Enantioselective synthesis of novel homochiral α-substituted (S)-isoserine derivatives. Incorporation of this amino acid in a highly conformationally constrained dipeptide surrogate

Optically pure isoserine derivatives with a chiral polyfunctional bicyclo[3.1.0]hexyl substituent at the α-carboxyl position were synthesized from a common cyclopentene precursor bearing an α-epoxy ester function in a side-chain. Cyclopropanation of the double bond and nucleophilic oxirane-ring opening by using a homochiral amine were the key steps. One of the synthesized derivatives was condensed with Cbz-cyclo-Asp-OMe affording a highly conformationally constrained dipeptide surrogate.     

Design and synthesis by click triazole formation of paclitaxel mimics with simplified core and side-chain structures

A library of paclitaxel (taxol) mimics was obtained by a straightforward strategy involving rational design and an efficient synthesis of a simplified taxane core substitute, together with a click-chemistry combinatorial search for phenylisoserine side-chain surrogates.     

Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes as conformationally constrained peptide inhibitors of Src SH2 domain binding.

Isothermal titration calorimetry and X-ray crystallography have been used to determine the structural and thermodynamic consequences associated with constraining the pTyr residue of the pYEEI ligand for the Src Homology 2 domain of the Src kinase (Src SH2 domain). The conformationally constrained peptide mimics that were used are cyclopropane-derived isosteres whereby a cyclopropane ring substitutes to the N-Calpha-Cbeta atoms of the phosphotyrosine. Comparison of the thermodynamic data for the binding of the conformationally constrained peptide mimics relative to their equivalent flexible analogues as well as a native tetrapeptide revealed an entropic advantage of 5-9 cal mol(-1) K(-1) for the binding of the conformationally constrained ligands. However, an unexpected drop in enthalpy for the binding of the conformationally constrained ligands relative to their flexible analogues was also observed. To evaluate whether these differences reflected conformational variations in peptide binding modes, we have determined the crystal structure of a complex of the Src SH2 domain bound to one of the conformationally constrained peptide mimics. Comparison of this new structure with that of the Src SH2 domain bound to a natural 11-mer peptide (Waksman et al. Cell 1993, 72, 779-790) revealed only very small differences. Hence, cyclopropane-derived peptides are excellent mimics of the bound state of their flexible analogues. However, a rigorous analysis of the structures and of the surface areas at the binding interface, and subsequent computational derivation of the energetic binding parameters, failed to predict the observed differences between the binding thermodynamics of the rigidified and flexible ligands, suggesting that the drop in enthalpy observed with the conformationally constrained peptide mimic arises from sources other than changes in buried surface areas, though the exact origin of the differences remains unclear.     

Synthesis of Novel Bioactive Dipeptides: i-PrTyr-Tic

Peptide side-chain conformations, especially the aromatic side-chain residues, play an important role in the molecular recognition processes between peptide ligands and their corresponding receptors. The modifications on peptide side-chain can result in biological activity changes and many other property changes. β-alkyl constrained α- amino acids have been applied for peptide molecular design, and have resulted in some important results in peptideresearch in recent years.[1～3]     

Substituent effects on the gas-phase fragmentation reactions of sulfonium ion containing peptides

The multistage mass spectrometric (MS/MS and MS3) gas-phase fragmentation reactions of methionine side-chain sulfonium ion containing peptides formed by reaction with a series of para-substituted phenacyl bromide (XBr where X=CH2COC6H4R, and R=--COOH, --COOCH3, --H, --CH3 and --CH2CH3) alkylating reagents have been examined in a linear quadrupole ion trap mass spectrometer. MS/MS of the singly (M+) and multiply ([M++nH](n+1)+) charged precursor ions results in exclusive dissociation at the fixed charge containing side chain, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility). However, loss of the methylphenacyl sulfide side-chain fragment as a neutral versus charged (protonated) species was observed to be highly dependent on the proton mobility of the precursor ion, and the identity of the phenacyl group para-substituent. Molecular orbital calculations were performed at the B3LYP/6-31+G** level of theory to calculate the theoretical proton affinities of the neutral side-chain fragments. The log of the ratio of neutral versus protonated side-chain fragment losses from the derivatized side chain were found to exhibit a linear dependence on the proton affinity of the side-chain fragmentation product, as well as the proton affinities of the peptide product ions. Finally, MS3 dissociation of the nominally identical neutral and protonated loss product ions formed by MS/MS of the [M++H]2+ and [M++2H]3+ precursor ions, respectively, from the peptide GAILM(X)GAILK revealed significant differences in the abundances of the resultant product ions. These results suggest that the protonated peptide product ions formed by gas-phase fragmentation of sulfonium ion containing precursors in an ion trap mass spectrometer do not necessarily undergo intramolecular proton 'scrambling' prior to their further dissociation, in contrast to that previously demonstrated for peptide ions introduced by external ionization sources.     

Synthesis of precursors of phomactins using [2,3]-Wittig rearrangements

o-Toluic acid has been converted into methyl (8RS,9SR)-7-(bromomethyl)-8,9-dimethyl-1,4-dioxaspiro[4.5]dec-6-ene-8-carboxylate, the stereochemical defining step being a conjugate addition of lithium dimethylcuprate to a cyclohexadienone prepared using a Birch reduction followed by an allylic oxidation. Displacement of the bromide with various propargylic alcohols followed by reduction of the ester and protection of the primary alcohol so formed then gave a series of propargyl cyclohexenylmethyl ethers. [2,3]-Wittig rearrangements of these and related propargylic ethers were studied as an approach to precursors of phomactins. The rearrangements were found to proceed by regioselective deprotonation of the propargylic side-chain to give substituted methylenecyclohexanes but mixtures of stereoisomers were obtained.Aspects of the chemistry of the Wittig rearrangement products were investigated including epoxidation, oxidation of the side-chain hydroxyl groups to give 2-ynones and reactions of the 2-ynones with lithium dimethylcuprate. The propargyl side-chain of a Wittig rearrangement precursor was elaborated to prepare an intermediate, which was fully functionalised for incorporation into a phomactin.     

Functionalized analogues of an unnatural amino acid that mimics a tripeptide beta-strand

This paper introduces polar and hydrophobic variants of the unnatural amino acid Hao, which mimics the hydrogen-bonding functionality of one edge of a beta-strand. In these variants, the methyl side chain of Hao is replaced with acidic, basic, and hydrophobic groups. These modifications can impart improved solubility and additional side-chain interactions to peptides containing Hao.     

Modeling the protein-nucleic acid base interactions through hydrogen-bonded complexes of N-heterocyclic analogs of Indene with amino acid side-chain mimics

A series of hydrogen-bonded complexes between N-heterocyclic analogs of Indene and amino acid side-chain mimics have been analyzed employing second-order Møller-Plesset perturbation (MP2) theory and density functional theory with dispersion function (DFT-D) calculations with the aim of gaining greater insight in to the nature of intermolecular interactions in these systems. In this study, the hydrogen bonding ability of N-heterocyclic analogs of Indene towards amino acid side-chain mimics follows the sequence Azaindazole (AIND) > Indazole (IND) > Azaindole (AIN) > Indole (IN) whereas the hydrogen bonding ability of amino acid side-chain mimics towards N-heterocyclic analogs of Indene follows the sequence AcOH > MeNH₂ > MeOH > MeSH. Bader’s theory of atoms in molecules (AIM) and natural bond orbitals (NBO) analyses are employed to elucidate the interaction characteristics in the complexes under study. The purpose of conducting these studies is to measure the relative strength of hydrogen bonding interactions such as N-H···O=C, N-H···O, N-H···S, N-H···N, and O-H···N in these complexes and their role in providing stability to the complexes. The AIM theory shows good correlation of the electron density and its Laplacian at the bond critical points (BCP) with the computed stabilization energy for all the complexes under study.

     

Conformationally Constrained Peptidomimetics as Inhibitors of the Protein Arginine Methyl Transferases

Protein arginine N‐methyl transferases (PRMTs) belong to a family of enzymes that modulate the epigenetic code through modifications of histones. In the present study, peptides emerging from a phage display screening were modified in the search for PRMT inhibitors through substitution with non‐proteinogenic amino acids, N‐alkylation of the peptide backbone, and incorporation of constrained dipeptide mimics. One of the modified peptides ( 23 ) showed an increased inhibitory activity towards several PRMTs in the low μm range and the conformational preference of this peptide was investigated and compared with the original hit using circular dichroism and NMR spectroscopy. Introducing two constrained tryptophan residue mimics (l ‐Aia) spaced by a single amino acid was found to induce a unique turn structure stabilized by a hydrogen bond and aromatic π‐stacking interaction between the two l ‐Aia residues.     

Design, synthesis, evaluation, and structure of vitamin D analogues with furan side chains

Based on the crystal structures of human vitamin D receptor (hVDR) bound to 1α,25-dihydroxy-vitamin D(3) (1,25 D) and superagonist ligands, we previously designed new superagonist ligands with a tetrahydrofuran ring at the side chain that optimize the aliphatic side-chain conformation through an entropy benefit. Following a similar strategy, four novel vitamin D analogues with aromatic furan side chains (3a, 3b, 4a, 4b) have now been developed. The triene system has been constructed by an efficient stereoselective intramolecular cyclization of an enol triflate (A-ring precursor) followed by a Suzuki-Miyaura coupling of the resulting intermediate with an alkenyl boronic ester (CD-side chain, upper fragment). The furan side chains have been constructed by gold chemistry. These analogues exhibit significant pro-differentiation effects and transactivation potency. The crystal structure of 3a in a complex with the ligand-binding domain of hVDR revealed that the side-chain furanic ring adopts two conformations.     

Synthesis of protected ω-mercapto amino acids: precursors for incorporation of elongated cysteines into peptides

A series of protected ω-mercapto amino acids with side-chain lengths ranging from 3–5 methylene units has been synthesized via nucleophilic substitution of ω-bromo-α-azido acids by 4-methoxy-α-toluenethiol followed by reduction of the azido functionality with SnCl₂. These enantiomerically pure protected cysteine analogues can be used to optimize the length of disulfide connections in cyclically constrained peptide pharmacophores.     

Structure-activity relationship studies on CXCR4 antagonists having cyclic pentapeptide scaffolds

Structure-activity relationship studies on CXCR4 antagonists, which were previously found by using cyclic pentapeptide libraries, were performed to optimize side-chain functional groups, involving conformationally constrained analogues. In addition, a new lead of cyclic pentapeptides with the introduction of a novel pharmacophore was developed.     

Design and Asymmetric Synthesis of beta-Strand Peptidomimetics

We describe the asymmetric synthesis of non-peptidic compounds that feature rigid backbone conformations and present various side-chain functions. The key step in the synthesis of these compounds is the C-acylation of an appropriate ketone with a suitably protected aspartic acid derivative. The resulting dipeptide modules may be connected to form tetrapeptide mimics. Specifically is described the mimicry of a four-residue segment of CD4, the cellular receptor of HIV-1. The design was based on molecular modeling and the X-ray crystal structures of CD4 and intended to present the most important side chains and backbone elements of the Phe43-Lys46 segment.     

Cone voltage and collision cell collision-induced dissociation study of triphenylethylenes of pharmaceutical interest.

Fragmentations of three triphenylethylene compounds (toremifene and its two metabolites) with different functional side-chain groups (alcohol, acid and amine) were studied. The compounds were dissociated by collision-induced dissociation (CID) in the interface region of an electrospray ionization source (ESI(+)) and in the collision cell of a triple quadrupole mass spectrometer. Fragmentation pathways for these molecules are proposed, based on accurate mass measurements of in-source fragment ions and MS/MS experiments using product and precursor ion scanning. The side-chain functional groups were found to strongly affect the fragmentations of the molecular ions. The fragmentation pathways of the protonated molecule and sodium ion adduct were quite similar, but the subsequent stabilities of certain common fragments were surprisingly different.     

Ionization and Photofragmentation of Isolated Metalloporphyrin Cations Investigated by VUV Action Spectroscopy**

We investigated the photoionization and fragmentation of isolated metal protoporphyrin IX cations (MPPIX⁺ with M=Fe, Co, Zn) by means of vacuum-ultraviolet (VUV) action spectroscopy in the energy range of 8.5–35 eV. Experiments were carried out in the gas phase by interfacing an electrospray ionization tandem mass spectrometer with a synchrotron beamline. The mass spectra and partial ion yields show that photoexcitation of the precursor ions predominantly leads to ^.CH₂COOH radical side-chain losses of the macrocycle with additional methyl radical (^.CH₃) side-chain losses. Ionization, in contrast, leads to the formation of the intact ionized precursor and various doubly charged fragments which are mostly due to side-chain cleavages. Although statistical fragmentation dominates, we found evidence for non-statistical processes such as new fragments involving for example single and double H₂O losses, indicating that different relaxation mechanisms are at play upon photoionization compared to photoexcitation. The measured ionization energies were 9.6±0.2 eV, 9.4±0.2 eV and 9.6±0.2 eV for FePPIX⁺, CoPPIX⁺ and ZnPPIX⁺, respectively.     

New chiral polyfunctional cyclobutane derivatives from (−)-verbenone: possible surfactant behaviour

New enantiopure cyclobutane derivatives have been synthesized from a chiral precursor derived from (?)-verbenone. The cyclobutane moiety acts as a chiral platform to afford a γ-amino acid function in a branched side-chain containing an additional stereogenic centre as well as additional C₆ or C₁₆-alkyl chains linked to the ring by means of an amine or an amide function. One of these compounds, obtained as a 1:2 mixture with its TFA salt has been investigated, suggesting behaviour as a good surfactant and its critical micellar concentration has been determined.     

Synthesis and conformational analysis of a cyclic peptide obtained via i to i+4 intramolecular side-chain to side-chain azide-alkyne 1,3-dipolar cycloaddition

Intramolecular side-chain to side-chain cyclization is an established approach to achieve stabilization of specific conformations and a recognized strategy to improve resistance toward proteolytic degradation. To this end, cyclizations, which are bioisosteric to the lactam-type side-chain to side-chain modification and do not require orthogonal protection schemes, are of great interest. Herein, we report the employment of Cu(I)-catalyzed 1,3-dipolar cycloaddition of side chains modified with azido and alkynyl functions and explore alternative synthetic routes to efficiently generate 1,4-disubstituted [1,2,3]triazolyl-containing cyclopeptides. The solid-phase assembly of the linear precursor including epsilon-azido norleucine and the propargylglycine (Pra) in positions i and i+4, respectively, was accomplished by either subjecting the resin-bound peptide to selective on-resin diazo transformation of a Lys into the Nle(epsilon-N3) or the incorporation of Fmoc-Nle(epsilon-N3)-OH during the stepwise build-up of the resin-bound peptide 1b. Solution-phase Cu(I)-catalyzed 1,3-dipolar cycloaddition converts the linear precursor Ac-Lys-Gly-Nle(epsilon-N3)-Ser-Ile-Gln-Pra-Leu-Arg-NH2 (2) into the 1,4-disubstituted [1,2,3]triazolyl-containing cyclopeptide [Ac-Lys-Gly-Xaa(&(1))-Ser-Ile-Gln-Yaa(&(2))-Leu-Arg-NH2][(&(1)(CH2)4-1,4-[1,2,3]triazolyl-CH2&(2))] (3). The conformational preferences of the model cyclopeptide 3 (III), which is derived from the sequence of a highly helical and potent i to i+4 side-chain to side-chain lactam-containing antagonist of parathyroid hormone-related peptide (PTHrP), are compared to the corresponding lactam analogue Ac[Lys(13)(&(1)),Asp(17)(&(2))]hPTHrP(11-19)NH2 (II). CD and NMR studies of 3 and II in water/hexafluoroacetone (HFA) (50:50, v/v) revealed a high prevalence of turn-helical structures involving in particular the cyclic regions of the molecule. Despite a slight difference of the backbone arrangement, the side-chains of Ser, Gln, and Ile located at the i+1 to i+3 of the ring-forming sequences share the same spatial orientation. Both cyclopeptides differ regarding the location of the turn-helical segment, which in II involves noncyclized residues while in 3 it overlaps with residues involved in the cyclic structure. Therefore, the synthetic accessibility and conformational similarity of i to i+4 side-chain to side-chain cyclopeptide containing the 1,4-disubstituted [1,2,3]triazolyl moiety to the lactam-type one may result in similar bioactivities.     

Synthesis of substituted conformationally constrained 6,5- and 7,5-fused bicyclic lactams as dipeptide mimics

Using a convenient and practical route we report the preparation of a series of rigid surrogates of amino acids and dipeptides for application within constrained peptide analogues, and for employment as input for combinatorial science. These substituted 2-oxo-1-azabicycloalkane amino acids have the potential of replicating the backbone geometry and side-chain function of dipeptide residues like serine, lysine, glutamate, and related amino acids.     

Dmab/ivDde protected diaminodiacids for solid-phase synthesis of peptide disulfide-bond mimics

The use of pre-prepared diaminodiacids has been established as an effective approach for the chemical synthesis of peptide disulfide bond mimics. A technical problem often encountered in the implementation of the diaminodiacids strategy is the use of heavy metal reagents to remove the side-chain protecting groups. In the present work, we reported the development of diaminodiacid that carry 4-(N-[1-(4,4-dimethyl-2,6-dioxocyclo-hexylidene)-3-methylbutyl]amino)benzyl (Dmab) and 1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)-3-methylbutyl (ivDde) protecting groups. This pair of protecting groups can be readily removed by mild hydrazinolysis during the solid-phase synthesis on resin. We demonstrated the use of Dmab/ivDde protected diaminodiacids in the successful synthesis of a disulfide surrogate of oxytocin.