i VIETNAM NATIONAL UNIVERSITY, HANOI VNU UNIVERSITY OF SCIENCE FACULTY OF CHEMISTRY Trần Thị Minh Châu Synthesis of Cyclic β Peptidomimetics by Ring Closing Metathesis Submitted in partial fulfillment of the requirements for the course of CHE4050 in Chemistry (Advanced program in Chemistry) Hanoi 2021 ITY OF SCIENCE ii VIETNAM NATIONAL UNIVERSITY, HANOI VNU UNIVERSITY OF SCIENCE FACULTY OF CHEMISTRY Trần Thị Minh Châu Synthesis of Cyclic β Peptidomimetics by Ring Closing Metathesis Submi.
Literature Review
Overview of peptides
Proteins, or polypeptides, are essential organic molecules found abundantly in living organisms, serving a wide array of functions Each cell can house thousands of distinct proteins, each fulfilling a specific role These versatile macromolecules contribute to cell membranes, act as enzymes and co-factors in biochemical processes, and function as chemical messengers within the human immune system.
The major building block of proteins are called α-amino acids (Figure 1) [5]
Amino acids are organic compounds that contain both a carboxylic acid functional group and an amine functional group, with the alpha designation indicating that these groups are separated by a single carbon atom In addition to the amine and carboxylic acid, the alpha carbon is bonded to a hydrogen atom and a variable R-group, which can differ in size and length In living organisms, there are 20 distinct amino acids that serve as the building blocks of proteins, differing only at the R-group position.
Figure 1 General structure of an α-amino acid
Protein function is primarily regulated by protein-protein interactions (PPI), which involve physical contacts and molecular docking between proteins within cells Disruption of these interactions can lead to various diseases, including the recent COVID-19 pandemic caused by the SARS-CoV-2 virus The binding of the viral spike proteins to ACE2 receptors on human lung cells is a crucial step for viral entry, resulting in respiratory complications Consequently, designing molecules that can target these protein sites to act as agonists or antagonists is a vital focus in drug development to mitigate undesirable health effects.
Peptides are promising candidates for inhibiting protein-protein interactions (PPIs) due to their ability to mimic protein surfaces and compete for binding They are synthetically accessible and can be chemically modified for stabilization It is estimated that 15% to 40% of cellular interactions involve PPIs By rationally designing peptides based on natural sequences that mediate these interactions, they can effectively mask critical binding sites Additionally, peptides have the capability to modulate intracellular targets by crossing cell membranes independently or through conjugation with cell-penetrating peptides.
Insulin, the first therapeutic peptide isolated, has been used to treat diabetes since 1922 The field of synthetic pharmaceutical peptides gained momentum in the early 1950s due to du Vigneaud's groundbreaking work on sequencing and synthesizing oxytocin and vasopressin Today, the use of natural and novel peptides as therapeutics is widespread, with around 60 peptide-based drugs available for various conditions, including diabetes, gastrointestinal disorders, osteoporosis, cancers, and infections Most therapeutic peptides function as receptor agonists, with only a small percentage of receptors (5-20%) needing to be occupied to achieve the desired therapeutic effect.
Since the 1950s, there has been significant interest in natural endogenous peptides; however, their unfavorable physicochemical properties often hinder their use as effective therapeutics These peptides typically exhibit limited stability against proteolysis, leading to a short half-life of only a few minutes.
Peptide therapeutics often face challenges in absorption and transport due to their relatively high molecular mass and the absence of specific transport systems, leading to rapid excretion through the liver and kidneys Their interaction with multiple biological targets results in poor selectivity and potential side effects, a consequence of the inherent flexibility from the rotatable bonds in amino acids Furthermore, oral administration is typically ineffective due to rapid degradation in the digestive system, prompting the need for parenteral injection as the preferred method of delivery.
Overview of peptidomimetics
Peptidomimetics are compounds designed to replicate the three-dimensional structure of natural peptides or proteins, allowing them to effectively interact with biological targets and elicit similar biological effects.
Peptidomimetics offer enhanced selectivity and efficiency compared to native peptides, leading to reduced side effects Additionally, they demonstrate improved oral bioavailability and prolonged biological activity, primarily due to their lower susceptibility to enzymatic degradation.
The creation of peptidomimetics relies on an understanding of the electronic and conformational characteristics of both the native peptide and its receptor or binding site Therefore, when developing peptidomimetics with potential biological activity, it is essential to consider fundamental principles.
• Replacement of peptide backbone with a non-peptide framework
• Preservation of sidechains involved in biological activity, as they constitute the pharmacophore
• Maintenance of flexibility in first-generation peptidomimetics
• Selection of proper targets based on a pharmacophore hypothesis
An important goal in the development of rationally designed mimics is to restrict the backbone and the side chain moieties into protein secondary structure
7 motifs (e.g., α-helix, β-strand or β-turn) [20] These structures are defined by their φ (phi), ψ (psi) and ω (omega) angles, while the side chain geometry is defined by
Figure 2 Dihedral angles that define peptide structure The backbone is defined by φ, ψ, ω, the side chain geometry is defined by 𝜒
Peptidomimetics may be divided into three types depending on their structural and functional characteristics [2]:
• Type I mimetics, or structural mimetics, show a strict analogy with the native substrate, as they carry all the functionalities in the same spatial orientation
Type II mimetics, also known as functional mimetics, lack structural similarities to the native substrate yet effectively replicate its function They achieve this by interacting with the target receptor or enzyme in a manner akin to the original substrate.
• Type III mimetics, or functional-structural mimetics, possess a scaffold significantly different from the native substrate, while displaying the interacting elements in the same spatial orientation
2.2.3 Synthetic approaches towards peptidomimetics design
There are various approaches to generating peptidomimetics, with the choice of design strategy influenced by the target protein's structure, sequence, function, and binding site characteristics This article discusses synthetic strategies that aim to restrict the φ, ψ, ω, and 𝜒 angles of peptidomimetics, which can be broadly classified into three categories.
8 categories, side chain modification, backbone modification, and introduction of global restrictions
The side chain orientation of an α-amino acid is critical for molecular recognition and transduction processes [21] There are three low energy staggered conformations that are possible (Figure 3)
Figure 3 Newman projections of low energy staggered conformers in α-amino acids
In peptide conformations, the gauche (-) orientation positions the side chain towards the N-terminus, while the gauche (+) orientation aligns it perpendicularly to the peptide backbone, and the anti-conformation directs it towards the C-terminus These three conformations are typically accessible due to the low energy barrier between them However, during peptide-receptor interactions, each side chain will adopt the specific conformation necessary for effective binding Constraining the χ angles to fix side chain geometry is a valuable strategy in peptidomimetic synthesis, as side chain modifications generally do not limit the peptide backbone's conformation.
Figure 4 Natural phenylalanine and β-alkyl analogue 1.01
Side chain orientation can be constrained by alkylation of the β-carbon (Figure 4) The rationale behind this is to isolate the biologically active χ rotomer
Steric hindrance of rotation about the χ1 bond plays a crucial role in the β-carbon alkylation of peptides, including endogenous opioids, oxytocin, somatostatin, and glucagon, to explore topographical requirements and structure-activity relationships Substituting natural amino acids with rigidified analogues can enhance activity and bio-stability; for instance, replacing phenylalanine with a rigid analogue in a peptide effectively modifies its activity at opioid receptors.
2.2.3.2 Strategies for restriction of φ, ψ, and ω torsion angles
Replacement of individual atoms Extension of peptide chain
NH-CO CH(OH)CH 2
Table 1 The most common forms of backbone modification of peptides to create peptidomimetics
The most common forms of backbone modification are given in Table 1
These modifications generally reduce the mimic’s affinity to proteolytic cleavage and, in some cases, restrict the flexibility of the backbone
Backbone modification in peptides can involve the replacement of individual atoms, extension of the peptide chain, or alteration of the amide bond to enhance cell permeation and bio-stability Specifically, substituting the NH group with an N-alkyl substituent can restrict the φ torsion angle and eliminate hydrogen bonding from the amide bond, thereby improving membrane penetration and proteolytic stability Naturally occurring peptides, like Cyclomarin C, exemplify the effectiveness of N-alkylation, which is widely used in creating synthetic peptidomimetic libraries for studying structure-activity relationships By removing hydrogen bonding capabilities through N-methylation, researchers can alkylate each backbone NH and assess the biological activity of derivatives to pinpoint crucial hydrogen bonds essential for activity.
The Thorpe-Ingold effect highlights the effectiveness of carbon substitution in restricting molecular conformation to promote ring closure This principle has led to extensive studies on the alkylation of α-carbons as a strategy for developing peptidomimetics, primarily due to the reduced rotation of α-alkyl amino acids around the φ and ψ torsion angles A prime example of a tetra-substituted amino acid is α-aminoisobutyric acid (Aib), which is naturally occurring.
Figure 5 Structure of tera-substituted Aib
The introduction of global restrictions on peptide conformation by cyclization is a recognized universal method for the preparation of peptidomimetics [20] The
Introducing rigid bridges of varying lengths within different segments of a peptide can enhance potency by stabilizing the backbone torsion angles and side chain orientation, effectively locking the ligand into an optimal bioactive conformation.
Cyclic peptidomimetics can be generated through three main approaches: backbone-backbone (including head-to-tail), backbone-side chain, or side chain-side chain cyclization The most prevalent method involves creating disulfide bridges or lactamization Numerous natural cyclic peptides, such as somatostatin, oxytocin, vasopressin, ciclosporin, and cyclotides, feature either amide linkages or disulfide bridges Given nature's tendency to utilize these cyclization methods, it is not surprising that many reported peptidomimetics, designed to target various proteins, incorporate lactam or disulfide bridges.
Figure 6 The three principles arrangements of peptide cyclization
Compounds featuring lactam and disulfide bridges, while capable of stabilizing secondary structures, are not optimal as peptidomimetics due to their susceptibility to degradation and recognition as substrates in vivo Natural hormones like oxytocin and vasopressin exemplify this limitation, as their therapeutic applications are restricted by short in vivo half-lives of just 2 to 5 minutes, necessitating intravenous administration for effective use.
Figure 7 Hormones containing a disulfide bridge.
Ring closing metathesis route to cyclic β-peptidomimetics
Ring closing metathesis has become a highly effective technique for creating carbon-carbon bonds in complex molecules, such as peptidomimetics This process involves the exchange of alkylidene groups in alkenes through a reversible mechanism, as proposed by Chauvin.
Figure 8 Ring closing metathesis mechanism
Metathesis became a viable synthetic technique for organic chemists with the development of air stable, functional group tolerant ruthenium catalysts,
The discovery of ruthenium-based catalysts in the early 1990s revolutionized ring-closing metathesis, making it a vital synthetic method in organic chemistry Unlike earlier transition metal catalysts, ruthenium catalysts are generally less active but offer greater versatility by preferentially reacting with olefins In contrast, molybdenum, tungsten, and titanium-based catalysts tend to interact with a wider range of functional groups, including esters, amides, and ketones.
The advancement of stable, highly active second-generation catalysts has significantly enhanced the versatility of ring closing metathesis reactions Among these, Grubbs’ second-generation catalyst, a ruthenium-based system, stands out due to its low sensitivity to moisture and air This catalyst's exceptional alkene activity and compatibility with various functional groups make it the preferred choice for olefin metathesis applications.
2.3.2 Peptidomimetics by ring closing metathesis
In 1996, Grubbs reported the first synthesis of a disulfide analogue through metathesis, resulting in the creation of cyclic tetra-peptide 1.03 Conformational studies indicated that the dicarba analogue exhibited identical hydrogen bonds, characteristic of a β-turn, similar to those found in the corresponding disulfide.
Figure 9 An early example of the use of RCM to mimic a disulfide bond
Ring closing metathesis is an effective method for synthesizing peptidomimetics that incorporate three essential binding motifs: α-helix mimics, β-turn mimics, and β-strand mimics.
Figure 10 Recent peptidomimetics cyclized by RCM
The bond highlighted red indicates the alkene formed in metathesis
Amylin (1-8) is an octa-peptide that promotes the proliferation of osteoblasts, enhancing bone volume and strength, making it a potential treatment for osteoporosis However, its instability in vivo, caused by a labile disulfide bridge, led researchers, including Kowalczyk and colleagues, to explore dicarba analogues as a replacement The dicarba analogues exhibited biological activity comparable to the parent peptide in in vitro assays, with two promising candidates advancing to in vivo testing Although the secondary structure of analogue 1.04 is not specified, variations in biological activity were noted between cis and trans isomers, likely due to the distinct secondary structures influenced by the olefin moieties.
Cyclic peptide 1.05 was synthesized by Henchey et al to explore its helical forming properties and its binding affinity to MDM2 P53, a tumor suppressor protein, plays a crucial role in signaling cell apoptosis in response to DNA damage or cellular stress MDM2 inhibits the action of P53 by binding to it at an α-helical interface, which is essential for understanding the regulation of tumor suppression.
The interaction between the tumor suppressor protein P53 and MDM2 plays a crucial role in cancer cell proliferation, making peptides that disrupt this binding potential anticancer agents Peptidomimetic 1.05 has been engineered to replace a hydrogen bond with a dicarba linkage, effectively stabilizing the peptide in an α-helix conformation This modification significantly enhances its selective binding to MDM2, with mimic 1.05 demonstrating a propensity to adopt an α-helix that is nearly double that of the original peptide Furthermore, the binding affinity of 1.05 to MDM2 is approximately twice that of the parent peptide, with a Kd value of 160 nM compared to 340 nM.
Cyclic structures represent a crucial category of peptidomimetics that effectively address challenges linked to linear peptides, such as poor bioavailability, low solubility, and instability against hydrolysis Prominent classes of constrained β-turn mimics include Freidinger lactams, spiro- bi- and tri-cyclic lactams, ring-fused lactams like benzodiazepines and azabicycloalkanes, as well as macrocycles made up of di-, tri-, and tetra-peptides.
Cyclic peptides made from β-amino acids represent a promising new category of peptidomimetics that are still underexplored These β-amino acid-based peptides offer a compelling alternative to traditional α-amino acid peptides in drug design, primarily due to their superior chemical stability, which leads to greater resistance against enzymatic degradation within the body.
β-peptides are known to form stable secondary structures, including turns, helices, and sheets, which closely resemble those found in natural proteins These unique structures not only enhance stability but also provide a versatile scaffold for interactions with α-amino acids.
Since the early 1990s, the discovery of well-defined molybdenum and ruthenium catalysts has significantly increased the popularity of metathesis as a method for synthesizing both small and large rings Despite this advancement, the application of ring-closing metathesis has seen limited exploration.
16 relatively recently been used to successfully prepare medium sized rings, for examples see Figure 11 [55-57] and Figure 12 [58-60]
Figure 11 Examples of bi-cyclics lactams where RCM is facilitates cyclic constraint
The metathesis-mediated cyclization of medium-sized rings has been successfully achieved by introducing conformational constraints into precursor dienes, utilizing either cyclic constraints like 1.06, 1.08, and 1.10 or acyclic constraints such as 1.14 Significant research in ring-closing metathesis has concentrated on β-turn mimics, particularly in the synthesis of cyclic lactams from α-amino acids, exemplified by the 8-membered ring 1.15.
RCM (Ring Closing Metathesis) is ineffective with trans-amide configurations due to the excessive distance between diene groups, which hinders the intramolecular reaction In contrast, the presence of the DMB group stabilizes the cis geometry of the amide bond, thereby facilitating the RCM process.
An acyclic constraint can be illustrated by the introduction of an N-alkylate on an amide nitrogen with a 2,4-dimethoxy-benzyl (DMB) group, which stabilizes the cis-amide conformation in the dipeptide This stabilization facilitates ring-closing metathesis (RCM) While diene 1.12 fails to undergo RCM with Grubbs’ second-generation catalyst, diene 1.14 benefits from the DMB group, which promotes a cis geometry around the central amide, allowing successful cyclization to yield compound 1.15.
Figure 13 Cyclization of Cβ-N’ by RCM to give 8-membered ring 1.17
Finally, cyclization of 1.16 from Cβ to N’ gives Homo-Freidinger lactam 1.17 (Figure 13) Freidinger lactams are examples of conformationally restrained peptidomimetics that are effective as inhibitors for a wide variety of proteases
[61] Hoffmann and coworkers have used ring closing metathesis to produce
18 unsaturated Homo-Freidinger lactams, which are of interest due to the enhanced metabolic stability of β-amino acids over α-amino acids [62].
Research described in this thesis
This article emphasizes the effectiveness of ring closing metathesis (RCM) in controlling the structure and pharmacological properties of peptidomimetics The growing research interest in cyclized peptidomimetics highlights the potential of this field This thesis focuses on the design and synthesis of a medium-sized ring peptidomimetic composed of β-amino acids, specifically aiming to create a cyclic derivative linked by two peptide-amide moieties The synthesis involves a 9-atom-membered ring peptide utilizing Grubbs’ catalyst through the RCM reaction.
Experimental Method
Subject and purpose
We aim to develop a synthesis procedure for medium-sized rings made from β-amino acids through ring-closing metathesis Utilizing β-glycine as the starting material, we successfully synthesized a dipeptide that was subsequently cyclized to create a 9-membered ring β-peptidomimetic.
Experimental procedure
All reactions were conducted under a nitrogen atmosphere, utilizing commercially sourced reagents without additional purification unless specified Solvents were dried using standard methods; tetrahydrofuran was dried over sodium and benzophenone before immediate use post-distillation, while dichloromethane was dried with diphosphorus pentoxide (P2O5), and pentane was distilled and then dried with sodium Analytical thin-layer chromatography (TLC) was performed on 0.25 mm Merck precoated silica gel plates (60-F254), and column chromatography utilized the same silica gel Visualization of TLC plates was achieved using a UV lamp at 254 nm and 366 nm.
20 visualizing solutions activated with heat, including: p-anisaldehyde solution and potassium permanganate solution
Proton and carbon nuclear magnetic resonance spectra (^1H NMR and ^13C NMR) were obtained using BRUKER 500 MHz Ascend instruments at Hanoi University of Science, Vietnam National University, with tetramethyl silane (TMS) as the internal standard and CDCl3 as the solvent The chemical shifts were measured in parts per million (ppm), with TMS at 0.00 ppm and CDCl3 at 7.26 ppm for ^1H NMR, and CDCl3 at 77.0 ppm for ^13C NMR The reported data includes chemical shift, multiplicity (s for singlet, d for doublet, t for triplet, q for quartet, m for multiplet), coupling constants in Hertz, and integration values Additionally, mass spectral analysis was conducted using an LTQ Orbitrap XL at the same institution.
In a reaction setup, β-glycine methyl ester 2 (1.5 equiv.) was mixed with powdered K2CO3 (3 equiv.) in acetonitrile and stirred at room temperature for 15 minutes Subsequently, bromide alkenyl was added, and the mixture was stirred for an additional 16 hours before being quenched with 30 mL of water The resulting mixture underwent extraction with diethyl ether (3 x 50 mL), and the organic phase was washed with brine (50 mL) and water (50 mL) After drying over anhydrous Na2SO4, the organic phase was filtered and evaporated under vacuum, yielding a crude product that was used for the next step without further purification.
Scheme 2 Synthesis of mono-alkylated product a) SOCl 2 , MeOH, r.t., overnight; b) allyl bromide, K 2 CO 3 , DMF
A solution of amine 3 (1 equivalent) in 50 mL of methanol was treated with 5 equivalents of 2M NaOH and stirred at room temperature for 4 hours The mixture was then evaporated under vacuum, and the resulting crude product was dissolved in 50 mL of water Extraction was performed using dichloromethane (2 x 50 mL), followed by acidification of the aqueous phase to pH 2-3 with 6M HCl, and further extraction with dichloromethane (3 times).
The organic phase, totaling 50 mL, was collected and washed with water (2 x 50 mL), then dried using Na2SO4 After filtration, the solution was evaporated under vacuum, resulting in crude acid that was utilized in the subsequent step without additional purification.
Scheme 3 Amine protection c) Cbz-Cl, CH 2 Cl 2 , Et 3 N, r.t., 4h; MeOH/NaOH 2M, 2h, r.t
The reaction was quenched using water and extracted with ethyl acetate in three 50 mL portions The combined organic phase underwent washing with 50 mL of 2M HCl, followed by water and brine solutions, each also measuring 50 mL After drying the organic phase over Na2SO4, it was filtered and evaporated under vacuum The resulting crude product was then purified through column chromatography on silica gel, utilizing a hexane and ethyl acetate mixture in a 2:1 ratio, yielding diamide 5 as a viscous liquid.
Scheme 4 Synthesis of dienes EDCI, HOBt, CH 2 Cl 2 , Et 3 N, and 4, r.t
Grubbs’ second-generation catalyst (5 mol%) was added to a 10 -3 M solution of diene 5 in degassed dichloromethane under an atmosphere of dry nitrogen
The mixture was heated to reflux for 4 hours in flame-dried glassware, followed by the addition of another 5 mol% of catalyst It continued to reflux overnight, and after the solution was evaporated, the residue was purified using column chromatography on Merck silica gel (40-60 mesh) with a hexane to ethyl acetate gradient of 1:1 to 1:9.
Scheme 5 Ring closing metathesis reaction.
Results and Discussions
Synthesis of N-alkylated β-amino acid
To synthesize the bis-N-alkenylated peptide with two terminal alkene chains for the RCM reaction, β-glycine was first transformed into its methyl ester This methyl ester then underwent N-alkylation, resulting in a mono-alkylated product with a yield of 68%.
The secondary amine was protected using Cbz-Cl, and subsequently underwent saponification to produce acid product 4 with a high yield Ultimately, the β-amino acid was coupled with N-alkenyl methyl ester 3 through the EDCI-HOBt coupling method.
Et3N coupling procedure to give desired dipeptide 5 with excellent yield (80%)
The 1 H NMR analysis of compound 4 indicates successful protection, as evidenced by the signals from the Cbz protecting group within the aromatic proton chemical shift range of 7.29 - 7.39 ppm Notably, a deshielding effect caused by the double bond and electronegative oxygen atom resulted in a shift of 5.14 ppm for four hydrogen atoms, while an additional signal at 5.77 ppm corresponds to a hydrogen associated with the double bond Furthermore, the nitrogen and oxygen deshielding effects led to chemical shifts of δ = 3.93 ppm, δ = 3.55 ppm, and δ = 2.65 ppm for the CH2 signals.
The 1H NMR analysis of compound 5 confirmed that the coupling of N-alkenyl methyl ester 3 successfully produced the desired dipeptide, with a total of 28 hydrogen atoms corresponding to its chemical formula The presence of nitrogen atoms led to overlapping signals and a complex splitting pattern in the hydrogen signals of dipeptide 5 Notably, new signal clusters in the chemical shift range of 3.54 - 3.65 ppm were identified, representing the hydrogen atoms of the -COOMe group Additionally, signals for two double bonds and the CH2 of the carbamate group were observed in the 5.11 - 5.82 ppm region.
3-(allyl((benzyloxy)carbonyl) amino) propanoic acid (4)
1H NMR (400 MHz, Chloroform-d) δ 7.39 – 7.29 (m, 5H), 5.77 (s, 1H), 5.14 (s, 4H), 3.93 (d, J = 5.8 Hz, 2H), 3.55 (t, J = 7.1 Hz, 2H), 2.65 (d, J = 25.4 Hz, 2H)
Methyl 3-(N-allyl-3-(allyl((benzyloxy)carbonyl) amino) propanamido) propanoate (5)
1H NMR (500 MHz, Chloroform-d) δ 7.33 (d, J = 5.3 Hz, 5H), 5.82 – 5.52 (m, 2H), 5.11 (td, J = 12.3, 9.9, 5.5 Hz, 7H), 3.95 – 3.77 (m, 4H), 3.65 (s, 2H), 3.54 (dt, J = 14.3, 6.3 Hz, 4H), 2.72 – 2.40 (m, 4H)
HRMS m/z calculated for [M + Na] + C21H28N2NaO5 Exact Mass: 411.1896 Found 411.1899
Synthesis of cyclic β-peptidomimetic
The obtained N-alkylated β-amino acid 5 were subjected to RCM by using
Grubbs' catalyst facilitated the formation of a 9-membered cyclic product, confirmed by 1H and 13C NMR and MS spectral analysis Initially, the reaction was conducted in toluene with 5% of Grubbs' second-generation catalyst However, switching the solvent to dichloromethane resulted in improved yields, likely due to the lower reaction temperature providing a more stable environment for the catalyst.
In a reaction using 5% Grubbs’ second-generation catalyst, a cyclic product was produced alongside unreacted starting material in a 2:1 ratio, a common occurrence in ring-closing metathesis (RCM) attributed to the catalyst's decomposition at high dilution To enhance the conversion rate, an additional portion of catalyst was introduced after 4 hours Ultimately, employing a total of 10% catalyst in a reflux system facilitated an effective quantitative synthesis, as evidenced by crude NMR results indicating a 45% isolated yield and confirmed through thin-layer chromatography.
A comparison of the 1H NMR data for compounds 5 and 6 reveals notable similarities, yet distinct differences in hydrogen signal intensities Specifically, in the 5.70 - 5.99 ppm range, peptide 6 exhibits hydrogen atom signals that shift further downfield compared to compound 5, with peaks splitting into three multiplets, likely due to the formation of a 9-membered ring Additionally, a significant increase in the intensity of the -COOMe peak was observed, along with a similar rise in the CH2 peak within the 2.63 - 2.73 ppm region.
Benzyl5-(3-methoxy-3-oxopropyl)-4-oxo-2,3,4,5,6,9-hexahydro-1H-1,5 diazonine-1-carboxylate (6)
13C NMR (126 MHz, CDCl3) δ 172.5, 172.5, 172.2, 171.9, 156.0, 155.2, 136.5, 136.4, 132.7, 132.1, 128.6, 128.4, 128.2, 128.1, 128.0, 127.9, 126.1, 126.0, 67.5, 67.5, 51.7, 47.2,47.0, 46.4, 46.4, 45.3, 45.3, 42.2, 42.1, 35.3, 34.8, 32.3 HRMS m/z calculated for [M + Na] + C19H24N2NaO5 Exact Mass: 383.1583 Found 383.1588
We successfully synthesized a 9-membered ring cyclic peptidomimetic through ring closing metathesis, achieving good yield and selectivity at high dilution of reactants This synthesis strategy provides a novel approach for creating cyclic peptidomimetics from β-amino acids, paving the way for exploring new structural variants that can enhance chemical biology and drug design Future research will focus on evaluating the biological activity and incorporating chiral β-amino acids into the cyclic structure.
[1] Fosgerau, K.; Hoffmann, Drug Discovery Today 2015, 20 (1), 122–128
[2] Lenci, E.; Trabocchi, A., Chemical Society Reviews 2020, 49 (11), 3262–
[3] Steer, D.; Lew, R.; Perlmutter, P.; Smith, A.; Aguilar, M.-I., Current Medicinal Chemistry 2002, 9 (8), 811–822
[4] Seebach, D.; Gardiner, J., Accounts of Chemical Research 2008, 41 (10),
[5] https://wou.edu/chemistry/courses/online-chemistry-textbooks/ch450-and- ch451-biochemistry-defining-life-at-the-molecular-level/chapter-2-protein- structure/ (accessed May 17, 2021)
[6] Gonzalez, M W.; Kann, M G., PLoS Computational Biology 2012, 8 (12)
[7] Shang, J.; Wan, Y.; Luo, C.; Ye, G.; Geng, Q.; Auerbach, A.; Li, F.,
Proceedings of the National Academy of Sciences 2020, 117 (21), 11727-
[8] Leung, D.; Abbenante, G.; Fairlie, D P., Journal of Medicinal Chemistry
[9] Mabonga, L.; Kappo, A P., International Journal of Peptide Research and
[10] Petsalaki, E.; Russell, R B., Current Opinion in Biotechnology 2008, 19 (4), 344-350
[11] Cunningham, A D.; Qvit, N.; Mochly-Rosen, D., Current Opinion in Structural Biology 2017, 44, 59–66
[13] du Vigneaud, V.; Ressler, C.; Trippett, S., Journal of Biological Chemistry
[14] Vlieghe, P.; Lisowski, V.; Martinez, J.; Khrestchatisky, M., Drug Discovery
[15] Pauletti, G M.; Gangwar, S.; Siahaan, T J.; Jeffrey, A.; T Borchardt, R.,
[16] Qvit, N.; Rubin, S J S.; Urban, T J.; Mochly-Rosen, D.; Gross, E R., Drug
[17] J Vagner, H Qu and V J Hruby, Curr Opin Chem Biol., 2008, 12, 292–
[18] Ripka, A S.; Rich, D H., Current Opinion in Chemical Biology 1998, 2 (4), 441–452
[19] Farmer, P.S., Drug Design 1980, Vol X, Academic Press, New York, 119-
[20] Hruby, V J.; Balse, P M., Current Medicinal Chemistry 2000, 7 (9), 945-
[22] Jensen, K J., Peptide and Protein Design for Biopharmaceutical Applications Wiley: West Sussex, UK; Hoboken, NJ, 2009
[23] Toth, G.; Russell, K C.; Landis, G.; Kramer, T H.; Fang, L.; Knapp, R.;Davis, P.; Burks, T F.; Yamamura, H I.; Hruby, V J., Journal of Medicinal Chemistry 1992, 35 (13), 2384-2391
[24] Mosberg, H I.; Omnaas, J R.; Lomize, A.; Heyl, D L.; Nordan, I.; Mousigian, C.; Davis, P.; Porreca, F., Journal of Medicinal Chemistry 1994,
[25] Lebl, M.; Toth, G.; Slaninova, J.; Hruby, V J., International Journal of Peptide and Protein Research 1992, 40 (2), 148-151
[26] Huang, Z.; He, Y B.; Raynor, K.; Tallent, M.; Reisine, T.; Goodman, M.,
Journal of the American Chemical Society 1992, 114 (24), 9390-9401
[27] Azizeh, B Y.; Shenderovich, M D.; Trivedi, D.; Li, G.; Sturm, N S.; Hruby,
[28] Tourwe, D.; Mannekens, E.; Diem, T N T.; Verheyden, P.; Jaspers, H.; Toth, G.; Peter, A.; Kertesz, I.; Torok, G.; Chung, N N.; Schiller, P W., Journal of Medicinal Chemistry 1998, 41 (26), 5167-5176
[30] Rajeswaran, W G.; Hocart, S J.; Murphy, W A.; Taylor, J E.; Coy, D H.,
[31] Beesley, R M.; Ingold, C K.; Thorpe, J F., Journal of the Chemical Society,
[32] Toniolo, C.; Crisma, M.; Formaggio, F.; Peggion, C., Peptide Science 2001,
[33] Grubbs, R H.; Trnka, T M., Accounts of Chemical Research 2001, 34 (1),
[34] Peterson, D H.; Reineke, L M., Journal of Biological Chemistry 1949, 181
[35] Tutschka, P J.; Beschorner, W E.; Allison, A C.; Burns, W H.; Santos, G W., Nature 1979, 280 (5718), 148-151
[36] Wiley, R A.; Rich, D H., Medicinal Research Reviews 1993, 13 (3), 327-
[37] Estieu-Gionnet, K.; Guichard, G., Expert Opinion on Drug Discovery 2011,
[38] Loughlin, W A.; Tyndall, J D A.; Glenn, M P.; Hill, T A.; Fairlie, D P.,
[39] Pộrez de Vega, M J.; Garcớa-Aranda, M I.; Gonzỏlez-Muủiz, R., Medicinal
[40] Aitken, S G.; Abell, A D., Australian Journal of Chemistry 2005, 58 (1), 3-
[41] Jean-Louis Hérisson, P.; Chauvin, Y., Die Makromolekulare Chemie 1971,
[42] Trnka, T M.; Grubbs, R H., Accounts of Chemical Research 2000, 34 (1),
[43] Nguyen, S T.; Johnson, L K.; Grubbs, R H.; Ziller, J W., Journal of the American Chemical Society 1992, 114 (10), 3974-3975
[44] Scholl, M.; Ding, S.; Lee, C W.; Grubbs, R H., Organic Letters 1999, 1 (6), 953-956
[45] Miller, S J.; Blackwell, H E.; Grubbs, R H., Journal of the American
[46] Kowalczyk, R.; Brimble, M A.; Callon, K E.; Watson, M.; Cornish, J.,
[47] Henchey, L K.; Porter, J R.; Ghosh, I.; Arora, P S., ChemBioChem 2010,
[48] Che, Y.; Marshall, G R., Expert Opinion on Therapeutic Targets 2008, 12
[49] Kaul, R.; Surprenant, S.; Lubell, W., Journal of Organic Chemistry 2005, 70
[51] Humuro, Y.; Schneider, J P.; DeGrado, W F., Journal of the American
[52] Schrock, R R., Accounts of Chemical Research 1990, 23 (5), 158-165
[53] Dias, E L.; Nguyen, S T.; Grubbs, R H., Journal of the American Chemical Society 1997, 119 (17), 3887-3897
[54] Novak, B M.; Grubbs, R H., Journal of the American Chemical Society
[57] Tarling, C.; Holmes, A.; Markwell, R.; Pearson, N., Journal of the Chemical
[58] Derrer, S.; Davies, J E.; Holmes, A B., Journal of the Chemical Society, Perkin Transactions 1 2000, (17), 2943-2956
[59] Creighton, C.; Leo, G.; Du, T.; Reitz, A., Bioorganic and Medicinal
[61] Wolfe, M S.; Dutta, D.; Aube, J., Journal of Organic Chemistry 1997, 62,
Methyl 3-(N-allyl-3-(allyl((benzyloxy)carbonyl) amino) propanamido) propanoate (5a) )
Benzyl 5-(3-methoxy-3-oxopropyl)-4-oxo-2,3,4,5,6,9-hexahydro-1H-1,5-diazonine-1- carboxylate (6a) ).