Design, Synthesis, and Solution Structure of a Pyrrolinone-Based β-Turn Peptidomimetic

Protein synthesis with conformationally constrained cyclic dipeptides

We have synthesized several conformationally constrained dipeptide analogues as possible substrates for incorporation into proteins. These have included three cyclic dipeptides formed from Boc derivatives of 2,4-diaminobutyric acid, ornithine and lysine, having 5-, 6-, and 7-membered lactam rings, respectively. These dipeptides were used to activate a suppressor tRNA transcript, the latter of which had been prepared by in vitro transcription. Using modified E. coli ribosomes described previously, these activated suppressor tRNAs enabled the incorporation of the three cyclic dipeptides into dihydrofolate reductase (DHFR) at positions 18 and 49. The suppression yields increased with increasing lactam ring size and were found to proceed in suppression yields ranging from 3.4 to 8.9% at two different protein sites for the 5-, 6- and 7-membered lactam dipeptides. The greater facility of incorporation of the 7-membered lactam prompted us to prepare two 7-membered cyclic acylhydrazides (4 and 5) by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDCI)-mediated cyclization of amino acids having selectively protected hydrazine functional groups in their side chains. In common with the lactam dipeptides, acylhydrazide dipeptides 4 and 5 could be used to activate the same suppressor tRNA transcript and to incorporate the cyclic dipeptides into DHFR. They were incorporated into the same two DHFR sites in suppression yields ranging from 8.3 to 11.2%.

Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS

HIV-1 protease inhibitors continue to play an important role in the treatment of HIV/AIDS, transforming this deadly ailment into a more manageable chronic infection. Over the years, intensive research has led to a variety of approved protease inhibitors for the treatment of HIV/AIDS. In this review, we outline current drug design and medicinal chemistry efforts toward the development of next-generation protease inhibitors beyond the currently approved drugs.

Pyrrolinone-based peptidomimetics. "Let the enzyme or receptor be the judge"

Peptides and proteins, evolved by nature to perform vital biological functions, would constitute ideal candidates for therapeutic intervention were it not for their generally poor pharmacokinetic profiles. Nonpeptide peptidomimetics have thus been pursued because they might overcome these limitations while maintaining both the potency and selectivity of the parent peptide or protein. Since the late 1980s, we have sought to design, synthesize, and evaluate a novel, proteolytically stable nonpeptide peptidomimetic scaffold consisting of a repeating structural unit amenable to iterative construction; a primary concern is maintaining both the appropriate peptide-like side-chains and requisite hydrogen bonding. In this Account, we detail how efforts in the Smith-Hirschmann laboratories culminated in the identification of the 3,5-linked polypyrrolinone scaffold. We developed effective synthetic protocols, both in solution and on solid supports, for iterative construction of diverse polypyrrolinones that present functionalized peptide-like side-chains. As a result of the rigid nature of the pyrrolinone scaffold, control over the backbone conformation could be exerted by modulation of the stereogenicity of the constituent monomers and the network of intramolecular hydrogen bonding. The extended conformation of the homochiral 3,5-linked polypyrrolinone scaffold proved to be an excellent mimic for β-strands and β-sheets. Application to enzyme inhibitor design and synthesis led not only to modest inhibitors of the aspartic acid protease renin and the matrix metalloprotease class of enzymes, but importantly to bioavailable HIV-1 protease inhibitors with subnanomolar binding constants. The design and synthesis of a competent peptide-pyrrolinone hybrid ligand for the class II major histocompatibility complex (MHC) antigen protein HLA-DR1 further demonstrated the utility of the 3,5-polypyrrolinone motif as a mimic for the extended polyproline type II peptide backbone. Equally important, we sought to define, by synthesis, the additional conformational space accessible to the polypyrrolinone structural motif, with the ultimate goal of accessing pyrrolinone-based turn and helix mimetics. Toward this end, a mono-N-methylated bispyrrolinone was found to adopt an extended helical array in the solid state. Subsequent synthesis of d,l-alternating (heterochiral) tetrapyrrolinones both validated the expected turn conformations in solution and led to a functionally active mimetic of a peptidal β-turn (similar to somatostatin). Finally, the design, synthesis, and structural evaluation of both acyclic and cyclic heterochiral (that is, d,l-alternating) hexapyrrolinones yielded nanotube-like assemblies in the solid state. Taken together, these results illustrate the remarkable potential of the 3,5-linked polypyrrolinone scaffold as β-strand, β-sheet, β-turn, and potentially helical peptidomimetics.

Design, synthesis, and structural analysis of D,L-mixed polypyrrolinones. 2. Macrocyclic hexapyrrolinones

The design, synthesis, and structural analysis of two macrocyclic D,L-alternating hexapyrrolinones have been achieved. These cyclic peptide mimics adopt a flat, hexagonal conformation, stabilized by intramolecular hydrogen bonding between adjacent pyrrolinone rings. Extensive NMR studies and X-ray analysis reveal, respectively, that the macrocyclic hexapyrrolinones aggregate in solution and in the solid state form staggered stacked nanotube-like assemblies.

Design, synthesis, and structural analysis of D,L-mixed polypyrrolinones. 1. From nonpeptide peptidomimetics to nanotubes

To expand the potential conformational space available to the polypyrroline structural motif, an open chain, D,L-alternating hexapyrrolinone was designed and synthesized. Structural studies, including solution NMR and X-ray crystallographic analysis, revealed that the hexapyrrolinone adopts a turn conformation both in solution and in the solid state, with aggregation in solution and a nanotube-like quaternary structure in the crystal.

Privileged scaffolds targeting reverse-turn and helix recognition

BACKGROUND

Protein-protein interactions dominate molecular recognition in biologic systems. One major challenge for drug discovery arises from the very large surfaces that are characteristic of many protein-protein interactions.

OBJECTIVES

To identify 'drug-like' small molecule leads capable of modulating protein-protein interactions based on common protein-recognition motifs, such as alpha-helices, beta-strands, reverse-turns and polyproline motifs for example.

OVERVIEW

Many proteins/peptides are unstructured under physiologic conditions and only fold into ordered structures on binding to their cellular targets. Therefore, preorganization of an inhibitor into its protein-bound conformation reduces the entropy of binding and enhances the relative affinity of the inhibitor. Accordingly, this review describes a general strategy to address the challenge based on the 'privileged structure hypothesis' [Che, PhD thesis, Washington University, 2003] that chemical templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as small-molecule inhibitors of protein-protein interactions. The authors highlight recent advances in the design of privileged scaffolds targeting reverse-turn and helical recognition.

CONCLUSIONS

Privileged scaffolds targeting common protein-recognition motifs are useful to help elucidate the receptor-bound conformation and to provide non-peptidic, bioavailable substructures suitable for optimization to modulate protein-protein interactions.

Artificial protein sensors

Protein recognition by synthetic molecules is a challenging endeavour, since these materials must bind to a large relatively flat surface domain and recognize a unique distribution of amino acid residues of varying charge, size and shape. The most promising routes involve specific metal coordination, epitope-docking on miniature proteins, aptamer selection, nonnatural peptide isosteres, functionalized platforms, secondary structure mimetics, molecular imprinting and receptors embedded in lipid layers.

Development of small molecules designed to modulate protein-protein interactions

Protein-protein interactions are ubiquitous, essential to almost all known biological processes, and offer attractive opportunities for therapeutic intervention. Developing small molecules that modulate protein-protein interactions is challenging, owing to the large size of protein-complex interface, the lack of well-defined binding pockets, etc. We describe a general approach based on the "privileged-structure hypothesis" [Che, Ph.D. Thesis, Washington University, 2003] - that any organic templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as protein-complex antagonists--to address the challenges inherent in the discovery of small-molecule inhibitors of protein-protein interactions.

Design, synthesis, and biological evaluation of monopyrrolinone-based HIV-1 protease inhibitors possessing augmented P2' side chains

A series of monopyrrolinone-based HIV-1 protease inhibitors possessing rationally designed P2' side chains have been synthesized and evaluated for activity against wild-type HIV-1 protease. The most potent inhibitor displays subnanomolar potency in vitro for the wild-type HIV-1 protease. Additionally, the monopyrrolinone inhibitors retain potency in cellular assays against clinically significant mutant forms of the virus. X-ray structures of these inhibitors bound in the wild-type enzyme reveal important insights into the observed biological activity.

Bottom-up design of biomimetic assemblies

Nature has evolved the ability to assemble a variety of molecules into functional architectures that can specifically bind cellular ligands. Mimicking this strategy requires the design of a set of multifaceted molecules, where elements that direct assembly were conjugated to biologically specific components. The development of functional molecular building-blocks that assemble to form compartments for therapeutics addresses the desire to have controllable morphologies that interact with biological interfaces at nanometer length scales. The practical application of such 'bottom-up' assemblies requires the ability to predict the type of aggregated structure and to synthesize molecules in a highly controlled fashion. This bottom-up approach results in a molecular platform that mimics biological systems with potential for encapsulating and delivering drug molecules.

A Reverse Turn Structure Induced by a d,l-α-Aminoxy Acid Dimer

Our previous work revealed that two adjacent D-alpha-aminoxy acids could form two homochiral N-O turns, with the backbone folding into an extended helical structure (1.8(8)-helix). Here, we report the conformational studies of linear peptides 3-6, which contain a D,L-alpha-aminoxy acid dimer segment. The NMR and X-ray analysis of 3 showed that it folded into a loop conformation with two heterochiral N-O turns. This loop segment can be used to constrain tetrapeptides 4 and 6 to form a reverse turn structure. (1)H NMR dilution studies, DMSO-d6 addition studies, and 2D-NOESY data indicated that tetrapeptides 4 and 6 folded into reverse turn conformations featured by a head-to-tail 16-membered-ring intramolecular hydrogen bond. In contrast, tetrapeptide 5 with L-Ala instead of Gly or D-Ala as the N-terminal amino acid could not form the desired reverse turn structure for steric reasons. Quantum mechanics calculations showed that model pentamide 7, with the same substitution pattern of 4, adopted a novel reverse turn conformation featuring two heterochiral N-O turns (each of an 8-membered ring hydrogen bond), a cross-strand 16-membered ring hydrogen bond, and a 7-membered ring gamma-turn.

Stereoselective synthesis of beta-substituted phenylalanine-beta-phenylisoserine-derived tripeptides using N-cinnamoyl-L-proline as template: synthesis of structural analogues of HIV protease inhibitors

N-Cinnamoyl-L-proline can be used as a template on which beta-substituted phenylalanine and beta-phenylisoserine residues can be synthesized leading to tripeptide derivatives as structural analogues of HIV protease inhibitors.

Diastereoselective synthesis of psi[(E)-CMe=CH]- and psi[(E)-CMe=CMe]- type dipeptide isosteres based on organocopper-mediated anti-S(N)2' reaction

[reaction: see text] A straightforward synthetic route for the synthesis of diastereomerically pure psi[(E)-CMe=CH]- and psi[(E)-CMe=CMe]-type dipeptide isosteres was developed on the basis of regio- and stereoselective anti-S(N)2' alkylation of 3-(N-Boc-5-methyl-4-substituted-oxazolidin-2-on-5-yl)acrylates with organocopper reagents.