Tissue-specific genome engineering using CRISPR-Cas9

A compound of any one of Formulas (A-1), (A-2), or (A-3):

• or a pharmaceutically acceptable salt thereof,
• wherein:
• RXX is H, alkyl, cycloalkyl, alkenyl, alkynyl, aryl, heteroaryl, —OR5, —N(R4)R5, or —SR5, wherein any one or more —CH2— groups of said RXX are each optionally replaced independently with a first heteroatom group selected from the group consisting of —O—, —S—, —N(R4)—;
• wherein any one or more —CH3 groups of said RXX are each optionally replaced independently with a second heteroatom group selected from the group consisting of —N(R4)2, —OR4, and —SR4, wherein any two of said second heteroatom groups are separated by at least two carbon atoms;
• and wherein said alkyl, alkenyl, alkynyl, or cycloalkyl is optionally substituted with one or more halogen atoms;
• Ryy is —CN, —CH2CN, —C≡CH, —CH2N3, —CH2NH2—CH2N(R4)SO2R5, —CH2CO2H, —CO2H, —CH2OH, —CH2SH, —CH═C(H)R5, —CH2R5, —CH2SR5, —CH2N(R4)R5, —CH2N(R4)C(O)R5, —CH2N(R4)CO2R5, —CH2N(R4)C(O)N(R4)R5, —CH2OR5, —CH2OC(O)R5, —CH2OC(O)N(R4)R5, —CH2OCO2R5, —CH2S(O)R5, —CH2SO2R5, —CH2SO2N(R4)R5, —C(O)NH2, —CO2R5, —C(O)N(R4)R5, aryl, or heteroaryl, wherein said aryl or heteroaryl is optionally substituted with R5;
• each R1 is independently —CN, —CH2CN, —C═CH, —CH2N3, —CH2NH2, —CH2N(R4)SO2R5, —CH2CO2H, —CO2H, —CH2SH, —CH═CHR5, —CH2R5, —CH2SR5, —CH2N(R4)R5, CH2N(R4)C(O)R5, CH2N(R4)CO2R5, —CH2N(R4)C(O)N(R4)R5, —CH2OR5, —CH2OC(O)R5, —CH2OC(O)N(R4)R5, —CH2OCO2R5, —CH2S(O)R5, —CH2SO2R5, —CH2SO2N(R4) R5, —C(O)NH2, —C(O)N(R4)R5, aryl, or heteroaryl, wherein the aryl or heteroaryl is optionally substituted with R5,
• or R1 is —Z—X—Y, —Z—Y, —X—Y, —Z—X+Y−, —X+Y−, —X−Y+, or —Y;
• X is a linker;
• X+ is a positively charged linker;
• X− is a negatively charged linker;
• Y is selected from the group consisting of a ribonucleoprotein comprising a site-directed modifying polypeptide, an endonuclease comprising a site-directed modifying polypeptide, a site-directed modifying polypeptide, a single guide RNA sequence (sgRNA), and a dual guide RNA sequence comprising a CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA), optionally wherein Y is a Cas9 ribonucleoprotein or a Cas9 protein;
• Y+ is selected from the group consisting of a positively charged ribonucleoprotein comprising a site-directed modifying polypeptide, a positively charged endonuclease comprising a site-directed modifying polypeptide, and a positively charged site-directed modifying polypeptide, optionally wherein r is a positively charged Cas9 protein;
• Y− is selected from the group consisting of a negatively charged ribonucleoprotein comprising a site-directed modifying polypeptide, a negatively charged endonuclease comprising a site-directed modifying polypeptide, a negatively charged site-directed modifying polypeptide, a negatively charged sgRNA, and a negatively charged dual guide RNA sequence comprising a CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA), optionally wherein Y− is a negatively charged Cas9 ribonucleoprotein;
• Z is a covalent bond, —C≡C—, —CH═CH—, —CH2—, —CH2O—, —C(O)N(R4)—, —CH2S—, —CH2S(O)—, —CH2SO2—, —CH2SO2N(R4)—, —CO2—, —CH2N(R4)—, —CH2N(R4)C(O)—, —CH2N(R4)SO2—, —CH2N(R4)CO2—, —CH2N(R4)C(O)N(R4)—, —CH2OC(O)—, —CH2OC(O)N(R4)—, —CH2OCO2—, aryl, or heteroaryl, wherein said aryl or heteroaryl is optionally substituted with R5;
• R2 is —OH, —N3, —N(R3)2, —N(R3)C(O)R3, —N(R3)C(O)N(R3)2, —N(R3)CO2R3, —N(R3)SO2R3, tetrazole, or triazole, wherein said tetrazole or triazole is optionally substituted with R3;
• each R3 is independently H, (C1-C5)alkyl, halo-substituted (C1-C5)alkyl, halo-substituted (C3-C6)cycloalkyl, (C1-C5)alkenyl, (C1-C5)alkynyl, halo-substituted (C1-C5)alkenyl, halo-substituted (C1-C5)alkynyl, or (C3-C6)cycloalkyl, wherein any one or more —CH2— groups of said (C1-C5)alkyl, halo-substituted (C1-C5)alkyl, halo-substituted (C3-C6)cycloalkyl, and (C3-C6)cycloalkyl are each optionally replaced independently with a first heteroatom group selected from the group consisting of —O—, —S— and —N(R4)—, wherein any two of said first heteroatom groups are separated by at least two carbon atoms;
• and wherein any one or more —CH3 groups of said (C1-C5)alkyl and halo-substituted (C1-C5)alkyl are each optionally replaced independently with a second heteroatom group selected from the group consisting of —N(R4)2, —OR4, and —SR4, wherein any two of said second heteroatom groups are separated by at least two carbon atoms;
• each R4 is independently H, (C1-C20)alkyl, (C1-C20)alkenyl, (C1-C20)alkynyl, or (C3-C6)cycloalkyl, wherein one to six —CH2— groups of said (C1-C20)alkyl and (C3-C6)cycloalkyl are each optionally replaced independently with a heteroatom group that is —O— or —S;
• and wherein any two of said heteroatom groups are separated by at least two carbon atoms;
• and wherein said (C1-C20)alkyl, (C1-C20)alkenyl, (C1-C20)alkynyl, or (C3-C6)cycloalkyl is optionally substituted with one or more halogen atoms;
• each R5 is independently (C3-C20)cycloalkyl, (C1-C60)alkenyl, (C1-C60)alkynyl, or (C1-C60)alkyl, wherein one to six —CH2— groups of said (C3-C20)cycloalkyl or one to 20 —CH2— groups of the (C1-C60)alkyl are each optionally replaced independently with a first heteroatom group selected from the group consisting of —O—, —S—, and —N(R4)—, wherein any two of said first heteroatom groups are separated by at least two carbon atoms;
• wherein any one or more —CH3 groups of said (C1-C60)alkyl are each optionally replaced independently with a second heteroatom group selected from the group consisting of —N(R4)2, —OR4, and —S(R4), wherein any two of said second heteroatom groups are separated by at least two carbon atoms;
• and wherein said (C3-C20)cycloalkyl, (C1-C60)alkenyl, (C1-C60)alkynyl, or (C1-C60)alkyl is optionally substituted with one or more halogen atoms.