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Table 1

Interfering strategy	Target RNA/protein	Interference site(s)	Mechanism	References

Anti-sense RNA	Cellular CCR5 and CXCR4 co-receptors	Viral entry	Inhibition of CCR5 and CXCR4 gene expression	6, 18, 19
	Psi-gag and U3-5'UTR-gag-env regions	Pre-integration	Co-packaged with genomic RNA, inhibits RT in incoming virions	6
	Cellular CyPA gene	Pre-integration	The skipping of internal CyPA encoding exons reduces CyPA biosynthesis and thereby inhibits the reverse transcription	37
	Tat/TAR interaction	HIV-1 transcription	Inhibits transcriptional regulation of HIV-1 gene expression	6, 7, 45, 76
	Rev/RRE interaction	Nuclear export	Inhibits transport of unspliced and single spiced viral RNAs	6
	5'UTR	HIV-1 translation	Inhibits the translation process	6
	Psi-gag region	Viral assembly	Inhibits packaging of genomic RNA	6, 7, 45
	5'-leader-gag region	Viral assembly	Inhibits the formation of Gag and Env multimeric complexes during viral assembly.	7, 18
	Env and Vif encoding regions	Viral assembly	Inhibits env and vif gene expression	70
	Nef encoding region	Viral release	Inhibits nef gene expression and thereby CD4 and MHC I downregulation	7
	Pol encoding region	Viral maturation	Inhibits pol gene expression	70
RNA decoys	RT enzyme	Pre-integration	Competes with HIV-1 RNA for the binding of RT	6
	HIV-1 TAR region	Pre-integration	Competes with cellular tRNA₃^Lysfor the binding to RT and primes the reverse transcription from the TAR region instead of the PBS region	6
	Tat and Tat-containing RNA polymerase II transcription complexes	HIV-1 transcription	Inhibits Tat regulated transcription	6, 7, 18, 51
	Rev protein	Nuclear export	Recruits Rev molecules and thereby prevents their interaction with the viral transcript	6
	NC domain of the Gag protein	Viral assembly	Inhibits packaging by interfering with the NC domains ability to recognize the genomic RNA	6, 45
Ribozymes	Cellular CCR5 and CXCR4 co-receptors	Viral entry	Cleaves CCR5 and CXCR4 mRNAs	6, 18
	HIV-1 Gag and Pol encoding region and the U5 region	Pre-integration	Cleaves the viral RNA before reverse transcription is completed	6, 36
	RRE and the Rev encoding region	Nuclear export	Cleaves the viral RNA	6, 7
	U5	HIV-1 translation	Cleaves off the 5'-cap structure localized on HIV-1 mRNAs	6, 7
	Psi	Viral assembly	Cleaves HIV-1 RNAs before packaging	6, 7
	Gag encoding transcripts	Viral assembly	Inhibits the formation of multimeric Gag and Env complexes	7, 18
	SU encoding region	Viral assembly	Cleaves different conserved regions in the SU sequence	7
	Nef encoding region	Viral release	Inhibits downregulation of CD4 and MHC I	7
RNA aptamers	RT enzyme	Pre-integration	Displays high affinity and specificity for the RT enzyme and acts as templates analogues	31
	Rev protein	Nuclear export	Possesses higher affinity for Rev than the RRE sequence and can therefore interfere with Rev function	57
siRNA	Cellular CCR5 and CXCR4 co-receptors	Viral entry	Impairs the SU-chemokine co-receptor interaction	21, 22
	CD4 protein	Viral entry	CD4 protein expression inhibited	23, 24
	CD4-binding domain of the SU protein	Viral entry	Inhibits the CD4-SU interaction	26
	The viral LTR region or the vif and nef encoding regions	Pre-integration	Guides the viral genomic RNA towards a siRNA-mediated destruction	34, 52
	RT encoding region	Pre-integration	Inhibits RT gene expression	35
	Cellular CyPA gene	Pre-integration	Reduces CyPA biosynthesis and thereby the reverse transcription	37
	CA encoding region	Pre-integration	Mediates cleavage of pre-spliced viral RNA in the cytoplasm and prevents integration	23, 24, 42
	Tat encoding region	HIV-1 transcription	Inhibits Tat transactivation	35, 49, 50
	NF-κB p65 subunit	HIV-1 transcription	Inhibits NF-κB transcriptional activation	35, 49
	3'-terminus of the nef gene	HIV-1 transcription	Mediates cleavage of all spliced and unspliced RNA produced from the provirus	42
	Rev transcript	Nuclear export	Inhibits Rev mediated export of unspliced and single spliced RNAs	49, 61
	Gag and Nef encoding regions	HIV-1 translation	Mediates cleavage of both spliced and unspliced RNA produced from the provirus	23, 24, 34, 42
shRNA/ miRNA	Nef encoding region	HIV-1 translation	nef shRNAs act by blocking RNA stability or RNA translation	62
Transdominant negative proteins (TNPs)	Interactions between Tat/TAR complex and cellular co-factors	HIV-1 transcription	Tat-mutants inhibit the function of the Tat protein by recruiting important cellular co-factors	7, 18, 45
	Rev protein	Nuclear export	Rev-mutants e.g. act by preventing the interaction with cellular co-factors or by sequestering the Rev protein in the cytoplasm	7, 18, 25, 57, 58, 59
	Cellular Sam68	Nuclear export	Sam68 mutants inhibit Sam68 transactivation of RRE and Rev function	60
	Cellular Tsg101	Viral assembly	Tsg101 mutants inhibit the transport of the Gag polyprotein into multivesicular bodies	71
	Vif protein	Viral assembly	Vif mutants block an early processing of the Gag protein	66
	Cellular INI1	Viral assembly	INI1 mutants e.g. interact with the integrase domain of the Gag-Pol polyprotein and interfere with prober multimerization of Gag and Gag-Pol	39
	The formation of Gag and Env multimeric complexes	Viral assembly	E.g. interferes with complex formation	4, 6, 18
	Nef protein	Viral release	Nef mutants e.g. inhibit CD4 downregulation	66
	SU protein	Viral release	Overexpressed CD4 variants bind and sequester virion progeny within the cell	19
	HIV-1 protease	Viral maturation	Pro-mutants prevent protease activation	7
Chimeric / fusion proteins	SU protein	Viral entry	A tetrameric version of sCD4, PRO542, which is fused to the conserved region of IgG2, prevents the CD4-SU interaction	8, 13
	Proviral DNA	Pre-integration	An IN targeted sFv-nuclease fusion protein associates with the pre-integration complex and cleaves proviral DNA after integration has occurred	7, 18
	TAR element	HIV-1 transcription	Designed Tat-nuclease fusion proteins recognize and cleave all HIV-1 RNA transcripts	5
	RRE sequence	Nuclear export	Designed Rev-nuclease fusion proteins recognize and cleave all HIV-1 RNAs carrying the RRE sequence	5
	Rev protein	Nuclear export	A NS1RM-Rev mutant, with a dominant retention activity, forms mixed oligomers together with Rev and inhibits nuclear export	7, 57
	The TAR and RRE elements	HIV-1 transcription / nuclear export	A designed fusion protein, Tev, containing the RNA binding domains of both Tat and Rev fused to a nuclease, inhibits both early and late viral gene products	5
	Viral genomic RNAs	Viral assembly	Gag-, Vpr- and Nef-nuclease fusion proteins cleaves viral RNA, either during or after the viral assembly	5, 7
	Psi-element	Viral assembly	A NC-nuclease fusion protein recognizes and cleaves all unspliced RNAs in the cytoplasm	5
	HIV-1 protease	Viral maturation	An overexpressed Vpr fused to several protease cleavage sites overwhelms the protease activity by a competitive mechanism	7, 74
Nucleases	Tat encoding region	HIV-1 transcription	Inhibits Tat transactivation	6, 7, 45
	TAR element	HIV-1 transcription	Inhibits Tat transactivation	6, 7, 45
Chemokine ligands	Cellular CCR5 and CXCR4 co-receptors	Viral entry	E.g. interacts directly with the co-receptors, mediates receptor blockade or mediates receptor down-regulation	8, 9, 11, 12, 13, 14, 16
Anti-infectious cellular proteins	SU protein	Viral entry	A truncated form of CD4, sCD4, inhibits the fusion event by binding to the SU protein and thereby extending the distance to the TM protein	8, 13, 19
Intracellular antibodies (sFvs)	SU protein	Viral entry	Inhibits the CD4-SU interaction	18
	The TM pre-hairpin intermediate	Viral entry	Inhibits the interaction between the fusion peptide and the cell membrane	29
	RT enzyme	Pre-integration	Inhibits RT function	7, 18
	IN enzyme	Pre-integration	Inhibits IN function	7, 18
	Tat protein	HIV-1 transcription	Interacts with the Tat protein and restrains it in the cytoplasm	7, 18
	Rev protein	Nuclear export	Recruits Rev in the cytoplasm	7, 18, 25, 57
	The CD4 binding region of the SU protein	Viral assembly	Interacts with the Env protein and restrains it in the ER	7, 18
Monoclonal antibodies (Mabs)	Cellular CCR5 and CXCR4 co-receptors	Viral entry	E.g. inhibit the SU-chemokine co-receptor interaction, HIV-1 fusion or entry	12
	Extracellular loop on CCR5	SU-chemokine co-receptor interaction	Inhibits HIV-1 fusion and entry	12
Nucleoside analogues (NRTIs)	RT enzyme	Pre-integration	Prevents the continued polymerization of the DNA chain	8
Non-nucleoside analogues (NNRTIs)	RT enzyme	Pre-integration	Interact directly and non-competitively with the RT enzyme and inhibits its function	8
Integrase inhibitors (Oligonucleotides, dinucleotides and chemical agents)	IN enzyme	Pre-integration	These inhibiting agents either block the catalytic function of the IN enzyme by binding to the integrase binding site located in the viral DNA, or by interacting with the catalytic core domain of the IN enzyme itself	40, 41
Protease inhibitors	Protease enzyme	Viral maturation	Act as transition state analogous and bind to the protease more tightly than the natural substrate	11, 8, 73
Examples of other inhibiting agents	Cellular CCR5 and CXCR4 co-receptor	Viral entry	Chemokine ligands potently inhibit the SU-chemokine co-receptor interaction	8, 9, 10, 11, 12, 13
	Cellular CCR5 and CXCR4 co-receptors	Viral entry	Designed peptides e.g. act by disrupting helix-helix interactions, which may influence co-receptor structure, or by associating with the co-receptor surfaces and thereby inhibit the interaction with the SU protein	8, 12
	Cellular CXCR4 co-receptor	Viral entry	AMD3100, a small organic molecule, acts by spanning the main ligand-binding cavity of CXCR4, which constrains the co-receptor in an inactive conformation	12
	Cellular CCR5 co-receptor	Viral entry	Cyclophilin-18, a protein derived from T. Gondii acts as a CCR5 antagonist and thereby inhibits fusion and infectivity of R5 HIV-1 isolates	17
	SU protein	Viral entry	CV-N, a 11 kDa protein with high affinity for the SU protein, inhibits the SU-CD4 interaction	15
	The N- and C-peptide regions on the TM pre-hairpin intermediate	Viral entry	Designed N-, C-, and D-peptides interacts with the pre-hairpin intermediate and inhibit the fusion event	13, 27, 28
	RT enzyme	Pre-integration	Small peptides, about 15–19 amino acid long, act by interfering the dimerization process of the RT enzyme	30
	The Tat/TAR interaction	HIV-1 transcription	The TR87 compound acts by competing with Tat for binding to TAR-RNA	46
	Protein /TAR RNA interaction	HIV-1 transcription	Pyrrolo [2,1-c][1,4]benzodiazepine-oligopyrrolo hybrids act by interrupting binding of cellular proteins and Tat to the TAR-RNA	47
	Protein /TAR RNA interaction	HIV-1 transcription	Aromatic polyamidines carrying a Br atom inhibit cellular and viral protein-TAR RNA interactions	48
	Cellular NF-κB	HIV-1 transcription	NF-κB activity is inhibited by minocycline, a second-generation tetracycline	38, 54
	Rev	Nuclear export	Peptides targeted against the NES domain inhibit Rev function	57
	The cellular protease furin	Viral assembly	Peptides mimicking a conserved target sequence inhibit furin activity and thereby cleavage of the Env protein within the ER	72
	HIV-1 infected cells	All	A Tat-Casp3 fusion protein induces apoptosis after cleavage and activation by the HIV-1 protease	79

Nielsen et al. Retrovirology 2005 2:10 doi:10.1186/1742-4690-2-10

Table 1