Arginine mimetics

Synthesis of Novel Arginine Building Blocks with Increased Lipophilicity Compatible with Solid-Phase Peptide Synthesis

Arginine, due to the guanidine moiety, increases peptides' hydrophilicity and enables interactions with charged molecules, but at the same time, its presence in a peptide chain might reduce its permeability through biological membranes. This might be resolved by temporary coverage of the peptide charge by lipophilic, enzyme-sensitive alkoxycarbonyl groups. Unfortunately, such a modification of a guanidine moiety has not been reported to date and turned out to be challenging. Here, we present a new, optimized strategy to obtain arginine building blocks with increased lipophilicity that were successfully utilized in the solid-phase peptide synthesis of novel arginine vasopressin prodrugs.

Targeting Melanocortin Receptors Using SNAr-Type Macrocyclization: A Doubly Orthogonal Route to Cyclic Peptide Conjugates

While a range of strategies exist to accomplish peptide macrocyclization, they are frequently limited by the need for orthogonal protection or provide little opportunity for structural diversification. We have evaluated an efficient macrocyclization method that employs nucleophilic aromatic substitution (S_NAr) to create thioether macrocycles. This versatile macrocyclization, orthogonal to conventional peptide synthesis, can be performed in solution on unprotected peptidomimetics or on resin-bound peptides with side-chain protection in place. We show that the electron-withdrawing groups present in the products can be further utilized in subsequent orthogonal reactions to alter the peptide properties or to add prosthetic groups. The macrocyclization strategy was applied to the design of melanocortin ligands, generating a library of potent melanocortin agonists that exhibit distinct subtype selectivity.

Direct, Late-Stage Mono-N-arylation of Pentamidine: Method Development, Mechanistic Insight, and Expedient Access to Novel Antiparastitics against Diamidine-Resistant Parasites

A selective mono‐N‐arylation strategy of amidines under Chan‐Lam conditions is described. During the reaction optimization phase, the isolation of a mononuclear Cu(II) complex provided unique mechanistic insight into the operation of Chan‐Lam mono‐N‐arylation. The scope of the process is demonstrated, and then applied to access the first mono‐N‐arylated analogues of pentamidine. Sub‐micromolar activity against kinetoplastid parasites was observed for several analogues with no cross‐resistance in pentamidine and diminazene‐resistant trypanosome strains and against Leishmania mexicana. A fluorescent mono‐N‐arylated pentamidine analogue revealed rapid cellular uptake, accumulating in parasite nuclei and the kinetoplasts. The DNA binding capability of the mono‐N‐arylated pentamidine series was confirmed by UV‐melt measurements using AT‐rich DNA. This work highlights the potential to use Chan‐Lam mono‐N‐arylation to develop therapeutic leads against diamidine‐resistant trypanosomiasis and leishmaniasis.

Copper-Catalyzed One-Pot Synthesis of N-Sulfonyl Amidines from Sulfonyl Hydrazine, Terminal Alkynes and Sulfonyl Azides

N-Sulfonyl amidines are developed from a Cu-catalyzed three-component reaction from sulfonyl hydrazines, terminal alkynes and sulfonyl azides in toluene at room temperature. Particularly, the intermediate N-sulfonylketenimines was generated via a CuAAC/ring-opening procedure and took a nucleophilic addition with the weak nucleophile sulfonyl hydrazines. In addition, the stability of the product was tested by a HNMR spectrometer.

Calcium mediated efficient synthesis of N-arylamidines from organic nitriles and amines

Amidines are a preeminent group of organic compounds having wide applications in various industries. Here, we have developed a simple one-step reaction protocol for the facile synthesis of N-arylamidines catalysed by calcium bis(hexamethyldisilazide) [Ca{N(SiMe3)2}2(THF)2]. The amidine synthesis was readily achieved from organic nitriles and amines which provided a broad substrate scope ranging from electron-withdrawing to electron-donating substitutions as well as heterocyclic substitution. The reaction was carried out in a solvent-free medium under ambient conditions. The nucleophilic addition of aromatic amines to aryl nitriles led to good to excellent yields of the corresponding amidines. The reactivity of the amidines was further examined and the respective urea derivatives were achieved in excellent yields. The plausible mechanism involves the generation of an active calcium amido pre-catalyst that helps in the activation of nitriles in the reaction course.

The reaction mechanism of Zika virus NS2B/NS3 serine protease inhibition by dipeptidyl aldehyde: a QM/MM study

Zika virus (ZIKV) infection has become a global public health problem, associated with microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there are no commercially available anti-ZIKV drugs. The viral protease NS2B/NS3, which is involved in viral replication and maturation, is a potential drug target. Peptidomimetic aldehyde inhibitors bind covalently to the catalytic S135 of the NS3 protease. Here, we apply hybrid quantum mechanics/molecular mechanics (QM/MM) free-energy simulations at the PDDG-PM3/ff14SB level to investigate the inhibition mechanism of the ZIKV protease by a dipeptidyl aldehyde inhibitor (acyl-KR-aldehyde). The results show that proton transfer from the catalytic S135 to H51 occurs in concert with nucleophilic addition on the aldehyde warhead by S135. The anionic covalent complex between the dipeptidyl aldehyde and the ZIKV protease is analogous to the tetrahedral intermediate for substrate hydrolysis. Spontaneous protonation by H51 forms the hemiacetal. In addition, we use correlated ab initio QM/MM potential energy path calculations at levels up to LCCSD(T)/(aug)-cc-pVTZ to obtain accurate potential energy profiles of the reaction, which also support a concerted mechanism. These results provide detailed insight into the mechanism of ZIKV protease inhibition by a peptidyl aldehyde inhibitor, which will guide in the design of inhibitors.

Phosphonate inhibitors of West Nile virus NS2B/NS3 protease

West Nile virus (WNV) is a member of the flavivirus genus belonging to the Flaviviridae family. The viral serine protease NS2B/NS3 has been considered an attractive target for the development of anti-WNV agents. Although several NS2B/NS3 protease inhibitors have been described so far, most of them are reversible inhibitors. Herein, we present a series of α-aminoalkylphosphonate diphenyl esters and their peptidyl derivatives as potent inhibitors of the NS2B/NS3 protease. The most potent inhibitor identified was Cbz-Lys-Arg-(4-GuPhe)^P(OPh)₂ displaying K_i and k₂/K_i values of 0.4 µM and 28 265 M⁻¹s⁻¹, respectively, with no significant inhibition of trypsin, cathepsin G, and HAT protease.

One-pot synthesis of diverseN,N′-disubstituted guanidines fromN-chlorophthalimide, isocyanides and aminesvia N-phthaloyl-guanidines

A sequential one-pot approach towardsN,N′-disubstituted guanidines fromN-chlorophthalimide, isocyanides and amines is reported.

Intramolecular alkene hydroamination and degradation of amidines: divergent behavior of rare earth metal amidinate intermediates

The methods for catalytic intramolecular alkene hydroamination and degradation of amidines have been established. Furthermore, a tandem reconstruction/cyclization of amidines has also been developed.

Broad-spectrum agents for flaviviral infections: dengue, Zika and beyond

Infections with flaviviruses, such as dengue, West Nile virus and the recently re-emerging Zika virus, are an increasing and probably lasting global risk. This Review summarizes and comments on the opportunities for broad-spectrum agents that are active against multiple flaviviruses. Broad-spectrum activity is particularly desirable to prepare for the next flaviviral epidemic, which could emerge from as-yet unknown or neglected viruses. Potential molecular targets for broad-spectrum antiflaviviral compounds include viral proteins, such as the viral protease or polymerase, and host targets that are exploited by these viruses during entry and replication, including α-glucosidase and proteins involved in nucleoside biosynthesis. Numerous compounds with broad-spectrum antiviral activity have already been identified by target-specific or phenotypic assays. For other compounds, broad-spectrum activity can be anticipated because of their mode of action and molecular targets.

Exploration of the P3 region of PEXEL peptidomimetics leads to a potent inhibitor of the Plasmodium protease, plasmepsin V

The use of arginine isosteres is a known strategy to overcome poor membrane permeability commonly associated with peptides or peptidomimetics that possess this highly polar amino acid. Here, we apply this strategy to peptidomimetics that are potent inhibitors of the malarial protease, plasmepsin V, with the aim of enhancing their activity against Plasmodium parasites, and exploring the structure-activity relationship of the P3 arginine within the S3 pocket of plasmepsin V. Of the arginine isosteres trialled in the P3 position, we discovered that canavanine was the ideal and that this peptidomimetic potently inhibits plasmepsin V, efficiently blocks protein export and inhibits parasite growth. Structure studies of the peptidomimetics bound to plasmepsin V provided insight into the structural basis for the enzyme activity observed in vitro and provides further evidence why plasmepsin V is highly sensitive to substrate modification.

Macrosteres: The Deltic Guanidinium Ion

The "deltic guanidinium" ion is described here as a "macrostere" of the guanidinium ion. The use of the 2,4-dimethoxybenzyl protecting group allows for the synthesis of the fully unsubstituted parent compound and a variety of derivatives bearing multiple N-H functions for the first time. Deltic urea, deltic thiourea, and deltic benzamidine are also synthesized. A comparison of the physical properties of guanidinium and deltic guanidinium ions is provided. The use of a deltic guanidinium dendrimer for cell transport is demonstrated.

Structural basis for plasmepsin V inhibition that blocks export of malaria proteins to human erythrocytes

Plasmepsin V, an essential aspartyl protease of malaria parasites, has a key role in the export of effector proteins to parasite-infected erythrocytes. Consequently, it is an important drug target for the two most virulent malaria parasites of humans, Plasmodium falciparum and Plasmodium vivax. We developed a potent inhibitor of plasmepsin V, called WEHI-842, which directly mimics the Plasmodium export element (PEXEL). WEHI-842 inhibits recombinant plasmepsin V with a half-maximal inhibitory concentration of 0.2 nM, efficiently blocks protein export and inhibits parasite growth. We obtained the structure of P. vivax plasmepsin V in complex with WEHI-842 to 2.4-Å resolution, which provides an explanation for the strict requirements for substrate and inhibitor binding. The structure characterizes both a plant-like fold and a malaria-specific helix-turn-helix motif that are likely to be important in cleavage of effector substrates for export.

Recent development of synthetic preparation methods for guanidines via transition metal catalysis

This article provides an overview of guanidine synthesis via transition-metal-catalyzed reactions including cycloaddition, guanylation and tandem guanylation/cyclization.

Catalytic addition of amines to carbodiimides by bis(β-diketiminate)lanthanide(ii) complexes and mechanistic studies

Bis(β-diketiminate)lanthanide(ii) complexes L₂Ln(THF)_n were found to be excellent pre-catalysts for catalytic addition of amines to carbodiimides and a possible catalytic mechanism was proposed on the basis of the isolation of monoguanidinate Eu(ii) and bis(guanidinate) Yb(iii) species.

Peptidomimetics of Arg-Phe-NH2 as small molecule agonists of Mas-related gene C (MrgC) receptors

A series of Arg-Phe-NH2 peptidomimetics containing an Arg mimetic were synthesized and tested as agonists of human MrgX1, rat MrgC, and mouse MrgC11 receptors. As predicted from the previously established species specificity, these peptidomimetics were found to be devoid of MrgX1 agonist activity. In contrast, these compounds acted as agonists of MrgC and/or MrgC11 with varying degrees of potency. These new peptidomimetics should complement the existing small molecule human MrgX1 agonists and enhance our ability to assess the therapeutic utility of targeting Mrg receptors in rodent models.

The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems

The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.

Methyl N-(3-cyano-picolino-yl)-l-tryptophanate

In the title compound, C₁₉H₁₆N₄O₃, the stereocenter has an l configuration; l-tryptophan methyl ester hydro­chloride being used as a starting material. The indole ring system and the pyridine ring are inclined to one another by 13.55 (14)°. In the crystal, adjacent mol­ecules are linked via N—H⋯O hydrogen bonds, forming chains propagating along the c-axis direction.

Amine-free approach toward N-toluenesulfonyl amidine construction: a phosphite-mediated Beckmann-like coupling of oximes and p-toluenesulfonyl azide

Atom hopping: A chlorophosphite-mediated Beckmann ligation of oximes and p-toluenesulfonyl azide gives access to N-sulfonyl phosphoramidines in good to excellent yields. The reaction proceeds under exceptionally mild conditions and constitutes a bioorthogonal approach toward amidines by avoiding the use of amines and transition-metal catalysts. dmp-ol=3,3-dimethylpropanediol.

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.

Arginine mimetics using α-guanidino acids: introduction of functional groups and stereochemistry adjacent to recognition guanidiniums in peptides

Arginine residues are broadly employed for specific biomolecular recognition, including in protein-protein, protein-DNA, and protein-RNA interactions. Arginine recognition commonly exploits the potential for bidentate electrostatic and hydrogen-bonding interactions. However, in arginine residues, the guanidinium functional group is located at the terminus of a flexible hydrocarbon side chain, which lacks the functionality to contribute to specific arginine-mediated recognition and may entropically disfavor binding. In order to enhance the potential for specificity and affinity in arginine-mediated molecular recognition, we have developed an approach to the synthesis of peptides that incorporates an α-guanidino acid as a novel arginine mimetic. α-Guanidino acids, derived from α-amino acids, with guanidinylation of the amino group, were incorporated stereospecifically into peptides on solid phase via coupling of an Fmoc amino acid to diaminopropionic acid (Dap), Fmoc deprotection, guanidinylation of the amine on solid phase, and deprotection, generating a peptide containing an α-functionalized arginine mimetic. This approach was examined by incorporating arginine mimetics into ligands for the Src, Grb, and Crk SH3 domains at the site of the key recognition arginine. Protein binding was examined for peptides containing guanidino acids derived from Gly, L-Val, L-Phe, L-Trp, D-Val, D-Phe, and D-Trp. We demonstrate that paralogue specificity and target site affinity may be modulated with the use of α-guanidino acid-derived arginine mimetics, generating peptides that exhibit enhanced Src specificity by selection against Grb and peptides that reverse the specificity of the native peptide ligand, with enhancements in Src target specificity of up to 15-fold (1.6 kcal mol(-1)).

On-resin synthesis of novel arginine-isostere peptides bearing substituted amidine headgroups

A methodology is presented for the facile synthesis of Arg-containing peptides modified at the guanidine headgroup as substituted amidine cores. This process allows for the iterative construction of these Arg isosteres while the peptide is being built out on the solid support, providing a high potential for diversity in substitution pattern in the resulting peptide. A series of N-Pmc-substituted thioamides were condensed with deprotected δ-N Orn-bearing peptides while attached to the solid support using Mukaiyama's reagent as coupling reagent, yielding isosteric Arg-containing analogs. Peptides were cleaved using trimethylsilyl trifluoromethanesulfonate/TFA and analyzed in their crude form in order to illustrate the amenability of this process toward production of peptide isolates in high crude purity. Arg-containing peptides having a single Arg isostere were utilized to show the general utility of this approach as well as a multiple-Arg-containing construct, illustrating the amenability of this method toward stepwise construction of differently substituted amidine headgroups within the same peptide.