative substitutions include those that significantly affect: the structure of the peptide backbone in the area of the alteration (e.g., the alpha-helical or beta-sheet structure); the charge or hydrophobicity of the molecule at the target site; or the bulk of the side chain. Non-conservative substitutions which in general are expected to produce the greatest changes in the proteins's properties are those in which (i) a hydrophilic residue (e.g. S or T) can be substituted for (or by) a hydrophobic residue (e.g. L, I, F, V, or A); (ii) a C or P can be substituted for (or by) any other residue; (iii) a residue having an electropositive side chain (e.g. K, R, or H) can be substituted for (or by) an electronegative residue (e.g. Q or D); or (iv) a residue having a bulky side chain (e.g. F), can be substituted for (or by) one not having a bulky side chain, (e.g. G). Additional information is found in Creighton (1984) Proteins, W.H. Freeman and Company.
Variants of protein sequences disclosed herein also include proteins with at least 70% sequence identity, at least 80% sequence identity, at least 85% sequence identity, at least 90% sequence identity, at least 95% sequence identity, at least 96% sequence identity, at least 97% sequence identity, at least 98% sequence identity, or at least 99% sequence identity to a protein sequence disclosed herein.
Variants of proteins disclosed herein include proteins that share: 70% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 75% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 80% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 81% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 82% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 83% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 84% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 85% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 86% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 87% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 88% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 89% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 90% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 91% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 92% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 93% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 94% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 95% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 96% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 97% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); 98% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50); or 99% sequence identity with any of SEQ ID NOs: 1-124, 126, or 134-146 (and particularly SEQ ID NO: 50).
“Percent_(%) amino acid sequence identity” with respect to the sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference sequence for each of the gp120 domain, the C4b multimerization domain, and/or the complete fusion after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared. For example,_% amino acid sequence identity values generated using the WU-BLAST-2 computer program (Altschul et al., Methods in Enzymology, 266:460-480 (1996)) uses several search parameters, most of which are set to the default values. Those that are not set to default values (i.e., the adjustable parameters) are set with the following values: overlap span=1, overlap fraction=0.125, word threshold (T)=11 and scoring matrix BLOSUM62.
Variants will typically exhibit the same qualitative biological activity and elicit a substantially similar immune response as a reference peptide, although variants can be selected to modify the characteristics of a reference peptide as needed. Screening of variants can be performed using assays of gp210 peptide activities, as known in the art. In particular embodiments, there is no statistically-significant difference in an immunization effect between a variant peptide and a reference peptide.
Covalent modifications of e/m Env are included within the scope of the disclosure. One type of covalent modification includes reacting targeted amino acid residues of e/m Env with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of e/m Env. Derivatization with bifunctional agents can be useful, for instance, for crosslinking e/m Env to a water-insoluble support matrix or surface for use in the methods described below, or for in vivo stability. Commonly used crosslinking agents include 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters (e.g., esters with 4-azidosalicylic acid), homobifunctional imidoesters, including disuccinimidyl esters (e.g., 3,3′-dithiobis(succinimidylpropionate), bifunctional maleimides (e.g., bis-N-maleimido-1,8-octane) and agents such as methyl-3-((p-azidophenyl)dithio)propioimidate, and 1-ethyl-3-(-3-dimethylaminopropyl)carbodiimide hydrochloride.
Other modifications include deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues, respectively, hydroxylation of P and L, phosphorylation of hydroxyl groups of S or T residues, methylation of the amino groups of L, R, and H side chains (see, e.g., T. E. Creighton, Proteins: Structure and Molecular Properties, W.H. Freeman & Co., San Francisco, pp. 79-86 (1983)), acetylation of the N-terminal amine, and/or amidation of any C-terminal carboxyl group. In addition, modifications such as derivitization with polyethylene glycols (and other glycols) to increase the in vivo stability half-life are also included.
Compositions.
Generally, e/m Env can be formulated into pharmaceutically useful compositions, whereby therapeutically effective amounts of e/m Env are combined in admixture with a pharmaceutically acceptable carrier. Salts and/or pro-drugs of e/m Env can also be used.
A pharmaceutically acceptable salt includes any salt that retains the activity of the e/m Env and is acceptable for pharmaceutical use. A pharmaceutically acceptable salt also refers to any salt which may form in vivo as a result of administration of an acid, another salt, or a prodrug which is converted into an acid or salt.
Suitable pharmaceutically acceptable acid addition salts can be prepared from an inorganic acid or an organic acid. Examples of such inorganic acids are hydrochloric, hydrobromic, hydroiodic, nitric, carbonic, sulfuric and phosphoric acid. Appropriate organic acids can be selected from aliphatic, cycloaliphatic, aromatic, arylaliphatic, heterocyclic, carboxylic and sulfonic classes of organic acids.
Suitable pharmaceutically acceptable base addition salts include metallic salts made from aluminum, calcium, lithium, magnesium, potassium, sodium and zinc or organic salts made from N,N′-dibenzylethylene-diamine, chloroprocaine, choline, diethanolamine, ethylenediamine, N-methylglucamine, lysine, arginine and procaine.
A prodrug includes an active ingredient which is converted to a therapeutically active compound after administration, such as by cleavage of a e/m Env or by hydrolysis of a biologically labile group.
In some embodiments, the compositions include e/m Env of at least 0.1% w/v of the composition; at least 1% w/v of composition; at least 10% w/v of composition; at least 20% w/v of composition; at least 30% w/v of composition; at least 40% w/v of composition; at least 50% w/v of composition; at least 60% w/v of composition; at least 70% w/v of composition; at least 80% w/v of composition; at least 90% w/v of composition; at least 95% w/v of composition; or at least 99% w/v of composition.
In other embodiments, e/m Env can be provided as part of a composition that can include, for example, at least 0.1% w/w of composition; at least 1% w/w of composition; at least 10% w/w of composition; at least 20% w/w of composition; at least 30% w/w of composition; at least 40% w/w of composition; at least 50% w/w of composition; at least 60% w/w of composition; at least 70% w/w of composition; at least 80% w/w of composition; at least 90% w/w of composition; at least 95% w/w of composition; or at least 99% w/w of composition.
Exemplary generally used pharmaceutically acceptable carriers include any and all absorption delaying agents, antioxidants, binders, buffering agents, bulking agents or fillers, chelating agents, coatings, disintegration agents, dispersion media, gels, isotonic agents, lubricants, preservatives, salts, solvents or co-solvents, stabilizers, surfactants, and/or delivery vehicles.
Exemplary antioxidants include ascorbic acid, methionine, and vitamin E.
Exemplary buffering agents include citrate buffers, succinate buffers, tartrate buffers, fumarate buffers, gluconate buffers, oxalate buffers, lactate buffers, acetate buffers, phosphate buffers, histidine buffers, and/or trimethylamine salts.
An exemplary chelating agent is EDTA.
Exemplary isotonic agents include polyhydric sugar alcohols including trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol, or mannitol.
Exemplary preservatives include phenol, benzyl alcohol, meta-cresol, methyl paraben, propyl paraben, octadecyldimethylbenzyl ammonium chloride, benzalkonium halides, hexamethonium chloride, alkyl parabens such as methyl or propyl paraben, catechol, resorcinol, cyclohexanol, and 3-pentanol.
Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which solubilizes the e/m Env or helps to prevent denaturation or adherence to the container wall. Typical stabilizers can include polyhydric sugar alcohols; amino acids, such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, and threonine; organic sugars or sugar alcohols, such as lactose, trehalose, stachyose, mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol, glycerol, and cyclitols, such as inositol; PEG; amino acid polymers; sulfur-containing reducing agents, such as urea, glutathione, thioctic acid, sodium thioglycolate, thioglycerol, alpha-monothioglycerol, and sodium thiosulfate; low molecular weight polypeptides (i.e., <10 residues); proteins such as human serum albumin, bovine serum albumin, gelatin or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; monosaccharides such as xylose, mannose, fructose and glucose; disaccharides such as lactose, maltose and sucrose; trisaccharides such as raffinose, and polysaccharides such as dextran. Stabilizers are typically present in the range of from 0.1 to 10,000 parts by weight based on e/m Env weight.
The compositions disclosed herein can be formulated for administration by, for example, injection, inhalation, infusion, perfusion, lavage, or ingestion. The compositions disclosed herein can further be formulated for intravenous, intradermal, intraarterial, intranodal, intralymphatic, intraperitoneal, intralesional, intraprostatic, intravaginal, intrarectal, topical, intrathecal, intratumoral, intramuscular, intravesicular, oral and/or subcutaneous administration and more particularly by intravenous, intradermal, intraarterial, intranodal, intralymphatic, intraperitoneal, intralesional, intraprostatic, intravaginal, intrarectal, intrathecal, intratumoral, intramuscular, intravesicular, and/or subcutaneous injection.
For injection, compositions can be formulated as aqueous solutions, such as in buffers including Hanks' solution, Ringer's solution, or physiological saline. The aqueous solutions can contain formulatory agents such as suspending, stabilizing, and/or dispersing agents. Alternatively, the formulation can be in lyophilized and/or powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
For oral administration, the compositions can be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like. For oral solid formulations such as powders, capsules and tablets, suitable excipients include binders (gum tragacanth, acacia, cornstarch, gelatin), fillers such as sugars, e.g. lactose, sucrose, mannitol and sorbitol; dicalcium phosphate, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate; cellulose preparations such as maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxy-methylcellulose, and/or polyvinylpyrrolidone (PVP); granulating agents; and binding agents. If desired, disintegrating agents can be added, such as corn starch, potato starch, alginic acid, cross-linked polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. If desired, solid dosage forms can be sugar-coated or enteric-coated using standard techniques. Flavoring agents, such as peppermint, oil of wintergreen, cherry flavoring, orange flavoring, etc. can also be used.
Compositions can be formulated as an aerosol. In one embodiment, the aerosol is provided as part of an anhydrous, liquid or dry powder inhaler. Aerosol sprays from pressurized packs or nebulizers can also be used with a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol, a dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of gelatin for use in an inhaler or insufflator may also be formulated containing a powder mix of e/m Env and a suitable powder base such as lactose or starch.
Compositions can also be formulated as depot preparations. Depot preparations can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as sparingly soluble salts.
Additionally, compositions can be formulated as sustained-release systems utilizing semipermeable matrices of solid polymers containing at least one e/m Env.
Various sustained-release materials have been established and are well known by those of ordinary skill in the art. Sustained-release systems may, depending on their chemical nature, release e/m Env following administration for a few weeks up to over 100 days. Depot preparations can be administered by injection; parenteral injection; instillation; or implantation into soft tissues, a body cavity, or occasionally into a blood vessel with injection through fine needles.
Depot formulations can include a variety of bioerodible polymers including poly(lactide), poly(glycolide), poly(caprolactone) and poly(lactide)-co(glycolide) (PLG) of desirable lactide:glycolide ratios, average molecular weights, polydispersities, and terminal group chemistries. Blending different polymer types in different ratios using various grades can result in characteristics that borrow from each of the contributing polymers.
The use of different solvents (for example, dichloromethane, chloroform, ethyl acetate, triacetin, N-methyl pyrrolidone, tetrahydrofuran, phenol, or combinations thereof) can alter microparticle size and structure in order to modulate release characteristics. Other useful solvents include water, ethanol, dimethyl sulfoxide (DMSO), N-methyl-2-pyrrolidone (NMP), acetone, methanol, isopropyl alcohol (IPA), ethyl benzoate, and benzyl benzoate.
Exemplary release modifiers can include surfactants, detergents, internal phase viscosity enhancers, complexing agents, surface active molecules, co-solvents, chelators, stabilizers, derivatives of cellulose, (hydroxypropyl)methyl cellulose (HPMC), HPMC acetate, cellulose acetate, pluronics (e.g., F68/F127), polysorbates, Span® (Croda Americas, Wilmington, Del.), poly(vinyl alcohol) (PVA), Brij® (Croda Americas, Wilmington, Del.), sucrose acetate isobutyrate (SAIB), salts, and buffers.
Excipients that partition into the external phase boundary of microparticles such as surfactants including polysorbates, dioctylsulfosuccinates, poloxamers, PVA, can also alter properties including particle stability and erosion rates, hydration and channel structure, interfacial transport, and kinetics in a favorable manner.
Additional processing of the disclosed sustained release depot formulations can utilize stabilizing excipients including mannitol, sucrose, trehalose, and glycine with other components such as polysorbates, PVAs, and dioctylsulfosuccinates in buffers such as Tris, citrate, or histidine. A freeze-dry cycle can also be used to produce very low moisture powders that reconstitute to similar size and performance characteristics of the original suspension.
Any composition disclosed herein can advantageously include any other pharmaceutically acceptable carriers which include those that do not produce significantly adverse, allergic, or other untoward reactions that outweigh the benefit of administration. Exemplary pharmaceutically acceptable carriers and formulations are disclosed in Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990. Moreover, formulations can be prepared to meet sterility, pyrogenicity, general safety, and purity standards as required by U.S. FDA Office of Biological Standards and/or other relevant foreign regulatory agencies.
Kits.
Also disclosed herein are kits including one or more containers including one or more of the e/m Env and/or compositions described herein. Associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use, or sale for human administration.
Optionally, the kits described herein further include instructions for using the kit in the methods disclosed herein. In various embodiments, the kit may include instructions regarding preparation of the e/m Env and/or compositions for administration; administration of the e/m Env and/or compositions; appropriate reference levels to interpret results associated with using the kit; proper disposal of the related waste; and the like. The instructions can be in the form of printed instructions provided within the kit or the instructions can be printed on a portion of the kit itself. Instructions may be in the form of a sheet, pamphlet, brochure, CD-Rom, or computer-readable device, or can provide directions to instructions at a remote location, such as a website. In various embodiments, possible side effects and contraindications to further use of components of the kit based on a subject's symptoms can be included.
Methods of Use.
Once formed, the compositions find use in a number of applications. In particular embodiments, the compositions find use in the treatment of disease. “Treatment” refers to both therapeutic treatment and prophylactic treatment or preventative measures, wherein the object is to prevent, reduce the occurrence or severity of, or slow down or lessen a targeted pathologic condition or disorder. “Subjects” include those in need of treatment, such as, those with an infection, as well as those prone to have or develop an infection, or those in whom infection is to be prevented, such as those in a high risk group for exposure to a pathogen.
Thus, in various exemplary embodiments, a subject can be a human subject. Other types of subjects include veterinary animals (dogs, cats, reptiles, birds, etc. and also including animals found within zoos), livestock (horses, cattle, goats, pigs, chickens, etc.), and research animals (monkeys, rats, mice, fish, etc.).
The compositions can be administered prophylactically in subjects who are at risk of developing HIV infection, or who have been exposed to HIV, to prevent, reduce, or delay the development of HIV infection or disease. For example, the compositions can be administered to a subject likely to have been exposed to HIV or to a subject who is at high risk for exposure to HIV.
In particular embodiments, compositions can be administered to a subject in a therapeutically effective amount. A “therapeutically effective amount” is an amount sufficient to produce a desired physiological effect and/or an amount capable of achieving a desired result, particularly for treatment of a disorder or disease condition, including reducing or eliminating one or more symptom of the disorder or disease or prevention or delaying the onset of at least one a disease symptom. Therapeutically effective amounts can provide therapeutic treatments and/or prophylactic treatments.
Particular uses of the compositions include use as prophylactic vaccines. Vaccines increase the immunity of a subject against a particular disease. Therefore, “HIV vaccine” can refer to a treatment that increases the immunity of a subject against HIV. Therefore, in some embodiments, a vaccine may be administered prophylactically, for example to a subject that is immunologically naive (e.g., no prior exposure or experience with HIV). In some embodiments, a vaccine may be administered therapeutically to a subject who has been exposed to HIV. Thus, a vaccine can be used to ameliorate a symptom associated with AIDS or HIV infection, such as a reduced T cell count.
In particular embodiments, an HIV vaccine is a therapeutically effective composition comprising one or more e/m Env disclosed herein that induce an immune response in a subject against HIV. The skilled artisan will appreciate that the immune system generally is capable of producing an innate immune response and an adaptive immune response. An innate immune response generally can be characterized as not being substantially antigen specific and/or not generating immune memory. An adaptive immune response can be characterized as being substantially antigen specific, maturing over time (e.g., increasing affinity and/or avidity for antigen), and in general can produce immunologic memory. Even though these and other functional distinctions between innate and adaptive immunity can be discerned, the skilled artisan will appreciate that the innate and adaptive immune systems can be integrated and therefore can act in concert.
“Immune response” refers to a response of the immune system to an e/m Env disclosed herein. In various exemplary embodiments, an immune response to an e/m Env can be an innate and/or adaptive response. In some embodiments, an adaptive immune response can be a “primary immune response” which refers to an immune response occurring on the first exposure of a “naive” subject to an e/m Env. For example, in the case of a primary antibody response, after a lag or latent period of from approximately 3 to 14 days depending on, for example, the composition, dose, and subject, antibodies to the e/m Env can be produced. Generally, IgM production lasts for several days followed by IgG production and the IgM response can decrease. Antibody production can terminate after several weeks but memory cells can be produced. In some embodiments, an adaptive immune response can be a “secondary immune response”, “anamnestic response,” or “booster response” which refer to the immune response occurring on a second and subsequent exposure of a subject to an e/m Env disclosed herein. Generally, in a secondary immune response, memory cells respond to the e/m Env and therefore the secondary immune response can differ from a primary immune response qualitatively and/or quantitatively. For example, in comparison to a primary antibody response, the lag period of a secondary antibody response can be shorter, the peak antibody titer can be higher, higher affinity antibody can be produced, and/or antibody can persist for a greater period of time.
Thus, in particular embodiments, an immune response against HIV will include antibody production against the gp120 domain of an e/m Env.
“Antibodies” refer to polyclonal or monoclonal antibodies that can be induced by an e/m Env according to the methods disclosed herein. In some embodiments, an antibody can bind to a gp120 domain of an e/m Env. In some embodiments, an antibody prevents AIDS and/or ameliorates a symptom of AIDS or HIV infection in a subject. Thus, in some embodiments, an antibody can bind to gp120 (i.e., an etiologic agent of HIV). Without being bound by theory, in some embodiments, the binding of an antibody can substantially neutralize or inactivate HIV gp120. Thus, antibodies are capable of reducing or eliminating a pathologic effect of HIV. That is, the binding of antibodies to gp120 of HIV may decrease or eliminate HIV infectivity and/or virulence factor activity, including replication, synthesis, and/or toxicity. In particular embodiments, at least a 25% decrease of one of these parameters is required to determine that a dose provides a therapeutically effective amount.
The actual dose amount administered to a particular subject can be determined by a physician, veterinarian, or researcher taking into account parameters such as physical and physiological factors including target, body weight, severity of infection, stage of infection, previous or concurrent therapeutic interventions, idiopathy of the subject, and route of administration.
For administration, therapeutically effective amounts (also referred to herein as doses) can be initially estimated based on results from in vitro assays and/or animal model studies. Exemplary doses include 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240 or 250 μg/kg body mass or mg/kg body mass although higher and/or lower doses can be used. The number of doses that can be administered as a function of time can be from 1, 2, 3, 4 or 5 doses over 1, 2, 3, 4, 5 or 6 weeks but can be increased or decreased depending at least in part on the immune status of a subject.
In particular embodiments, a composition can be administered initially, and thereafter maintained by further administration. For example, a composition can be administered by intravenous injection to bring blood levels to a suitable level. The subject's levels are then maintained by an oral dosage form, although other forms of administration, dependent upon the patient's condition, may be used. In the instance of a vaccine composition, the vaccine may be administered as a single dose, or the vaccine may incorporate set booster doses. For example, booster doses may include variants in order to provide protection against multiple clades of HIV.
The e/m Env can be prepared by expressing polynucleotide sequences in vectors or other expression vehicles in compatible prokaryotic or eukaryotic host cells using standard molecular biology methods (e.g., Sambrook et al. 1989, Molecular Cloning a Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; incorporated herein by reference).
A “polynucleotide sequence” is at least two nucleotides covalently linked together. A polynucleotide sequence will generally contain phosphodiester bonds, although in some cases, polynucleotide sequence analogs are included that may have alternate backbones, including, for example, phosphoramide, phosphorothioate, phosphorodithioate, O-methylphophoroamidite linkages, and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones; and non-ribose backbones. Polynucleotide sequences containing one or more carbocyclic sugars are also included within the definition of nucleic acids. These modifications of the ribose-phosphate backbone may be included to facilitate the addition of additional moieties such as labels, or to increase the stability and half-life of such molecules in physiological environments. Determining the type of nucleotides and their position within a polynucleotide sequence depends at least in part on the intended use of the polynucleotide sequence and is within the abilities of the skilled artisan.
The polynucleotide sequences may be single stranded or double stranded, as specified, or contain portions of both double stranded or single stranded sequences. The polynucleotide sequence may be DNA, both genomic and cDNA, RNA or a hybrid, where the nucleic acid contains any combination of deoxyribo- and ribo-nucleotides, and any combination of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xathanine hypoxathanine, isocytosine, isoguanine, etc.
In particular embodiments, a polynucleotide sequence can express a domain or an e/m Env disclosed herein. As such, polynucleotide sequences can include polynucleotide sequences encoding a polypeptide(s) of interest, operably linked to additional regulatory or accessory elements required or helpful for its expression and use. Generally, “operably linked” means that the nucleic acid sequences being linked are contiguous and arranged so that they function in concert for their intended purposes—for example, transcription initiates in the promoter and proceeds through the coding polynucleotide segment to the terminator. Where necessary to join two protein coding regions, the polynucleotide coding sequences should be contiguous and in reading frame.
Regulatory or accessory elements can include promoter and terminator sequences, enhancer sequences, polyadenylation signals, translational regulatory elements, including ribosomal binding sites. The transcriptional and translational regulatory or accessory elements employed are functional in the host cell used for expression, and may include those naturally associated with HIV genes. Therefore, in some embodiments a polynucleotide sequence can include sequences such as a promoter (e.g., inducible or constitutive), enhancer sequences (e.g., IE1 enhancer), introns sequences, transcriptional regulatory elements, and polyadenylation sequences (e.g., BGH polyadenylation sequence).
Promoters such as the trp, lac and phage promoters, tRNA promoters and glycolytic enzyme promoters may be used in prokaryotic hosts. Useful yeast promoters include the promoter regions for metallothionein, 3-phosphoglycerate kinase or other glycolytic enzymes such as enolase or glyceraldehyde-3-phosphate dehydrogenase, enzymes responsible for maltose and galactose utilization, and others. Appropriate non-native mammalian promoters may include the early and late promoters from SV40 or promoters derived from murine moloney leukaemia virus, mouse mammary tumour virus, avian sarcoma viruses, adenovirus II, bovine papilloma virus or polyoma. In particular embodiments, the expression vector comprises a CMV promoter.
Polynucleotide sequences encoding protein sequences disclosed herein can be derived by commercially and publicly-available databases.
In another aspect, the disclosure provides a vector comprising a polynucleotide sequence that encodes an e/m Env comprising a gp120 domain and a C4b multimerization domain.
In particular embodiments, the vector is selected from a DNA vector, a RNA vector, a viral vector, a bacterial vector, a plasmid vector, a cosmid vector, an artificial chromosome vector, such as a yeast artificial chromosome vector.
Viral vectors are usually non-replicating or replication-impaired vectors, which means that the viral vector cannot replicate to any significant extent in normal cells (e.g., normal human cells), as measured by conventional means (e.g. via measuring DNA synthesis and/or viral titer). Non-replicating or replication-impaired vectors may have become so naturally (i.e., they have been isolated as such from nature) or artificially (e.g., by breeding in vitro or by genetic manipulation). There will generally be at least one cell-type in which the replication-impaired viral vector can be grown—for example, modified vaccinia Ankara (MVA) can be grown in CEF cells. Typically, viral vectors are incapable of causing a significant infection in a subject, typically in a mammalian subject.
In particular embodiments, the vector is selected from an adenovirus or a poxvirus vector. Examples of viral vectors that are useful in this context include attenuated vaccinia virus vectors such as modified vaccinia Ankara (MVA) and NYVAC, or strains derived therefrom. Other examples of vectors include an avipox vector, such as a fowlpox vectors (e.g., FP9) or canarypox vectors (e.g., ALVAC and strains derived therefrom). Alternative viral vectors include adenoviral vectors (e.g., non-human adenovirus vectors), alphavirus vectors, flavivirus vectors, herpes viral vectors (e.g., herpes simplex, CMV and EBV), influenza virus vectors and retroviral vectors.
In particular embodiments, the vector is a human adenovirus. In another embodiment, the vector is a simian adenovirus. In another embodiment, the vector is a chimpanzee adenovirus. A chimpanzee as referred to herein may include Pan troglodytes (common chimpanzee) and Pan paniscus (Bonobo). In particular embodiments, the vector is selected from adenovirus 5 (Ad5), adenovirus 35 (Ad35), adenovirus 11 (Ad11), adenovirus 26 (Ad26), adenovirus 48 (Ad48) or adenovirus 50 (Ad50).
“Host cells”, and other such terms denoting microorganisms or higher eukaryotic cell lines cultured as unicellular entities refer to cells which can be, or have been, used as recipients for recombinant vector or other transfer DNA, and include the progeny of the original cell which has been transformed. It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental or deliberate mutation.
The most commonly used prokaryotic hosts are strains of E. coli, although other prokaryotes, such as B. subtilis or Pseudomonas may be used. Mammalian or other eukaryotic host cells, such as those of yeast, filamentous fungi, plant, insect, amphibian or avian species, may also be useful. Propagation of mammalian cells in culture is per se well known. Examples of commonly used mammalian host cell lines are VERO and HeLa cells, Chinese hamster ovary (CHO) cells, and W138, BHK, and COS cell lines, although other cell lines may be appropriate, e.g., to provide higher expression.
Expression and cloning vectors may contain a selectable marker, a gene encoding a protein necessary for the survival or growth of a host cell transformed with the vector. This gene ensures the growth of only those host cells which express the inserts. Conventional selection genes encode proteins that (i) confer resistance to antibiotics or other toxic substances, e.g., ampicillin, neomycin, methotrexate, etc.; (ii) complement auxotrophic deficiencies; or (iii) supply critical nutrients not available from complex media, e.g. the gene encoding D-alanine racemase for Bacilli. The choice of appropriate selectable marker will depend on the host cell.
The transformed host cell can be cultured in accordance with known methods, and the expressed polypeptide may be harvested i.e. recovered and isolated (eg. from the culture medium) using conventional protocols.
1. An engineered and multimerized (e/m) human immunodeficiency virus (HIV) envelope glycoprotein (Env) including SEQ ID NO: 50.
2. An e/m Env including an artificial human immunodeficiency virus (HIV) envelope glycoprotein selected from SEQ ID NOs: 52-121 and a heptamerization domain selected from SEQ ID NOs: 14-49 or 51.
3. An e/m Env including an artificial HIV envelope glycoprotein selected from SEQ ID NO: 52 and a heptamerization domain selected from SEQ ID NO: 14 or SEQ ID NOs: 46-49 or 51.
4. An e/m Env including an HIV envelope glycoprotein and a heptamerization domain.
5. An e/m Env of embodiment 4, wherein the heptamerization domain is selected from SEQ ID NOs: 14-49 or 51.
6. An e/m Env of embodiment 4 or 5, wherein the HIV envelope glycoprotein is an artificial gp120.
7. An e/m Env of any of embodiments 4-6, wherein the artificial gp120 is selected from SEQ ID NOs: 52-121.
8. An e/m Env of any one of embodiments 1-7, multimerized into a heptamer or a larger order multimer based on a heptamer.
9. A composition including a fusion protein of embodiment 8 or an e/m Env of any of embodiments 1-8.
10. A kit including an e/m Env of any one of embodiments 1-9.
11. A vector encoding an e/m Env of any one of embodiments 1-9.
12. A host cell including a vector of embodiment 11.
13. An e/m Env including: (i) mutations: N460D; N463D; S278R; G471S; V65C; and S115C; (ii) removal of the V1 loop and the V2 loop; (iii) replacement of the V3 loop with a flexible linker; (iv) an N-terminal truncation; and (v) a heptamerization domain; wherein the e/m Env does not include a mutation at position 276.
14. An e/m Env of embodiment 13 wherein the N-terminal truncation is before residue 49, 48, 47, 46, 45, 44, 43, 42, 41, 40 or 39.
15. An e/m Env of embodiment 13 wherein the N-terminal truncation is before residue 44.
16. An e/m Env of any one of embodiments 13-15 further including a C-terminal truncation after residue 499, 498, 497, 496, 495, 494, 493, 492, 491, 490 or 389.
17. An e/m Env of any one of embodiments 13-15 wherein the C-terminal truncation is after residue 494.
18. An e/m Env of any one of embodiments 13-17 wherein the flexible linker is selected from SEQ ID NOs: 3-13, or 126.
19. An e/m Env of any one of embodiments 13-18 wherein the V3 loop includes 296-331.
20. An e/m Env of any one of embodiments 13-19 wherein the heptamerization domain is selected from SEQ ID NOs: 14-49 or 51.
21. An e/m Env of any one of embodiments 13-20 wherein removal of the V1 loop includes removal of 131-152 and/or removal of the V2 loop includes removal of 161-196.
22. An e/m Env of any one of embodiments 13-20 wherein removal of the V1 loop and removal of the V2 loop includes removal of 123-196.
23. An e/m Env of any one of embodiments 13-22, multimerized into a heptamer or a larger order multimer based on a heptamer.
24. A composition including a fusion protein of embodiment 23 or an e/m Env of any of embodiments 13-23.
25. A kit including an e/m Env of any of embodiments 13-23.
26. A vector including an e/m Env of any of embodiments 13-23.
27. A host cell including a vector of embodiment 26.
DG75 B cells that were transduced to stably express the gl-reverted (gl)VRC01, 12A21, and NIH45-46 B cell receptors (as indicated), were loaded with the Calcium binding indicator dye Fluo-4. B cells were then challenged with the indicated 426c.TM4ΔV1-3 gp140 trimer (
75 ug of the 426c.TM4ΔV1-3 gp120 monomer (
METHODS. Cell lines. Recombinant HIV-1 Envelope and antibodies were expressed in Freestyle 293F cells (Life technologies) that were not tested for mycoplasma contamination.
Antibody production. Expression plasmids for the gl forms of VRC01, NIH45-46, 3BNC60 and 12A21 were previously described. Hoot, et al., Recombinant HIV envelope proteins fail to engage gl versions of anti-CD4bs bNAbs. PLoS pathogens 9, e1003106 (2013); Scheid, et al., Science 333, 1633-1637 (2011). This method was used to design plasmids expressing the gl forms of VRC-PG19, VRC-PG20, VRC-PG04 and VRC-CH31 based on the published sequences. Jardine, et al., Science 340, 711-716 (2013).
Plasmids expressing the Fab forms of these antibodies were produced by inserting a 6-His tag followed by a stop codon directly after the C1 region of the heavy chain expression plasmids (forward Fab mutagenesis primer, 5′-caaatcttgtgacaaaactcaccatcaccatcaccattgacagcacctgaactcctggggggac-3′ (SEQ ID NO: 125)).
sIgGs were produced by co-transfecting the appropriate heavy and light chain plasmids at a 1:1 ratio into Freestyle 293F cells at a density of 106 cells/ml in Freestyle 293 media (Life Technologies) using the 293Free transfection reagent (EMD Millipore). Antibody expression was carried out in Freestyle 293 media for 6 days with gentle shaking at 37° C. in the presence of 5% CO2 after which cells and cellular debris were removed by centrifugation at 10,000×g followed by filtration through a 0.2 μM filter. Supernatants were then applied to Pierce Protein A Agarose (Thermo Scientific) followed by washing with PBS. Antibodies were eluted in 1 ml fractions with Pierce IgG Elution Buffer pH 2.0 (Thermo Scientific) into 1.5 ml centrifuge tubes containing 0.1 ml of 1M Tris-HCl pH 8.0. Fractions containing protein were pooled and exchanged into PBS using Zebra spin desalting columns (Thermo Scientific).
Fab fragments were produced in a similar manner. Following filtration the clarified supernatant was then passed over Ni-NTA resin (Qiagen, Valencia, Calif.), pre-equilbrated with Ni-NTA binding buffer, followed by extensive washing with Ni-NTA binding buffer supplemented with 10 mM imidazole, and then eluted with 250 mM imidazole, 0.3 M NaCl, 20 mM Tris, pH 8.0. Ni-NTA FAb fragments were further purified by size exclusion chromatography (SEC) using a 10/300 S200 column (GE healthcare) equilibrated in PBS.
Recombinant Envelopes. All constructs are based on the clade C 426c gp140 (GenBank: KC79518.1) (McGuire, et al., J. Exp. Med. 210, 655-663 (2013)) or the 426c.NLGS.TMΔV1-3 (herein called 426c.TM1ΔV1-3) expressed from the pTT3 vector with or without a C-terminal Avi-Tag (McGuire, et al., Science 346, 1380-1383 (2014)) unless otherwise noted. Amino acid substitutions (summarized in
gp160 plasmids encoding 426c. N276D. N460D. N463D, 426c. 5276A.T462A.T465A, 426c. S278R. N460D. N463D, Q168a2. N462D. N465D, Q461e2. N276D. N463D, Bal. N276D. N463D, 823c. N276D. N463D, and 706c.N276D.N463D were generated by introducing mutations into the parental gp160 plasmids (Genbank numbers, KC79518.1, AF407148.1, AF407156.1, DQ318210.1, KC769511.1, and KC769513.1, respectively) using Agilent's QuikChange Primer Design Program and synthesized by Integrated DNA Technologies (IDT, Coralville, Iowa). All mutations were confirmed by Sanger sequencing.
cDNA for 426cTM4ΔV1-3 amino acids 44-494 (HXB2 numbering) followed by a GSGGGGSG (SEQ ID NO: 126) and the previously described helicobacter pylori bullfrog ferritin (Kanekiyo, et al., Cell 162, 1090-1100 (2015) was codon optimized for human, synthesized by IDT technologies, and cloned into the pTT3 expression vector to create pTT3-426cTM4ΔV1-3-Ferritin.
cDNA for 426cTM4ΔV1-3 amino acids 44-494 was PCR amplified from pTT3-426cTM4ΔV1-3-Ferritin and subcloned into the pCVL-UCOE0.7-SFFV-C4b-IRES-GFP parental vector encoding the C4b heptamerization motif of SEQ ID NO: 46 (Genbank: 416733). The resulting e/m Env contains SEQ ID NO: 5 as a linker, derived from the NotI cloning site combined with sequence from the previously crystallized construct (Hofmeyer, et al., J. of Mol. Biol. 425, 1302-1317 (2013), as well as a C-terminal thrombin-6×His tag.
His-tagged 426c gp120 was engineered by disrupting the 426c furin cleavage site (RNKR→RNKG) followed immediately by the addition of a 7×-polyhisitidine tag and stop codon (forward gp120-His mutagenesis primer, 5′-ggaacaagggcgctcatcatcaccaccatcaccattgataggtggggatcggagc-3′ (SEQ ID NO: 127)).
Recombinant Env-expression and purification. Plasmids encoding His-tagged Env proteins were transfected into 293F cells at a density of 106 cells/ml in Freestyle 293 media (Life Technologies) using the 293Free transfection reagent (EMD Millipore) according to the manufacturer's instructions. Expression was carried out in Freestyle 293 media for 6 days with gentle shaking at 37° C. in the presence of 5% CO2 after which cells and cellular debris were removed by centrifugation at 10,000×g followed by filtration through a 0.2 μM filter. Clarified cell supernatant was passed over Ni-NTA resin (Qiagen), pre-equilbrated with Ni-NTA binding buffer (containing 5 mM imidizole), followed by extensive washing with Ni-NTA binding buffer (supplemented with 10 mM imidazole), and then eluted with 250 mM imidazole, 0.3 M NaCl, 20 mM Tris, pH 8.0. Purified gp120 proteins were then buffer exchanged into PBS using Zebra desalting columns (Thermo Scientific). Soluble trimeric gp140 Envs were expressed in 293F cells and purified as previously described. McGuire, et al., J. Exp. Med. 210, 655-663 (2013).
AVI-tagged Env variants were biotinylated in vitro using the In Vitro Biotin Ligase Kit (Avidity) according to the manufacturer's instructions, followed by SEC using a 10/300 S 200 column (GE healthcare) equilibrated in PBS to remove un-ligated biotin and BirA enzyme.
Multimerized Env. Dextramers were formed as follows. Purified biotinylated-avi tagged 426cTM4ΔV1-3 gp120 or gp140 was mixed with a biotinylated dextran (Life Technologies, Cat # D-7142) at a 3:1 ratio (Env:biotin), with the assumption that the modified dextran had 77 biotins molecules/multimer (lot dependent value). Streptavidin (New England Biolabs Cat# N7021S) was then added to achieve a 3:1:1 Env to streptavidin to biotin ratio.
pTT3-426cTM4ΔV1-3-ferritin was transfected into 293E cells at a density of 106 cells/ml in Freestyle 293 media (Life Technologies) using the 293Free transfection reagent (EMD Millipore) and half the amount of DNA recommended by the manufacturer. Expression was carried out in 293Freestyle media for 6 days with gentle shaking at 37° C. in the presence of 5% CO2 after which cells and cellular debris were removed by centrifugation at 10, 000×g followed by filtration through a 0.2 μM filter. Clarified supernatant was passed over a GNL agarose column (Vector laboratories) pre-equilibrated in GNL binding buffer (20 mM Tris, 100 mM NaCl, 1 mM EDTA, pH 7.4) followed by extensive washing and then eluted with GNL binding buffer containing 1M methylmannopyranoside. Ferritin nano-particles were further purified by SEC using a 16/60 S200 column (GE healthcare) equilibrated in PBS, followed by a second final SEC purification step on a 10/300 superose 6 column equilibrated in PBS (GE healthcare).
426cTM4ΔV1-3-C4b was expressed in 293 Freestyle cells (Invitrogen) using the Daedalus system. Briefly, recombinant lentivirus was produced by transient co-transfection of 293T using 25-kDa PEI with pCVL-UCOE0.7-SFFV-426cTM4ΔV1-3-C4b-IRES-GFP, and psPAX2 (Addgene#12260) and pMD2.G (Addgene#12259) packaging vectors. Transduction was carried out in 150 mL flasks containing 1×107 cells in 10 mL of expression media, then cultures were expanded to a 4 L terminal culture volume. Conditioned medium was harvested by centrifugation and recombinant protein was purified using Ni-NTA.
Biolayer Interferometry (BLI). BLI assays were performed on the Octet QKe or the Octet Red instrument (ForteBio, Inc, Menlo Park, Calif.) at 30° C. with shaking at 1,000 RPM. All measurements of Env-Ab binding were corrected by subtracting the signal obtained from simultaneous traces performed with the corresponding envelopes in the absence of antibody, using PBS only. Experiments to detect glAb-binding to Env were performed as follows: Initial screening for Ab-binding was determined by immobilizing His-tagged gp120 onto Ni-NTA biosensors (Fortebio) for 300 seconds, sensors were then incubated with BSA (1 mg/ml in PBS) for 1 minute, and the baseline signal (nm shift) was recorded for 1 minute in kinetics buffer (KB: 1×PBS, 0.01% BSA, 0.02% Tween 20, and 0.005% NaN3). Sensors were then immersed into solutions of antibody (20 ug/ml in PBS) for 300 seconds, followed by immersion in KB for 300 seconds.
Kinetic analysis with FAbs was performed as follows: gp140s were biotinylated using EZ-Link NHS-PEG4-Biotin (Thermo Scientific) at a ratio of one biotin molecule/gp140 trimer (0.33 biotin molecules/monomer). Unligated biotin was removed using Zebra desalting columns (Thermo Scientific) according to the manufacturer's instructions. Biotinylated trimeric recombinant gp140s were immobilized on streptavidin biosensors (Forte Bio) at concentrations that yielded the same Rmax for all Envs tested (1-2 μM). The baseline signal was recorded for 1 min in KB, then the sensors were immersed into wells containing dilutions of purified recombinant FAbs (1-32 μM) for 4 min (association phase). Sensors were then immersed in kinetic buffer (KB) without Env for an additional 8 min (dissociation phase). Curve fitting was performed using a 1:1 binding model and the Data analysis software (Fortebio). Mean kon and koff and apparent KD values were determined by averaging all binding curves that matched the theoretical fit with an R2 value of >0.95.
Generation and characterization of gl3BNC60 knock-in mice. HC-Knock-in mice were generated as previously described. Dosenovic, et al., Cell 161, 1505-1515 (2015); Pelanda, et al., Immunity 7, 765-775 (1997); Shih, et al., Nat. Immunol. 3, 399-406 (2002). LC knock-in mice were generated in a similar way using the VJL sequence of the predicted gl version of human 3BNC60. Hoot, et al., Recombinant HIV envelope proteins fail to engage gl versions of anti-CD4bs bNAbs. PLoS pathogens 9, e1003106 (2013). A targeting vector with homologous regions flanking the J segments of the endogenous mouse kappa locus was generated. Homologous recombination results in deletion of endogenous J segments; which minimizes rearrangement of the WT locus. The HC and LC knock-in mice were generated independently and bred to homozygosity. They were then crossed with each other to generate double heterozygous and eventually double homozygous mice. Knock-in HC and LC genotype were verified by PCR using specific primers for the 3BNC60 gl HC or LC sequences as well as primers specific for the WT untargeted loci of IgH and IgK. Naive B cell development of the newly generated KI mice were characterized by flow cytometry. A single cell suspension of BM was stained to identify immature (IgM−/low, IgD−), and mature (IgM+/int, IgD+) B cell populations. Single cell suspensions of splenocytes were stained to identify marginal zone B cells (CD23-CD21+) and follicular B cells (CD23+, CD21lo/−) and to determine kappa and lambda usage of total B cells. The following antibodies were used; anti-mouse CD4 PE-CF594, anti-mouse CD8 PE-CF594, anti-mouse Ly-6G and Ly-6C PE-CF594 and anti-mouse Ig kappa BV421 (BD biosciences), anti-Hu/Mo B220 APC-eFlour 780, anti-mouse CD19 Pe-Cy7, anti-mouse IgM PerCP-eFluor 710, anti-mouse CD21/CD35 eFluor 450 (eBiosciences). Anti-mouse Ig lambda PE, and anti-mouse IgD Pacific Blue, anti-mouse CD23 PE (BioLegend). Live dead aqua stain was used to separate dead cells (Life Technologies).
B cell-sorting. Memory B cells of immunized knock-in mice were single cell sorted as previously described. Dosenovic, et al., Cell 161, 1505-1515 (2015). In brief, splenocytes were stained with anti-mouse CD4 PE-CF594, anti-mouse CD8 PE-CF594, anti-mouse Ly-6G and Ly-6C (Gr1) PE-CF594, anti-mouse IgG1 BV421 (BD biosciences), anti-Hu/Mo B220 FITC, anti-mouse CD38 A700, anti-mouse IgM PerCP-eFluor 710 (eBiosciences) and PE-Streptavidin conjugated 426c.TM4ΔV1-3 gp140-biotin and APC-Streptavidin conjugated 426c.TM4ΔV1-3. D368R.E370A-biotin (426c.TM4ΔV1-3 gp140-KO). Live dead aqua stain was used to separate dead cells (Life Technologies). The sorted cells were live cells, CD4−, CD8−, Gr-1−, B220+, CD38+, IgM−, IgG1+, 426c.TM4ΔV1-3 gp140+, 426c.TM4ΔV1-3 gp140-KO−. The VDJ knock-in sequence was amplified by nested PCR using the following primer pairs; 1_3BNC60_F_HK GGGATGGTCATGTATCATCCTTTTTCTAG (SEQ ID NO: 128) with 1mRG AGAAGGTGTGCACACCGCTGGAC (SEQ ID NO: 129) and 2_3BNC60_F_HK GTAGCAACTGCAACCGGTGTACATTCT (SEQ ID NO: 130) with 2mRG GCTCAGGGAARTAGCCCTTGAC (SEQ ID NO: 131). The VJ knock-in sequence was amplified by nested PCR using the following primer pairs; SEQ ID NO: 128 with 1mRK ACTGAGGCACCTCCAGATGTT (SEQ ID NO: 132) and SEQ ID NO: 130 with 2mRK TGGGAAGATGGATACAGTT (SEQ ID NO: 133).
Immunizations. 6-8 weeks old female or male WT and gl3BNC60 knock-in mice were immunized with 10 μg of rEnv. 3-5 mice/group were used in each experiment. Immunizations of 426c gp140, gp120-dextramer and gp140-dextramer were performed with Imject Alum (Thermo Scientific). Immunizations with gp120-dextramer were also performed with Ribi (Sigma). Immunizations with gp120 were performed with Ribi. Serum was collected for analysis at two weeks after immunization. No randomization or blinding of the experiments were performed. All experiments were performed according to the protocols approved by the IACUC at Rockefeller University. In the case of immunizations with dextrameric Env, the dextrameric complexes were formed for 10-15 min before the addition of Alum or Ribi. All experiments were performed according to the protocols approved by the IACUC at Rockefeller University.
Serum ELISA. High binding 96-well plates (Corning Incorporated) were coated with 200 ng/well of 426c.TM4 ΔV1-3 and 426c.TM4 ΔV1-3 CD4-BS KO (Corning Incorporated) with 200 ng/well of protein. After incubation overnight (ON) at 4° C., plates were washed in wash buffer (3× in PBS with 0.05% TWEEN 20 (Sigma)) and blocked in blocking buffer (PBS with 2% milk). Serum samples were added to coated wells at the indicated dilutions and incubated for 1 hr at 37° C. Plates were washed and secondary antibody, HRP conjugated anti-mouse (Jackson Immuno Research), was added and incubated for 30 minutes at 37° C. Plates were washed again and then developed by adding ABTS solution (Life Technologies) and the absorbance was measured at 405 nm using a FLUOstar Omega microplate reader (BMG Labtech) which gives a maximum reading of 4.0.
Neutralization Assay. Serum IgG were tested against a panel of HIV-1 pseudoviruses using the TZM-bl neutralization assay as previously described. Li, et al., J. of Virol. 79, 10108-10125 (2005).
Capture ELISA: Plasmids expressing 426c. N276D. N460D. N463D, Q168a2. N462D. N465D, Q461e2. N276D. N463D, Bal. N276D. N463D, 823c. N276D.N463D, and 706c.N276D.N463D gp160 proteins were transfected into 293 cells using GeneJuice (Merck Millipore) according to the manufacturer's instructions. 72 h later, the cells were lysed with PBS containing 1% Triton X-100. Cell lysates were clarified by centrifugation, passed through a 0.2 μM filter, and then incubated in triplicate on ELISA plates coated with the anti-C-terminal D7324 anti-gp120 sheep antibody (Aalto Bioreagents). ELISA was performed with mature and gl NIH45-46 and VRC01 as previously described. Hoot, et al., Recombinant HIV envelope proteins fail to engage gl versions of anti-CD4bs bNAbs. PLoS pathogens 9, e1003106 (2013).
The disruption of the NLGS at position 276 (N276D) from the clade C recombinant Env 426c, results in glVRC01 and glNIH45-46 antibody-binding. McGuire, et al., J. Exp. Med. 210, 655-663 (2013). The parallel disruption of two NLGS in V5 (positions 460 and 463) improves this binding; although by themselves N460D and N463D are insufficient to confer glVRC01- or glNIH-45-46-binding. McGuire, et al., J. Exp. Med. 210, 655-663 (2013). The 426c Env lacking these three NLGS is referred to as a “triple mutant 1” (TM1) or “426c.NLGS.TM1Δ1-3” as compared to 426c.NLGS.TM4Δ1-3. The disruption of the 276 and V5 NLGS from other Envs does not result in glVRC01-binding (
The reasons for the differential recognition of TM1 by the different glVRC01-class antibodies are not well understood. Information on this topic will help to better understand the features of Env that prevent the engagement of the various glVRC01-class BCRs in the context of HIV-1 infection and will facilitate the design of immunogens capable of activating a broader range of these receptors.
Although the VH domains of all known VRC01-class bNAbs are derived from the VH1-2*02 allele and a few J genes, their CDRH3 regions differ extensively in amino acid sequence and length. Zhou, et al., Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell (2015); Scheid, et al., Science 333, 1633-1637 (2011); Wu, et al., Science 333, 1593-1602 (2011); Wu, et al., Cell 161, 470-485 (2015); Georgiev, et al., Science 340, 751-756 (2013). Therefore, one possible explanation for the differential recognition of TM1 by different members of the glVRC01-class antibodies may be due to the different CDRH3 regions expressed by these antibodies. It is also possible that the above-mentioned differences in TM1 recognition by the various glVRC01-class antibodies is linked to the different light chains (LCs) used by these antibodies. Relevant to the latter possibility is the observation that when the gl heavy chains (glHCs) of 3BNC60 and gl12A21 are paired with the gl light chains (glLC) of VRC01/NIH45-46, the chimeric antibodies bind TM1. McGuire, et al., J. Exp. Med. 210, 655-663 (2013).
These results suggest that the glLCs of 12A21 and 3BNC60 (derived from VK1-33 while those of VRC01/NIH45-46 are derived from VK3-11) are incompatible with TM1-binding. The N to D substitutions used to generate TM1, were initially selected to maintain structural similarity at positions 276, 460 and 463. However, they introduce negative charges at those positions; which potentially create unfavorable electrostatic interactions with the more negatively-charged CDRLs on the glLCs of 12A21 and 3BNC60 (as compared to the CDRL regions of the VRC01/NIH45-46 glLC;
Alternatively, the NLGS at position 276 was disrupted by mutating S278. Interestingly, a S278A substitution (TM2) conferred gl12A21 binding, while it reduced binding of glNIH45-46, glVRC01, and glVRC-PG20, and improved binding of glVRC-PG19 compared to TM1 (although this Ab still had a relatively fast off rate) (
In addition to the S278R modification discussed above, Jardine et al., identified a combination of five additional amino acid mutations (L260F, K357R, I371F, N386D, and G471S) which on the background of the engineered outer domain of eOD-base (which also contains the N276D and the N463D modifications) resulted in eOD-GT6 that bound glVRC01, glNIH45-46, glVRC-PG19/20 and gl12A21, and to gl3BNC60, glVRC-CH31 and glVRC-PG04. Jardine, et al., Science 340, 711-716 (2013).
eOD-GT6 is derived from HxB2 which is a CXCR4-tropic tier 1 virus while TM1 is a CCR5-tropic tier 2 virus. Furthermore, TM1 includes the outer and inner domains of gp120, while eOD-GT6 is designed to recapitulate only the outer domain structure of Env. Therefore it was assessed whether these additional mutations would improve binding of glVRC01 class Abs on the background of TM1 as they did on eOD-GT6. On the TM1 background the combination of these six mutations abrogated the binding of all glVRC01-class antibodies tested (
The lengths and glycosylation patterns of variable regions 1, 2 and 3 of gp120 (V1, V2, V3 respectively) influence the accessibility of diverse mature anti-CD4-BS antibodies. Deletion of the V1, V2 and V3 from TM1 gp140 improves the activation of B cells expressing the glNIH45-46 BCR. McGuire, et al., Science 346, 1380-1383 (2014). To investigate whether these regions restrict binding to glVRC01 class antibodies on various modified 426c constructs, versions of TM1, TM4 and TM5 lacking V1, V2 and V3 (ΔV1-3) were engineered. gl3BNC60-binding to TM4ΔV1-3 and TM5ΔV1-3 (
Mice, rats, rabbits and NHPs do not express a human VH1-2*02 ortholog and thus are not suitable to evaluate immunogens designed to stimulate glBCRs of VRC01-class Abs. Jardine, et al., Science 340, 711-716 (2013); West, et al., PNAS 109, E2083-2090 (2012); Tran, et al., PNAS 111, E738-747 (2014). To study the activation of naïve B cells expressing the predicted gl version of a VRC01-class Ab in vivo, knock-in mice homozygous for the VH and VL of gl3BNC60 (gl3BNC60-KI) were engineered. Because gl3BNC60 has the lowest binding affinity for TM4ΔV1-3 among the glVRC01-class antibodies tested (
In contrast to WT mice, gl3BNC60 KI mice showed very few IgD+IgM+ B cells in the bone marrow (
WT or gl3BNC60 KI mice were immunized with the soluble gp140 trimeric form (gp140) of TM4ΔV1-3 Env (
The ability of antigens with low binding affinities (due to fast off rates) to activate B cells can be improved by increasing their valency. Batista & Neuberger, Immunity 8, 751-759 (1998). Multimerizing an antigen can also overcome poor B cell responses related to anergy in a manner that allows these B cells to receive T cell help and to produce somatically hypermutated BCRs and antibodies displaying no, or limited autoreactivity. Cooke, et al., The J. of Exp. Med. 179, 425-438 (1994); Sabouri, et al., PNAS, 111, E2567-2575 (2014). To that end, the following multimerization approaches were tested with the TM4ΔV1-3 construct: (a) a dextran-based antigen-multimerization approach that can lead to up to 70 Env molecules per dextran molecule. This approach was previously used to stimulate B cells in knock-in mice expressing the gl 3BNC60 HC only (gl3BNC60 HC) (Dosenovic, et al., Cell 161, 1505-1515 (2015)); (b) addition of the multimerization domain of the human C4b-binding protein to the carboxy terminus of Env (this approach leads to the formation of ring-like structures expressing seven Env molecules) (Hofmeyer, et al., J. of Mol. Biol. 425, 1302-1317 (2013)); and (c) a ferritin-based approach, which leads to the formation of particles with 24 copies of Env. Kanekiyo, et al., Cell 162, 1090-1100 (2015).
WT or gl3BNC60 KI mice were immunized with dextrameric gp140 (gp140-dex) (
The presence of anti-CD4-BS Abs in immune sera from WT and gl3BNC60 KI mice was inferred by comparing the antibody titers to the immunogen (filled circles) to those against CD4-BS KO (D368R and E370A) version of the immunogen (open circles,
In WT mice, 95% of naïve B cells in the spleen express λLCs and only 5% express λLCs (
Most of these HC and LC transcripts were unmutated, with 2 VH and 3 VL chains having 1-3 amino acid changes from gl, indicative of having undergone limited somatic hypermutation (
The disclosure supports the notion that immunogens rationally designed to overcome evolutionary-selected, steric blocks on HIV-1 Env that prevent its recognition by specific gl BCRs, lead to the activation of the corresponding glBCRs in vivo. Furthermore the described results corroborate the proposal that a major reason for the lack of elicitation of VRC01-like bNAbs by previous Env immunogens is the inability of such proteins to activate the appropriate naïve B cells upon immunization. Jardine, et al., Science 340, 711-716 (2013); McGuire, et al., J. Exp. Med. 210, 655-663 (2013). As such the disclosure further illuminates a path to overcome the earliest block in the elicitation of VRC01-class bNAbs by immunization.
As will be understood by one of ordinary skill in the art, each embodiment disclosed herein can comprise, consist essentially of or consist of its particular stated element, step, ingredient or component. Thus, the terms “include” or “including” should be interpreted to recite: “comprise, consist of, or consist essentially of.” The transition term “comprise” or “comprises” means includes, but is not limited to, and allows for the inclusion of unspecified elements, steps, ingredients, or components, even in major amounts. The transitional phrase “consisting of” excludes any element, step, ingredient or component not specified. The transition phrase “consisting essentially of” limits the scope of the embodiment to the specified elements, steps, ingredients or components and to those that do not materially affect the embodiment. A material effect would cause a statistically-significant reduction in an e/m Env's ability to induce an immune response (e.g., B-cell activation as measured by Ca2+ flux).
Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as molecular weight, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about.” Accordingly, unless indicated to the contrary, the numerical parameters set forth in the specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. When further clarity is required, the term “about” has the meaning reasonably ascribed to it by a person skilled in the art when used in conjunction with a stated numerical value or range, i.e. denoting somewhat more or somewhat less than the stated value or range, to within a range of ±20% of the stated value; ±19% of the stated value; ±18% of the stated value; ±17% of the stated value; ±16% of the stated value; ±15% of the stated value; ±14% of the stated value; ±13% of the stated value; ±12% of the stated value; ±11% of the stated value; ±10% of the stated value; ±9% of the stated value; ±8% of the stated value; ±7% of the stated value; ±6% of the stated value; ±5% of the stated value; ±4% of the stated value; ±3% of the stated value; ±2% of the stated value; or ±1% of the stated value.
Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard deviation found in their respective testing measurements.
The terms “a,” “an,” “the” and similar referents used in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. Recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention otherwise claimed. No language in the specification should be construed as indicating any non-claimed element essential to the practice of the invention.
Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member may be referred to and claimed individually or in any combination with other members of the group or other elements found herein. It is anticipated that one or more members of a group may be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.
Certain embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Of course, variations on these described embodiments will become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventor expects skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.
Furthermore, numerous references have been made to patents, printed publications, journal articles and other written text throughout this specification (referenced materials herein). Each of the referenced materials are individually incorporated herein by reference in their entirety for their referenced teaching.
In closing, it is to be understood that the embodiments of the invention disclosed herein are illustrative of the principles of the present invention. Other modifications that may be employed are within the scope of the invention. Thus, by way of example, but not of limitation, alternative configurations of the present invention may be utilized in accordance with the teachings herein. Accordingly, the present invention is not limited to that precisely as shown and described.
The particulars shown herein are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of various embodiments of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for the fundamental understanding of the invention, the description taken with the drawings and/or examples making apparent to those skilled in the art how the several forms of the invention may be embodied in practice.
Definitions and explanations used in the present disclosure are meant and intended to be controlling in any future construction unless clearly and unambiguously modified in the following examples or when application of the meaning renders any construction meaningless or essentially meaningless. In cases where the construction of the term would render it meaningless or essentially meaningless, the definition should be taken from Webster's Dictionary, 3rd Edition or a dictionary known to those of ordinary skill in the art, such as the Oxford Dictionary of Biochemistry and Molecular Biology (Ed.
Anthony Smith, Oxford University Press, Oxford, 2004).
This application is a U.S. national stage entry of International Application No. PCT/US2016/023985, filed Mar. 24, 2016, which application claims the benefit of U.S. Provisional Application No. 62/137,764 filed on Mar. 24, 2015 and U.S. Provisional Application No. 62/266,532 filed on Dec. 11, 2015, the entire contents of each of which are incorporated by reference herein.
This invention was made with government support under A1094419 and AI109632 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2016/023985 | 3/24/2016 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2016/154422 | 9/29/2016 | WO | A |
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| Number | Date | Country | |
|---|---|---|---|
| 20180117140 A1 | May 2018 | US |
| Number | Date | Country | |
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| 62266532 | Dec 2015 | US | |
| 62137764 | Mar 2015 | US |
