Structure-based HIV drug design
One of the most remarkable examples of structure-guided drug design effort has been the development of drugs for the treatment of human immunodeficiency virus (HIV) infection. The three-dimensional structure of HIV protease was solved in 1989 and, based on its structure-activity relation, it was considered to be a good target for drug discovery.
The protease hydrolyzes the Gag and Gag-Pol polyproteins of the virus at different cleavage sites producing the structural proteins (viral envelope glycoproteins), and the reverse transcriptase (RT), integrase (IN) and protease (PR) enzymes which are all packed into new virion particles.
PR is a homodimer with each of the two subunits containing 99 amino acid residues. Two aspartate residues (Asp25) belonging to the two subunits come together at the dimer interface and form the catalytic site of the enzyme. Two flexible glycine-rich beta sheets form flaps over the top of the active site. The flaps move closer to the catalytic residues when the enzyme binds a substrate.
Publication of the protease structure led to the development of some successful antivirals. The first one to reach the market in 1995, with prompt approval from the Food and Drug Administration (FDA), was saquinavir, developed by Roche Pharmaceuticals. The time of six years ‘from bench to bedside’ is still a record for any novel drug.
Saquinavir binds to the protease dimer forming several H-bonds with the catalytic aspartates and surrounding residues. Binding of the normal substrate to the protease is thus prevented.
Saquinavir and other HIV protease inhibitors which followed were not free from problems of efficacy and toxicity. Subsequently, drug resistance mutations brought in additional complexity. Research continued towards formulations and development of drugs that would work by different mechanisms and target different steps in the HIV replication process.
Another major class of antiretroviral (anti-HIV) drugs emerged in 2007 with the FDA approval of raltegravir, an integrase inhibitor. Eleven years later, in 2018, the FDA approved biktarvy developed by Gilead Sciences, Inc., one of the leading biotech companies in the USA. Biktarvy contains a novel integrase strand transfer inhibitor (INSTI) bictegravir.
In the cytoplasm of the host cell, the genomic RNA of the virus is reverse transcribed to produce a copy of viral DNA (vDNA). Integration of the vDNA into the host cell chromosome is an absolute requirement for HIV replication cycle. The minimum functional complex (synaptic complex) for integration involves the vDNA and IN. It is a large nucleoprotein assembly, referred to as the intasome.
IN catalyzes an endonucleolytic cleavage at 3′-end of the vDNA, thereby releasing a GT dinucleotide and generating a nucleophilic CA-3′-hydroxyl. The cleaved synaptic complex (CSC) is now “catalytically competent” for the next step – strand transfer. IN catalyzes insertion of the two vDNA ends into the host chromosome.
The intasome is a suitable target for antiretroviral INSTIs. Bictegravir (on any other INSTI) binds HIV CSC within a pocket formed by the interface between two IN protomers and vDNA. For binding, two Mg2+ coordinate three electronegative heteroatoms in bictegravir and specific amino acid residues of IN.
National Institute of Allergy and Infectious Diseases (National Institutes of Health, USA) continues to support the development of new antiretroviral drugs and further improved HIV treatment can be expected in the near future.
* For basic concepts: Fundamentals of Molecular Structural Biology (Elsevier/Academic Press) Section 18.3
Reference
Ghosh, A.K., Osswald, H.L., Prato, G., 2016. Recent progress in the development of HIV-1 protease inhibitors for the treatment of HIV/AIDS. J. Med. Chem. 59 (11), 5172–5208.
Krohn, A., et al. (1991) Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere. J Med Chem 34: 3340-3342
Marchand, C. et al. (2006) Mechanisms and inhibition of HIV integration. Drug Discov Today Dis Mech. 3(2): 253–260.