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Journal articles on the topic 'Pseudopeptidic molecules'

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Author: Grafiati

Published: 6 September 2023

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1

Alfonso, Ignacio. "From simplicity to complex systems with bioinspired pseudopeptides." Chemical Communications 52, no. 2 (2016): 239–50. http://dx.doi.org/10.1039/c5cc07596c.

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This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).

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2

Bijesh, M. B., N. U. Dheepthi, Appa Rao Sapala, Ashutosh Shandilya, Kedar Khare, and V. Haridas. "Chiral and non-chiral assemblies from lipidated serine-based pseudopeptidic molecules." Molecular Systems Design & Engineering 1, no. 2 (2016): 163–68. http://dx.doi.org/10.1039/c6me00009f.

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Through various examples, we demonstrated serine as an excellent building block for the design of chiral and non-chiral self-assembled materials. The fine parameters such as pitch, angle and helicity can be altered using clever molecular engineering.

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3

Ostankovitch, Marina, Gilles Guichard, Francine Connan, Sylviane Muller, Aude Chaboissier, Johan Hoebeke, Jeannine Choppin, Jean-Paul Briand, and Jean-Gérard Guillet. "A Partially Modified Retro-Inverso Pseudopeptide Modulates the Cytokine Profile of CTL Specific for an Influenza Virus Epitope." Journal of Immunology 161, no. 1 (July 1, 1998): 200–208. http://dx.doi.org/10.4049/jimmunol.161.1.200.

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Abstract There is considerable evidence that peptides corresponding to MHC class I-restricted epitopes can be used as immunogens or immunomodulators. Pseudopeptides containing isosteric replacements of the amide bond provide more stable analogues, which may even have enhanced biologic activity. But there have been very few studies on the use of pseudopeptides to initiate or modulate the cellular immune response. This study describes the immunogenicity of a partially modified retro-inverso pseudopeptide of an influenza virus epitope and shows that this pseudopeptide modulates the cytokine profile expressed by CD8+CTL generated from primed precursors. Moreover, the pseudopeptide is much more efficient at low concentration than the wild-type epitope to stimulate IFN-γ secretion by CD8+ T effector cells. These results are analyzed with reference to changes in the conformation of the MHC molecule/peptide complex deduced from molecular modeling. The findings support the idea that partially modified retro-inverso analogues can be used as altered peptide ligands to enhance the stimulation of natural epitope-specific CTL and to modify their functional properties. Hence, pseudopeptide ligands might be promising tools for use in immunotherapy.

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4

Faggi, Enrico, Santiago V. Luis, and Ignacio Alfonso. "Minimalistic amino amides as models to study N–H⋯π interactions and their implication in the side chain folding of pseudopeptidic molecules." RSC Advances 3, no. 29 (2013): 11556. http://dx.doi.org/10.1039/c3ra41843j.

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5

Mehrazma, Banafsheh, Anahit Petoyan, Stanley K. A. Opare, and Arvi Rauk. "Interaction of the N-AcAβ(13–23)NH2 segment of the beta amyloid peptide with beta-sheet-blocking peptides: site and edge specificity." Canadian Journal of Chemistry 94, no. 6 (June 2016): 583–92. http://dx.doi.org/10.1139/cjc-2016-0033.

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The region encompassing residues 13–23 of the amyloid beta peptide (Aβ(13–23)) of Alzheimer’s disease is the self-recognition site that initiates toxic oligomerization and fibrillization and also is the site of interaction of Aβ with many other proteins. We describe herein a study by molecular dynamics of the complexes formed by R (= N-AcAβ(13–23)NH2(N-CH3C(O)HHQKLVFFAEDNH2)) with several pseudopeptides designed to form β-sheets with Aβ(1-40,42) and prevent oligomer and fibril formation. Adhesion to both edges of the R β-strand is examined by structure analysis. Umbrella sampling along a dissociation pathway reveals approximate free energies of binding in the submicromolar range. One of the three pseudopeptides binds strongly to one edge of the R β-strand and another to the opposite edge, while the third displays strong binding to both edges. It is desirable to block both edges of the self-recognition site of Aβ to prevent oligomer formation. The study reveals that this may be accomplished by a single pseudopeptide or two in combination. Thus the pseudopeptides, used singly or in pairs, may be competitive inhibitors of Aβ oligomerization at stoichiometric concentrations.

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6

Esteve, Ferran, Alexis Villanueva-Antolí, Belén Altava, Eduardo García-Verdugo, and Santiago V. Luis. "Unravelling the Supramolecular Driving Forces in the Formation of CO2-Responsive Pseudopeptidic Low-Molecular-Weight Hydrogelators." Gels 8, no. 6 (June 20, 2022): 390. http://dx.doi.org/10.3390/gels8060390.

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A new family of C2-symmetric pseudopeptides with a high functional density for supramolecular interactions has been synthetized through the attachment of four amino acid subunits to a diamino aliphatic spacer. The resulting open-chain compounds present remarkable properties as low-molecular-weight hydrogelators. The self-assembled 3D networks were characterized by SEM analyses, observing regular nanofibres with 80–100 nm diameters. Spectroscopic and molecular modelling experiments revealed the presence of strong synergic effects between the H-bonding and π–π interactions, with the best results obtained for the homoleptic tetra-pseudopeptide derived from l-Phe. In addition, these bioinspired hydrogels possessed pH- and CO2-responsive sol–gel transitions. The formation of ammonium carbamate derivatives in the presence of carbon dioxide led to a detrimental change in its adequate self-assembly. CO2 desorption temperatures of ca. 70 °C were assigned to the thermodynamically favoured recovery of the supramolecular gel.

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7

Dharmashekar, Chandan, Bhargav Shreevatsa, Anisha S. Jain, Bhavana Harendra, Sushma Pradeep, Prashanth M. Vishwanath, Pranav Singh, et al. "Evaluating the Antimicrobial and Anti-Hemolytic Activity of Synthesized Pseudopeptide against Leptospiral Species: In Silico and In Vitro Approach." Molecules 28, no. 3 (January 22, 2023): 1106. http://dx.doi.org/10.3390/molecules28031106.

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Bacterial infections are one of the leading causes of morbidity, mortality, and healthcare complications in patients. Leptospirosis is found to be the most prevalent, re-emergent, and neglected tropical zoonotic disease worldwide. The adaptation to various environmental conditions has made Leptospira acquire a large genome (~4.6 Mb) and a complex outer membrane, making it unique among bacteria that mimic the symptoms of jaundice and hemorrhage. Sph2 is another important virulence factor that enhances hemolytic sphingomyelinase—capable of moving inside mitochondria—which increases the ROS level and decreases the mitochondrial membrane potential, thereby leading to cell apoptosis. In the present study, 25 suspected bovine serum samples were subjected to the Microscopic Agglutination Test (MAT) across the Mysuru region. Different samples, such as urine, serum, and aborted materials from the confirmed MAT-positive animals, were used for isolation and genomic detection by conventional PCR targeting virulence gene, Lipl32, using specific primers. Further, in vitro and in silico studies were performed on isolated cultures to assess the anti-leptospiral, anti-hemolytic, and sphingomyelinase enzyme inhibition using novel pseudopeptides. The microdilution technique (MDT) and dark field microscope (DFM) assays revealed that at a concentration of 62.5 μg/mL, the pseudopeptide inhibited 100% of the growth of Leptospira spp., suggesting its efficiency in the treatment of leptospirosis. The flow cytometry analyses show the potency of the pseudopeptide against sphingomyelinase enzymes using human umbilical vein endothelial cells (HUVECs). Thus, the present study demonstrated the efficacy of the pseudopeptide in the inhibition of the growth of Leptospira, and therefore, this can be used as an alternative drug for the treatment of leptospirosis.

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8

Calbo, Sébastien, Gilles Guichard, Philippe Bousso, Sylviane Muller, Philippe Kourilsky, Jean-Paul Briand, and Jean-Pierre Abastado. "Role of Peptide Backbone in T Cell Recognition." Journal of Immunology 162, no. 8 (April 15, 1999): 4657–62. http://dx.doi.org/10.4049/jimmunol.162.8.4657.

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Abstract T cells recognize self and nonself peptides presented by molecules of the MHC. Amino acid substitutions in the antigenic peptide showed that T cell specificity is highly degenerate. Recently, determination of the crystal structure of several TCR/MHC-peptide complexes suggested that the peptide backbone may significantly contribute to the interaction with the TCR. To directly investigate the role of the peptide backbone in T cell recognition, we performed a methylene-amino scan on the backbone of an antigenic peptide and measured the capacity of such pseudopeptides to bind their cognate MHC molecule, to sensitize target cells for T cell lysis, and to stimulate IL-2 secretion by two T cell hybridomas. For one of these pseudopeptides, we prepared fluorescent tetramers of MHC molecules and compared the staining of two T cell hybridomas. Our results demonstrate that the peptide backbone has an important contribution to TCR binding and suggest that some interactions between the peptide backbone and the TCR may be partially conserved. We discuss this finding in the perspective of TCR plasticity and T cell function.

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9

Amini, Zohreh, Mohammad Hossein Fatemi, and Arvi Rauk. "Molecular dynamics studies of a β-sheet blocking peptide with the full-length amyloid beta peptide of Alzheimer’s disease." Canadian Journal of Chemistry 94, no. 10 (October 2016): 833–41. http://dx.doi.org/10.1139/cjc-2016-0267.

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The region encompassing residues 13–23 of the amyloid beta peptide (Aβ(13–23)) of Alzheimer’s disease is the self-recognition site that initiates toxic oligomerization and fibrillization. A number of pseudopeptides have been designed to bind to Aβ(13–23) and been computationally shown to do so with high affinity. More interactions are available in full-length Aβ than are available in the shorter peptide. We describe herein a study by molecular dynamics (MD) of nine distinct complexes formed by one such pseudopeptide, SGA1, with full-length beta amyloid, Aβ(1–42). The relative stabilities of the Aβ–SGA1 complexes were estimated by a combination of MD and ab initio methods. The most stable complex, designated AB1, was found to be one in which SGA1 is bound to the self-recognition site of Aβ(1–42) in an antiparallel β-sheet fashion. Another complex, designated AB3, also involved SGA1 binding to the self-recognition region of Aβ(1–42), albeit with lower affinity. In both AB1 and AB3, SGA1 formed antiparallel β-sheets but to opposite edges of Aβ. A complex, AB4, with similar stability to AB3, was found with a parallel β-sheet in the self-recognition site. A fourth complex, AB7, also with similar stability, formed a parallel β-sheet in the hydrophobic central region of Aβ. In all cases, complexation of SGA1 induced extensive β-sheet structure in Aβ(1–42).

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10

Moure, Alejandra, Santiago V. Luis, and Ignacio Alfonso. "Efficient Synthesis of Pseudopeptidic Molecular Cages." Chemistry - A European Journal 18, no. 18 (March 29, 2012): 5496–500. http://dx.doi.org/10.1002/chem.201104045.

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11

Faggi, Enrico, Cristian Vicent, Santiago V. Luis, and Ignacio Alfonso. "Stereoselective recognition of the Ac-Glu-Tyr-OH dipeptide by pseudopeptidic cages." Organic & Biomolecular Chemistry 13, no. 48 (2015): 11721–31. http://dx.doi.org/10.1039/c5ob01889g.

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Pseudopeptidic cages derived from Ser and Thr displayed stereoselective molecular recognition of the Ac-Glu-Tyr-OH dipeptide, both in mixed aqueous solution (NMR) and in the gas phase (ESI-MS). The results allowed proposing a mode of binding that explains the observed trends.

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12

Faggi, Enrico, Santiago V. Luis, and Ignacio Alfonso. "Sensing, Transport and Other Potential Biomedical Applications of Pseudopeptides." Current Medicinal Chemistry 26, no. 21 (September 19, 2019): 4065–97. http://dx.doi.org/10.2174/0929867325666180301091040.

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Pseudopeptides are privileged synthetic molecules built from the designed combination of peptide-like and abiotic artificial moieties. Consequently, they are benefited from the advantages of both families of chemical structures: modular synthesis, chemical and functional diversity, tailored three-dimensional structure, usually high stability in biological media and low non-specific toxicity. Accordingly, in the last years, these compounds have been used for different biomedical applications, ranging from bio-sensing, ion transport, the molecular recognition of biologically relevant species, drug delivery or gene transfection. This review highlights a selection of the most remarkable and recent advances in this field.

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13

Sharma, Sakshi, Shridhar H. Thorat, Rajesh G. Gonnade, Jerry P. Jasinski, Ray Butcher, and V. Haridas. "Engineering Molecular Topology: A Pseudopeptidic Macrocyclic Figure-Eight Motif." European Journal of Organic Chemistry 2017, no. 7 (December 12, 2016): 1120–24. http://dx.doi.org/10.1002/ejoc.201601365.

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14

Giuri, Demetra, Nicola Zanna, and Claudia Tomasini. "Low Molecular Weight Gelators Based on Functionalized l-Dopa Promote Organogels Formation." Gels 5, no. 2 (May 14, 2019): 27. http://dx.doi.org/10.3390/gels5020027.

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We prepared the small pseudopeptide Lau-l-Dopa(OBn)2-d-Oxd-OBn (Lau = lauric acid; l-Dopa = l-3,4-dihydroxyphenylalanine; d-Oxd = (4R,5S)-4-methyl-5-carboxyl-oxazolidin-2-one; Bn = benzyl) through a number of coupling reactions between lauric acid, protected l-Dopa and d-Oxd with an excellent overall yield. The ability of the product to form supramolecular organogels has been tested with different organic solvents of increasing polarity and compared with the results obtained with the small pseudopeptide Fmoc-l-Dopa(OBn)2-d-Oxd-OBn. The mechanical and rheological properties of the organogels demonstrated solvent-dependent properties, with a storage modulus of 82 kPa for the ethanol organogel. Finally, to have a preliminary test of the organogels’ ability to adsorb pollutants, we treated a sample of the ethanol organogel with an aqueous solution of Rhodamine B (RhB) for 24 h. The water solution slowly lost its pink color, which became trapped in the organogel.

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15

Martí, Inés, M. Isabel Burguete, Philip A. Gale, and Santiago V. Luis. "Acyclic Pseudopeptidic Hosts as Molecular Receptors and Transporters for Anions." European Journal of Organic Chemistry 2015, no. 23 (July 3, 2015): 5150–58. http://dx.doi.org/10.1002/ejoc.201500390.

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16

Kotynia, Aleksandra, Benita Wiatrak, Wojciech Kamysz, Damian Neubauer, Paulina Jawień, and Aleksandra Marciniak. "Cationic Peptides and Their Cu(II) and Ni(II) Complexes: Coordination and Biological Characteristics." International Journal of Molecular Sciences 22, no. 21 (November 6, 2021): 12028. http://dx.doi.org/10.3390/ijms222112028.

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Antimicrobial peptides are a promising group of compounds used for the treatment of infections. In some cases, metal ions are essential to activate these molecules. Examples of metalloantibiotics are, for instance, bleomycin and dermcidin. This study is focused on three new pseudopeptides with potential biological activity. The coordination behavior of all ligands with Cu(II) and Ni(II) ions has been examined. Various analytical methods such as potentiometric titration, UV-Vis and CD spectroscopies, and mass spectrometry were used. All compounds are convenient chelators for metal ion-binding. Two of the ligands tested have histidine residues. Surprisingly, imidazole nitrogen is not involved in the coordination of the metal ion. The N-terminal amino group, Dab side chains, and amide nitrogen atoms of the peptide bonds coordinated Cu(II) and Ni(II) in all the complexes formed. The cytotoxicity of three pseudopeptides and their complexes was evaluated. Moreover, their other model allowed for assessing the attenuation of LPS-induced cytotoxicity and anti-inflammatory activities were also evaluated, the results of which revealed to be very promising.

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17

Koistinen, Hannu, Erik Wallén, Henna Ylikangas, Kristian Meinander, Maija Lahtela-Kakkonen, Ale Närvänen, and Ulf-Håkan Stenman. "Development of molecules stimulating the activity of KLK3 – an update." Biological Chemistry 397, no. 12 (December 1, 2016): 1229–35. http://dx.doi.org/10.1515/hsz-2016-0189.

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Abstract Kallikrein-related peptidase-3 (KLK3, known also as prostate-specific antigen, PSA) is highly expressed in the prostate. KLK3 possess antiangiogenic activity, which we have found to be related to its proteolytic activity. Thus, it may be possible to slow down the growth of prostatic tumors by enhancing this activity. We have developed peptides that enhance the proteolytic activity of KLK3. As these peptides are degraded in circulation and rapidly excreted, we have started to modify them and have succeeded in creating bioactive and more stable pseudopeptides. We have also identified small molecules stimulating the activity of KLK3, especially in synergy with peptides.

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18

Angulo-Pachón, César A., Diego Navarro-Barreda, Celia M. Rueda, Francisco Galindo, and Juan F. Miravet. "Deamidation of pseudopeptidic molecular hydrogelators and its application to controlled release." Journal of Colloid and Interface Science 505 (November 2017): 1111–17. http://dx.doi.org/10.1016/j.jcis.2017.07.003.

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19

Abdelbaky, Ahmed S., Ivan A. Prokhorov, Igor P. Smirnov, Kristina M. Koroleva, Vitaliy I. Shvets, and Yulia G. Kirillova. "Synthesis of α-(R)-/γ-(S)-Dimethyl Substituted Peptide Nucleic Acid Submonomer Using Mitsunobu Reaction." Letters in Organic Chemistry 16, no. 5 (April 1, 2019): 437–46. http://dx.doi.org/10.2174/1570178616666190118155031.

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One of the major challenges facing modern biochemical and biomedical technologies are finding molecular tools for diagnosis and detection of genetic diseases. In this connection, several classes of oligonucleotides have been developed that can recognize and bind to DNA and RNA with high affinity and sequence selectivity and withstand enzymatic degradation by proteases and nucleases; however, few can traverse the cell membrane on their own. One such promising class of nucleic acid mimics developed in the last two decades which showed good results in vitro, are the peptide nucleic acids (PNAs). New chiral α- and γ-peptide Nucleic Acid (PNA) submonomer with methyl substituents in pseudopeptide backbone were synthesized via Mitsunobu reaction. The α-(R)-/γ-(S)-configuration of the chiral centres will ensure the preorganization of the PNA oligomer into a right-handed helix. The results obtained showed that Boc/Fmoc-submonomer compatible with Boc-protocol PNAs solid-phase synthesis on an MBHA resin. We synthesized simple and efficient α-R-, γ-S-disubstituted PNA submonomer based on L-Ala and D-Ala with the construction of the intermediate pseudopeptide moiety by Mitsunobu reaction for subsequent use in the Boc-Protocol of solid phase PNA synthesis.

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20

Robinson, Morgan, Jennifer Lou, Banafsheh Mehrazma, Arvi Rauk, Michael Beazely, and Zoya Leonenko. "Pseudopeptide Amyloid Aggregation Inhibitors: In Silico, Single Molecule and Cell Viability Studies." International Journal of Molecular Sciences 22, no. 3 (January 21, 2021): 1051. http://dx.doi.org/10.3390/ijms22031051.

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Neurodegeneration in Alzheimer’s disease (AD) is defined by pathology featuring amyloid-β (Aβ) deposition in the brain. Aβ monomers themselves are generally considered to be nontoxic, but misfold into β-sheets and aggregate to form neurotoxic oligomers. One suggested strategy to treat AD is to prevent the formation of toxic oligomers. The SG inhibitors are a class of pseudopeptides designed and optimized using molecular dynamics (MD) simulations for affinity to Aβ and experimentally validated for their ability to inhibit amyloid-amyloid binding using single molecule force spectroscopy (SMFS). In this work, we provide a review of our previous MD and SMFS studies of these inhibitors and present new cell viability studies that demonstrate their neuroprotective effects against Aβ(1–42) oligomers using mouse hippocampal-derived HT22 cells. Two of the tested SG inhibitors, predicted to bind Aβ in anti-parallel orientation, demonstrated neuroprotection against Aβ(1–42). A third inhibitor, predicted to bind parallel to Aβ, was not neuroprotective. Myristoylation of SG inhibitors, intended to enhance delivery across the blood-brain barrier (BBB), resulted in cytotoxicity. This is the first use of HT22 cells for the study of peptide aggregation inhibitors. Overall, this work will inform the future development of peptide aggregation inhibitors against Aβ toxicity.

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21

Formicola, Lucia, Xavier Maréchal, Nicolas Basse, Michelle Bouvier-Durand, Danièle Bonnet-Delpon, Thierry Milcent, Michèle Reboud-Ravaux, and Sandrine Ongeri. "Novel fluorinated pseudopeptides as proteasome inhibitors." Bioorganic & Medicinal Chemistry Letters 19, no. 1 (January 2009): 83–86. http://dx.doi.org/10.1016/j.bmcl.2008.11.012.

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22

Mehrazma, Banafsheh, Stanley Opare, Anahit Petoyan, and Arvi Rauk. "d-Amino Acid Pseudopeptides as Potential Amyloid-Beta Aggregation Inhibitors." Molecules 23, no. 9 (September 18, 2018): 2387. http://dx.doi.org/10.3390/molecules23092387.

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A causative factor for neurotoxicity associated with Alzheimer’s disease is the aggregation of the amyloid-β (Aβ) peptide into soluble oligomers. Two all d-amino acid pseudo-peptides, SGB1 and SGD1, were designed to stop the aggregation. Molecular dynamics (MD) simulations have been carried out to study the interaction of the pseudo-peptides with both Aβ13–23 (the core recognition site of Aβ) and full-length Aβ1–42. Umbrella sampling MD calculations have been used to estimate the free energy of binding, ∆G, of these peptides to Aβ13–23. The highest ∆Gbinding is found for SGB1. Each of the pseudo-peptides was also docked to Aβ1–42 and subjected up to seven microseconds of all atom molecular dynamics simulations. The resulting structures lend insight into how the dynamics of Aβ1–42 are altered by complexation with the pseudo-peptides and confirmed that SGB1 may be a better candidate for developing into a drug to prevent Alzheimer’s disease.

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23

Giuri, Demetra, Marianna Barbalinardo, Nicola Zanna, Paolo Paci, Marco Montalti, Massimiliano Cavallini, Francesco Valle, Matteo Calvaresi, and Claudia Tomasini. "Tuning Mechanical Properties of Pseudopeptide Supramolecular Hydrogels by Graphene Doping." Molecules 24, no. 23 (November 28, 2019): 4345. http://dx.doi.org/10.3390/molecules24234345.

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Supramolecular hydrogels, obtained from small organic molecules, may be advantageous over polymeric ones for several applications, because these materials have some peculiar properties that differentiate them from the traditional polymeric hydrogels, such as elasticity, thixotropy, self-healing propensity, and biocompatibility. We report here the preparation of strong supramolecular pseudopeptide-based hydrogels that owe their strength to the introduction of graphene in the gelling mixture. These materials proved to be strong, stable, thermoreversible and elastic. The concentration of the gelator, the degree of graphene doping, and the nature of the trigger are crucial to get hydrogels with the desired properties, where a high storage modulus coexists with a good thixotropic behavior. Finally, NIH-3T3 cells were used to evaluate the cell response to the presence of the most promising hydrogels. The hydrogels biocompatibility remains good, if a small degree of graphene doping is introduced.

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24

Graham, Samuel L., S. Jane deSolms, Elizabeth A. Giuliani, Nancy E. Kohl, Scott D. Mosser, Allen I. Oliff, David L. Pompliano, Elaine Rands, and Michael J. Breslin. "Pseudopeptide Inhibitors of Ras Farnesyl-Protein Transferase." Journal of Medicinal Chemistry 37, no. 6 (March 1994): 725–32. http://dx.doi.org/10.1021/jm00032a004.

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25

Ten Brink, Ruth E., Donald T. Pals, Douglas W. Harris, and Garland A. Johnson. "Renin inhibitors containing .psi.[CH2O] pseudopeptide inserts." Journal of Medicinal Chemistry 31, no. 3 (March 1988): 671–77. http://dx.doi.org/10.1021/jm00398a029.

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26

Galéotti, Nathalie, Joël Poncet, and Patrick Jouin. "Post-Source Decay Analysis of Dolastatin 10 and Dolastatin 15 by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry." European Journal of Mass Spectrometry 8, no. 4 (August 2002): 311–21. http://dx.doi.org/10.1255/ejms.502.

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Dolastatin 10 and dolastatin 15 have been analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry. Interestingly, in-source fragmentations could be easily detected for both compounds. Determination of the primary structure of both pseudopeptides could be done by using post-source decay (PSD) analysis. The molecular ion was used as the precursor ion in the case of dolastatin 10, whereas two in-source fragment ions and cationized (Na and K) precursors were selected in the case of dolastatin 15. An analogue of dolastatin 15 containing an amino alkyl linkage (compound 1) was also studied. Despite its close chemical structure its PSD spectrum exhibited a quite different pattern.

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Mavridis, George, Richa Arya, Alexander Domnick, Jerome Zoidakis, Manousos Makridakis, Antonia Vlahou, Anastasia Mpakali, et al. "A systematic re-examination of processing of MHCI-bound antigenic peptide precursors by endoplasmic reticulum aminopeptidase 1." Journal of Biological Chemistry 295, no. 21 (March 17, 2020): 7193–210. http://dx.doi.org/10.1074/jbc.ra120.012976.

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Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims antigenic peptide precursors to generate mature antigenic peptides for presentation by major histocompatibility complex class I (MHCI) molecules and regulates adaptive immune responses. ERAP1 has been proposed to trim peptide precursors both in solution and in preformed MHCI-peptide complexes, but which mode is more relevant to its biological function remains controversial. Here, we compared ERAP1-mediated trimming of antigenic peptide precursors in solution or when bound to three MHCI alleles, HLA-B*58, HLA-B*08, and HLA-A*02. For all MHCI-peptide combinations, peptide binding onto MHCI protected against ERAP1-mediated trimming. In only a single MHCI-peptide combination, trimming of an HLA-B*08-bound 12-mer progressed at a considerable rate, albeit still slower than in solution. Results from thermodynamic, kinetic, and computational analyses suggested that this 12-mer is highly labile and that apparent on-MHC trimming rates are always slower than that of MHCI-peptide dissociation. Both ERAP2 and leucine aminopeptidase, an enzyme unrelated to antigen processing, could trim this labile peptide from preformed MHCI complexes as efficiently as ERAP1. A pseudopeptide analogue with high affinity for both HLA-B*08 and the ERAP1 active site could not promote the formation of a ternary ERAP1/MHCI/peptide complex. Similarly, no interactions between ERAP1 and purified peptide-loading complex were detected in the absence or presence of a pseudopeptide trap. We conclude that MHCI binding protects peptides from ERAP1 degradation and that trimming in solution along with the dynamic nature of peptide binding to MHCI are sufficient to explain ERAP1 processing of antigenic peptide precursors.

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28

Pispisa, B., L. Stella, M. Venanzi, and A. Palleschi. "A spectroscopic and molecular modeling study on novel pseudopeptides exhibiting biological activity." Journal of Peptide Research 54, no. 4 (October 1999): 353–60. http://dx.doi.org/10.1034/j.1399-3011.1999.00124.x.

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29

Balboni, Gianfranco, Severo Salvadori, Remo Guerrini, Clementina Bianchi, Vincenzo Santagada, Giuseppe Calliendo, Sharon D. Bryant, and Lawrence H. Lazarus. "Opioid pseudopeptides containing heteroaromatic or heteroaliphatic nuclei." Peptides 21, no. 11 (November 2000): 1663–71. http://dx.doi.org/10.1016/s0196-9781(00)00315-6.

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30

Liu, Keyuan, Long Ye, Yao Wang, Ganhong Du, and Liming Jiang. "A Pseudopeptide Polymer Micelle Used for Asymmetric Catalysis of the Aldol Reaction in Water." Polymers 10, no. 9 (September 10, 2018): 1004. http://dx.doi.org/10.3390/polym10091004.

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Micelles assembled from amphiphilic molecules have proved to be ideal scaffolds to construct artificial catalysts mimicking enzymatic catalytic behavior. In this paper, we describe the synthesis of amphiphilic poly(2-oxazoline) derivatives with l-prolinamide units in the side chain and their application in asymmetric aldol reactions. Upon dissolution in water, the pseudopeptide polymers self-assembled into particles with different sizes, relying on the copolymer composition and distribution of hydrophilic/hydrophobic segments in the polymer chain. A preliminary study has demonstrated that the catalytic activity of these polymeric organocatalysts are strongly dependent on the aggregated architecture. The micelle-type assemblies can act as nanoreactors to efficiently promote the direct aldolisation of cyclohexanone with aromatic aldehydes in aqueous media, affording anti-aldol products in excellent yields (88–99%) and higher stereoselectivities (90/10 dr, 86% ee) compared to their nonmicellar systems under identical conditions.

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31

Perez, Juan J. "Designing Peptidomimetics." Current Topics in Medicinal Chemistry 18, no. 7 (July 9, 2018): 566–90. http://dx.doi.org/10.2174/1568026618666180522075258.

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The concept of a peptidomimetic was coined about forty years ago. Since then, enormous effort and interest have been devoted to mimic the properties of peptides with small molecules or pseudopeptides. The present report aims to review different approaches described in the past to succeed in this goal. Basically, there are two different approaches to design peptidomimetics: a medicinal chemistry approach, where parts of the peptide are successively replaced by non-peptide moieties until getting a non-peptide molecule and a biophysical approach, where a hypothesis of the bioactive form of the peptide is sketched and peptidomimetics are designed based on hanging the appropriate chemical moieties on diverse scaffolds. Although both approaches have been used in the past, the former has been more widely used to design peptidomimetics of secretory peptides, whereas the latter is nowadays getting momentum with the recent interest in designing protein-protein interaction inhibitors. The present report summarizes the relevance of the information gathered from structure-activity studies, together with a short review of the strategies used to design new peptide analogs and surrogates. In the following section, there is a short discussion on the characterization of the bioactive conformation of a peptide, to continue describing the process of designing conformationally constrained analogs producing first and second generation peptidomimetics. Finally, there is a section devoted to reviewing the use of organic scaffolds to design peptidomimetics based on the information available on the bioactive conformation of the peptide.

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32

Pinnen, Francesco, Grazia Luisi, Gino Lucente, Enrico Gavuzzo, and Silvio Cerrini. "Approaches to pseudopeptidic ergopeptines. Synthesis and molecular structure of an α-aza-phenylalanine-containing oxa-cyclol." J. Chem. Soc., Perkin Trans. 1, no. 7 (1993): 819–24. http://dx.doi.org/10.1039/p19930000819.

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33

Valls, Adriana, Adrián Castillo, Raúl Porcar, Sami Hietala, Belén Altava, Eduardo Garcı́a-Verdugo, and Santiago V. Luis. "Urea-Based Low-Molecular-Weight Pseudopeptidic Organogelators for the Encapsulation and Slow Release of (R)-Limonene." Journal of Agricultural and Food Chemistry 68, no. 26 (June 8, 2020): 7051–61. http://dx.doi.org/10.1021/acs.jafc.0c01184.

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34

Previti, Santo, Roberta Ettari, Carla Di Chio, Rahul Ravichandran, Marta Bogacz, Ute A. Hellmich, Tanja Schirmeister, Sandro Cosconati, and Maria Zappalà. "Development of Reduced Peptide Bond Pseudopeptide Michael Acceptors for the Treatment of Human African Trypanosomiasis." Molecules 27, no. 12 (June 11, 2022): 3765. http://dx.doi.org/10.3390/molecules27123765.

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Human African Trypanosomiasis (HAT) is an endemic protozoan disease widespread in the sub-Saharan region that is caused by T. b. gambiense and T. b. rhodesiense. The development of molecules targeting rhodesain, the main cysteine protease of T. b. rhodesiense, has led to a panel of inhibitors endowed with micro/sub-micromolar activity towards the protozoa. However, whilst impressive binding affinity against rhodesain has been observed, the limited selectivity towards the target still remains a hard challenge for the development of antitrypanosomal agents. In this paper, we report the synthesis, biological evaluation, as well as docking studies of a series of reduced peptide bond pseudopeptide Michael acceptors (SPR10–SPR19) as potential anti-HAT agents. The new molecules show Ki values in the low-micro/sub-micromolar range against rhodesain, coupled with k2nd values between 1314 and 6950 M−1 min−1. With a few exceptions, an appreciable selectivity over human cathepsin L was observed. In in vitro assays against T. b. brucei cultures, SPR16 and SPR18 exhibited single-digit micromolar activity against the protozoa, comparable to those reported for very potent rhodesain inhibitors, while no significant cytotoxicity up to 70 µM towards mammalian cells was observed. The discrepancy between rhodesain inhibition and the antitrypanosomal effect could suggest additional mechanisms of action. The biological characterization of peptide inhibitor SPR34 highlights the essential role played by the reduced bond for the antitrypanosomal effect. Overall, this series of molecules could represent the starting point for further investigations of reduced peptide bond-containing analogs as potential anti-HAT agents

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35

D'Angeli, Ferruccio, Paolo Marchetti, Severe Salvador, and Gianfranco Balboni. "2-Bromoamides as synthons for pseudopeptides containing aminodicarboxy units." Journal of the Chemical Society, Chemical Communications, no. 3 (1993): 304. http://dx.doi.org/10.1039/c39930000304.

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36

Zaretsky, Serge, and Andrei K. Yudin. "Recent advances in the synthesis of cyclic pseudopeptides." Drug Discovery Today: Technologies 26 (December 2017): 3–10. http://dx.doi.org/10.1016/j.ddtec.2017.11.004.

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37

Abdelbaky, Ahmed S., Ivan A. Prokhorov, Elena V. Gnuskova, Olga V. Esipova, and Yulia G. Kirillova. "Convenient and Efficient Syntheses of Peptide Nucleic Acid Purine Monomers." Current Organic Chemistry 23, no. 19 (December 19, 2019): 2122–30. http://dx.doi.org/10.2174/1385272823666191014161442.

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Currently, peptide nucleic acids (PNAs) play an important role as therapeutic agents, molecular tools for diagnosis and detection of genetic diseases as well as in biosensor probes. This research aims to optimize the synthesis of aeg- and γ-(S)-Me PNA monomers based on L-Ala, intended for oligomerization according to the Boc protocol. The monomers were obtained through the condensation of the corresponding pseudopeptides with carboxymethyl purine nucleic bases. During the work, the optimization of benzyloxycarbonyl- N6-adenine-9-yl-acetic acid and benzyloxycarbonyl-N2-guanine-9-ylacetic acid was carried out. The synthesis of benzyloxycarbonyl-N6-adenine-9-yl-acetic acid was conducted in three stages based on adenine with an overall yield of 22%. At the same time, the conditions for effective recrystallization of the mixture after alkylation of benzyloxycarbonyl-N6-adenine with ethyl bromoacetic acid ether have been developed to isolate the desired N9-regioisomer. Also, the optimization of a known method for producing benzyloxycarbonyl-N2-guanine-9-ylacetic acid from 2-amino-6-chloropurine was carried out. The total yield of the five-stage scheme was 55%. Condensation of aeg- and γ-(S)-Me pseudopeptides with benzyloxycarbonyl-N6-adenine-9-yl-acetic acid and benzyloxycarbonyl-N2-guanine-9-yl-acetic acid was performed by the standard carbodiimide method, DCC/HOBt in DMF followed by the removal of C-terminal methyl protective group by alkaline hydrolysis. The structure of the new compounds obtained was confirmed by spectral analysis methods. This work provides simple and optimized methods for obtaining protected carboxymethyl purine bases and increasing the efficiency of the synthesis and synthesized purine PNA monomers in an acceptable yield.

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38

Byk, Gerardo, Marc Duchesne, Fabienne Parker, Yves Lelievre, Jean D. Guitton, François F. Clerc, Jérôme Becquart, Bruno Tocque, and Daniel Scherman. "Local constrained shifty pseudopeptides inhibitors of rasfarnesyl transferase." Bioorganic & Medicinal Chemistry Letters 5, no. 22 (November 1995): 2677–82. http://dx.doi.org/10.1016/0960-894x(95)00482-9.

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39

Scognamiglio, Pasqualina Liana, Chiara Platella, Ettore Napolitano, Domenica Musumeci, and Giovanni Nicola Roviello. "From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides." Molecules 26, no. 12 (June 10, 2021): 3558. http://dx.doi.org/10.3390/molecules26123558.

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Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.

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40

Guichard, Gilles, Sébastien Calbo, Sylviane Muller, Philippe Kourilsky, Jean-Paul Briand, and Jean-Pierre Abastado. "Efficient Binding of Reduced Peptide Bond Pseudopeptides to Major Histocompatibility Complex Class I Molecule." Journal of Biological Chemistry 270, no. 44 (November 3, 1995): 26057–59. http://dx.doi.org/10.1074/jbc.270.44.26057.

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41

Qian, J. M., D. H. Coy, N. Y. Jiang, J. D. Gardner, and R. T. Jensen. "Reduced Peptide Bond Pseudopeptide Analogues of Substance P." Journal of Biological Chemistry 264, no. 28 (October 1989): 16667–71. http://dx.doi.org/10.1016/s0021-9258(19)84757-9.

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42

Sharma, Sakshi, Shridhar H. Thorat, Rajesh G. Gonnade, Jerry P. Jasinski, Ray Butcher, and V. Haridas. "Front Cover: Engineering Molecular Topology: A Pseudopeptidic Macrocyclic Figure-Eight Motif (Eur. J. Org. Chem. 7/2017)." European Journal of Organic Chemistry 2017, no. 7 (February 10, 2017): 1099. http://dx.doi.org/10.1002/ejoc.201700131.

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43

Giastas, Petros, Anastasia Mpakali, Athanasios Papakyriakou, Aggelos Lelis, Paraskevi Kokkala, Margarete Neu, Paul Rowland, John Liddle, Dimitris Georgiadis, and Efstratios Stratikos. "Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1." Proceedings of the National Academy of Sciences 116, no. 52 (December 16, 2019): 26709–16. http://dx.doi.org/10.1073/pnas.1912070116.

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Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that optimizes the peptide cargo of major histocompatibility class I (MHC-I) molecules and regulates adaptive immunity. It has unusual substrate selectivity for length and sequence, resulting in poorly understood effects on the cellular immunopeptidome. To understand substrate selection by ERAP1, we solved 2 crystal structures of the enzyme with bound transition-state pseudopeptide analogs at 1.68 Å and 1.72 Å. Both peptides have their N terminus bound at the active site and extend away along a large internal cavity, interacting with shallow pockets that can influence selectivity. The longer peptide is disordered through the central region of the cavity and has its C terminus bound in an allosteric pocket of domain IV that features a carboxypeptidase-like structural motif. These structures, along with enzymatic and computational analyses, explain how ERAP1 can select peptides based on length while retaining the broad sequence-specificity necessary for its biological function.

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44

Shaaban, Saad, Florenz Sasse, Torsten Burkholz, and Claus Jacob. "Sulfur, selenium and tellurium pseudopeptides: Synthesis and biological evaluation." Bioorganic & Medicinal Chemistry 22, no. 14 (July 2014): 3610–19. http://dx.doi.org/10.1016/j.bmc.2014.05.019.

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45

Zhao, Ming, Hynda K. Kleinman, and Michael Mokotoff. "Synthetic Laminin-like Peptides and Pseudopeptides as Potential Antimetastatic Agents." Journal of Medicinal Chemistry 37, no. 20 (September 1994): 3383–88. http://dx.doi.org/10.1021/jm00046a023.

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46

Ewenson, Ariel, Ralph Laufer, Michael Chorev, Zvi Selinger, and Chaim Gilon. "Ketomethylene pseudopeptide analogs of substance P: synthesis and biological activity." Journal of Medicinal Chemistry 29, no. 2 (February 1986): 295–99. http://dx.doi.org/10.1021/jm00152a020.

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47

Marastoni, Mauro, Martina Bazzaro, Fabrizio Bortolotti, and Roberto Tomatis. "Synthesis and activity of N-Benzyl pseudopeptides HIV protease inhibitors." Bioorganic & Medicinal Chemistry 11, no. 11 (May 29, 2003): 2477–83. http://dx.doi.org/10.1016/s0968-0896(02)00563-1.

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48

Harrington, Edmund M., James J. Kowalczyk, Sharon L. Pinnow, Karen Ackermann, Ana Maria Garcia, and Michael D. Lewis. "Cysteine and methionine linked by carbon pseudopeptides inhibit farnesyl transferase." Bioorganic & Medicinal Chemistry Letters 4, no. 23 (December 1994): 2775–80. http://dx.doi.org/10.1016/s0960-894x(01)80593-x.

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49

Sieńczyk, Marcin, Dawid Podgórski, Aleksandra Błażejewska, Julita Kulbacka, Jolanta Saczko, and Józef Oleksyszyn. "Phosphonic pseudopeptides as human neutrophil elastase inhibitors—a combinatorial approach." Bioorganic & Medicinal Chemistry 19, no. 3 (February 2011): 1277–84. http://dx.doi.org/10.1016/j.bmc.2010.12.008.

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50

Georgsson, Jennie, Ulrika Rosenström, Charlotta Wallinder, Hélène Beaudry, Bianca Plouffe, Gunnar Lindeberg, Milad Botros, et al. "Short pseudopeptides containing turn scaffolds with high AT2 receptor affinity." Bioorganic & Medicinal Chemistry 14, no. 17 (September 2006): 5963–72. http://dx.doi.org/10.1016/j.bmc.2006.05.019.

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