Polymerization is a common reaction, due to excessive use of amino acids to ensure coupling during each synthesis phase. As a result, a series of deprotection phases are added to the synthesis process which takes the following form:
t- Boc protecting group: This group requires more number of acid stable groups for side chain protection in orthogonal strategies. It was most commonly used to protect the terminal amine of the peptide being synthesized. This group can be added to amino acids with t-Boc anhydride and a suitable base. It reduces aggregation of peptides during synthesis.
Fmoc protecting group: It is currently being most widely used in the iterative synthesis of a peptide from amino acid units. It is usually removed from the N-terminus of the peptide during iterative synthesis. It is also cleaved under very mild basic conditions and is stable under acidic conditions. Fmoc group is preferred over BOC due to ease of cleavage, but it is less atom-economical.
Nucleoside analogs are replications of natural nucleosides. They prevent the production of new virus, when incorporated into virus DNA or RNA, during virus replication. The nucleoside analogues replace the natural nucleosides to block the completion of the viral DNA chain when they infect a new cell by HIV. They inhibit reverse transcriptase, hence are called nucleoside reverse transcriptase inhibitors. And unlike natural nucleosides that are active only in cells that can produce the drug by a process called phosphorylation, nucleoside analogues are active in their native form. They are active against HIV for a wider range of infected cells. 
Treatment for various stages of HIV are:
1) Binding and Fusion:- Blocked by entry inhibitors. HIV virus binds to the CD4 molecule (receptor) on the outside surface of the T4 cell, activating other proteins on the cell surface and allowing the HIV envelope to fuse to the outside of the cell.
2) Reverse Transcription:- Blocked by Nucleoside Reverse Transcriptase inhibitors. Virus penetrates the host cell and releases its contents in it i.e. enzymes, RNA. The HIV virus infects the host cell by "reverse transcription", i.e. a DNA copy of the virus's RNA is made by a viral enzyme called reverse transcriptase. This new DNA copy is called "proviral DNA".
3) Integration:- Blocked by Integrase Inhibitors. Viral DNA combines with the host cell's own DNA by the integrase enzyme.