Discovery and development of integrase inhibitors
The body uses its immune system to protect itself from bacteria, viruses and other disease-causing beings, and when it fails to do so immunodeficiency diseases occur.
Raltegravir (brand name Isentress) was granted accelerated approval from the U.S. Food and Drug Administration (FDA) in October 2007 and from EMEA (now EMA) in December 2007.
Raltegravir, Elvitegravir, Dolutegravir, Bictegravir and Cabotegravir are the only HIV-1 integrase inhibitor being used to treat HIV infections S/GSK1349572.
[10] Since IN has no equivalent in the host cell, integrase inhibitors have a high therapeutic index as they do not interfere with normal cellular processes.
[11] IN belongs, both mechanistically and structurally, to the superfamily of polynucleotidyl transferases 10 and is composed of 288 amino acids that form the 32 kDa protein.
The C-terminal domain (CTD), which encompasses amino acids 213–288, binds DNA nonspecifically and its interaction with NTD and CCD is required for IN 3´-processing and strand-transfer activities.
[6] In 3´processing IN binds to a short sequence located at either end of the long terminal repeat (LTR) of the viral DNA and catalyzes endonucleotide cleavage.
[9] Strand transfer is a trans-esterification reaction involving a direct nucleophilic attack of the 3´hydroxy group of the two newly processed viral 3´-DNA ends on the phosphodiester backbone of the host target DNA.
Strand transfer occurs simultaneously at both ends of the viral DNA molecule, with an offset of precisely five base pairs between the two opposite points of insertion.
[9][14] Divalent metals, Mg2+ or Mn2+, are required for 3'-processing and strand transfer steps as well as for assembly of IN onto specific viral donor DNA to form a complex that is competent to carry out either function.
[6] There are several ways to target integrase but strand transfer inhibition is the most intuitively obvious and readily pursued to date.
In fact, all small molecule HIV-1 INIs that are now being researched contain a structural motif that coordinates the two divalent magnesium ions in the enzyme's active site.
[8] Lens epithelial derived growth factor (LEDGF/p75) is a host protein that binds to integrase and is crucial for viral replication.
The mechanism of action is not precisely known but evidence suggest that LEDGF/p75 guides integrase to insert viral DNA into transcriptionally active sites of the host genome.
[16] INSTIs bind tightly and specifically to the IN that is associated with the ends of the DNA by chelating the divalent metal ions (Mg2+) which is coordinated by the catalytic triad i.e. the DDE motif.
[17] In fact, all potent integrase inhibitors possess a substituted benzyl component that is critical for maintaining 3‘end joining potency.
[6] When catechol-based inhibitors of IN were researched it was observed that maintaining a planar relationship with the bis-hydroxylated aryl ring increases potency.
The inhibitory activity could be further optimized by including a meta-chloro substituent, enhancing the interaction of the benzyl group with the adjacent hydrophobic pocket (see figure 4: Structures A-G).
[18] Benard et al (2004) synthesized INIs with a quinoline subunit and an ancillary aromatic ring linked by functionalized spacers such as amide, hydrazide, urea and hydroxyprop-1-en-3-one moiety.
[18] Since critical structure information is scarce on HIV integrase catalysis it is difficult to find the exact pharmacophore for its inhibition.
Wang et al (2010) hoped that by studying the SAR and pharmacophore of a dual inhibitor scaffold, focusing both on integrase and reverse transcriptase (RT) it would be possible to observe anti-integrase activity.
A DKA functionality or its heterocyclic bioisostere that selectively inhibit strand transfer seem to be present in all major chemotypes of integrase inhibitors.
[17] As detailed in the SAR discussion above the two necessary structural components of INI are a benzyl hydrophobic moiety and a chelating triad to bind the Mg2+ ions.
[11][17] However, despite previous success in clinical development (raltegravir), a detailed binding model is lacking so it has proven difficult to structure base the design of integrase inhibitors.
The adjacent hydroxyl and carboxylic groups on salicylic acid could bind with the metal ions and serve as their pharmacophore.
Polyhydroxylated aromatic inhibitors are mostly active against strand transfer reactions and 3‘-processing which suggests a mechanism that targets both steps.
When it was assessed alongside the primary mutations of raltegravir and elvitegravir it did not show cross-resistance which means that it could be useful against drug resistant viruses.
Newer drugs are warranted to overcome this pharmacological disadvantage and gain plasma concentrations high enough to target raltegravir-resistant viruses.
Development of a successful INSTI treatment was accomplished when raltegravir was discovered by Merck Sharp & Dohme Limited.
[22] Since there have been problems with resistance to raltegravir and elvitegravir, scientists have started to work on new second generation integrase inhibitors, such as MK-2048 which in 2009 was developed by Merck.
