Co-lethality studied as an asset against viral drug escape: the HIV protease case

Abstract

Background: Co-lethality, or synthetic lethality is the documented genetic situation where two, separately non-lethal mutations, become lethal when combined in one genome. Each mutation is called a "synthetic lethal" (SL) or a co-lethal. Like invariant positions, SL sets (SL linked couples) are choice targets for drug design against fast-escaping RNA viruses: mutational viral escape by loss of affinity to the drug may induce (synthetic) lethality.

Results: From an amino acid sequence alignment of the HIV protease, we detected the potential SL couples, potential SL sets, and invariant positions. From the 3D structure of the same protein we focused on the ones that were close to each other and accessible on the protein surface, to possibly bind putative drugs. We aligned 24,155 HIV protease amino acid sequences and identified 290 potential SL couples and 25 invariant positions. After applying the distance and accessibility filter, three candidate drug design targets of respectively 7 (under the flap), 4 (in the cantilever) and 5 (in the fulcrum) amino acid positions were found.

Conclusions: These three replication-critical targets, located outside of the active site, are key to our anti-escape strategy. Indeed, biological evidence shows that 2/3 of those target positions perform essential biological functions. Their mutational variations to escape antiviral medication could be lethal, thus limiting the apparition of drug-resistant strains.

Reviewers: This article was reviewed by Arcady Mushegian, Shamil Sunyaev and Claus Wilke.

Figure 1

Spatially close SLs. The whole graph represents the "spatially close SLs". The blue-shaded ovals, represents only the "accessible, spatially close SLs". Each oval contains the amino acid (one-letter codename) found in the HIV-1 protease ancestral sequence, followed by its position in this sequence. The accessible residues are all shaded in blue. The black edges linking the nodes mean "is co-lethal with and is within 10 Angström from". The four orange, boxed amino acids (N37, P39, K41, D60) are the locked targets jointly called SG flap. The three red, boxed amino acids (H69, K70, I72) are the locked targets called SG canti. The two yellow, boxed amino acids (L10, T12) are the locked targets called SG fulc1 and the two yellow double-boxed amino acids (K14, L19) are the locked targets called SG fulc2. SG fulc1 plus SG fulc2 are called all together SG fulc. The graph was built with Graphviz software.

Figure 2

locked targets (accessible, spatially close locked sets). All nodes shown here are accessible and spatially close amino acids The nodes in ovals are the accessible synthetic lethals which were shaded in blue on Figure 1, boxed with the same colour codes and linked by black edges. Each black edge means "is co-lethal with, and within 10 Angström from". The corresponding p-value is shown above each edge. Invariant amino acids are boxed in green, linked by dotted green edges meaning "is within 10 Angström from". All the nodes are shaded in blue because they are all accessible. Each invariant is also linked to all the other nodes by implicit edges, not shown, for the sake of clarity. The locked target represented subgraph "a" is called SGI flap (orange+green) The locked target represented subgraph "b" is called SGI canti (red+green) The locked target represented subgraph "c" is called SGI fulc (yellow+green) The graph was built using the Graphviz software.

Figure 3

3D view of the locked targets. 3D representation of the HIV-1 homodimer (1HSG) protease. Same colour codes as Figures 1 and 2. a: SGI flap (4 orange SLs + 3 green invariants) b: SGI flap + SGI canti (2 red SLs + 1 green invariant) c: SGI fulc (2 yellow SLs + 1 green invariant) d: SGI fulc + SGI canti (4 yellow SLs + 1 green invariant) The 3D molecules were built by pymol software.