Engineering of a 129-residue tripod protein by chemoselective ligation of proline-II helices

Proline Analogues

Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.

Conformational studies of proline-, thiaproline- and dimethylsilaproline-containing diketopiperazines

As proline plays an important role in biologically active peptides, many analogues of this residue have been developed to modulate the proportion of cis and trans conformers. A correlation between the pyrrolidine ring shape and structural properties of proline has been established. Diketopiperazine (DKP) is the model of choice to study the influence of the proline ring modification. In this contribution, cyclo(Gly-Pro) and two analogues cyclo(Sip-Pro) and cyclo(Thz-Pro) have been studied with proton NMR. We showed that both analogues with heteroatoms in gamma position, silicon and sulfur respectively, display a more rigid five-member ring. The usual flexibility of proline ring is restrained in both cases and only the two C(beta)-exo and C(beta)-endo conformations are observed.

Evidence for Through-Space Electron Transfer in the Distance Dependence of Normal and Inverted Electron Transfer in Oligoproline Arrays

Four new helical oligoproline assemblies containing 16, 17, 18, and 19 proline residues and ordered arrays of a Ru(II)-bipyridyl chromophore and a phenothiazine electron-transfer donor have been synthesized in a modular fashion by solid-phase peptide synthesis. These arrays are illustrated and abbreviated as CH(3)CO-Pro(6)-Pra(PTZ)-Pro(n)()-Pra(Ru(II)b(2)m)(2+)-Pro(6)-NH(2), where PTZ is 3-(10H-phenothiazine-10)propanoyl and (Ru(II)b'(2)m)(2+) is bis(4,4'-diethylamide-2,2'-bipyridine)(4-methyl,4'-carboxylate,2,2'-bipyridine)ruthenium(II) dication with n = 2 (2), 3 (3), 4 (4), and 5 (5). They contain PTZ as an electron-transfer donor and (Ru(II)b'(2)m)(2+) as a metal-to-ligand charge transfer (MLCT) light absorber and are separated by proline-to-proline through-space distances ranging from 0 (n = 2) to 12.9 A (n = 5) relative to the n = 2 case. They exist in the proline-II helix form in water, as shown by circular dichroism measurements. Following laser flash Ru(II) --> b'(2)m MLCT excitation at 460 nm in water, excited-state PTZ --> Ru(2+) quenching (k(2)) occurs by reductive electron transfer, followed by Ru(+) --> PTZ(+) back electron transfer (k(3)), as shown by transient absorption and emission measurements in water at 25 degrees C. Quenching with DeltaG degrees = -0.1 eV is an activated process, while back electron transfer occurs in the inverted region, DeltaG degrees = -1.8 eV, and is activationless, as shown by temperature dependence measurements. Coincidentally, both reactions have comparable distance dependences, with k(2)( )()varying from = 1.9 x 10(9) (n = 2) to 2.2 x 10(6) s(-)(1) (n = 4) and k(3) from approximately 2.0 x 10(9) (n = 2) to 2.2 x 10(6) s(-)(1) (n = 4). For both series there is a rate constant enhancement of approximately 10 for n = 5 compared to n = 4 and a linear decrease in ln k with the through-space separation distance, pointing to a significant and probably dominant through-space component to intrahelical electron transfer.

Solvent Dependence of Intramolecular Electron Transfer in a Helical Oligoproline Assembly

The helical oligoproline assembly CH3-CO-Pro-Pro-Pro-Pra(Ptzpn)-Pro-Pro-Pra(RuIIb2m2+ -Pro-Pro-Pra(Anq)-Pro-Pro-Pro-NH2, having a spatially ordered array of functional sites protruding from the proline backbone, has been prepared. The 13-residue assembly formed a linear array containing a phenothiazine electron donor, a tris(bipyridine)ruthenium(II) chromophore, and an anthraquinone electron acceptor with the proline II secondary structure as shown by circular dichroism measurements. Following RuII --> b2m metal-to-ligand charge-transfer (MLCT) excitation at 457 nm, electron-transfer quenching occurs, ultimately to give a redox-separated (RS) state containing a phenothiazine (PTZ) radical cation at the Pra(Ptzpn) site and an anthraquinone (ANQ) radical anion at the Pra(Anq) site. The redox-separated state was formed with 33-96% efficiency depending on the solvent, and the transient stored energy varied from -1.46 to -1.71 eV at 22 +/- 2 degrees C. The dominant quenching mechanism is PTZ reductive quenching of the initial RuIII(b2m*-) MLCT excited state which is followed by m*- --> ANQ electron transfer to give the RS state. Back electron transfer is highly exergonic and occurs in the inverted region. The rate constant for back electron transfer is solvent dependent and varies from 5.2 x 10(6) to 7.7 x 10(6) s-1 at 22 +/- 2 degrees C. It is concluded that back electron transfer occurs by direct ANQ*- --> PTZ*+ electron transfer. Based on independently evaluated kinetic parameters, the electron-transfer matrix element is HDA approximately 0.13 cm-1.

Short, highly efficient syntheses of protected 3-azido- and 4-azidoproline and their precursors

[structure: see text] An improved synthesis of protected cis- and trans-3-azido-L-proline and cis- and trans-4-azido-L- and -D-proline is reported. These compounds have been synthesized from the corresponding hydroxyproline precursors using diphenylphosphoryl azide under Mitsunobu conditions. Short, highly efficient syntheses of these precursors are described, based on a new lactone-opening reaction and p-nitrobenzoate hydrolysis under very mild conditions.

Design, synthesis, and conformational analysis of azacycloalkane amino acids as conformationally constrained probes for mimicry of peptide secondary structures

Conformationally constrained amino acid and dipeptide units can serve in mimics of specific secondary structures for studying relationships between peptide conformation and biological activity. A variety of mimics are required to study systematically the structure-activity relationships in biologically relevant peptides. We present our efforts on the design, synthesis, and conformational analysis of a series of rigid surrogates of amino acid and dipeptide units for application within constrained peptide analogues, and for employment as inputs for combinatorial science. Conceived to be general and versatile, our methodology has delivered a variety of azacycloalkane and azabicycloalkane amino acids in enantiomerically pure form, via practical methods, from readily available and inexpensive starting materials.

Separation of positional isomers of oxidation catalyst precursors

A series of polypyridyl ruthenium complexes of the general formula [Ru(tpy)(bpy')Cl]+ where tpy is 2,2':6',2"-terpyridine and bpy' is 4-carboxy-4'-methyl-2,2'-bipyridine (4-CO2H-4'-Mebpy), a proline derviative (4-CO-Pra-(Boc)(OMe)-4'-Mebpy), or 4-((diethoxyphosphinyl)methyl)-4'-methyl-2,2'-bipyridine (4-CH2PO3Et2-4'-Mebpy) are prepared. For each complex, two isomers exist, and these are separated chromatographically. The structure of the hexafluorophosphate salt of cis-[Ru(tpy)(4-CO2H-4'-Mebpy)Cl]+, cis-1, is determined by X-ray crystallography. The salt crystallizes in the monoclinic space group Cc with a = 12.4778(6) A, b = 12.6086(6) A, c = 20.1215(9) A, beta = 107.08200(1) degrees, Z = 4, R = 0.058, and Rw = 0.072. The structures of the remaining complexes are assigned by 1H NMR comparisons with cis-1. The complexes are potentially important precursors for the incorporation of RuIV=O2+ oxidants into polymers or peptides or for their adsorption onto oxide surfaces. Preliminary electrochemical results for the isomers of [Ru(tpy)(4-CH2PO3H2-4'-Mebpy)(H2O)]2+, 4, adsorbed on ITO (In2O3:Sn) surfaces add support to a recently proposed electron-transfer mechanism involving cross-surface proton-coupled electron transfer.

Chemical synthesis of proteins

The manipulation of protein structure enables a better understanding of the principles of protein folding, as well as the development of novel therapeutics and drug-delivery vehicles. Chemical synthesis is the most powerful approach for constructing proteins of novel design and structure, allowing for variation of covalent structure without limitations. Here we describe the various chemical methods that are currently used for creating proteins of unique architecture and function.

Design and evaluation of benzophenone-containing conformationally constrained ligands as tools for photoaffinity scanning of the integrin alphaVbeta3-ligand bimolecular interaction

Integrins are cell-surface adhesion molecules involved in mediating cell-extracellular matrix interactions. High-resolution structural data are not available for these heterodimeric receptors. In order to generate tools for photoaffinity scanning of the RGD-binding site of human integrin alphaVbeta3. new conformationally constrained ligands were designed. The ligands were based on five different cyclic peptidic or peptidomimetic scaffolds with high affinity for alphaVbeta3. A single photoreactive group (a benzophenone moiety) was introduced at different positions relative to the RGD triad. In addition, an 125I or a biotin group was introduced as a reporting tag. Twenty-four cyclic ligands were prepared and their binding affinity for alphaVbeta3 was determined. In most cases, the modifications resulted in a 5- to 500-fold decrease in affinity relative to the unmodified scaffold. Analogs representing three of the five families were screened for their cross-linking efficiency. Ligands with submicromolar affinities cross-linked efficiently and specifically to the integrin receptor, whereas ligands with weaker affinities gave specific cross-linking, but with lower efficiency. Almost all of the screened ligands cross-linked predominantly to the beta3 subunit.

An examination of the steric effects of 5-tert-butylproline on the conformation of polyproline and the cooperative nature of type II to type I helical interconversion

The influence of steric effects on the helical geometry and the interconversion of type II to type I polyproline in water was examined by the synthesis and analysis of proline dimers and hexamers containing up to three (2S,5R)-5-tert-butylproline residues. In the dimers, the bulky 5-tert-butyl substituent was found to exert a significant influence on the local prolyl amide geometry such that the predominant trans-isomer in N-(acetyl)prolyl-prolinamide (1) was converted to 63% cis isomer in N-(acetyl)prolyl-5-tert-butylprolinamide (2) as measured by (1)H-nmr spectroscopy. Similarly, the presence of a 5-tert-butyl group on the C-terminal residue in the polyproline hexamer Ac-Pro(5)-t-BuPro-NH(2) (4) produced a local 5-tert-butylprolyl amide population containing 61% cis isomer in water. In spite of the presence of a local prolyl cis amide geometry, the downstream prolyl amides in 4 remained in the trans isomer as determined by NOESY spectroscopy. Conformational analysis by (13)C-nmr and CD spectroscopy indicated that Ac-Pro(6)-NH(2) (3) adopted the all-trans amide polyproline type II helix in water. As the amount of 5-tert-butylproline increased from one to three residues in hexamers 4-6, a gradual destabilization of the polyproline type II helical geometry was observed by CD spectroscopy in water; however, no spectrum was obtained, indicative of a complete conversion to a polyproline type I helix. The implications of these results are discussed with respect to the previously proposed theoretical mechanisms for the helical interconversion of polyproline, which has been suggested to occur by either a cooperative C- to N-terminal isomerization of the prolyl amide bonds or via a conformational intermediate composed of dispersed sequences of prolyl amide cis and trans isomers.