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New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Bioactives and Nutraceuticals".

Deadline for manuscript submissions: closed (28 February 2024) | Viewed by 24514

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Dr. Flavia Anna Mercurio

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CNR-IBB (National Research Council-Institute of Biostructures and Bioimaging), Via Tommaso De Amicis 95, Naples, Italy
Interests: structural biology; NMR; drug discovery; conformational analysis of proteins and peptides; protein–protein interactions (PPIs); design and evaluation of PPI inhibitors; structure-based drug design; molecular modeling; docking
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Dr. Marilisa Leone

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Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), Via Mezzocannone 16, 80134 Naples, Italy
Interests: structural biology; NMR; drug discovery; conformational analysis of proteins and peptides; protein–protein interactions (PPIs); design and evaluation of PPI inhibitors; structure-based drug design; molecular modeling; docking; cancer
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Peptides consist of amino acids linked by covalent bonds similarly to proteins but with a shorter chain. Synthetic and natural peptides may hold interesting biological functions and consequently they have aroused increasing attention in drug design / drug discovery research fields. Peptide sequences may reflect proteins spots responsible for molecular recognition and biological activities, thus can act as enzyme inhibitors or protein-protein interaction modulators and interfere with signaling pathways. Peptides may possess therapeutic potential and be employed to set-up original therapies in alternative to small molecules and protein drugs due to their unique features of potency, specificity, and low toxicity profile. Since the discovery of Insulin for diabetes treatment, peptide drugs have been implemented to treat a wide range of diseases, including cancer, osteoporosis, multiple sclerosis, HIV infection and chronic pain. Moreover, peptides can play a supporting role in disease diagnosis and drug delivery. As peptides may be affected by high protease sensitivity and defective pharmacokinetics, different chemical strategies have been proposed for overcoming these issues, such as peptide stapling and cyclization and peptidomimetics design. Several computational tools have been also devoted to peptide ligand design and screening against biological macromolecular targets, and peptide structure manipulation.

The present Special Issue aims to cover the above-described topics by means of contributions (communication, full papers and reviews) particularly focused on innovative experimental and computational approaches towards the development of bioactive peptides.

Dr. Flavia Anna Mercurio
Dr. Marilisa Leone
Guest Editors

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Keywords

peptides
protein-peptide interactions
PPI inhibition and modulation
peptide drugs
peptidomimetics
cyclic peptides
stapled peptides
diagnostic peptides
peptides for drug delivery
multidisciplinary approaches

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New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship (2nd Edition) in International Journal of Molecular Sciences (3 articles)

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Research

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16 pages, 2637 KiB

Open AccessArticle

Liquid Chromatographic Enantioseparation of Newly Synthesized Fluorinated Tryptophan Analogs Applying Macrocyclic Glycopeptides-Based Chiral Stationary Phases Utilizing Core-Shell Particles

by Dániel Tanács, Róbert Berkecz, Zsolt Bozsó, Gábor K. Tóth, Daniel W. Armstrong, Antal Péter and István Ilisz

Int. J. Mol. Sci. 2024, 25(9), 4719; https://doi.org/10.3390/ijms25094719 - 26 Apr 2024

Viewed by 922

Abstract

Due to the favorable features obtained through the incorporation of fluorine atom(s), fluorinated drugs are a group with emerging pharmaceutical importance. As their commercial availability is still very limited, to expand the range of possible candidates, new fluorinated tryptophan analogs were synthesized. Control of enantiopurity during the synthesis procedure requires that highly efficient enantioseparation methods be available. In this work, the enantioseparation of seven fluorinated tryptophans and tryptophan was studied and compared systematically to (i) develop analytical methods for enantioselective separations and (ii) explore the chromatographic features of the fluorotrytophans. For enantioresolution, macrocyclic glycopeptide-based selectors linked to core-shell particles were utilized, applying liquid chromatography-based methods. Application of the polar-ionic mode resulted in asymmetric and broadened peaks, while reversed-phase conditions, together with mobile-phase additives, resulted in baseline separation for all studied fluorinated tryptophans. The marked differences observed between the methanol and acetonitrile-containing eluent systems can be explained by the different solvation abilities of the bulk solvents of the applied mobile phases. Among the studied chiral selectors, teicoplanin and teicoplanin aglycone were found to work effectively. Under optimized conditions, baseline separations were achieved within 6 min. Ionic interactions were semi-quantitatively characterized and found to not influence enantiorecognition. Interestingly, fluorination of the analytes does not lead to marked changes in the chromatographic characteristics of the methanol-containing eluents, while larger differences were noticed when the polar but aprotic acetonitrile was applied. Experiments conducted on the influence of the separation temperature indicated that the separations are enthalpically driven, with only one exception. Enantiomeric elution order was found to be constant on both teicoplanin and teicoplanin aglycone-based chiral stationary phases (L < D) under all applied chromatographic conditions. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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14 pages, 3399 KiB

Open AccessArticle

The 12-Membered TNFR1 Peptide, as Well as the 16-Membered and 6-Membered TNF Peptides, Regulate TNFR1-Dependent Cytotoxic Activity of TNF

by Daria M. Yurkina, Elena A. Romanova, Anna V. Tvorogova, Zlata K. Naydenysheva, Alexey V. Feoktistov, Denis V. Yashin and Lidia P. Sashchenko

Int. J. Mol. Sci. 2024, 25(7), 3900; https://doi.org/10.3390/ijms25073900 - 31 Mar 2024

Viewed by 1302

Abstract

Understanding the exact mechanisms of the activation of proinflammatory immune response receptors is very important for the targeted regulation of their functioning. In this work, we were able to identify the sites of the molecules in the proinflammatory cytokine TNF (tumor necrosis factor) and its TNFR1 (tumor necrosis factor receptor 1), which are necessary for the two-stage cytotoxic signal transduction required for tumor cell killing. A 12-membered TNFR1 peptide was identified and synthesized, interacting with the ligands of this receptor protein’s TNF and Tag7 and blocking their binding to the receptor. Two TNF cytokine peptides interacting with different sites of TNFR1 receptors were identified and synthesized. It has been demonstrated that the long 16-membered TNF peptide interferes with the binding of TNFR1 ligands to this receptor, and the short 6-membered peptide interacts with the receptor site necessary for the transmission of a cytotoxic signal into the cell after the ligands’ interaction with the binding site. This study may help in the development of therapeutic approaches to regulate the activity of the cytokine TNF. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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14 pages, 3089 KiB

Open AccessArticle

Beneficial Effects of Small-Molecule Oligopeptides Isolated from Panax Ginseng C. A. Meyer on Cellular Fates in Oxidative Stress-Induced Damaged Human Umbilical Vein Endothelial Cells and PC-12

by Na Zhu, Yong Li and Meihong Xu

Int. J. Mol. Sci. 2024, 25(5), 2906; https://doi.org/10.3390/ijms25052906 - 2 Mar 2024

Cited by 1 | Viewed by 1246

Abstract

Cell fate instability is a crucial characteristic of aging and appears to contribute to various age-related pathologies. Exploring the connection between bioactive substances and cell fate stability may offer valuable insights into longevity. Therefore, the objective of this study was to investigate the potential beneficial effects of ginseng oligopeptides (GOPs) isolated from Panax ginseng C. A. Meyer at the cellular level. Disruption of homeostasis of human umbilical vein endothelial cells (HUVECs) and PC-12 was achieved by culturing them in the growth medium supplemented with 200 µM of H₂O₂, and 25, 50, and 100 µg/mL GOPs for 4 h. Then, they were cultured in a H₂O₂-free growth medium containing different concentration of GOPs. We found that GOP administration retards the oxidative stress-induced cell instability in HUVECs by increasing cell viability, inhibiting the cell cycle arrest, enhancing telomerase (TE) activity, suppressing oxidative stress and an inflammatory attack, and protecting mitochondrial function. Furthermore, we hypothesized that GOPs may promote mitochondrial biosynthesis by upregulating PGC-1α expression. Similarly, GOPs positively regulated cell stability in PC-12; notably, the protective effect of GOPs on PC-12 mainly occurred through the inhibition of autophagic cell death of neuronal cells, while the protective effect on mitochondria was weak. In conclusion, it is evident that GOPs demonstrate potential beneficial effects in maintaining cell fate stability, thereby potentially contributing to an enhanced health span and overall well-being. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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18 pages, 4917 KiB

Open AccessArticle

Rational Design, Synthesis and Binding Affinity Studies of Anthraquinone Derivatives Conjugated to Gonadotropin-Releasing Hormone (GnRH) Analogues towards Selective Immunosuppression of Hormone-Dependent Cancer

by Georgia Biniari, Christos Markatos, Agathi Nteli, Haralambos Tzoupis, Carmen Simal, Alexios Vlamis-Gardikas, Vlasios Karageorgos, Ioannis Pirmettis, Panagiota Petrou, Maria Venihaki, George Liapakis and Theodore Tselios

Int. J. Mol. Sci. 2023, 24(20), 15232; https://doi.org/10.3390/ijms242015232 - 16 Oct 2023

Cited by 1 | Viewed by 2310

Abstract

Gonadotropin-releasing hormone (GnRH) is pivotal in regulating human reproduction and fertility through its specific receptors. Among these, gonadotropin-releasing hormone receptor type I (GnRHR I), which is a member of the G-protein-coupled receptor family, is expressed on the surface of both healthy and malignant cells. Its presence in cancer cells has positioned this receptor as a primary target for the development of novel anti-cancer agents. Moreover, the extensive regulatory functions of GnRH have underscored decapeptide as a prominent vehicle for targeted drug delivery, which is accomplished through the design of appropriate conjugates. On this basis, a rationally designed series of anthraquinone/mitoxantrone–GnRH conjugates (con1–con8) has been synthesized herein. Their in vitro binding affinities range from 0.06 to 3.42 nM, with six of them (con2–con7) demonstrating higher affinities for GnRH than the established drug leuprolide (0.64 nM). Among the mitoxantrone based GnRH conjugates, con3 and con7 show the highest affinities at 0.07 and 0.06 nM, respectively, while the disulfide bond present in the conjugates is found to be readily reduced by the thioredoxin (Trx) system. These findings are promising for further pharmacological evaluation of the synthesized conjugates with the prospect of performing future clinical studies. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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10 pages, 2199 KiB

Open AccessArticle

Insecticidal Effects of Receptor-Interference Isolated Bioactive Peptides on Fire Ant Colonies

by Satya Chinta, Robert Vander Meer, Erin O’Reilly and Man-Yeon Choi

Int. J. Mol. Sci. 2023, 24(18), 13978; https://doi.org/10.3390/ijms241813978 - 12 Sep 2023

Cited by 2 | Viewed by 1323

Abstract

Receptor-interference (Receptor-i) is a novel technology used to identify bioactive peptides as agonists or antagonists against a specific receptor, primarily targeting G-protein-coupled receptors (GPCRs). Using Receptor-i methodology, we targeted the pheromone biosynthesis activating neuropeptide receptor (PBAN-R) of the red imported fire ant (Solenopsis invicta). Based on previous studies, we selected four bioactive peptides cyclized with two cysteines: CVKLGSHFC, CIQQGSHFC, CERVGSHFC, and CMARYMSAC, and we conducted small-scale feeding bioassays, measuring fire ant worker mortality. All peptides reduced ant survival; however, CMARYMSAC (MARY) and CIQQGSHFC (IQQG) were the most effective and were selected for feeding trials against large, fully functional fire ant field colonies containing queen, brood, and up to 8000 workers. At the end of the experiment, day 84, synthetic peptide MARY killed over 80% of the workers and two of four queens. IQQG killed over 70% of the workers and three of four queens. The surviving two MARY queens lost an average of 21% of their starting weight. The surviving IQQG queen lost 31% of its weight. In contrast, control colony queens gained an average of 11% of their starting weight. These results provide proof-of-concept for the Receptor-i technology and will synergize applications to other agricultural and medical pests. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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13 pages, 2682 KiB

Open AccessArticle

Interaction of Blenoxane and Congeners Bleomycins A2 and B2 with Human Plasma Proteins Using Circular Dichroism Spectroscopy

by Edoardo Longo, Giuliano Siligardi and Rohanah Hussain

Int. J. Mol. Sci. 2023, 24(17), 13598; https://doi.org/10.3390/ijms241713598 - 2 Sep 2023

Cited by 1 | Viewed by 1539

Abstract

Bleomycin is a glycopeptide congeners’ family of antitumor antibiotics employed for the treatment of several types of tumors such as squamous cell carcinomas and malignant lymphomas. The general chemical structure is constituted by three main portions: (i) a metal binding domain that is recognized to be responsible for the DNA cleavage activity; (ii) a DNA binding domain via the 1-4’ bithiazole moiety; and (iii) a carbohydrate domain thought to be responsible for the accumulation of bleomycin in some cancer cells. To date, a limited number of protein interactions with bleomycin have been studied, but the plasma binding has not yet been determined. Here, we explore this aspect of the protein binding capacity of bleomycin to the two most abundant plasma proteins, human serum albumin (HSA) and α1-acid glycoprotein (AGP), which are known to bind and to be carriers of many drug molecules using spectroscopic techniques, such as circular dichroism, UV-vis absorbance, and fluorescence. The results showed that bleomycin binds to plasma proteins with an order-of-magnitude higher affinity for AGP than HSA. This is particularly important as AGP is an acute phase protein and is overexpressed in cancer patients. This should be taken into consideration as it could affect the therapeutic effect of the bleomycin dosage. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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13 pages, 3275 KiB

Open AccessArticle

Isolation and Characterization of Poeciguamerin, a Peptide with Dual Analgesic and Anti-Thrombotic Activity from the Poecilobdella manillensis Leech

by Chaoming Wang, Mengrou Chen, Xiaoyu Lu, Shuo Yang, Min Yang, Yaqun Fang, Ren Lai and Zilei Duan

Int. J. Mol. Sci. 2023, 24(13), 11097; https://doi.org/10.3390/ijms241311097 - 4 Jul 2023

Cited by 7 | Viewed by 2133

Abstract

When Poecilobdella manillensis attacks its prey, the prey bleeds profusely but feels little pain. We and other research teams have identified several anticoagulant molecules in the saliva of P. manillensis, but the substance that produces the paralyzing effect in P. manillensis is not known. In this study, we successfully isolated, purified, and identified a serine protease inhibitor containing an antistasin-like domain from the salivary secretions of P. manillensis. This peptide (named poeciguamerin) significantly inhibited elastase activity and slightly inhibited FXIIa and kallikrein activity, but had no effect on FXa, trypsin, or thrombin activity. Furthermore, poeciguamerin exhibited analgesic activity in the foot-licking and tail-withdrawal mouse models and anticoagulant activity in the FeCl₃-induced carotid artery thrombosis mouse model. In this study, poeciguamerin was found to be a promising elastase inhibitor with potent analgesic and antithrombotic activity for the inhibition of pain and thrombosis after surgery or in inflammatory conditions. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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11 pages, 4832 KiB

Open AccessArticle

Investigating the Effects of NaCl on the Formation of AFs from Gluten in Cooked Wheat Noodles

by Ying Liang, Jiayang Song, Jiayi Wang, Hao Liu, Xingquan Wu, Baoshan He, Xia Zhang and Jinshui Wang

Int. J. Mol. Sci. 2023, 24(12), 9907; https://doi.org/10.3390/ijms24129907 - 8 Jun 2023

Cited by 4 | Viewed by 1617

Abstract

To clarify the effect of NaCl concentration (0–2.0%) on the formation of amyloid fibrils (AFs) in cooked wheat noodles, the morphology, surface hydrophobicity, secondary structure, molecular weight distribution, microstructure, and crystal structure of AFs were investigated in this paper. Fluorescence data and Congo red stain images confirmed the presence of AFs and revealed that the 0.4% NaCl concentration promoted the production of AFs. The surface hydrophobicity results showed that the hydrophobicity of AFs increased significantly from 3942.05 to 6117.57 when the salt concentration increased from 0 to 0.4%, indicating that hydrophobic interactions were critical for the formation of AFs. Size exclusion chromatography combined with gel electrophoresis plots showed that the effect of NaCl on the molecular weight of AFs was small and mainly distributed in the range of 5–7.1 KDa (equivalent to 40–56 amino acid residues). X-ray diffraction and AFM images showed that the 0.4% NaCl concentration promoted the formation and longitudinal growth of AFs, while higher NaCl concentrations inhibited the formation and expansion of AFs. This study contributes to the understanding of the mechanism of AF formation in wheat flour processing and provides new insight into wheat gluten aggregation behavior. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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17 pages, 2494 KiB

Open AccessArticle

Bradykinin and Neurotensin Analogues as Potential Compounds in Colon Cancer Therapy

by Magdalena Szaryńska, Agata Olejniczak-Kęder, Kamila Podpłońska, Adam Prahl and Emilia Iłowska

Int. J. Mol. Sci. 2023, 24(11), 9644; https://doi.org/10.3390/ijms24119644 - 1 Jun 2023

Cited by 2 | Viewed by 2087

Abstract

Colorectal cancer (CRC) is one of the most lethal malignancies worldwide, so the attempts to find novel therapeutic approaches are necessary. The aim of our study was to analyze how chemical modifications influence physical, chemical, and biological properties of the two peptides, namely, bradykinin (BK) and neurotensin (NT). For this purpose, we used fourteen modified peptides, and their anti-cancers features were analyzed on the HCT116 CRC cell line. Our results confirmed that the spherical mode of a CRC cell line culture better reflects the natural tumour microenvironment. We observed that the size of the colonospheres was markedly reduced following treatment with some BK and NT analogues. The proportion of CD133+ cancer stem cells (CSCs) in colonospheres decreased following incubation with the aforementioned peptides. In our research, we found two groups of these peptides. The first group influenced all the analyzed cellular features, while the second seemed to include the most promising peptides that lowered the count of CD133+ CSCs with parallel substantial reduction in CRC cells viability. These analogues need further analysis to uncover their overall anti-cancer potential. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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21 pages, 6397 KiB

Open AccessArticle

Novel Polymyxin-Inspired Peptidomimetics Targeting the SARS-CoV-2 Spike:hACE2 Interface

by Kelly Bugatti, Andrea Sartori, Lucia Battistini, Crescenzo Coppa, Emiel Vanhulle, Sam Noppen, Becky Provinciael, Lieve Naesens, Annelies Stevaert, Alessandro Contini, Kurt Vermeire and Franca Zanardi

Int. J. Mol. Sci. 2023, 24(10), 8765; https://doi.org/10.3390/ijms24108765 - 15 May 2023

Cited by 2 | Viewed by 1907

Abstract

Though the bulk of the COVID-19 pandemic is behind, the search for effective and safe anti-SARS-CoV-2 drugs continues to be relevant. A highly pursued approach for antiviral drug development involves targeting the viral spike (S) protein of SARS-CoV-2 to prevent its attachment to the cellular receptor ACE2. Here, we exploited the core structure of polymyxin B, a naturally occurring antibiotic, to design and synthesize unprecedented peptidomimetics (PMs), intended to target contemporarily two defined, non-overlapping regions of the S receptor-binding domain (RBD). Monomers 1, 2, and 8, and heterodimers 7 and 10 bound to the S-RBD with micromolar affinity in cell-free surface plasmon resonance assays (K_D ranging from 2.31 μM to 2.78 μM for dimers and 8.56 μM to 10.12 μM for monomers). Although the PMs were not able to fully protect cell cultures from infection with authentic live SARS-CoV-2, dimer 10 exerted a minimal but detectable inhibition of SARS-CoV-2 entry in U87.ACE2⁺ and A549.ACE2.TMPRSS2⁺ cells. These results validated a previous modeling study and provided the first proof-of-feasibility of using medium-sized heterodimeric PMs for targeting the S-RBD. Thus, heterodimers 7 and 10 may serve as a lead for the development of optimized compounds, which are structurally related to polymyxin, with improved S-RBD affinity and anti-SARS-CoV-2 potential. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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Review

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44 pages, 2081 KiB

Open AccessReview

Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools

by Marian Vincenzi, Flavia Anna Mercurio and Marilisa Leone

Int. J. Mol. Sci. 2024, 25(3), 1798; https://doi.org/10.3390/ijms25031798 - 1 Feb 2024

Cited by 6 | Viewed by 4032

Abstract

Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein–protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation). Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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18 pages, 1455 KiB

Open AccessReview

Are Antimicrobial Peptides a 21st-Century Solution for Atopic Dermatitis?

by Manuela Machado, Sara Silva and Eduardo M. Costa

Int. J. Mol. Sci. 2023, 24(17), 13460; https://doi.org/10.3390/ijms241713460 - 30 Aug 2023

Cited by 2 | Viewed by 2546

Abstract

Atopic dermatitis (AD) is a chronic inflammatory skin disorder that is the result of various environmental, bacterial and genetic stimuli, which culminate in the disruption of the skin’s barrier function. Characterized by highly pruritic skin lesions, xerosis and an array of comorbidities among which skin infections are the most common, this condition results in both a significant loss of quality of life and in the need for life-long treatments (e.g., corticosteroids, monoclonal antibodies and regular antibiotic intake), all of which may have harmful secondary effects. This, in conjunction with AD’s rising prevalence, made the development of alternative treatment strategies the focus of both the scientific community and the pharmaceutical industry. Given their potential to both manage the skin microbiome, fight infections and even modulate the local immune response, the use of antimicrobial peptides (AMPs) from more diverse origins has become one of the most promising alternative solutions for AD management, with some being already used with some success towards this end. However, their production and use also exhibit some limitations. The current work seeks to compile the available information and provide a better understanding of the state of the art in the understanding of AMPs’ true potential in addressing AD. Full article

(This article belongs to the Special Issue New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship)

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