Design and synthesis of conformationally constrained amino acids as versatile scaffolds and peptide mimetics

My 50-Plus Years of Academic Research Collaborations with Industry. A Retrospective

A retrospective is presented highlighting the synthesis of selected "first-in-kind" natural products, their synthetic analogues, structure elucidations, and rationally designed bioactive synthetic compounds that were accomplished because of collaborations with past and present pharmaceutical and agrochemical companies. Medicinal chemistry projects involving structure-based design exploiting cocrystal structures of small molecules with biologically relevant enzymes, receptors, and bacterial ribosomes with synthetic small molecules leading to marketed products, clinical candidates, and novel drug prototypes were realized in collaboration. Personal reflections, historical insights, behind the scenes stories from various long-term projects are shared in this retrospective article.

Catalytic Reductive Recyclization of Functionalized Isoxazoline N-Oxides to Pyrrolizidine-3-ones

Pyrrolizidine is among the saturated N-heterocyclic scaffolds most frequently found in natural products and pharmaceutically relevant substances. Herein, a strategy for the synthesis of polysubstituted pyrrolizidine-3-ones by catalytic reductive domino-type recyclization of properly functionalized isoxazoline N-oxides was developed. The process is diastereoselective, and one diastereomer (out of four possible ones) is predominant in many of the studied cases. Using the developed method, modifications of potent GSK's PDE4 inhibitor and MSD's potent hNK1 antagonist were prepared.

β-Turn Induction by a Diastereopure Azepane-Derived Quaternary Amino Acid

β-Turns are one of the most common secondary structures found in proteins. In the interest of developing novel β-turn inducers, a diastereopure azepane-derived quaternary amino acid has been incorporated into a library of simplified tetrapeptide models in order to assess the effect of the azepane position and peptide sequence on the stabilization of β-turns. The conformational analysis of these peptides by molecular modeling, NMR spectroscopy, and X-ray crystallography showed that this azepane amino acid is an effective β-turn inducer when incorporated at the i + 1 position. Moreover, the analysis of the supramolecular self-assembly of one of the β-turn-containing peptide models in the solid state reveals that it forms a supramolecular helical arrangement while maintaining the β-turn structure. The results here presented provide the basis for the use of this azepane quaternary amino acid as a strong β-turn inducer in the search for novel peptide-based bioactive molecules, catalysts, and biomaterials.

Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics

The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and β-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed β-turn conformation preferred in solution and in solid state.

Pseudoprolines as stereoelectronically tunable proline isosteres

The cyclic structure of proline (Pro) confers unique conformational properties on this natural amino acid that influences polypeptide structure and function. Pseudoprolines are a family of Pro isosteres that incorporate a heteroatom, most prominently oxygen or sulfur but also silicon and selenium, to replace the C_β or C_γ carbon atom of the pyrrolidine ring. These readily synthetically accessible structural motifs can facilitate facile molecular editing in a fashion that allows modulation of the amide bond topology of dipeptide elements and influence over ring pucker. While the properties of pseudoprolines have been exploited most prominently in the design of oligopeptide analogues, they have potential application in the design and optimization of small molecules. In this Digest, we summarize the physicochemical properties of pseudoprolines and illustrate their potential in drug discovery by surveying examples of applications in the design of bioactive molecules.

Chiral-Boron-Complex-Catalyzed Asymmetric [3 + 2] Cycloaddition of 2'-Hydroxychalcones with N,N'-Cyclic Azomethine Imines

We report the (R)-3,3'-I₂-BINOL-boron-complex-catalyzed asymmetric 1,3-dipolar cycloaddition of 2'-hydroxychalcones with N,N'-cyclic azomethine imines, providing the corresponding N,N'-bicyclic pyrazolidine derivatives with three contiguous tertiary stereocenters in high yields with excellent diastereo- and enantioselectivities (up to >99:1 diastereomeric ratio and >99% enantiomeric excess). This catalytic system exhibits advantages of mild reaction conditions, high efficiency, and broad substrate scopes.

Synthesis, structural characterization, and evaluation of new peptidomimetic Schiff bases as potential antithrombotic agents

New Schiff bases functionalized with amide and phenolic groups synthesized by the condensation of 2-hydroxybenzaldehyde and 2-hydroxyacetophenone with amino acid amides which in turn were prepared in two steps from N-Boc-amino acids and homoveraltrylamine through intermediate compounds N-Boc-amino acids amides. The compounds were characterized by elemental analysis, FT-IR, UV–Vis, and NMR spectroscopy. The crystal structures of three Schiff bases were determined by single crystal X-ray diffraction. There exists O–H\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\cdots $$\end{document}⋯N, N–H\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\cdots $$\end{document}⋯O, and C–H\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\cdots $$\end{document}⋯O types of hydrogen bonds and C–H\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\cdots\uppi $$\end{document}⋯π secondary bonding interactions in these crystalline solids. The Schiff bases have been screened for anticoagulant and antiplatelet aggregation activities. All the compounds showed procoagulant activity which shortens the clotting time of citrated human plasma in both platelet-rich plasma and platelet-poor plasma except the derivatives of L-methionine which showed anticoagulant activity by prolonging the clotting time. In addition, the compounds derived from benzyl cysteine and phenylalanine showed adenosine diphosphate induced antiplatelet aggregation activity, whereas others did not show any role. Moreover, all these compounds revealed non-hemolytic activity with red blood cells.

Asymmetric Synthesis of Bicyclic Pyrazolidinones through Alkaloid-Catalyzed [3+2]-Cycloadditions of Ketenes and Azomethine Imines

A versatile asymmetric synthesis of bicyclic pyrazolidinones through alkaloid‐catalyzed formal [3+2]‐ and [3+2+2]‐cycloadditions of ketenes with azomethine imines is described. The methodology was found to be tolerant of ketene and a variety of monosubstituted ketenes (R=alkyl, OAc). The products were formed in good to excellent yields (71–99 % for 24 examples, 39 examples in all), with good to excellent diastereoselectivity in many cases (dr 3 : 1 to 27 : 1 for 22 examples), and with excellent enantioselectivity for most examples (≥93 % ee for 34 products). In the case of most disubstituted ketenes, the reaction proceeded through a [3+2+2]‐cycloaddition to form structurally interesting bicyclic pyrazolo‐oxadiazepinediones with moderate diastereoselectivity (dr up to 3.7 : 1) and as racemic mixtures (3 examples). The method represents the first unambiguous example of an enantioselective reaction between ketenes and a 1,3‐dipole.

Synthesis, crystal structure and Hirshfeld surface analysis of dimethyl 3-(3-bromophenyl)-6-methyl-7-oxo-3,5,6,7-tetrahydropyrazolo[1,2-a]pyrazole-1,2-dicarboxylate

In the title compound, one of the fused pyrazole rings adopts an envelope conformation while the other displays a twisted conformation. In the crystal, the mol­ecules are linked by C—H⋯O hydrogen bonds and aromatic π–π inter­actions.

The title compound, C₁₇H₁₇BrN₂O₅, resulted from the 1,3-dipolar cyclo­addition reaction between dimethyl acetyl­enedi­carboxyl­ate and (3-bromo­benzyl­idene)-4-methyl-5-oxopyrazolidin-2-ium-1-ide in CHCl₃. The dihedral angle between the pyrazole rings (all atoms) is 32.91 (10)°; the oxo-pyrazole ring displays an envelope conformation whereas the other pyrazole ring adopts a twisted conformation. The bromo­phenyl ring subtends a dihedral angle of 88.95 (9)° with the mean plane of its attached pyrazole ring. In the crystal, the mol­ecules are linked by C—H⋯O hydrogen bonds and aromatic π–π inter­actions with an inter-centroid distance of 3.8369 (10) Å. The Hirshfeld surface analysis and fingerprint plots reveal that the mol­ecular packing is governed by H⋯H (37.1%), O⋯H/H⋯O (31.3%), Br⋯H/H⋯Br (13.5%) and C⋯H/H⋯C (10.6%) contacts. The energy framework indicates that dispersion energy is the major contributor to the mol­ecular packing.

Amine-functionalized MCM-41 as an efficient catalyst for the synthesis of sulfur/dinitrogen-fused heterocycles via [3+3] cycloaddition in water

The sulfur/dinitrogen-containing heterocycle is an important chemical motif and is found widely in natural products, drug molecules, catalysts and functional materials.

DBU-catalyzed dearomative annulation of 2-pyridylacetates with α,β-unsaturated pyrazolamides for the synthesis of multisubstituted 2,3-dihydro-4H-quinolizin-4-ones

DBU-catalyzed dearomative [3 + 3] annulation of 2-pyridylacetates and α,β-unsaturated pyrazolamides for the synthesis of multisubstituted 2,3-dihydro-4H-quinolizin-4-ones was developed.

A DFT study on the formation of heterocycles via iodine(iii)-promoted ring expansion reactions

Combined computational–experimental study to elucidate the mechanism of HTIB-promoted ring expansion reaction of bicyclic heterocycles bearing an exocyclic double bond.

Constrained Dipeptide Surrogates: 5- and 7-Hydroxy Indolizidin-2-one Amino Acid Synthesis from Iodolactonization of Dehydro-2,8-diamino Azelates

The constrained dipeptide surrogates 5- and 7-hydroxy indolizidin-2-one N-(Boc)amino acids have been synthesized from L-serine as a chiral educt. A linear precursor ∆⁴-unsaturated (2S,8S)-2,8-bis[N-(Boc)amino]azelic acid was prepared in five steps from L-serine. Although epoxidation and dihydroxylation pathways gave mixtures of hydroxy indolizidin-2-one diastereomers, iodolactonization of the ∆⁴-azelate stereoselectively delivered a lactone iodide from which separable (5S)- and (7S)-hydroxy indolizidin-2-one N-(Boc)amino esters were synthesized by sequences featuring intramolecular iodide displacement and lactam formation. X-ray analysis of the (7S)-hydroxy indolizidin-2-one N-(Boc)amino ester indicated that the backbone dihedral angles embedded in the bicyclic ring system resembled those of the central residues of an ideal type II’ β-turn indicating the potential for peptide mimicry.

6-Hydroxymethyl Indolizidin-2-one Amino Acid Synthesis, Conformational Analysis, and Biomedical Application as Dipeptide Surrogates in Prostaglandin-F2α Modulators

6-Hydroxymethyl indolizidin-2-one amino acids were synthesized in 10 steps from l-serine by intramolecular ring opening of a symmetrical epoxide and lactam formation. X-ray analyses indicated the bicycles replicated ideal peptide type II' β-turn central dihedral angle geometry. Inside a prostaglandin-F_2α receptor modulator, the 6-hydroxymethyl analogue retained inhibitory activity on myometrial contractility.

Cyclisation strategies for stabilising peptides with irregular conformations

Cyclisation is a common synthetic strategy for enhancing the therapeutic potential of peptide-based molecules. While there are extensive studies on peptide cyclisation for reinforcing regular secondary structures such as α-helices and β-sheets, there are remarkably few reports of cyclising peptides which adopt irregular conformations in their bioactive target-bound state. In this review, we highlight examples where cyclisation techniques have been successful in stabilising irregular conformations, then discuss how the design of cyclic constraints for irregularly structured peptides can be informed by existing β-strand stabilisation approaches, new computational design techniques, and structural principles extracted from cyclic peptide library screening hits. Through this analysis, we demonstrate how existing peptide cyclisation techniques can be adapted to address the synthetic design challenge of stabilising irregularly structured binding motifs.

Synthesis of Chromeno[3,4-b]piperazines by an Enol-Ugi/Reduction/Cyclization Sequence

Keto piperazines and aminocoumarins are privileged building blocks for the construction of geometrically constrained peptides and therefore valuable structures in drug discovery. Combining these two heterocycles provides unique rigid polycyclic peptidomimetics with drug-like properties including many points of diversity that could be modulated to interact with different biological receptors. This work describes an efficient multicomponent approach to condensed chromenopiperazines based on the novel enol-Ugi reaction. Importantly, this strategy involves the first reported post-condensation transformation of an enol-Ugi adduct.

A three-component, general and practical route for diastereoselective synthesis of aza-spirocyclic pyrazolones via a decarboxylative annulation process

An efficient, general, and practical route for highly diastereoselective synthesis of aza-spirocyclic pyrazolones from easily available α-amino acids, aldehydes, and alkylidene pyrazolones by means of a decarboxylative annulation process is reported.

Ru(ii)-Catalyzed C–H activation/annulation reactions of N-aryl-pyrazolidinones with sulfoxonium ylides: synthesis of cinnoline-fused pyrazolidinones

The first Ru(ii)-catalyzed cascade C–H activation/annulation reactions of N-aryl-pyrazolidinones with sulfoxonium ylides are reported.

Selective and reversible 1,3-dipolar cycloaddition of 6-aryl-1,5-diazabicyclo[3.1.0]hexanes with 1,3-diphenylprop-2-en-1-ones under microwave irradiation

The first example of the cycloaddition of in situ-generated azomethine imine under microwave conditions is described. The reaction of 6-aryl-1,5-diazabicyclo[3.1.0]hexanes with 1,3-diphenylprop-2-en-1-ones proceeds regio- and stereoselectively giving mostly good yields of the corresponding perhydropyrazolopyrazoles. The products of the reaction undergo cycloreversion under the reaction conditions.

Strategies for Fine-Tuning the Conformations of Cyclic Peptides

Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.

Peptidomimetic toolbox for drug discovery

The art of transforming peptides into drug leads is still a dynamic and fertile field in medicinal chemistry and drug discovery. Peptidomimetics can respond to peptide limitations by displaying higher metabolic stability, good bioavailability and enhanced receptor affinity and selectivity. Various synthetic strategies have been developed over the years in order to modulate the conformational flexibility and the peptide character of peptidomimetic compounds. This tutorial review aims to outline useful tools towards peptidomimetic design, spanning from local modifications, global restrictions and the use of secondary structure mimetics. Selected successful examples of each approach are presented to document the relevance of peptidomimetics in drug discovery.

New frontiers in the transition-metal-free synthesis of heterocycles from alkynoates: an overview and current status

This review highlights the successful utilization of transition-metal-free approaches for the modular assembly of various heterocycles from alkynoates.

Chiral ScIII-N,N'-Dioxide-Catalyzed 1,3-Dipolar Cycloaddition of Diaziridines with Chalcones

A highly enantioselective 1,3-dipolar cycloaddition of meso-diaziridines with chalcones was realized by utilizing the Sc^III-N,N'-dioxide complex as the catalyst. In this transformation, the 1,3-dipole intermediates generated from the C-N bond cleavage of diaziridine were trapped by chiral N,N'-dioxide/scandium(III) complex activated chalcones to undergo enantioselective 1,3-dipolar cycloaddition. A range of chiral 1,5-diazabicylo[3.3.0]octane derivatives were readily synthesized in good yields with high diastereo- and enantioselectivities.

Synthesis of Functionalized 6,5- and 7,5-Azabicycloalkane Amino Acids by Metathesis Reactions

Azabicyclo[4.3.0]- and [5.3.0]alkanone amino acid derivatives were easily prepared by submitting the same starting dipeptide to a direct ring-closing enyne metathesis or an ethylene-mediated cross-enyne metathesis/ring-closing metathesis, respectively. The reactivity of the newly synthesized 6,5- and 7,5-fused bicyclic scaffolds was then investigated to obtain variously functionalized derivatives with potential applications in the field of peptides/peptidomimetics.

Multicomponent Synthesis of Polyphenols and their in vitro Evaluation as Potential β-Amyloid Aggregation Inhibitors

While plant polyphenols possess a variety of biological properties, exploration of chemical diversity around them is still problematic. Here, an example of application of the Ugi multicomponent reaction to the combinatorial assembly of artificial, yet "natural-like", polyphenols is presented. The synthesized compounds represent a second-generation library directed to the inhibition of β-amyloid protein aggregation. Chiral enantiopure compounds, and polyphenol-β-lactam hybrids have been prepared too. The biochemical assays have highlighted the importance of the key pharmacophores in these compounds. A lead for inhibition of aggregation of truncated protein AβpE3-42 was selected.

Solvent incorporated sequential [3 + 2] annulation/substitution reaction of azomethine imines and propargyl sulfur ylide

A novel solvent incorporated sequential [3 + 2] cycloaddition/substitution reaction of azomethine imines with propargyl sulfur ylide was developed. In the actual three-component reaction, propargyl sulfur ylide acts as a dipole reagent to furnish the annulation with azomethine imines, followed by the protic solvents acting as nucleophiles. The simple, mild, catalyst-free and practical protocol allows for the formation of N,N-bicyclic pyrazolidinones in moderate to excellent yields. Further transformation and gram-scale operations could also be achieved efficiently.

Selection and optimization of enzyme reporters for chemical cytometry

Chemical cytometry, sensitive analytical measurements of single cells, reveals inherent heterogeneity of cells within a population which is masked or averaged out when using bulk analysis techniques. A particular challenge of chemical cytometry is the development of a suitable reporter or probe for the desired measurement. These reporters must be sufficiently specific for measuring the desired process; possess a lifetime long enough to accomplish the measurement; and have the ability to be loaded into single cells. This chapter details our approach to rationally design and improve peptide substrates as reporters of enzyme activity utilizing chemical cytometry. This method details the iterative approach used to design, characterize, and identify a peptidase-resistant peptide reporter which acts as a kinase substrate within intact cells. Small-scale, rationally designed peptide libraries are generated to rapidly and economically screen candidate reporter peptides for substrate suitability and peptidase resistance. Also detailed are strategies to characterize and validate the designed reporters by determining kinetic parameters, intracellular substrate specificity, resistance to degradation by intracellular peptidases, and behavior within lysates and intact cells.

Synthesis of Enantiopure Constrained α,β-Cycloaliphatic Cystines via Diels-Alder Reaction with Homochiral Thiazolines

The behavior of homochiral 2,3-dihydrothiazoles, easily available from l-cysteine in Diels-Alder reaction with different dienes, "en route" to sterically constrained modified cystines, has been studied. The oxidation level of the sulfur atom of the heterocyclic ring was crucial for the course of the reaction. Whereas 2,3-dihydrothiazoles did not lead to Diels-Alder adducts, 1-oxide and 1,1-dioxide derivatives afforded the exo adduct enantiopurely in high yields and diastereoselectivities. Further elaboration of the resulting adducts provided conformationally restricted quaternary cystines. DFT calculations correctly predict both the reactivity and stereoselectivity observed experimentally.

Nα-Amino acid containing privileged structures: design, synthesis and use in solid-phase peptide synthesis

Fmoc-protected Nα-amino acid containing heterocyclic privileged structures, O-(1-methyl-5-oxo-2,5-dihydro-1H-pyrrol-3-yl)-l-serine and O-((S)-5-oxo-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl)-l-serine, were synthesized on the solid phase from simple commercially available building blocks under mild conditions. The amino acid side-chain is composed of tetramic acid, a natural product derived privileged structure. The key transformation was the formation of cyclic enol ethers via nonclassical Wittig olefinations of the esters. Solid-phase synthesis represents a method of choice, particularly for the synthesis of peptides. This route is compatible with traditional Merrifield solid-phase peptide synthesis (SPPS), as documented on the preparation of the pentapeptide Leu-enkephalin amide H-Tyr-Gly-Gly-Phe-Leu-NH2 with Phe or Tyr replaced by a novel amino acid.

Traceless Solid-Phase Synthesis of [6,7,8 + 5,6,7]-Fused Molecular Frameworks

We report two synthetic strategies for traceless solid-phase synthesis of molecular scaffolds comprising 6- to 8-membered rings fused with 5- to 7-membered rings. Traceless synthesis facilitated preparation of target molecules without any trace of polymer-supported linkers. The cyclization proceeded via acid-mediated tandem N-acylium ion formation followed by the nucleophilic addition of O- and C-nucleophiles. The presented synthetic strategy enabled, through the use of simple building blocks without any conformational preferences, the evaluation of the predisposition of different combinations of ring sizes to form fused ring molecular scaffolds. Compounds with any combination of [6,7 + 5,6,7] ring sizes were accessible with excellent crude purity. The 8-membered cyclic iminium was successfully fused only with the 5-membered cycle and larger fused ring systems were not formed, probably due to their instability.

New enolate-carbodiimide rearrangement in the concise synthesis of 6-amino-2,3-dihydro-4-pyridinones from homoallylamines

Three-step synthesis of 6-amino-2,3-dihydro-4-pyridinones from homoallylamines involving NBS-mediated cyclization of N-(3-butenyl)ureas to 6-(bromomethyl)-2-iminourethanes, dehydrohalogenation and a novel rearrangement as a key step has been developed. The scope and limitations of the method, as well as the mechanism of the rearrangement, supported by kinetic studies and the isolation of N-(1-adamantyl)carbodiimide, are discussed. The final products, imino-analogues of well known piperidine-2,4-diones, are promising building blocks in the synthesis of bio-/pharmacological compounds.