Design of HIV‐1‐PR inhibitors that do not create resistance: Blocking the folding of single monomers

Abstract

The main problems found in designing drugs are those of optimizing the drug-target interaction and of avoiding the insurgence of resistance. We suggest a scheme for the design of inhibitors that can be used as leads for the development of a drug and that do not face either of these problems, and then apply it to the case of HIV-1-PR. It is based on the knowledge that the folding of single-domain proteins, such as each of the monomers forming the HIV-1-PR homodimer, is controlled by local elementary structures (LES), stabilized by local contacts among hydrophobic, strongly interacting, and highly conserved amino acids that play a central role in the folding process. Because LES have evolved over many generations to recognize and strongly interact with each other so as to make the protein fold fast and avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding-inhibitor molecules suggest themselves: short peptides (or eventually their mimetic molecules) displaying the same amino acid sequence of that of LES (p-LES). Aside from being specific and efficient, these inhibitors are expected not to induce resistance; in fact, mutations in HIV-1-PR that successfully avoid the action of p-LES imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations, we first identify the LES of the HIV-1-PR and then show that the corresponding p-LES peptides act as effective inhibitors of the folding of the protease.

More is Different: 50 Years of Nuclear BCS

“…56 Such peptides, called p-LES, can bind a complementary LES leading to misfolding and thus competing with productive folding. 39,51,57 Circular dichroism is consistent with such a scenario 58,59 , while NMR indicates that the only amino acids which give a signal similar to that associated with the native state of the protein are those which bind in the native state to the LES of which the peptide p-LES is a replica.…”

“…It only means that to do so a concerted mutation of a large number of amino acids evolution and thus forcing the protein to become again a random polymer) folding inhibitors are likely to be leads of drugs which do not create resistance. [51][52][53][54]58,59,[62][63][64][65] has to take place in a single step, an event which is very unlikely.…”

Protein folding: Understanding the role of water and the low Reynolds number environment as the peptide chain emerges from the ribosome and folds

“…This approach is in part based upon the decoupling of monomer folding and assembly of the dimer (Levy et al, 2004) and offers the hope of overcoming the development of resistance that is a problem with active site inhibitors (Broglia et al, 2005). Clearly, the effectiveness of this strategy should be increased by a better understanding of the mechanism of the early stages of protein folding.…”

Design of a folding inhibitor of the HIV-1 protease

“…A different strategy for the inhibition of an enzyme is to interfere with its folding, destabilizing the native state of the protein [5,6]. This is done exploiting the fact that the stabilization energy of a protein is not distributed evenly among the amino acids, but is concentrated in a core of mutually interacting residues [3,4,7].…”

“…The fragments of the protein which carry these "hot" residues (called local elementary structures (LES) in [8]) play a key role also for the folding kinetics [9,10]. The basic idea is to destabilize a protein in solution by adding short peptides with the same sequence as a LES of the protein [5,6]. We shall call these peptides p-LES.…”