Sexually transmitted disease vaccines

Abstract

The disclosure relates to sexually transmitted disease ribonucleic acid vaccines and combination vaccines, as well as methods of using the vaccines and compositions comprising the vaccines.

What is claimed is: 
     
         1 . A sexually transmitted disease (STD) vaccine, comprising:
 at least one RNA polynucleotide having an open reading frame encoding at least one STD antigenic polypeptide, formulated in a cationic lipid nanoparticle.   
     
     
         2 . The STD vaccine of  claim 1 , wherein the antigenic polypeptide is selected from human papillomavirus (HPV), herpes simplex virus (HSV) and  Chlamydia trachomatis  antigenic polypeptides. 
     
     
         3 . A human papillomavirus (HPV) vaccine, comprising:
 at least one ribonucleic acid (RNA) polynucleotide having an open reading frame encoding at least one HPV antigenic polypeptide or an immunogenic fragment thereof.   
     
     
         4 . The vaccine of  claim 3 , wherein the at least one antigenic polypeptide is selected from HPV E1 protein, HPV E2 protein, HPV E4 protein, HPV E5 protein, HPV E6 protein, HPV E7 protein, HPV L1 protein, and HPV L2 protein, optionally wherein the HPV serotype is selected from HPV serotypes 6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68, 73 and 82. 
     
     
         5 . The vaccine of  claim 3  or  4 , wherein the vaccine comprises at least one RNA polynucleotide having an open reading frame encoding at least two antigenic polypeptides or immunogenic fragments thereof selected from HPV E1 protein, HPV E2 protein, HPV E4 protein, HPV E5 protein, HPV E6 protein, HPV E7 protein, HPV L1 protein, and HPV L2 protein. 
     
     
         6 . The vaccine of any one of  claims 3 - 5 , wherein the vaccine comprises at least two RNA polynucleotides, each having an open reading frame encoding at least one antigenic polypeptide or an immunogenic fragment thereof selected from HPV E1 protein, HPV E2 protein, HPV E4 protein, HPV E5 protein, HPV E6 protein, HPV E7 protein, HPV L1 protein, and HPV L2 protein, wherein the HPV antigenic polypeptide encoded by one of the open reading frames differs from the HPV antigenic polypeptide encoded by another of the open reading frames. 
     
     
         7 . The vaccine of any one of  claims 3 - 6 , wherein the at least one antigenic polypeptide comprises an amino acid sequence identified by any one of SEQ ID NO: 31-61. 
     
     
         8 . The vaccine of any one of  claims 3 - 7 , wherein the at least one RNA polypeptide is encoded by a nucleic acid sequence identified by any one of SEQ ID NO: 1-30, and/or wherein the at least one RNA polypeptide comprises a nucleic acid sequence identified by any one of SEQ ID NO: 431-461. 
     
     
         9 . The vaccine of any one of  claims 3 - 8 , wherein the at least one antigenic polypeptide has an amino acid sequence that has at least 95% identity to an amino acid sequence identified by any one of SEQ ID NO: 31-61. 
     
     
         10 . The vaccine of any one of  claims 3 - 9 , wherein the at least one antigenic polypeptide has an amino acid sequence that has 95%-99% identity to an amino acid sequence identified by any one of SEQ ID NO: 31-61. 
     
     
         11 . The vaccine of any one of  claims 3 - 10 , wherein the at least one antigenic polypeptide has an amino acid sequence that has at least 90% identity to an amino acid sequence of SEQ ID NO: 31-61 and wherein the antigenic polypeptide or immunogenic fragment thereof has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected. 
     
     
         12 . The vaccine of any one of  claims 3 - 11 , wherein the at least one antigenic polypeptide has an amino acid sequence that has 90%-99% identity to an amino acid sequence of SEQ ID NO: 31-61 and wherein the antigenic polypeptide or immunogenic fragment thereof has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected. 
     
     
         13 . A  Chlamydia  vaccine, comprising:
 at least one ribonucleic acid (RNA) polynucleotide having an open reading frame encoding at least one  Chlamydia trachomatis  antigenic polypeptide or an immunogenic fragment thereof.   
     
     
         14 . The vaccine of  claim 13 , wherein the at least one antigenic polypeptide is a major outer membrane protein (MOMP) or an immunogenic fragment thereof, optionally having a  Chlamydia trachomatis  serovar selected serovar H, F, E, D, I, G, J and K. 
     
     
         15 . The vaccine of  claim 13  or  14 , wherein the vaccine comprises at least one RNA polynucleotide having an open reading frame encoding at least two antigenic polypeptides or immunogenic fragments thereof selected from a MOMP of serovar H, a MOMP of serovar F, a MOMP of serovar E, a MOMP of serovar D, a MOMP of serovar I, a MOMP of serovar G, a MOMP of serovar J, and a MOMP of serovar K. 
     
     
         16 . The vaccine of any one of  claims 13 - 15 , wherein the vaccine comprises at least two RNA polynucleotides, each having an open reading frame encoding at least one antigenic polypeptide or an immunogenic fragment thereof selected from a MOMP of serovar H, a MOMP of serovar F, a MOMP of serovar E, a MOMP of serovar D, a MOMP of serovar I, a MOMP of serovar G, a MOMP of serovar J, and a MOMP of serovar K, wherein the antigenic polypeptide encoded by one of the open reading frames differs from the antigenic polypeptide encoded by another of the open reading frames. 
     
     
         17 . The vaccine of any one of  claims 13 - 16 , wherein the at least one antigenic polypeptide comprises an amino acid sequence identified by any one of SEQ ID NO: 65-183. 
     
     
         18 . The vaccine of any one of  claims 13 - 17 , wherein the at least one RNA polypeptide is encoded by a nucleic acid sequence identified by any one of SEQ ID NO: 62-64 or 184-294, and/or wherein the at least one RNA polypeptide comprises a nucleic acid sequence identified by any one of SEQ ID NO: 317-430. 
     
     
         19 . The vaccine of any one of  claims 13 - 18 , wherein the at least one antigenic polypeptide has an amino acid sequence that has at least 95% identity to an amino acid sequence identified by any one of SEQ ID NO: 65-183. 
     
     
         20 . The vaccine of any one of  claims 13 - 19 , wherein the at least one antigenic polypeptide has an amino acid sequence that has 95%-99% identity to an amino acid sequence identified by any one of SEQ ID NO: 65-183. 
     
     
         21 . The vaccine of any one of  claims 13 - 20 , wherein the at least one antigenic polypeptide has an amino acid sequence that has at least 90% identity to an amino acid sequence of SEQ ID NO: 65-183 and wherein the antigenic polypeptide or immunogenic fragment thereof has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected. 
     
     
         22 . The vaccine of any one of  claims 13 - 21 , wherein the at least one antigenic polypeptide has an amino acid sequence that has 90%-99% identity to an amino acid sequence of SEQ ID NO: 65-183 and wherein the antigenic polypeptide or immunogenic fragment thereof has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected. 
     
     
         23 . A sexually transmitted disease (STD) vaccine, comprising:
 at least one ribonucleic acid (RNA) polynucleotide having an open reading frame encoding at least two antigenic polypeptides selected from human papillomavirus (HPV) antigenic polypeptides or immunogenic fragments thereof, herpes simplex virus (HSV) antigenic polypeptides or immunogenic fragments thereof, and  Chlamydia trachomatis  antigenic polypeptides or immunogenic fragments thereof.   
     
     
         24 . The vaccine of  claim 23 , wherein at least one HPV antigenic polypeptide is selected from HPV E1 protein, HPV E2 protein, HPV E4 protein, HPV E5 protein, HPV E6 protein, HPV E7 protein, HPV L1 protein, and HPV L2 protein; and/or wherein at least one HSV antigenic polypeptide is selected from glycoprotein B, HSV glycoprotein C, HSV glycoprotein D, HSV glycoprotein E, and HSV (glycoprotein I); and/or wherein at least one  Chlamydia trachomatis  antigenic polypeptide is a MOMP antigenic polypeptide. 
     
     
         25 . The vaccine of  claim 23 , wherein the vaccine comprises at least one RNA polynucleotide having an open reading frame encoding at least two antigenic polypeptides or immunogenic fragments thereof selected from HPV antigenic polypeptides or immunogenic fragments thereof, HSV antigenic polypeptides or immunogenic fragments thereof, and  Chlamydia trachomatis  antigenic polypeptides or immunogenic fragments thereof. 
     
     
         26 . The vaccine of any one of  claims 23 - 25 , wherein the vaccine comprises at least two RNA polynucleotides, each having an open reading frame encoding at least one antigenic polypeptide or an immunogenic fragment thereof selected from HPV antigenic polypeptides or immunogenic fragments thereof, HSV antigenic polypeptides or immunogenic fragments thereof, and  Chlamydia trachomatis  antigenic polypeptides or immunogenic fragments thereof, wherein the antigenic polypeptide encoded by one of the open reading frames differs from the antigenic polypeptide encoded by another of the open reading frames. 
     
     
         27 . The vaccine of any one of  claims 23 - 26 , wherein the at least one antigenic polypeptide comprises an amino acid sequence identified by any one of SEQ ID NO: 31-61 or 65-183. 
     
     
         28 . The vaccine of any one of  claims 23 - 27 , wherein the at least one RNA polypeptide is encoded by a nucleic acid sequence identified by any one of SEQ ID NO: 1-28, 62-64 or 184-294, and/or wherein the at least one RNA polypeptide comprises a nucleic acid sequence identified by any one of SEQ ID NO: 317-319 or 320-461. 
     
     
         29 . The vaccine of any one of  claims 23 - 25 , wherein the at least one antigenic polypeptide has an amino acid sequence that has at least 95% identity to an amino acid sequence identified by any one of SEQ ID NO: 31-61 or 65-183. 
     
     
         30 . The vaccine of any one of  claims 23 - 25 , wherein the at least one antigenic polypeptide has an amino acid sequence that has 95%-99% identity to an amino acid sequence identified by any one of SEQ ID NO: 31-61 or 65-183. 
     
     
         31 . The vaccine of any one of  claims 23 - 25 , wherein the at least one antigenic polypeptide has an amino acid sequence that has at least 90% identity to an amino acid sequence of SEQ ID NO: 31-61 or 65-183 and wherein the antigenic polypeptide or immunogenic fragment thereof has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected. 
     
     
         32 . The vaccine of any one of  claims 23 - 25 , wherein the at least one antigenic polypeptide has an amino acid sequence that has 90%-99% identity to an amino acid sequence of SEQ ID NO: 31-61 or 65-183 and wherein the antigenic polypeptide or immunogenic fragment thereof has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected. 
     
     
         33 . The vaccine of any one of  claims 1 - 32 , wherein the at least one RNA polynucleotide has less than 80% identity to wild-type mRNA sequence. 
     
     
         34 . The vaccine of any one of  claims 1 - 32 , wherein at least one RNA polynucleotide has at least 80% identity to wild-type mRNA sequence, but does not include wild-type mRNA sequence. 
     
     
         35 . The vaccine of any one of  claims 1 - 34 , wherein the at least one antigenic polypeptide has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected. 
     
     
         36 . The vaccine of any one of  claims 1 - 35 , wherein the at least one RNA polynucleotide comprises at least one chemical modification. 
     
     
         37 . The vaccine of  claim 36 , wherein the chemical modification is selected from pseudouridine, N1-methylpseudouridine, N1-ethylpseudouridine, 2-thiouridine, 4′-thiouridine, 5-methylcytosine, 5-methyluridine, 2-thio-1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-pseudouridine, 2-thio-5-aza-uridine, 2-thio-dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-pseudouridine, 4-methoxy-2-thio-pseudouridine, 4-methoxy-pseudouridine, 4-thio-1-methyl-pseudouridine, 4-thio-pseudouridine, 5-aza-uridine, dihydropseudouridine, 5-methoxyuridine and 2′-O-methyl uridine. 
     
     
         38 . The vaccine of  claim 36  or  37 , wherein the chemical modification is in the 5-position of the uracil. 
     
     
         39 . The vaccine of any one of  claims 36 - 38 , wherein the chemical modification is a N1-methylpseudouridine or N1-ethylpseudouridine. 
     
     
         40 . The vaccine of any one of  claims 36 - 39 , wherein at least 80% of the uracil in the open reading frame have a chemical modification. 
     
     
         41 . The vaccine of  claim 40 , wherein at least 90% of the uracil in the open reading frame have a chemical modification. 
     
     
         42 . The vaccine of  claim 41 , wherein 100% of the uracil in the open reading frame have a chemical modification. 
     
     
         43 . The vaccine of any one of  claims 1 - 42 , wherein at least one RNA polynucleotide further encodes at least one 5′ terminal cap. 
     
     
         44 . The vaccine of  claim 43 , wherein the 5′ terminal cap is 7mG(5′)ppp(5′)NlmpNp. 
     
     
         45 . The vaccine of any one of  claims 1 - 44 , wherein at least one antigenic polypeptide or immunogenic fragment thereof is fused to a signal peptide selected from: a HuIgGk signal peptide (METPAQLLFLLLLWLPDTTG; SEQ ID NO: 304); IgE heavy chain epsilon-1 signal peptide (MDWTWILFLVAAATRVHS; SEQ ID NO: 305); Japanese encephalitis PRM signal sequence (MLGSNSGQRVVFTILLLLVAPAYS; SEQ ID NO: 306), VSVg protein signal sequence (MKCLLYLAFLFIGVNCA; SEQ ID NO: 307) and Japanese encephalitis JEV signal sequence (MWLVSLAIVTACAGA; SEQ ID NO: 308). 
     
     
         46 . The vaccine of  claim 45 , wherein the signal peptide is fused to the N-terminus of at least one antigenic polypeptide. 
     
     
         47 . The vaccine of  claim 45 , wherein the signal peptide is fused to the C-terminus of at least one antigenic polypeptide. 
     
     
         48 . The vaccine of any one of  claims 1 - 47 , wherein the antigenic polypeptide or immunogenic fragment thereof comprises a mutated N-linked glycosylation site. 
     
     
         49 . The vaccine of any one of  claims 3 - 48  formulated in a nanoparticle. 
     
     
         50 . The vaccine of  claim 49 , wherein the nanoparticle is a lipid nanoparticle. 
     
     
         51 . The vaccine of  claim 1 ,  2 ,  50  or  51 , wherein the nanoparticle has a mean diameter of 50-200 nm. 
     
     
         52 . The vaccine of  claim 1 ,  2 ,  50  or  51 , wherein the lipid nanoparticle comprises a cationic lipid, a PEG-modified lipid, a sterol and a non-cationic lipid. 
     
     
         53 . The vaccine of  claim 52 , wherein the lipid nanoparticle carrier comprises a molar ratio of about 20-60% cationic lipid, 0.5-15% PEG-modified lipid, 25-55% sterol, and 25% non-cationic lipid. 
     
     
         54 . The vaccine of  claim 52  or  53 , wherein the cationic lipid is an ionizable cationic lipid and the non-cationic lipid is a neutral lipid, and the sterol is a cholesterol. 
     
     
         55 . The vaccine of any one of  claim 53  or  54 , wherein the cationic lipid is selected from 2,2-dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane (DLin-KC2-DMA), dilinoleyl-methyl-4-dimethylaminobutyrate (DLin-MC3-DMA), and di((Z)-non-2-en-1-yl) 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioate (L319). 
     
     
         56 . The vaccine of any one of  claims 1 ,  2 ,  50 - 55 , wherein the lipid nanoparticle comprises a compound of Formula (I), optionally Compound 3, 18, 20, 25, 26, 29, 30, 60, 108-112, or 122. 
     
     
         57 . The vaccine of any one of  claims 1 ,  2 ,  50 - 55 , wherein the lipid nanoparticle comprises a compound of Formula (II). 
     
     
         58 . The vaccine of any one of  claims 1 - 57 , wherein the nanoparticle has a polydispersity value of less than 0.4. 
     
     
         59 . The vaccine of any one of  claims 1 - 58 , wherein the nanoparticle has a net neutral charge at a neutral pH value. 
     
     
         60 . The vaccine of any one of  claims 1 - 59  further comprising an adjuvant. 
     
     
         61 . The vaccine of  claim 60 , wherein the adjuvant is a flagellin protein or peptide. 
     
     
         62 . The vaccine of  claim 61 , wherein the flagellin protein or peptide comprises an amino acid sequence identified by any one of SEQ ID NO: 301-303. 
     
     
         63 . The vaccine of any one of  claims 1 - 62 , wherein the open reading frame is codon-optimized. 
     
     
         64 . The vaccine of any one of  claims 1 - 63 , wherein the vaccine is multivalent. 
     
     
         65 . The vaccine of any one of  claims 1 - 64  formulated in an effective amount to produce an antigen-specific immune response. 
     
     
         66 . A method of inducing an immune response in a subject, the method comprising administering to the subject the vaccine of any one of  claims 1 - 65  in an amount effective to produce an antigen-specific immune response in the subject. 
     
     
         67 . The method of  claim 66 , wherein the antigen specific immune response comprises a T cell response or a B cell response. 
     
     
         68 . The method of  claim 66  or  67 , wherein the subject is administered a single dose of the vaccine. 
     
     
         69 . The method of  claim 66  or  67 , wherein the subject is administered a booster dose of the vaccine. 
     
     
         70 . The method of any one of  claims 66 - 69 , wherein the vaccine is administered to the subject by intradermal injection or intramuscular injection. 
     
     
         71 . The method of any one of  claims 66 - 70 , wherein an anti-antigenic polypeptide antibody titer produced in the subject is increased by at least 1 log relative to a control. 
     
     
         72 . The method of any one of  claims 66 - 71 , wherein an anti-antigenic polypeptide antibody titer produced in the subject is increased by 1-3 log relative to a control. 
     
     
         73 . The method of any one of  claims 66 - 72 , wherein the anti-antigenic polypeptide antibody titer produced in the subject is increased at least 2 times relative to a control. 
     
     
         74 . The method of any one of  claims 66 - 73 , wherein the anti-antigenic polypeptide antibody titer produced in the subject is increased 2-10 times relative to a control. 
     
     
         75 . The method of any one of  claims 71 - 74 , wherein the control is an anti-antigenic polypeptide antibody titer produced in a subject who has not been administered a vaccine against the virus. 
     
     
         76 . The method of any one of  claims 71 - 74 , wherein the control is an anti-antigenic polypeptide antibody titer produced in a subject who has been administered a live attenuated vaccine or an inactivated vaccine against the virus. 
     
     
         77 . The method of any one of  claims 71 - 74 , wherein the control is an anti-antigenic polypeptide antibody titer produced in a subject who has been administered a recombinant protein vaccine or purified protein vaccine against the virus. 
     
     
         78 . The method of any one of  claims 71 - 74 , wherein the control is an anti-antigenic polypeptide antibody titer produced in a subject who has been administered a VLP vaccine against the virus. 
     
     
         79 . The method of any one of  claims 66 - 78 , wherein the effective amount is a dose equivalent to an at least 2-fold reduction in the standard of care dose of a recombinant protein vaccine or a purified protein vaccine against the virus, and wherein an anti-antigenic polypeptide antibody titer produced in the subject is equivalent to an anti-antigenic polypeptide antibody titer produced in a control subject administered the standard of care dose of a recombinant protein vaccine or a purified protein vaccine against the virus, respectively. 
     
     
         80 . The method of any one of  claims 66 - 78 , wherein the effective amount is a dose equivalent to an at least 2-fold reduction in the standard of care dose of a live attenuated vaccine or an inactivated vaccine against the virus, and wherein an anti-antigenic polypeptide antibody titer produced in the subject is equivalent to an anti-antigenic polypeptide antibody titer produced in a control subject administered the standard of care dose of a live attenuated vaccine or an inactivated vaccine against the virus, respectively. 
     
     
         81 . The method of any one of  claims 66 - 78 , wherein the effective amount is a dose equivalent to an at least 2-fold reduction in the standard of care dose of a VLP vaccine against the virus, and wherein an anti-antigenic polypeptide antibody titer produced in the subject is equivalent to an anti-antigenic polypeptide antibody titer produced in a control subject administered the standard of care dose of a VLP vaccine against the virus. 
     
     
         82 . The method of any one of  claims 66 - 81 , wherein the effective amount is a total dose of 50 μg-1000 μg. 
     
     
         83 . The method of  claim 82 , wherein the effective amount is a dose of 25 μg, 100 μg, 400 μg, or 500 μg administered to the subject a total of two times. 
     
     
         84 . The method of any one of  claims 66 - 83 , wherein the efficacy of the vaccine against the virus is greater than 65%. 
     
     
         85 . The method of any one of  claims 66 - 84 , wherein the vaccine immunizes the subject against the virus for up to 2 years. 
     
     
         86 . The method of any one of  claims 66 - 84 , wherein the vaccine immunizes the subject against the virus for more than 2 years. 
     
     
         87 . The method of any one of  claims 66 - 86 , wherein the subject has an age of about 12 to about 50 years old. 
     
     
         88 . The method of any one of  claims 66 - 87 , wherein the subject has been exposed to the virus, wherein the subject is infected with the virus, or wherein the subject is at risk of infection by the virus. 
     
     
         89 . The method of any one of  claims 66 - 88 , wherein the subject is immunocompromised. 
     
     
         90 . The vaccine of any one of  claims 1 - 65  for use in a method of inducing an antigen specific immune response in a subject, the method comprising administering to the subject the vaccine in an amount effective to produce an antigen specific immune response in the subject. 
     
     
         91 . Use of the vaccine of any one of  claims 1 - 65  in the manufacture of a medicament for use in a method of inducing an antigen specific immune response in a subject, the method comprising administering to the subject the vaccine in an amount effective to produce an antigen specific immune response in the subject. 
     
     
         92 . An engineered nucleic acid encoding at least one RNA polynucleotide of a vaccine of any one of  claims 1 - 65 . 
     
     
         93 . A pharmaceutical composition for use in vaccination of a subject comprising an effective dose of mRNA encoding a sexually transmitted disease antigen, wherein the effective dose is sufficient to produce detectable levels of antigen as measured in serum of the subject at 1-72 hours post administration. 
     
     
         94 . The composition of  claim 93 , wherein the cut off index of the antigen is 1-2. 
     
     
         95 . A pharmaceutical composition for use in vaccination of a subject comprising an effective dose of mRNA encoding a sexually transmitted disease antigen, wherein the effective dose is sufficient to produce a 1,000-10,000 neutralization titer produced by neutralizing antibody against said antigen as measured in serum of the subject at 1-72 hours post administration. 
     
     
         96 . A vaccine comprising an mRNA encoding a sexually transmitted disease antigen formulated in a lipid nanoparticle comprising compounds of Formula (I): 
       
         
           
           
               
               
           
         
         or a salt or isomer thereof, wherein: 
         R 1  is selected from the group consisting of C 5-30  alkyl, C 5-20  alkenyl, —R*YR″, —YR″, and —R″M′R′; 
         R 2  and R 3  are independently selected from the group consisting of H, C 1-14  alkyl, C 2-14  alkenyl, —R*YR″, —YR″, and —R*OR″, or R 2  and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle; 
         R 4  is selected from the group consisting of a C 3-6  carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6  alkyl, where Q is selected from a carbocycle, heterocycle, —OR, —O(CH 2 ) n N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —N(R) 2 , —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —N(R)R 8 , —O(CH 2 ) n OR, —N(R)C(═NR 9 )N(R) 2 , —N(R)C(═CHR 9 )N(R) 2 , —OC(O)N(R) 2 , —N(R)C(O)OR, —N(OR)C(O)R, —N(OR)S(O) 2 R, —N(OR)C(O)OR, —N(OR)C(O)N(R) 2 , —N(OR)C(S)N(R) 2 , —N(OR)C(═NR 9 )N(R) 2 , —N(OR)C(═CHR 9 )N(R) 2 , —C(═NR 9 )N(R) 2 , —C(═NR 9 )R, —C(O)N(R)O R, and —C(R)N(R) 2 C(O)OR, and each n is independently selected from 1, 2, 3, 4, and 5; 
         each R 5  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H; 
         each R 6  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H; 
         M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group; 
         R 7  is selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H; 
         R 8  is selected from the group consisting of C 3-6  carbocycle and heterocycle; 
         R 9  is selected from the group consisting of H, CN, NO 2 , C 1-6  alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6  alkenyl, C 3-6  carbocycle and heterocycle; 
         each R is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H; 
         each R′ is independently selected from the group consisting of C 1-18  alkyl, C 2-18  alkenyl, —R*YR″, —YR″, and H; 
         each R″ is independently selected from the group consisting of C 3-14  alkyl and C 3-14  alkenyl; 
         each R* is independently selected from the group consisting of C 1-12  alkyl and C 2-12  alkenyl; 
         each Y is independently a C 3-6  carbocycle; 
         each X is independently selected from the group consisting of F, Cl, Br, and I; and 
         m is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13. 
       
     
     
         97 . The vaccine of  claim 96 , wherein a subset of compounds of Formula (I) includes those in which when R 4  is —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, or -CQ(R) 2 , then (i) Q is not —N(R) 2  when n is 1, 2, 3, 4 or 5, or (ii) Q is not 5, 6, or 7-membered heterocycloalkyl when n is 1 or 2. 
     
     
         98 . The vaccine of  claim 96 , wherein a subset of compounds of Formula (I) includes those in which
 R 1  is selected from the group consisting of C 5-30  alkyl, C 5-20  alkenyl, —R*YR″, —YR″, and —R″M′R′;   R 2  and R 3  are independently selected from the group consisting of H, C 1-14  alkyl, C 2-14  alkenyl, —R*YR″, —YR″, and —R*OR″, or R 2  and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;   R 4  is selected from the group consisting of a C 3-6  carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6  alkyl, where Q is selected from a C 3-6  carbocycle, a 5- to 14-membered heteroaryl having one or more heteroatoms selected from N, O, and S, —OR, —O(CH 2 )—N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —CRN(R) 2 C(O)OR, —N(R)R 8 , —O(CH 2 ) n OR, —N(R)C(═NR 9 )N(R) 2 , —N(R)C(═CHR 9 )N(R) 2 , —OC(O)N(R) 2 , —N(R)C(O)OR, —N(OR)C(O)R, —N(OR)S(O) 2 R, —N(OR)C(O)OR, —N(OR)C(O)N(R) 2 , —N(OR)C(S)N(R) 2 , —N(OR)C(═NR 9 )N(R) 2 , —N(OR)C(═CHR 9 )N(R) 2 , —C(═NR 9 )N(R) 2 , —C(═NR 9 )R, —C(O)N(R)O R, and a 5- to 14-membered heterocycloalkyl having one or more heteroatoms selected from N, O, and S which is substituted with one or more substituents selected from oxo (═O), OH, amino, mono- or di-alkylamino, and C 1-3  alkyl, and each n is independently selected from 1, 2, 3, 4, and 5;   each R 5  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R 6  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;   R 7  is selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   R 8  is selected from the group consisting of C 3-6  carbocycle and heterocycle;   R 9  is selected from the group consisting of H, CN, NO 2 , C 1-6  alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6  alkenyl, C 3-6  carbocycle and heterocycle;   each R is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R′ is independently selected from the group consisting of C 1-18  alkyl, C 2-18  alkenyl, —R*YR″, —YR″, and H;   each R″ is independently selected from the group consisting of C 3-14  alkyl and C 3-14  alkenyl;   each R* is independently selected from the group consisting of C 1-12  alkyl and C 2-12  alkenyl;   each Y is independently a C 3-6  carbocycle;   each X is independently selected from the group consisting of F, Cl, Br, and I; and   m is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,   or salts or isomers thereof.   
     
     
         99 . The vaccine of  claim 96 , wherein a subset of compounds of Formula (I) includes those in which
 R 1  is selected from the group consisting of C 5-30  alkyl, C 5-20  alkenyl, —R*YR″, —YR″, and —R″M′R′;   R 2  and R 3  are independently selected from the group consisting of H, C 1-14  alkyl, C 2-14  alkenyl, —R*YR″, —YR″, and —R*OR″, or R 2  and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;   R 4  is selected from the group consisting of a C 3-6  carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6  alkyl, where Q is selected from a C 3-6  carbocycle, a 5- to 14-membered heterocycle having one or more heteroatoms selected from N, O, and S, —OR, —O(CH 2 )—N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —CRN(R) 2 C(O)OR, —N(R)R 8 , —O(CH 2 ) n OR, —N(R)C(═NR 9 )N(R) 2 , —N(R)C(═CHR 9 )N(R) 2 , —OC(O)N(R) 2 , —N(R)C(O)OR, —N(OR)C(O)R, —N(OR)S(O) 2 R, —N(OR)C(O)OR, —N(OR)C(O)N(R) 2 , —N(OR)C(S)N(R) 2 , —N(OR)C(═NR 9 )N(R) 2 , —N(OR)C(═CHR 9 )N(R) 2 , —C(═NR 9 )R, —C(O)N(R)OR, and —C(═NR 9 ) N(R) 2 , and each n is independently selected from 1, 2, 3, 4, and 5; and when Q is a 5- to 14-membered heterocycle and (i) R 4  is —(CH 2 ) n Q in which n is 1 or 2, or (ii) R 4  is —(CH 2 ) n CHQR in which n is 1, or (iii) R 4  is —CHQR, and —CQ(R) 2 , then Q is either a 5- to 14-membered heteroaryl or 8- to 14-membered heterocycloalkyl;   each R 5  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R 6  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;   R 7  is selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   R 8  is selected from the group consisting of C 3-6  carbocycle and heterocycle;   R 9  is selected from the group consisting of H, CN, NO 2 , C 1-6  alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6  alkenyl, C 3-6  carbocycle and heterocycle;   each R is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R′ is independently selected from the group consisting of C 1-18  alkyl, C 2-18  alkenyl, —R*YR″, —YR″, and H;   each R″ is independently selected from the group consisting of C 3-14  alkyl and C 3-14  alkenyl;   each R* is independently selected from the group consisting of C 1-12  alkyl and C 2-12  alkenyl;   each Y is independently a C 3-6  carbocycle;   each X is independently selected from the group consisting of F, Cl, Br, and I; and   m is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,   or salts or isomers thereof.   
     
     
         100 . The vaccine of  claim 96 , wherein a subset of compounds of Formula (I) includes those in which
 R 1  is selected from the group consisting of C 5-30  alkyl, C 5-20  alkenyl, —R*YR″, —YR″, and —R″M′R′;   R 2  and R 3  are independently selected from the group consisting of H, C 1-14  alkyl, C 2-14  alkenyl, —R*YR″, —YR″, and —R*OR″, or R 2  and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;   R 4  is selected from the group consisting of a C 3-6  carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6  alkyl, where Q is selected from a C 3-6  carbocycle, a 5- to 14-membered heteroaryl having one or more heteroatoms selected from N, O, and S, —OR, —O(CH 2 ) n N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —CRN(R) 2 C(O)OR, —N(R)R 8 , —O(CH 2 ) n OR, —N(R)C(═NR 9 )N(R) 2 , —N(R)C(═CHR 9 )N(R) 2 , —OC(O)N(R) 2 , —N(R)C(O)OR, —N(OR)C(O)R, —N(OR)S(O) 2 R, —N(OR)C(O)OR, —N(OR)C(O)N(R) 2 , —N(OR)C(S)N(R) 2 , —N(OR)C(═NR 9 )N(R) 2 , —N(OR)C(═CHR 9 )N(R) 2 , —C(═NR 9 )R, —C(O)N(R)OR, and —C(═NR 9 ) N(R) 2 , and each n is independently selected from 1, 2, 3, 4, and 5;   each R 5  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R 6  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;   R 7  is selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   R 8  is selected from the group consisting of C 3-6  carbocycle and heterocycle;   R 9  is selected from the group consisting of H, CN, NO 2 , C 1-6  alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6  alkenyl, C 3-6  carbocycle and heterocycle;   each R is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R′ is independently selected from the group consisting of C 1-18  alkyl, C 2-18  alkenyl, —R*YR″, —YR″, and H;   each R″ is independently selected from the group consisting of C 3-14  alkyl and C 3-14  alkenyl;   each R* is independently selected from the group consisting of C 1-12  alkyl and C 2-12  alkenyl;   each Y is independently a C 3-6  carbocycle;   each X is independently selected from the group consisting of F, Cl, Br, and I; and   m is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,   or salts or isomers thereof.   
     
     
         101 . The vaccine of  claim 96 , wherein subset of compounds of Formula (I) includes those in which
 R 1  is selected from the group consisting of C 5-30  alkyl, C 5-20  alkenyl, —R*YR″, —YR″, and —R″M′R′;   R 2  and R 3  are independently selected from the group consisting of H, C 2-14  alkyl, C 2-14  alkenyl, —R*YR″, —YR″, and —R*OR″, or R 2  and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;   R 4  is —(CH 2 ) n Q or —(CH 2 ) n CHQR, where Q is —N(R) 2 , and n is selected from 3, 4, and 5;   each R 5  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R 6  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;   R 7  is selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R′ is independently selected from the group consisting of C 1-18  alkyl, C 2-18  alkenyl, —R*YR″, —YR″, and H;   each R″ is independently selected from the group consisting of C 3-14  alkyl and C 3-14  alkenyl;   each R* is independently selected from the group consisting of C 1-12  alkyl and C 1-12  alkenyl;   each Y is independently a C 3-6  carbocycle;   each X is independently selected from the group consisting of F, Cl, Br, and I; and   m is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,   or salts or isomers thereof.   
     
     
         102 . The vaccine of  claim 96 , wherein a subset of compounds of Formula (I) includes those in which
 R 1  is selected from the group consisting of C 5-30  alkyl, C 5-20  alkenyl, —R*YR″, —YR″, and —R″M′R′;   R 2  and R 3  are independently selected from the group consisting of C 1-14  alkyl, C 2-14  alkenyl, —R*YR″, —YR″, and —R*OR″, or R 2  and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;   R 4  is selected from the group consisting of —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, and —CQ(R) 2 , where Q is —N(R) 2 , and n is selected from 1, 2, 3, 4, and 5;   each R 5  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R 6  is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;   R 7  is selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R is independently selected from the group consisting of C 1-3  alkyl, C 2-3  alkenyl, and H;   each R′ is independently selected from the group consisting of C 1-18  alkyl, C 2-18  alkenyl, —R*YR″, —YR″, and H;   each R″ is independently selected from the group consisting of C 3-14  alkyl and C 3-14  alkenyl;   each R* is independently selected from the group consisting of C 1-12  alkyl and C 1-12  alkenyl;   each Y is independently a C 3-6  carbocycle;   each X is independently selected from the group consisting of F, Cl, Br, and I; and   m is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,   or salts or isomers thereof.   
     
     
         103 . The vaccine of  claim 96 , wherein a subset of compounds of Formula (I) includes those of Formula (IA): 
       
         
           
           
               
               
           
         
         or a salt or isomer thereof, wherein 1 is selected from 1, 2, 3, 4, and 5; m is selected from 5, 6, 7, 8, and 9; M 1  is a bond or M′; R 4  is unsubstituted C 1-3  alkyl, or —(CH 2 ) n Q, in which Q is OH, —NHC(S)N(R) 2 , —NHC(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)R 8 , —NHC(═NR 9 )N(R) 2 , —NHC(═CHR 9 )N(R) 2 , —OC(O)N(R) 2 , —N(R)C(O)OR, heteroaryl or heterocycloalkyl; M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —P(O)(OR′)O—, —S—S—, an aryl group, and a heteroaryl group; and R 2  and R 3  are independently selected from the group consisting of H, C 1-14  alkyl, and C 2-14  alkenyl.