Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers

One of the main problems of drug design is that of optimizing the drug--target interaction. In the case in which the target is a viral protein displaying a high mutation rate, a second problem arises, namely the eventual development of resistance. We wish to suggest a scheme for the design of non--conventional drugs which do not face any of these problems and apply it to the case of HIV--1 protease. It is based on the knowledge that the folding of single--domain proteins, like e.g. 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 which play a central role in the folding process. Because LES have evolved over myriads of generations to recognize and strongly interact with each other so as to make the protein fold fast as well as to avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding--inhibitor drugs 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 which successfully avoid their action imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations within the framework of a simple although not oversimplified model, which is able to reproduce the main thermodynamic as well as dynamic properties of monoglobular proteins, 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 which do not create resistance

Multiple Routes and Milestones in the Folding of HIV–1 Protease Monomer

Proteins fold on a time scale incompatible with a mechanism of random search in conformational space thus indicating that somehow they are guided to the native state through a funneled energetic landscape. At the same time the heterogeneous kinetics suggests the existence of several different folding routes. Here we propose a scenario for the folding mechanism of the monomer of HIV–1 protease in which multiple pathways and milestone events coexist. A variety of computational approaches supports this picture. These include very long all-atom molecular dynamics simulations in explicit solvent, an analysis of the network of clusters found in multiple high-temperature unfolding simulations and a complete characterization of free-energy surfaces carried out using a structure-based potential at atomistic resolution and a combination of metadynamics and parallel tempering. Our results confirm that the monomer in solution is stable toward unfolding and show that at least two unfolding pathways exist. In our scenario, the formation of a hydrophobic core is a milestone in the folding process which must occur along all the routes that lead this protein towards its native state. Furthermore, the ensemble of folding pathways proposed here substantiates a rational drug design strategy based on inhibiting the folding of HIV–1 protease

Mitochondrial GTP‐AMP phosphotransferase

GTP‐AMP phosphotransferase has been purified 116‐fold with a yield of 24% from beef heart mitochondria using freeze‐thawing, alkali and acid treatment and successive column chromatography on phosphocellulose, Sephadex G‐100 and blue‐dextran–Sepharose. It has crystallized from poly(ethylene glycol) and is essentially homogeneous by sodium dodecylsulfate electrophoresis and isoelectrofocusing. The specific activity of the crystalline preparation was 290 U/mg. The molecular weight was found to be 26000 and the isoelectric point to be 9.8. Amino acid analysis showed 21 aspartic acid or asparagine, 19 threonine, 12 serine, 26 glutamic acid or glutamine, 15 proline, 16 glycine, 14 alanine, 15 valine, 4 methionine, 12 isoleucine, 28 leucine, 7 tyrosine, 7 phenylalanine, 5 histidine, 14 lysine, 16 arginine, 2 tryptophan, no –SS– bonds or free –SH. Guanosine(5′)pentaphospho(5′)adenosine is a very strong inhibitor similar to adenosine(5′)pentaphospho(5′)adenosine as an inhibitor of cytosolic adenylate kinase

Preliminary X-ray studies on the GTP: AMP phosphotransferase from beef heart mitochondria

Crystals of GTP: AMP phosphotransferase from beef heart mitochondria suitable for X-ray analysis have been grown. They belong to space group I4 with unit cell dimensions: . The asymmetric unit contains two molecules each of Mr = 26,000. So far, two heavy-atom derivatives have been obtained

Mitochondrial adenylate kinase (AK2) from bovine heart Homology with the cytosolic isoenzyme in the catalytic region

The adenylate kinase isoenzyme located in the intermembrane space of mitochondria, AK2, is a monomeric protein of Mr 30000 which catalyzes the reaction ATP + AMP 〙 2ADP. 1 The protein was reduced and S‐carboxymethylated with iodo[14C2]acetate. Using a Laursen sequenator, the N‐terminal sequence of S‐carboxymethylated AK2 was determined as Ala‐Pro‐Asn‐; in some batches of the isolated protein the N‐terminal dipeptide portion was missing. The C‐terminus of AK2 was found to be Met. 2 Cleavage with CNBr yielded eight fragments which could be isolated in one step using high‐performance size‐exclusion chromatography. They ranged in size over 4–88 amino acid residues, the total being approximately 270 residues. All CNBr fragments were overlapped with Met‐containing tryptic peptides of AK2. 3 The N‐terminal 111 residues of AK2 were sequenced. Except for an N‐terminal extension of nine residues, this segment of AK2 could be aligned with the sequence 1–104 of cytosolic AK1. Allowing for two deletions in AK2, 43 of the 102 aligned residues are identical. Since this section contains the catalytic residues such as His‐36 and Asp‐93, we conclude that AK1 can serve as a three‐dimensional model of AK2 in mechanistic and drug‐designing studies. 4 Preliminary sequence results on AK2 beyond position 104 show that AK2 here contains a wing of approximately 50 residues which has no counterpart in AK1. The chain folds of the adenylate kinase isoenzymes are similar again from a position corresponding to residue 115 of AK1 onwards. The additional structural motifs of AK2 are probably related to the location of this isoenzyme in the mitochondrion

STRUCTURAL RELATIONSHIPS IN THE ADENYLATE KINASE FAMILY

The sequences of five distantly related adenylate kinases have been aligned. The local conservation of amino acids is discussed in the light of the known three-dimensional structure of one of the enzymes, the cytosolic isoenzyme 1 (AK1) from porcine muscle. The similarity profile outlines clearly the active site in the cleft of the spatial structure of AK1. The alignment reveals further that the enzyme family can be subdivided into small and large variants according to the presence or absence of a particular segment of about 30 residues in the middle of the chain. The extra segments of the large variants are strongly conserve