From Proteopedia

Complera: Emtricitabine/rilpivirine/tenofovir

• Marketed by: Gilead Sciences and Janssen Therapeutics
• Major Indication: HIV infection
• Drug Class: Combination of nucleoside/tide reverse transcriptase inhibitor and nonnucleoside reverse transcriptase inhibitor
• Date of FDA Approval: August 2011

Reverse Transcriptase: Upon infection, HIV binds to the CD4 receptor in a helper T cell or other CD4-presenting lymphocyte. The viral envelope is then fused with the cellular membrane allowing intracellular release of viral particles. The utilization of several enzymes helps to solidify the virus’s hold on the cell. HIV reverse transcriptase (RT) works to convert the viral single-stranded RNA (ssRNA) into DNA. HIV integrase then helps to incorporate the newly reverse transcribed DNA into the cellular genome. (Voet et al. 2008)

The structure of HIV-1 reverse transcriptase is a dimeric protein with a (p66) domain and a 51-kD RNase H domain (p51). The enzyme has a conformation and possesses one active site and three catalytic functions: RNA-dependent DNA polymerization, RNA hydrolysis, and DNA replication. The p66 domain is an RNA-dependent DNA polymerase which binds viral RNA as well as DNA in its single palm-like active site. This active site of the fingers is lined with (blue) which interact with the negatively charged phosphodiester backbone of the . This diversity of function is brought about by the flexible nature of the hand-like p66 subunit. The p51 subunit is the RNase H domain which degrades the viral RNA after a daughter DNA strand has been synthesized. A structural overview helps us understand the basis of the high mutability of HIV. RNA, which forms the basis of the viral genetic material, is less stable than DNA and is more subject to modification or damage. In addition the reverse transcriptase polymerase domain lacks proofreading exonuclease activity. This lowers the fidelity of the reverse transcription. ^[1],^[2].

Because of the high mutability of HIV, resistance develops quickly when the virus is exposed to antiretroviral drugs. Because HIV is not curable at this point, these drugs are therapeutic and only work to reduce viral load which can effectively reduce the patient’s symptoms and boost his/her immune system. Random mutations in the HIV genetic code can allow strains to develop resistance to antiretroviral drugs. Thus, antiretroviral therapy often consists of several different compounds which effect different aspects of HIV infection, reverse transcription, and integration. Combination drugs both reduce viral load, and delay development of resistance. Complera is a drug that combines the antiretroviral activity of three reverse transcriptase inhibitors: emtricitabine (ETB), tenofovir (TFV), and rilpivirine (RPV). ETB is a nucleoside RT inhibitor (NRTI), TFV is a nucleotide RT inhibitors (NtRTI), RPV is a second generation nonnucleoside RT inhibitor (NNRTI).

NRTI (Tenofovir and Emtricitabine)

Structure of tenofovir, 1hmv

ETB and TFV are highly similar in function and many drug formulations use them in tandem. Once activated by phosphorylation, these compounds compete with naturally occurring dNTPs as alternative substrates for viral DNA synthesis by RT. When these compounds are incorporated in the growing chain of viral DNA, they terminate chain extension by functioning as . In this scene the ligand, TFV, is shown as a space filling molecule in the polymerase site, having stopped the polymerization of additional nucleotides.

Emtricitabine (ECT)

[[Image:Emtricitabine3.png |left|200px|thumb|Structure of cytidine analog emtricitabine, 1hmv]]

ETB is a cytosine analog and specifically lack a 3’-OH group on its deoxyribose. TFV lacks a deoxyribose completely. Both prevent the next nucleotide from binding, as any incoming dNTP cannot form a phosphodiester bond without the presence of a 3’-OH group. Thus, these two compounds act as competitive substrate inhibitors.

Rilpivirine (RPV)

Rilpivirine is a diarylpyrimidine that functions as an NNRTI, which does not bind to the viral DNA. Instead, it binds to a (solvent shown as red, hydrophobic active site residues gray, RPV as teal) called the (NNIBP) which is located 10Å away from the polyermase active site (Iyidogan et al. 2012).In red are the binding pocket residues p66 (Leu-100, Lys-101, Lys-103, Val-106, Thr-107, Val-108, Val-179, Tyr-181, Tyr-188, Val-189, Gly-190, Phe-227, Trp-229, Leu- 234, and Tyr-318) and p51(Glu-138) ^[3]. This specific site is primarily contained in the p66 subunit, but contains one glutamic acid residue in the p51 subunit . The methods of NNRTI inhibition are threefold, that binding of the NNRTI limits the mobility of the thumb subdomain, alters the catalytic “hand” or triad, and changes the effectiveness of primer binding. Simply put, NNRTIs are noncompetitive allosteric inhibitors that cause the thumb and finger domains (flexible zone) from closing in active conformation and thus halt viral replication. Because of these multiple methods of attack, combination antiretroviral formulas like Complera® demonstrate a synergistic effect on viral load reduction. NRTI-resistant mutants are not resistant to NNRTIs, and the presence of an NNRTI helps to regain efficacy of the NRTI.

HIV can become resistant to NNRTIs through a variety of binding pocket mutations. However, due to the flexible nature of RPV, which classifies it as a second generation NNRTI, it is able to bind less optimal pockets that are the result of mutation. Of particular interest in RPV binding are the residues p51(E138) and p66(M184) where mutations have been shown by Singh et al. (2012) to drastically decrease the effectiveness of RPV. It was found that the entrance of the NNRTI to the NNIBP was due largely to a between p51(E138) and p66(K101) shown in scarlet. Mutation of the glutamate residue results in the breakage of this salt bridge and less access of RPV to the NNIBP. Both mutations act in tandem to increase the overall dissociation rate of RPV.

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