Practical and efficient synthesis of orthogonally protected constrained 4-guanidinoprolines

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.

N-Terminal Proline Editing for the Synthesis of Peptides with Mercaptoproline and Selenoproline: Mechanistic Insights Lead to Greater Efficiency in Proline Native Chemical Ligation

Native chemical ligation (NCL) at proline has been limited by cost and synthetic access. In addition, prior examples of NCL using mercaptoproline have exhibited stalling of the reaction after thioester exchange, due to inefficient S → N acyl transfer. Herein, we develop methods, using inexpensive Boc-4R-hydroxyproline, for the solid-phase synthesis of peptides containing N-terminal 4R-mercaptoproline and 4R-selenoproline. The synthesis proceeds via proline editing on the N-terminus of fully synthesized peptides on the solid phase, converting an N-terminal Boc-4R-hydroxyproline to the 4S-bromoproline, followed by an SN2 reaction with potassium thioacetate or selenobenzoic acid. After cleavage from the resin and deprotection, peptides with functionalized N-terminal proline amino acids were obtained. NCL reactions with mercaptoproline proceeded slowly under standard NCL conditions, with the S-acyl transthioesterification intermediate observed as a major species. Computational investigations indicated that the bicyclic intermediates and transition states for S → N acyl transfer are sufficiently low in energy (10-15 kcal mol-1 above starting material) that ring strain cannot explain the slow S → N acyl transfer. Instead, the bicyclic zwitterionic tetrahedral intermediate has a low barrier for reversion to the S-acyl intermediate, causing reversion to the thioester (reverse reaction) to occur preferentially over elimination to generate the amide (forward reaction). We hypothesized that a buffer capable of general acid and/or general base catalysis could promote S → N acyl transfer and thus achieve greater efficiency in proline NCL. In the presence of 2 M imidazole at pH 6.8, NCL with mercaptoproline proceeded efficiently to generate the peptide with a native amide bond. NCL with selenoproline also proceeded efficiently to generate the desired products when a thiophenol thioester was employed as a ligation partner. After desulfurization or deselenization, the products obtained were identical to those synthesized directly, confirming that the solid-phase proline editing reactions proceeded stereospecifically and without epimerization.

Application of (4R)-aminoproline in peptide engineering: conformational bias and pH-responsiveness revisited

How do we make proline residues pH sensitive?

Design and synthesis of fluorinated peptides for analysis of fluorous effects on the interconversion of polyproline helices

The unique interaction between fluorine atoms has been exploited to alter protein structures and to develop synthetic and analytical applications. To expand such fluorous interaction for novel applications, polyproline peptides represent an excellent molecular nanoscaffold for controlling the presentation of perfluoroalkyl groups on their unique secondary structure. We develop approaches to synthesis fluorinated peptides to systematically investigate how the number, location and types of the fluorous groups on polyproline affect the conformation by monitoring the transition between the two major polyproline structures PPI and PPII. This work provides valuable information on how fluorous interaction affects the peptide structure and also benefits the design of functional fluorous molecules.

Novel µ opioid antagonists derived from the µ opioid agonists endomorphin and [Dmt1 ]DALDA (H-Dmt-D-Arg-Phe-Lys-NH2 )

Hybrid analogues of the µ opioid agonists endomorphin and [Dmt¹ ]DALDA (H-Dmt-D-Arg-Phe-Lys-NH₂ , Dmt = 2',6'-dimethyltyrosine) containing cis-4-amino-Pro, trans-4-amino-Pro, cis-4-aminoethyl-Pro or cis-4-guanidinylethyl-Pro in the 2 position of the peptide sequence were synthesized. None of the compounds retained high µ opioid agonist activity and, unexpectedly, substitution of cis-4-amino-Pro resulted in a novel class of potent µ opioid antagonists. In particular, the compound H-Dmt-cis-4-amino-Pro-Trp-Lys-NH₂ (CZ-1) turned out to be a highly selective µ opioid antagonist with ~1 nM µ receptor binding affinity.

Pyrrolidine ring puckering and prolyl amide bond configurations of 2-methyl-allo-hydroxyproline-based dipeptides

An expeditious method for the synthesis of homo and heterochiral dipeptides containing l-alanine and d/l 2-methyl allo-hydroxyl prolines was developed using direct aminolysis of bicyclic lactones derived from d/l alanine. The impact of C-2 methylation and its spatial orientation on the pyrrolidine ring puckering and prolyl amide bond configuration was ascertained by solution NMR studies. The present studies reveal that C-2 methylation causes the prolyl amide bond to exist exclusively in the trans geometry in both homo- and heterochiral dipeptides. However, the spatial orientation of the C-2 methyl group and its i + 2 position in appropriately capped model dipeptides may nucleate into a turn like structure.

Discovery of a Branched Peptide That Recognizes the Rev Response Element (RRE) RNA and Blocks HIV-1 Replication

We synthesized and screened a unique 46 656-member library composed of unnatural amino acids that revealed several hits against RRE IIB RNA. Among the hit peptides identified, peptide 4A5 was found to be selective against competitor RNAs and inhibited HIV-1 Rev-RRE RNA interaction in cell culture in a p24 ELISA assay. Biophysical characterization in a ribonuclease protection assay suggested that 4A5 bound to the stem-loop region in RRE IIB while SHAPE MaP probing with 234 nt RRE RNA indicated additional interaction with secondary Rev binding sites. Taken together, our investigation suggests that HIV replication is inhibited by 4A5 blocking binding of Rev and subsequent multimerization.

Probing the Synergistic Catalytic Model: A Rationally Designed Urea-Tagged Proline Catalyst for the Direct Asymmetric Aldol Reaction

A urea tag was incorporated at the C-4 position of proline, cis to its COOH group, in order to explore the prospect of a synergistic effect between the two functional groups in the transition state of the enamine route to the asymmetric aldol reaction. The catalyst proved to be an excellent performer, delivering aldols in high yields and with excellent enantio- and diastereoselectivities using just 2 mol % loading in the presence of water; it also exhibited good levels of recyclability under aqueous conditions. The favorable results reveal the interesting possibility of an intramolecular host-guest interaction between the urea and the amino acid moieties, exerting a beneficial effect on catalysis. The concept could certainly offer a new direction toward more efficient catalyst design.

Development of a Cell-penetrating Peptide that Exhibits Responsive Changes in its Secondary Structure in the Cellular Environment

Cell-penetrating peptides (CPP) are received a lot of attention as an intracellular delivery tool for hydrophilic molecules such as drugs, proteins, and DNAs. We designed and synthesized nona-arginine analogues 1–5 [FAM-β-Ala-(l-Arg-l-Arg-l-Pro)₃-(Gly)₃-NH₂ (1), FAM-β-Ala-(l-Arg-l-Arg-l-Pro^NH2)₃-(Gly)₃-NH₂ (2), FAM-β-Ala-(l-Arg-l-Arg-l-Pro^Gu)₃-(Gly)₃-NH₂ (3), FAM-β-Ala-(l-Arg)₂-(l-Pro^Gu)₂-(l-Arg)₄-l-Pro^Gu-(Gly)₃-NH₂ (4), and FAM-β-Ala-(l-Arg)₆-(l-Pro^Gu)₃-(Gly)₃-NH₂ (5)] containing l-proline (l-Pro) or cationic proline derivatives (l-Pro^NH2 and l-Pro^Gu), and investigated their cell-penetrating abilities. Interestingly, only peptide 3 having the side-chain guanidinyl l-Pro^Gu exhibited a secondary structural change in cellular environment. Specifically, peptide 3 formed a random structure in hydrophilic conditions, whereas it formed a helical structure under amphipathic conditions. Furthermore, during cellular permeability tests, peptide 3 demonstrated greater cell-penetrating activity than other peptides and effectively transported plasmid DNA into HeLa cells. Thus, l-Pro^Gu-containing peptide 3 may be a useful candidate as a gene delivery carrier.

Proline editing: a general and practical approach to the synthesis of functionally and structurally diverse peptides. Analysis of steric versus stereoelectronic effects of 4-substituted prolines on conformation within peptides

Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase peptide synthesis to incorporate Fmoc-hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to "protect" the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR ((19)F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; (77)SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution-phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazine-trans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels-Alder reactions. These proline derivatives allowed three parallel bioorthogonal reactions to be conducted in one solution.

Crystal structure of (2S, 4R)-2-benzyl 1-tert-butyl 4-(tosyloxy)pyrrolidine- 1,2-dicarboxylate, C24H29NO7S

C24H29NO7S, triclinic, P1 (no. 1) , a = 6.5903(3) Å, b = 9.7193(5) Å, c = 9.9874(4) Å, α = 82.462(4)°, β = 77.197(3)°, γ = 85.6180(4)°,V = 617.7 Å3, Z = 1, Rgt(F) = 0.0351, wRref(F2) = 0.0967, T = 123 K.

Organic chemistry and biology: chemical biology through the eyes of collaboration

From a scientific perspective, efforts to understand biology including what constitutes health and disease has become a chemical problem. However, chemists and biologists "see" the problems of understanding biology from different perspectives, and this has retarded progress in solving the problems especially as they relate to health and disease. This suggests that close collaboration between chemists and biologists is not only necessary but essential for progress in both the biology and chemistry that will provide solutions to the global questions of biology. This perspective has directed my scientific efforts for the past 45 years, and in this overview I provide my perspective of how the applications of synthetic chemistry, structural design, and numerous other chemical principles have intersected in my collaborations with biologists to provide new tools, new science, and new insights that were only made possible and fruitful by these collaborations.

Substitution of arginine with proline and proline derivatives in melanocyte-stimulating hormones leads to selectivity for human melanocortin 4 receptor

A new series of melanotropin analogues with His or Arg residues in the core pharmacophores of MTII, SHU9119, and Ac-NDP-gamma-MSH-NH(2) replaced by Pro or trans-/cis-4-guanidinyl-Pro derivatives were designed and synthesized to introduce selectivity toward the human melanocortin 4 receptor (hMC4R). Analogues 1, 2, 3, 6, 7, 8 were found to be hMC4R selective. Second messenger studies have demonstrated that analogues 1 and 2 are insurmountable inhibitors of MTII agonist activity at the hMC4R. Molecular modeling studies suggest that the hMC4R selectivity is due to a beta-turn shift induced by the Pro ring that makes the global minimum structures of these analogues resemble the NMR solution structure of the hASIP melanocortin receptor binding motif. Substitution of His in MTII also provided functional selectivity for the hMC3R or the hMC4R. These findings are important for a better understanding of the selectivity mechanism at the hMC3R/hMC4R and the development of therapeutic ligands selectively targeting the hMC4R.

Highly Diastereo- and Enantioselective Direct Aldol Reactions of Aldehydes and Ketones Catalyzed by Siloxyproline in the Presence of Water

Proline-based organocatalysts have been developed for a highly enantioselective, direct aldol reaction of aldehydes and ketones in the presence of water. While several surfactant-proline combined catalysts have proved effective, proline derivatives with a hydrophobic moiety such as trans-siloxy-L-proline and cis-siloxy-D-proline, both of which are easily prepared from the same commercially available 4-hydroxy-L-proline, have been found to be the most effective organocatalysts examined in this study, affording the aldol product with excellent diastereo- and enantioselectivities, these two catalysts generating opposite enantiomers. Water affects the selectivity, and poor results are obtained under neat reaction conditions or in dry organic solvents. More than three equivalents of water are required for the best diastereo- and enantioselectivities, while three equivalents is the recommended amount from a synthetic point of view. The reaction proceeds in the organic phase, and also proceeds in the presence of a large amount of water. The large-scale preparation of aldols with the minimal use of an organic solvent, including in the purification step, is described.

Catalytic Addition of Amine NH Bonds to Carbodiimides by Half-Sandwich Rare-Earth Metal Complexes: Efficient Synthesis of Substituted Guanidines through Amine Protonolysis of Rare-Earth Metal Guanidinates

Reaction of [Ln(CH(2)SiMe(3))(3)(thf)(2)] (Ln=Y, Yb, and Lu) with one equivalent of Me(2)Si(C(5)Me(4)H)NHR' (R'=Ph, 2,4,6-Me(3)C(6)H(2), tBu) affords straightforwardly the corresponding half-sandwich rare-earth metal alkyl complexes [{Me(2)Si(C(5)Me(4))(NR')}Ln(CH(2)SiMe(3))(thf)(n)] (1: Ln = Y, R' = Ph, n=2; 2: Ln = Y, R' = C(6)H(2)Me(3)-2,4,6, n=1; 3: Ln = Y, R' = tBu, n=1; 4: Ln = Yb, R' = Ph, n=2; 5: Ln = Lu, R' = Ph, n=2) in high yields. These complexes, especially the yttrium complexes 1-3, serve as excellent catalyst precursors for the catalytic addition of various primary and secondary amines to carbodiimides, efficiently yielding a series of guanidine derivatives with a wide range of substituents on the nitrogen atoms. Functional groups such as C[triple chemical bond]N, C[triple chemical bond]CH, and aromatic C--X (X: F, Cl, Br, I) bonds can survive the catalytic reaction conditions. A primary amino group can be distinguished from a secondary one by the catalyst system, and therefore, the reaction of 1,2,3,4-tetrahydro-5-aminoisoquinoline with iPrN==C==NiPr can be achieved stepwise first at the primary amino group to selectively give the monoguanidine 38, and then at the cyclic secondary amino unit to give the biguanidine 39. Some key reaction intermediates or true catalyst species, such as the amido complexes [{Me(2)Si(C(5)Me(4))(NPh)}Y(NEt(2))(thf)(2)] (40) and [{Me(2)Si(C(5)Me(4))(NPh)}Y(NHC(6)H(4)Br-4)(thf)(2)] (42), and the guanidinate complexes [{Me(2)Si(C(5)Me(4))(NPh)}Y{iPrNC(NEt(2))(NiPr)}(thf)] (41) and [{Me(2)Si(C(5)Me(4))(NPh)}Y{iPrN}C(NC(6)H(4)Br-4)(NHiPr)}(thf)] (44) have been isolated and structurally characterized. Reactivity studies on these complexes suggest that the present catalytic formation of a guanidine compound proceeds mechanistically through nucleophilic addition of an amido species, formed by acid-base reaction between a rare-earth metal alkyl bond and an amine N--H bond, to a carbodiimide, followed by amine protonolysis of the resultant guanidinate species.

Solid Phase Synthesis of 3,4,7-Trisubstituted 4,5,8,9-Tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2(7H)-thiones and N-Alkyl-4,5,7,8-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2-amines

The solid-phase parallel synthesis of 3,4,7-trisubstituted 4,5,8,9-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2(7H)-thiones and N-alkyl-4,5,7,8-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2-amines starting from resin-bound dipeptides is described. The key synthetic steps involve the cylization of an amino and a guanidino functionality using thiocarbonyldiimidazole and the subsequent transformation of the resulting thiourea moiety to a substituted guanidine group using HgCl(2) and various amines. Following cleavage from the resin, the desired products were obtained in good yields and good to moderate purities, depending on the building blocks employed.

A practical synthesis of Nalpha-Fmoc-L-pyrazinylalanine via Schöllkopf's chiral auxiliary

A practical, gram-scale synthesis of L-pyrazinylalanine (Paa) is described, utilizing Schöllkopf's D-valine-derived bis-lactim ether chiral auxiliary.

A (4R)- or a (4S)-Fluoroproline Residue in Position Xaa of the (Xaa-Yaa-Gly) Collagen Repeat Severely Affects Triple-Helix Formation

The triple-helical fold of collagen requires the presence of a glycine residue at every third position in the peptide sequence and is stabilized by proline and (4R)-4-hydroxyproline residues in positions Xaa and Yaa of the (Xaa-Yaa-Gly) triplets, respectively. Regular down/up puckering of these Xaa/Yaa residues is possibly responsible for the tight packing of the three peptide strands, which have a polyproline-II-like structure, into the supercoiled helix. (4R)-Configured electronegative substituents such as a hydroxy group or a fluorine substituent on the pyrrolidine ring of the residue in the Yaa position favor the up pucker and thus significantly stabilize the triple helix. A similar effect was expected from the corresponding (4S)-isomers in the Xaa positions, but the opposite effect has been observed with (4S)-hydroxyproline, a result that has been speculatively attributed to steric effects. In this study, (4R)- and (4S)-fluoroproline residues were introduced into the Xaa position and potential steric effects were thus avoided. Contrary to expectations, (4S)-fluoroproline prevents triple-helix formation, whereas (4R)-fluoroproline stabilizes the polyPro II conformation, but without supercoiling of the three strands. The latter observation suggests that folding of the single chains into a polyproline II helix is not directly associated with triple helix formation and that fine tuning of van der Waals contacts, electrostatic interactions, and stereoelectronic effects is required for optimal packing into a triple helix.