Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold

Computer aided study on cyclic tetrapeptide based ligands as potential inhibitors of Proplasmepsin IV

The belief that we could always stay ahead of the pathogens was forced upon scientists in the whole world by antimicrobial resistance. According to several reports, there are medications that are yet to be made public in the pipeline and there are little motivations to design novel antimicrobials to combat the worldwide drug resistance issues. Presently, the desire to design and develop efficient novel anti-bacterial agents is very high by researchers; thus, this study focuses on identifying the interactions between the studied ligands and Proplasmepsin IV, as well as examining the relationship between the calculated descriptors and binding affinities. This work shows successful prediction of the reacting and inhibiting efficiency of ten (10) cyclic tetra-peptides using insilico method. The optimization of the studied compound revealed the proficiency of methyl (3S,9S,12S)-12-(1,3-dioxoisoindolin-2-yl)-9-(2-(methylthio)ethyl)-5,8,11-trioxo-4,7,10-triaza-1(1,3)-benzenacyclotridecaphane-3-carboxylate (F5) and 2-((3S,9S,12S)-12-(1,3-dioxoisoindolin-2-yl)-3-(methoxycarbonyl)-5,8,11-trioxo-4,7,10-triaza-1(1,3)-benzenacyclotridecaphane-9-yl)acetic acid (F7) to react more than the remaining molecules in term of HOMO and LUMO energies. In comparison, compound F9 demonstrated a higher inhibitory activity than the reference drug, Chloroquine, based on binding affinity. Molecular dynamics simulations over a 100 ns period further explored the binding affinity between F9 and the reference drug. The results showed that the reference drug (- 21.91 ± 1.16 kcal/mol) had a slightly stronger binding affinity than the F9_complex (- 13.85 ± 0.72 kcal/mol). Additionally, pharmacokinetic studies for F9 were compared with those of the reference compound and presented accordingly.

Synthesis of Mono-Boc-2,5-Diketopiperazine: A Key Building Block for Amide and Peptide Synthesis

Diketopiperazine (DKP), a versatile scaffold, is extensively used in the synthesis of complex natural products, bioactive molecules, and smart materials in organic chemistry. Recently, activated DKPs, such as Boc-DKPs, have emerged as key building blocks for peptide elongation in peptide synthesis. In this study, we developed a facile protocol for synthesizing mono-Boc-protected DKPs from readily accessible N-4-methoxybenzyl (N-PMB)-amino acids and amino acid methyl esters. This protocol involved a sequence of reactions encompassing the formation of dipeptides from N-PMB-amino acids and amino acid methyl esters, cyclization of N-PMB-dipeptides to form PMB-DKPs, Boc-protection of PMB-DKPs, and subsequent PMB-deprotection of PMB-DKP-Boc to afford mono-Boc-DKPs. The protocol demonstrated a broad substrate scope, accommodating diverse amino acids with various side chains, affording mono-Boc-DKPs in good yields with excellent stereoselectivities (>20:1 dr). The synthetic utility of mono-Boc-DKPs was showcased in peptide synthesis by synthesizing pentapeptide Boc-l-Tyr(t-Bu)-Gly-l-Phe-Gly-l-Val-OtBu by 2-fold peptide elongation with two mono-Boc-DKPs. Furthermore, we synthesized Leu-enkephalin pentapeptide by reacting cyclo(Boc-l-Tyr(t-Bu)-Gly-) with H-Gly-l-Phe-l-Leu-Ot-Bu, resulting in a good yield and excellent optical purity.

'Need for speed: high throughput' - mass spectrometry approaches for high-throughput directed evolution screening of natural product enzymes

Covering: 2015 to 2024Mass spectrometry (MS)-based methods have been implemented extensively for enzyme engineering due to their label-free nature, making them suitable for screening a wide range of biochemical systems. Over the past decade, advancements in mass spectrometry, separation science, and the implementation of hyphenated methods have allowed for more streamlined analysis of large volumes of samples while maximizing the richness and dimensionality of the data collected. In this review we highlight recent advancements in mass spectrometry that have allowed for more efficient, robust, and rigorous enzyme engineering for various applications relating to natural products chemistry.

In Vitro and In Silico Studies of Maculosin as a Melanogenesis and Tyrosinase Inhibitor

The investigation of melanogenesis and tyrosinase inhibitors is essential for developing safe and effective natural compounds to treat pigmentation disorders. This study aimed to evaluate the effects of maculosin, a cyclic dipeptide composed of tyrosine and proline, on melanin production and tyrosinase activity using the B16F10 melanoma cell model, while elucidating its mechanism of action through molecular docking and molecular dynamics (MD) simulations. Experimental results demonstrated that maculosin inhibited intracellular melanin content and tyrosinase activity in a concentration-dependent manner in B16F10 melanoma cells. Molecular docking analyses revealed that maculosin exhibited high binding affinities with mushroom tyrosinase (mTYR), tyrosinase-related protein 1 (TYRP1), and Bacillus megaterium tyrosinase (BmTYR) with binding energies of -7.7, -6.8, and -7.5 kcal/mol, respectively. Furthermore, MD simulations confirmed the structural stability and dynamic flexibility of maculosin-protein complexes, as indicated by RMSD, RMSF, Rg, SASA, hydrogen bond interactions, PCA, and DCCM analyses. Binding free energy calculations using the MM/PBSA method showed that maculosin exhibited binding energies of -28.76 kcal/mol with mTYR and -22.23 kcal/mol with TYRP1, outperforming standard co-crystal inhibitors such as tropolone (-12.47 kcal/mol) and kojic acid (-12.73 kcal/mol). Critical residues, including VAL-283 and HIS-263 in mTYR and HIS-381, GLY-389, and THR-391 in TYRP1, were identified as key contributors to maculosin binding, corroborating molecular docking findings and displaying strong correlations in DCCM analyses. Collectively, these results suggest that maculosin is a highly promising candidate for the treatment of pigmentation disorders, offering significant inhibitory effects on melanogenesis and tyrosinase activity.

Novel application of cyclo(-Phe-Pro) in mitigating aluminum toxicity through oxidative stress alleviation in wheat roots

Microbial secondary metabolites are crucial in plant-microorganism interactions, regulating plant growth and stress responses. In this study, we found that cyclo(-Phe-Pro), a proline-based cyclic dipeptide secreted by many microorganisms, alleviated aluminum toxicity in wheat roots by increasing root growth, decreasing callose deposition, and decreasing Al accumulation. Cyclo(-Phe-Pro) also significantly reduced Al-induced reactive oxygen species (ROS) with H2O2, O2•-, and •OH levels decreasing by 19.1%, 42.8%, and 17.9% in root tips, thus protecting the plasma membrane from oxidative damage. Although Al stress increased the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) in wheat roots, cyclo(-Phe-Pro) application reduced these enzyme activities. However, compared to the Al treatment, cyclo(-Phe-Pro) application increased DPPH and FRAP activities by 16.8% and 14.9%, indicating increased non-enzymatic antioxidant capacity in wheat roots. We observed that Al caused the oxidation of ascorbate (AsA) and glutathione (GSH) to dehydroascorbate (DHA) and glutathione disulfide (GSSG), respectively. Under Al stress, cyclo(-Phe-Pro) treatment maintained reduced AsA and GSH levels, as well as high AsA/DHA and GSH/GSSG redox pair ratios in wheat roots. High AsA/DHA and GSH/GSSG ratios can reduce Al toxicity by neutralizing free radicals and restoring redox homeostasis via antioxidant properties. These results suggest that cyclo(-Phe-Pro) maintains ASA- and GSH-dependent redox homeostasis to alleviate oxidative and Al stress in wheat roots. Findings of this study establishes a theoretical foundation for using microbial metabolites to mitigate Al toxicity in acidic soils, highlighting their potential in sustainable agriculture.

Novel Peptidomimetic Cyclo-{E(I)-E(W)}Na (CP-88) with Hematopoietic Activity Sustained in Invasive and Oral Administration: Experimental and Preclinical Evaluation

Over the last decades, significant progress has been made in studying agonistic and antagonistic hematopoietic peptides. The main disadvantage of this class of peptides is their low stability with noninvasive administration methods, which limits the widespread use of hematopoiesis-regulated peptide drugs in medical practice. The aim of this work is to study novel peptidomimetics with hematopoietic activity sustained in invasive and oral administration. The activity of the leading compound cyclopeptide Cyclo-[Glu(Ile)-Glu(Trp)] (CP-88) was compared to that of the pharmaceutical preparation Stemokin in stimulating the population of committed colony-forming cells in intact and irradiated mice. CP-88 peptide increases the relative number of CD34+ cells in the blood and bone marrow, leading to expanded hematopoietic stem cells. CP-88 peptide, applied 48 h before bone marrow extraction, stimulates the population of committed colony-forming cells in the normal bone marrow by 33-37% above the normal level. In recipient mice injected with irradiated bone marrow, this peptide was restored practically to normal levels of colony-forming cells in a wide range of doses at intraperitoneal and oral administration. The toxicological results conclude that in humans, considering interspecies extrapolation, the CP-88 peptide can be practically safe with a single and course administration in doses of up to 100 μg/kg. The results of this investigation underscore the significant potential of CP-88 peptide as a hematopoiesis-regulated drug and instill optimism for its future application in medical practice.

Cyclization of alanyl-valine dipeptides in the solid state. The effects of molecular radiator and heat capacity

Heating of linear dipeptides above a critical temperature initiates their cyclization even in the solid state. This method of obtaining cyclic dipeptides meets the requirements of "green chemistry", provides a high yield of the main product and releases only water as a by-product of the reaction, and does not require solvents. However, to date, the cyclization of only a small number of dipeptides in the solid state has been studied, and some correlations of the process were discovered. The influence of the structure of dipeptide molecules and their crystal packing on the kinetics of solid-state cyclization is still not fully understood. In this work, the cyclization of L-alanyl-L-valine in the solid state upon heating was studied. Using non-isothermal kinetic approaches, the kinetic parameters of this reaction and the optimal kinetic model describing this process were determined. The effect of the features of the crystal packing of dipeptides and their heat capacity on the temperature of the cyclization in the solid state was analyzed. This study expands our knowledge about solid-state reactions involving dipeptides and the ability to control such reactions.

Harnessing bacterial metabolites for enhanced cancer chemotherapy: unveiling unique therapeutic potentials

Cancer poses a serious threat to health globally, with millions diagnosed every year. According to Global Cancer Statistics 2024, about 20 million new cases were reported in 2022, and 9.7 million people worldwide died of this condition. Advanced therapies include combination of one or more treatment procedures, depending on the type, stage, and particular genetic constitution of the cancer, which may include surgery, radiotherapy, chemotherapy, immunotherapy, hormone therapy, targeted therapy, and stem cell transplant. Also, awareness about lifestyle changes, preventive measures and screening at early stages has reduced the incidence of the disease; still, there is a major failure in controlling the incidence of cancer because of its complex and multifaceted nature. With increasing interest in bacterial metabolites as possible novel and effective treatment options in cancer therapy, their main benefits include not only direct anticancer effects but also the modulation of the immune system and potential for targeted and combination therapies. They can therefore be used in combination with chemotherapy, radiotherapy, or immunotherapy to improve outcomes or reduce side effects. Furthermore, nanoparticle-based delivery systems have the potential to enhance the potency and safety of anticancer drugs by providing improved stability, targeted release, and controlled delivery.

A Novel Deinococcus Antioxidant Peptide Mitigates Oxidative Stress in Irradiated CHO-K1 Cells

Reactive oxygen species (ROS), byproducts of cellular metabolism and environmental factors, are linked to diseases like cancer and aging. Antioxidant peptides (AOPs) have emerged as effective countermeasures against ROS-induced damage. The Deinococcus genus is well known for its extraordinary resilience to ionizing radiation (IR) and possesses complex antioxidant systems designed to neutralize ROS generated by IR. In this study, we developed four peptides, each containing 9 to 11 amino acids, from the leaderless mRNA (lmRNA) sequences of D. deserti. Lacking a 5' untranslated region, lmRNAs directly initiate protein synthesis, potentially encoding small peptides such as AOPs. Of the four peptides, Ddes-P3 was found to exhibit significant antioxidant capabilities in vitro, effectively scavenging ABTS radicals. Ddes-P3 provided considerable defense against IR-induced oxidative stress in CHO-K1 cells, demonstrating a notable reduction in ROS production and lipid peroxidation. The peptide's potential was highlighted by its ability to enhance cell survival and maintain mitochondrial membrane potential under irradiative stress, suggesting its utility as a nontoxic and effective radioprotector in mitigating radiation-induced cellular damage. This study explores the potential role of lmRNA in synthesizing AOPs within Deinococcus. Identifying lmRNAs that encode AOPs could deepen our understanding of their cellular resistance to oxidative stress and pave the way for creating innovative biotechnological and therapeutic AOPs.

Exploring the Frontier of Cyclic Dipeptides: A Bioinformatics Approach to Potential Therapeutic Applications in Schizophrenia

Cyclic dipeptides (CDPs), known for their diverse biological activities, have potential therapeutic applications in mental and behavioral disorders (MBDs), particularly schizophrenia. This study explores the CDPs' therapeutic potential using bibliometric analysis, network pharmacology, molecular docking, and experimental verification, focusing on the interactions with the SIGMA1 receptor. A literature review over three decades utilizing the Web of Science Core Collection (WOSCC) was conducted to identify the emerging trends in CDPs research. A compound library was constructed from the PubChem database, and target prediction using SwissTargetPrediction revealed 800 potential protein targets. A compound-target network highlighted the key interactions with kinases, G protein-coupled receptors, and chromatin-modifying enzymes. Enrichment analysis revealed significant associations with schizophrenia and other MBDs. Schizophrenia-related targets among the potential protein targets were identified using the GEO database. Molecular docking results showed interactions of MC4R, OPRK1, SIGMA1, and CDK5R1 with various CDPs compounds, with SIGMA1 being especially noteworthy. Most CDPs exhibited lower binding energies than the control compounds NE-100 and duloxetine. Experimental validation demonstrated that CDPs such as Cyclo(Ala-Gln), Cyclo(Ala-His), and Cyclo(Val-Gly) exhibited IC50 values of 13.4, 19.4, and 11.5 μM, respectively, against SIGMA1, indicating biological activity. Our findings underscore their potential as therapeutic agents for schizophrenia, highlighting the need for further modifications to enhance specificity and efficacy. This work paves the way for future investigations into CDPs, contributing to developing targeted treatments for schizophrenia and related mental health disorders.

An experimental and computational investigation of the cyclopentene-containing peptide-derived compounds: focus on pseudo-cyclic motifs via intramolecular interactions

Conformational flexibility is one of the main disadvantages of peptide-based compounds. We focus on their molecular 'chameleonicity' related to forming pseudo-cyclic motifs via modulation of weak intramolecular interactions. It is an appealing strategy for controlling equilibrium between the polar open and the nonpolar closed conformations. Within this context, we report here the crystal structure of the (R)-(2-tert-butoxycarbonyl)amino-1-oxo-3-phenyl)propyl)-1-cyclopentene (1), synthesis of which in high yield was achieved by a facile multi-step protocol. Our Cambridge Structural Database (CSD) overview for the peptide-based crystals revealed the exclusivity of this compound from the viewpoint of the unusual pseudo-bicyclic system via C-H…O and C-O…π interactions, in which cyclopentene shields the amide bond. Notably, cyclopentene as a bioisostere of proline is an appealing scaffold in medicinal chemistry. An extensive combined experimental and computational study provided more profound insight into the supramolecular landscape of 1 with respect to similar derivatives deposited in the CSD, including the tendency of cyclopentene for the generation of pseudo-cyclic motifs through weak H-bonding and π-based intramolecular interactions. These weak interactions have been examined by either the quantum theory of 'atoms-in-molecules' (QTAIM) or complex Hirshfeld surface methodology, including enrichment ratios, molecular electrostatic potential surfaces and energy frameworks. In all analysed crystals, all types of H-bonded motifs involving cyclopentene are formed at all levels of supramolecular architecture. A library of cyclopentene-based H-bonding synthons is provided. A molecular docking study depicted vital interactions of cyclopentene with key amino acid residues inside the active sites of two prominent protein kinases, uncovering the therapeutic potential of 1 against breast cancer. To a large extent, dispersion forces have significance in stabilizing the supramolecular structure of both ligand and bio-complex ligand-protein. Finally, the satisfactory in silico bio-pharmacokinetic profile of 1 related to drug-likeness and blood-brain barrier permeation was also revealed.

Antibacterial, Antifungal, and Cytotoxic Effects of Endophytic Streptomyces Species Isolated from the Himalayan Regions of Nepal and Their Metabolite Study

Background/Objectives: Recently, antimicrobial-resistant pathogens and cancers have emerged as serious global health problems, highlighting the immediate need for novel therapeutics. Consequently, we aimed to isolate and characterize endophytic Streptomyces strains from the rhizospheres of the Himalayan region of Nepal and identify specialized metabolites with antibacterial, antifungal, and cytotoxic potential. Methods: To isolate Streptomyces sp., we collected two soil samples and cultured them on an ISP4 medium after pretreatment. We isolated and identified the strains PY108 and PY109 using a combination of morphological observations and 16S rRNA gene sequencing. Results: The BLAST results showed that PY108 and PY109 resembled Streptomyces hundungensis PSB170 and Streptomyces sp. Ed-065 with 99.28% and 99.36% nucleotide similarity, respectively. Antibacterial assays of ethyl acetate (EA) extracts from both isolates PY108 and PY109 in a tryptic soy broth (TSB) medium were conducted against four pathogenic bacteria. They showed significant antibacterial potential against Staphylococcus aureus and Klebsiella pneumoniae. Similarly, these extracts exhibited moderate antifungal activities against Saccharomyces cerevisiae and Aspergillus niger. Cytotoxicity assays on cervical cancer cells (HeLa) and breast cancer cells (MCF-7) revealed significant potential for both extracts. LC-MS/MS profiling of the EA extracts identified 27 specialized metabolites, including diketopiperazine derivatives, aureolic acid derivatives such as chromomycin A, and lipopeptide derivatives. In comparison, GC-MS analysis detected 34 metabolites, including actinomycin D and γ-sitosterol. Furthermore, a global natural product social molecular networking (GNPS)-based molecular networking analysis dereplicated 24 metabolites in both extracts. Conclusions: These findings underscore the potential of endophytic Streptomyces sp. PY108 and PY109 to develop new therapeutics in the future.

Short Peptides as Powerful Arsenal for Smart Fighting Cancer

Short peptides have been coming around as a strong weapon in the fight against cancer on all fronts-in immuno-, chemo-, and radiotherapy, and also in combinatorial approaches. Moreover, short peptides have relevance in cancer imaging or 3D culture. Thanks to the natural 'smart' nature of short peptides, their unique structural features, as well as recent progress in biotechnological and bioinformatics development, short peptides are playing an enormous role in evolving cutting-edge strategies. Self-assembling short peptides may create excellent structures to stimulate cytotoxic immune responses, which is essential for cancer immunotherapy. Short peptides can help establish versatile strategies with high biosafety and effectiveness. Supramolecular short peptide-based cancer vaccines entered clinical trials. Peptide assemblies can be platforms for the delivery of antigens, adjuvants, immune cells, and/or drugs. Short peptides have been unappreciated, especially in the vaccine aspect. Meanwhile, they still hide the undiscovered unlimited potential. Here, we provide a timely update on this highly active and fast-evolving field.

Co-Culture of Gut Bacteria and Metabolite Extraction Using Fast Vacuum Filtration and Centrifugation

This protocol describes a robust method for the extraction of intra and extracellular metabolites of gut bacterial mono and co-cultures. In recent years, the co-culture techniques employed in the field of microbiology have demonstrated significant importance in regard to understanding cell-cell interactions, cross-feeding, and the metabolic interactions between different bacteria, fungi, and microbial consortia which enable the mimicking of complex co-habitant conditions. This protocol highlights a robust reproducible physiologically relevant culture and extraction protocol for the co-culture of gut bacterium. The novel extraction steps are conducted without using quenching and cell disruption through bead-cell methods, freeze-thaw cycles, and sonication, which tend to affect the physical and biochemical properties of intracellular metabolites and secretome. The extraction procedure of inoculated bacterial co-cultures and monocultures use fast vacuum filtration and centrifugation. The extraction methodology is fast, effective, and robust, requiring 4 h to complete.

The Immobilization of a Cyclodipeptide Synthase Enables Biocatalysis for Cyclodipeptide Production

Cyclodipeptide synthases (CDPSs) are enzymes that use aminoacylated tRNAs as substrates to produce cyclic dipeptide natural products acting as anticancer and neuroprotective compounds. Many CDPSs, however, suffer from instability and poor recyclability, while enzyme immobilization can enhance catalyst efficiency and reuse. Here, the CDPS enzyme from Parcubacteria bacterium RAAC4_OD1_1 was immobilized using three different supports: biochar from waste materials, calcium-alginate beads, and chitosan beads. Immobilization of active PbCDPS was successful, and production of the cyclodipeptide cyclo (His-Glu) (cHE) was confirmed by HPLC-MS. Biochar from spent coffee activated with glutaraldehyde, alginate beads, and chitosan beads activated with glutaraldehyde led to a 5-fold improvement in cHE production, with the immobilized enzyme remaining active for seven consecutive cycles. Furthermore, we co-immobilized three enzymes participating in the cascade reaction yielding cHE (PbCDPS, histidyl-tRNA synthetase, and glutamyl-tRNA synthetase). The enzymatic cascade successfully produced the cyclic dipeptide, underscoring the potential of immobilizing various enzymes within a single support. Importantly, we demonstrated that tRNAs remained free in solution and were not adsorbed by the beads. We paved the way for the immobilization of enzymes that utilize tRNAs and other complex substrates, thereby expanding the range of reactions that can be exploited by using this technology.

The Immunosuppressive Properties of Cyclo-[D-Pro-Pro-β3-HoPhe-Phe-] Tetrapeptide Selected from Stereochemical Variants of Cyclo-[Pro-Pro-β3-HoPhe-Phe-] Peptide

The anti-inflammatory, antiviral, and anti-cancer properties, as well as the mechanism of action of cyclo-[Pro-Pro-β3-HoPhe-Phe-] tetrapeptide (denoted as 4B8M), were recently described. The aim of this work was to synthesize and evaluate the immunosuppressive actions of the stereochemical variants of 4B8M by sequential substitution of L-amino acids by D-amino acids (a series of peptides denoted as P01-P07) using parent 4B8M as a reference compound. In addition, diverse available bioinformatics tools using machine learning and artificial intelligence were tested to find the bio-pharmacokinetic and polypharmacological attributes of analyzed stereomers. All peptides were non-toxic to human peripheral blood mononuclear cells (PBMCs) and only cyclo-[D-Pro-Pro-β3-HoPhe-Phe-] peptide (P03) was capable of inhibiting mitogen-induced PBMC proliferation. The peptides inhibited the lipopolysaccharide (LPS)-induced production of tumor necrosis factor-alpha (TNF-α) to various degrees, with P04 (cyclo-[Pro-Pro-D-β3-HoPhe-Phe-]) and P03 being the most potent. For further in vivo studies, P03 was selected because it had the combined properties of inhibiting cell proliferation and TNF-α production. P03 demonstrated a comparable ability to 4B8M in the inhibition of auricle edema and lymph node cell number and in the normalization of a distorted blood cell composition in contact sensitivity to the oxazolone mouse model. In the mouse model of carrageenan-induced inflammation of the air pouch, P03 exhibited a similar inhibition of the cell number in the air pouches as 4B8M, but its inhibitory effects on the percentage of neutrophils and eosinophils in the air pouches and blood, as well as on mastocyte degranulation in the air pouches, were stronger in comparison to 4B8M. Lastly, in a mouse model of dextran sulfate-induced colitis, similar effects to 4B8M regarding thymocyte number restoration and normalization of the blood cell pictures by P03 were observed. In summary, depending on either experimental findings or in silico predictions, P03 demonstrated comparable, or even better, anti-inflammatory and bio-pharmacokinetic properties to 4B8M and may be considered as a potential therapeutic. The possibility of P00 and P03 identification by circular dichroism measurements was tested by quantum-chemical calculations.

Influence of proline and hydroxyproline as antimicrobial and anticancer peptide components on the silver(I) ion activity: structural and biological evaluation with a new theoretical and experimental SAR approach

Silver(I) complexes with proline and hydroxyproline were synthesized and structurally characterized and crystal structure analysis shows that the formulas of the compounds are {[Ag2(Pro)2(NO3)]NO3}n (AgPro) (Pro = L-proline) and {[Ag2(Hyp)2(NO3)]NO3}n (AgHyp) (Hyp = trans-4-hydroxy-L-proline). Both complexes crystallize in the monoclinic lattice with space group P21 with a carboxylate bidentate-bridging coordination mode of the organic ligands Pro and Hyp (with NH2+ and COO- groups in zwitterionic form). Both complexes have a distorted seesaw (C2v) geometry around one silver(I) ion with τ4 values of 58% (AgPro) and 51% (AgHyp). Moreover, the results of spectral and thermal analyses correlate with the structural ones. 1H and 13C NMR spectra confirm the complexes species' presence in the DMSO biological testing medium and their stability in the time range of the bioassays. In addition, molar conductivity measurements indicate complexes' behaviour like 1 : 1 electrolytes. Both complexes showed higher or the same antibacterial activity against Bacillus cereus, Pseudomonas aeruginosa and Staphylococcus aureus as AgNO3 (MIC = 0.063 mM) and higher than silver(I) sulfadiazine (AgSD) (MIC > 0.5 mM) against Pseudomonas aeruginosa. In addition, complex AgPro exerted a strong cytotoxic effect against the tested MDA-MB-231 and Jurkat cancer cell lines (IC50 values equal to 3.7 and 3.0 μM, respectively) compared with AgNO3 (IC50 = 6.1 (5.7) μM) and even significantly higher selectivity than cisplatin (cisPt) against MDA-MB-231 cancer cell lines (SI = 3.05 (AgPro); 1.16 (cisPt), SI - selectivity index). The binding constants and the number of binding sites (n) of AgPro and AgHyp complexes with bovine serum albumin (BSA) were determined at four different temperatures, and the zeta potential of BSA in the presence of silver(I) complexes was also measured. The in ovo method shows the safety of the topical and intravenous application of AgPro and AgHyp. Moreover, the complexes' bioavailability was verified by lipophilicity evaluation from the experimental and theoretical points of view.

Novel Niosome-Encapsulated 2,5-Diketopiperazine (BHPPD): Synthesis, Formulation, and Anti-breast Cancer Activity

In the course of this investigation, a brand-new noisome-encapsulated 2,5-diketopiperazine (BHPPD) was developed, synthesized, and assessed. Utilizing CCK-8, invasion screens, MTT test, flow cytometry, and cell cycle analysis, we evaluated the anti-breast cancer properties of niosome-encapsulated BHPPD. Apoptosis-related gene expression and cytotoxicity was measured using quantitative real-time PCR and MTT assays. This meta-analysis showed a significant drug-binding affinity for intestinal protease. The spherical mean diameters of the free BHPPD, the F1 niosomal-BHPPD, and the F2 niosomal-BHPPD were all determined to be108.91 ± 4.2, 129.13 ± 7.2 nm, and 149.43 ± 3.2 nm, respectively. Also, it was found that the entrapment efficiency (EE%) of the F1 formulations of BHPPD that was niosome-encapsulated was 81.01 0.09% and that it was 70.22 0.13%, respectively. Early, late, necrotic, and viable MCF-7 cells were present in the cells with F1 formulation in proportions of 38.24%, 34.34%, 4.02%, and 23.40%, respectively. Compared to the control group, the treatment group's expression of the genes P57, Prkca, MDM4, Map2k6, and FADD was considerably greater (P < 0.001). Furthermore, compared to control cells, cells in the treatment group expressed less BCL2 and survival genes (P < 0.001). Moreover, formulations of BHPPD encapsulated in niosomes showed a biocompatible nanoscale delivery method and exhibited little cytotoxicity against the HEK-293 standard cell line. According to the findings, formulations of BHPPD with niosome-encapsulation might be viable for boosting anticancer activity.

Novel 2,5-Diketopiperazines with In Vitro Activities against Protozoan Parasites of Tropical Diseases

Malaria, Chagas disease, and leishmaniasis are tropical diseases caused by protozoan parasites of the genera Plasmodium, Trypanosoma and Leishmania, respectively. These diseases constitute a major burden on public health in several regions worldwide, mainly affecting low-income populations in economically poor countries. Severe side effects of currently available drug treatments and the emergence of resistant parasites need to be addressed by the development of novel drug candidates. Natural 2,5-Diketopiperazines (2,5-DKPs) constitute N-heterocyclic secondary metabolites with a wide range of biological activities of medicinal interest. Its structural and physicochemical properties make the 2,5-DKP ring a versatile, peptide-like, and stable pharmacophore attractive for synthetic drug design. In the present work, twenty-three novel synthetic 2,5-DKPs, previously synthesized through the versatile Ugi multicomponent reaction, were assayed for their anti-protozoal activities against P. falciparum, T. cruzi, and L. infantum. Some of the 2,5-DKPs have shown promising activities against the target protozoans, with inhibitory concentrations (IC50) ranging from 5.4 to 9.5 µg/mL. The most active compounds also show low cytotoxicity (CC50), affording selectivity indices ≥ 15. Results allowed for observing a clear relationship between the substitution pattern at the aromatic rings of the 2,5-DKPs and their corresponding anti-Plasmodium activity. Finally, calculated drug-like properties of the compounds revealed points for further structure optimization of promising drug candidates.

Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater?

Seagrass meadows provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of waterborne pathogens linked to infections in humans and marine organisms in their vicinity. Among potential drivers, seagrass phenolics released into seawater have been linked to pathogen suppression, but the potential involvement of the seagrass microbiome has not been investigated. We hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and the surrounding seawater, inhibit waterborne pathogens thereby contributing to their removal. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots. We assessed the antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and mined the metabolome of the most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also displayed remarkable activities. UPLC-MS/MS-based untargeted metabolomics analyses showed rich specialized metabolite repertoires with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome in suppression of pathogens in seawater. Such effect is beneficial for the health of ocean and human, especially in the context of climate change that is expected to exacerbate all infectious diseases. It may also assist future seagrass conservation and management strategies.

Structural Analysis and Activity Correlation of Amphiphilic Cyclic Antimicrobial Peptides Derived from the [W4R4] Scaffold

In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and their interactions with membranes. The objective was to discern the nature of these interactions and understand how peptide sequence and structure influence antimicrobial activity. We introduced modifications into the established cyclic AMP peptide, [W4R4], incorporating an extra aromatic hydrophobic residue (W), a positively charged residue (R), or the unique 2,5-diketopiperazine (DKP). This study systematically explored the structure-activity relationships (SARs) of a series of cyclic peptides derived from the [W4R4] scaffold, including the first synthesis and evaluation of [W4R4(DKP)]. Structural, dynamic, hydrophobic, and membrane-binding properties of four cyclic peptides ([W4R4], [W5R4], [W4R5], [W4R4(DKP)]) were explored using molecular dynamics simulations within a DOPC/DOPG lipid bilayer that mimics the bacterial membrane. The results revealed distinct SARs linking antimicrobial activity to parameters such as conformational plasticity, immersion depth in the bilayer, and population of the membrane binding mode. Notably, [W4R5] exhibited an optimal "activity/binding to the bacterial membrane" pattern. This multidisciplinary approach efficiently decoded finely regulated SAR profiles, laying a foundation for the rational design of novel antimicrobial peptides.

Elucidating the mechanism of action of mycotoxins through machine learning-driven QSAR models: Focus on lipid peroxidation

Understanding the mechanisms of mycotoxin toxicity is crucial for establishing effective guidelines and preventive strategies. In this study, machine learning models based on quantitative structure-activity relationship (QSAR) were employed to predict the lipid peroxidation activity of mycotoxins. Two different algorithms using Linear Discriminant Analysis (LDA) and Artificial Neural Networks (ANNs) have been trained using a dataset of 70 mycotoxins. The LDA model had an average correct classification rate of 91%, while the ANN model achieved a perfect 100% classification rate. Following an internal validation process, the models were utilized to predict mycotoxins with known lipid peroxidation activity. The machine learning models achieved an 88% correct classification rate for these mycotoxins. Finally, by utilizing classified algorithms, the study aimed to infer the mechanism of action related to lipid peroxidation for 91 unstudied mycotoxins. These models provide a fast, accurate, and cost-effective means to assess the potential toxicity and mechanism of action of mycotoxins. The findings of this study contribute to a comprehensive understanding of mycotoxin toxicology and assist researchers and toxicologists in evaluating health risks associated with mycotoxin exposure and developing appropriate preventive strategies and potential therapeutic interventions to mitigate the effects of mycotoxins.

Diastereoselective Spirocyclization: Entry to Spirocyclic Diketopiperazines

We report a novel approach to access spirocyclic compounds containing a diketopiperazine (DKP) motif fused on a pyrrolidine ring. The shared spirocyclic carbon is at the ketone oxidation state, bearing two carbon-nitrogen bonds, one of which is introduced stereoselectively during the cyclization event. The reaction proceeds through an acid-catalyzed cyclization of a pendent chiral aminoamide unit onto a 2,3-dehydroproline amide moiety with up to >98:2 diastereoselectivity. We have demonstrated the generality of this methodology and its applicability to access chemically diverse DKP-containing structures. The extent of stereoinduction and how it varies according to the bulkiness of the substituent on the pendent aminoamide is demonstrated through a diverse substrate set. This methodology gives access to an underexplored spirocyclic diketopiperazine motif that may be useful in identifying new bioactive molecules.

Recent advances and applications of peptide-agent conjugates for targeting tumor cells

BACKGROUND

Cancer, being a complex disease, presents a major challenge for the scientific and medical communities. Peptide therapeutics have played a significant role in different medical practices, including cancer treatment.

METHOD

This review provides an overview of the current situation and potential development prospects of anticancer peptides (ACPs), with a particular focus on peptide vaccines and peptide-drug conjugates for cancer treatment.

RESULTS

ACPs can be used directly as cytotoxic agents (molecularly targeted peptides) or can act as carriers (guiding missile) of chemotherapeutic agents and radionuclides by specifically targeting cancer cells. More than 60 natural and synthetic cationic peptides are approved in the USA and other major markets for the treatment of cancer and other diseases. Compared to traditional cancer treatments, peptides exhibit anticancer activity with high specificity and the ability to rapidly kill target cancer cells. ACP's target and kill cancer cells via different mechanisms, including membrane disruption, pore formation, induction of apoptosis, necrosis, autophagy, and regulation of the immune system. Modified peptides have been developed as carriers for drugs, vaccines, and peptide-drug conjugates, which have been evaluated in various phases of clinical trials for the treatment of different types of solid and leukemia cancer.

CONCLUSIONS

This review highlights the potential of ACPs as a promising therapeutic option for cancer treatment, particularly through the use of peptide vaccines and peptide-drug conjugates. Despite the limitations of peptides, such as poor metabolic stability and low bioavailability, modified peptides show promise in addressing these challenges. Various mechanism of action of anticancer peptides. Modes of action against cancer cells including: inducing apoptosis by cytochrome c release, direct cell membrane lysis (necrosis), inhibiting angiogenesis, inducing autophagy-mediated cell death and immune cell regulation.

Total synthesis of complex 2,5-diketopiperazine alkaloids

The 2,5-diketopiperazine (DKP) motif is present in many biologically relevant, complex natural products. The cyclodipeptide substructure offers structural rigidity and stability to proteolysis that makes these compounds promising candidates for medical applications. Due to their fascinating molecular architecture, synthetic organic chemists have focused significant effort on the total synthesis of these compounds. This review covers many such efforts on the total synthesis of DKP containing complex alkaloid natural products.

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the P-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

Dimeric Benzodiazepines as Peptide Mimetics to Overcome p53-Dependent Drug Resistance of Tumors

Benzodiazepines that consist of one α- and one β-amino acid residues linked together in a seven-membered heterocyclic ring could be treated as small, rigid, cyclic dipeptides capable of exhibiting a wide range of biological activities. During our research on novel analogues of anthramycin, a tricyclic antibiotic benzodiazepine, we developed the synthesis of two benzodiazepine dimers, obtained through the cyclization of appropriate linear tripeptides. The synthesized compounds were tested on a panel of seven cancer and normal cell lines. The developed molecules exhibited promising cytotoxic activity against the lung cancer cell lines A549 and NCI-H1299 and the epidermoid carcinoma cell line A-431. Moreover, they showed significant selectivity compared to the reference cell lines (BJ-human normal skin fibroblasts and MRC-5-human normal lung cell line). When tested on two isogenic cell lines, HCT116 and HCT116p53^-/- (colon cancer), contrary to cisplatin being used as a positive control, the obtained compounds showed a cytotoxic effect independent of the p53 protein status. For the above reasons, the obtained compounds can be considered a new group of promising anticancer agents, useful in the fight against p53-dependent drug resistance in cancers. They can also be treated as convenient, leading structures suitable for further optimization and searching for more active and selective molecules.

Characterization of antifungal cyclic dipeptides of Lacticaseibacillus paracasei ZX1231 and active packaging film prepared with its cell-free supernatant and bacterial nanocellulose

Fungal infection and/or spoilage are major concerns of crop and food security worldwide, prompting the developments and application of various antimicrobial agents. In this study, nine strains of lactic acid bacteria (LAB) with antifungal activities were isolated from the traditional Chinese fermented wort of Meigui rice vinegar, where fungi coexist. The cell-free supernatant (CFS) of Lacticaseibacillus paracasei ZX1231 exhibited significant inhibitory activities against Aspergillus niger, Penicillium citrinum, Penicillium polonicum, Zygosaccharomyces rouxii, Talaromyces rubrifaciens, and Candida albicans. Among the four cyclic dipeptides (CDPs) uncovered from the CFS, cyclo(Phe-Leu) and cyclo(Anthranily-Pro) were found in the family Lactobacillaceae for the first time, which inhibited the C. albicans filamentation by targeting upon RAS1-cAMP-PKA pathway. CFS antifungal activities were optimally combined with a bacterial nanocellulose (BNC) matrix to prepare the active quality packaging CFS-BNC films. The challenge tests confirmed that CFS-BNC films significantly inhibited the fungi growth and thus prolonged the shelf life of bread, beef, cheese and soy sauce. L. paracasei ZX1231, its CFS, and the CFS-BNC film may have extensive applications in food preservation and food packaging.

Bispyrrolidinoindoline Epi(poly)thiodioxopiperazines (BPI-ETPs) and Simplified Mimetics: Structural Characterization, Bioactivities, and Total Synthesis

Within the 2,5-dioxopiperazine-containing natural products generated by "head-to-tail" cyclization of peptides, those derived from tryptophan allow further structural diversification due to the rich chemical reactivity of the indole heterocycle, which can generate tetracyclic fragments of hexahydropyrrolo[2,3-b]indole or pyrrolidinoindoline skeleton fused to the 2,5-dioxopiperazine. Even more complex are the dimeric bispyrrolidinoindoline epi(poly)thiodioxopiperazines (BPI-ETPs), since they feature transannular (poly)sulfide bridges connecting C3 and C6 of their 2,5-dioxopiperazine rings. Homo- and heterodimers composed of diastereomeric epi(poly)thiodioxopiperazines increase the complexity of the family. Furthermore, putative biogenetically generated downstream metabolites with C11 and C11'-hydroxylated cores, as well as deoxygenated and/or oxidized side chain counterparts, have also been described. The isolation of these complex polycyclic tryptophan-derived alkaloids from the classical sources, their structural characterization, the description of the relevant biological activities and putative biogenetic routes, and the synthetic efforts to generate and confirm their structures and also to prepare and further evaluate structurally simple analogs will be reported.

Peptide-Drug Conjugates: A New Hope for Cancer Management

Cancer remains the leading cause of death worldwide despite advances in treatment options for patients. As such, safe and effective therapeutics are required. Short peptides provide advantages to be used in cancer management due to their unique properties, amazing versatility, and progress in biotechnology to overcome peptide limitations. Several appealing peptide-based therapeutic strategies have been developed. Here, we provide an overview of peptide conjugates, the better equivalents of antibody-drug conjugates, as the next generation of drugs for required precise targeting, enhanced cellular permeability, improved drug selectivity, and reduced toxicity for the efficient treatment of cancers. We discuss the basic components of drug conjugates and their release action, including the release of cytotoxins from the linker. We also present peptide-drug conjugates under different stages of clinical development as well as regulatory and other challenges.

Cyclodipeptides: From Their Green Synthesis to Anti-Age Activity

Cyclodipeptides (CDPs) or diketopiperazines (DKPs) are often found in nature and in foodstuff and beverages and have attracted great interest for their bioactivities, biocompatibility, and biodegradability. In the laboratory, they can be prepared by green procedures, such as microwave-assisted cyclization of linear dipeptides in water, as performed in this study. In particular, five CDPs were prepared and characterized by a variety of methods, including NMR and ESI-MS spectroscopies and single-crystal X-ray diffraction (XRD), and their cytocompatibility and anti-aging activity was tested in vitro, as well as their ability to penetrate the different layers of the skin. Although their mechanism of action remains to be elucidated, this proof-of-concept study lays the basis for their future use in anti-age cosmetic applications.

Hunting for Novel Routes in Anticancer Drug Discovery: Peptides against Sam-Sam Interactions

Among the diverse protein binding modules, Sam (Sterile alpha motif) domains attract attention due to their versatility. They are present in different organisms and play many functions in physiological and pathological processes by binding multiple partners. The EphA2 receptor contains a Sam domain at the C-terminus (EphA2-Sam) that is able to engage protein regulators of receptor stability (including the lipid phosphatase Ship2 and the adaptor Odin). Ship2 and Odin are recruited by EphA2-Sam through heterotypic Sam-Sam interactions. Ship2 decreases EphA2 endocytosis and consequent degradation, producing chiefly pro-oncogenic outcomes in a cellular milieu. Odin, through its Sam domains, contributes to receptor stability by possibly interfering with ubiquitination. As EphA2 is upregulated in many types of tumors, peptide inhibitors of Sam-Sam interactions by hindering receptor stability could function as anticancer therapeutics. This review describes EphA2-Sam and its interactome from a structural and functional perspective. The diverse design strategies that have thus far been employed to obtain peptides targeting EphA2-mediated Sam-Sam interactions are summarized as well. The generated peptides represent good initial lead compounds, but surely many efforts need to be devoted in the close future to improve interaction affinities towards Sam domains and consequently validate their anticancer properties.

Identification of Cyclic Dipeptides and a New Compound (6-(5-Hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one) Produced by Streptomyces fungicidicus against Alternaria solani

As an important microbial resource, Actinomycetes, especially Streptomyces, have important application values in medicine and biotechnology. Streptomyces fungicidicus SYH3 was isolated from soil samples in tomato-growing areas and showed good inhibitory effects on Alternaria solani in tomato. To obtain pure active compounds, SYH3 fermentation broth was subjected to XAD-16 macroporous resin and silica gel column chromatography. Combined with the repeated preparation and separation of preparative high-performance liquid chromatography (HPLC), a total of four monomer compounds were obtained after activity tracking. Compound 4 was identified as a new six-membered lactone ring compound named 6-(5-hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one by 1D and 2D nuclear magnetic resonance (NMR) data and mass spectrometry (MS). The other three active compounds belong to the cyclodipeptide, and their half maximal inhibitory concentration (IC₅₀) values against A. solani were 43.4, 42.9, and 30.6 μg/mL, respectively. Compound 4 significantly inhibited the spore germination and induced swollen and deformed local hyphae of A. solani with an IC₅₀ value of 24.9 μg/mL. Compound 4 also had broad-spectrum antifungal activity and had a good antifungal effect on the tested plant-pathogenic fungi. The modes of action of new compound (4) still require further investigation, representing a novel and effective anti-fungal agent for future application.

Molecular Dynamics Investigation of Clustering in Aqueous Glycine Solutions

Recent experiments with undersaturated aqueous glycine solutions have repeatedly exhibited the presence of giant liquid-like clusters or nanodroplets around 100 nm in diameter. These nanodroplets re-appear even after careful efforts for their removal and purification of the glycine solution. The composition of these clusters is not clear, although it has been suggested that they are mainly composed of glycine, a small and very soluble amino acid. To gain insights into this phenomenon, we study the aggregation of glycine in aqueous solutions at concentrations below the experimental solubility limit using large-scale molecular dynamics simulations under ambient conditions. Three protonation states of glycine (zwitterion = GLZ, anion = GLA, and cation = GLC) are simulated using molecular force fields based on the 1.14*CM1A partial charge scheme, which incorporates the OPLS all-atom force field and TIP3P water. When initiated from dispersed states, we find that giant clusters do not form in our simulations unless salt impurities are present. Moreover, if simulations are initiated from giant cluster states, we find that they tend to dissolve in the absence of salt impurities. Therefore, the simulation results provide little support for the possibility that the giant clusters seen in experiments are composed purely of glycine (and water). Considering that strenuous efforts are made in experiments to remove impurities such as salt, we propose that the giant clusters observed might instead result from the aggregation of reaction products of aqueous glycine, such as diketopiperazine or other oligoglycines which may be difficult to separate from glycine using conventional methods, or their co-aggregation with glycine.

Structural and Biofunctional Insights into the Cyclo(Pro-Pro-Phe-Phe-) Scaffold from Experimental and In Silico Studies: Melanoma and Beyond

Short peptides have great potential as safe and effective anticancer drug leads. Herein, the influence of short cyclic peptides containing the Pro-Pro-Phe-Phe sequence on patient-derived melanoma cells was investigated. Cyclic peptides such as cyclo(Leu-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe-), called CLA, and cyclo(Pro-homoPro-β3homoPhe-Phe-), called P11, exert the cytotoxic and the cytostatic effects in melanoma cells, respectively. CLA was the most active peptide as it reduced the viability of melanoma cells to 50% of control at about 10 µM, whereas P11 at about 40 µM after 48 h incubation. Interestingly, a linear derivative of P11 did not induce any effect in melanoma cells confirming previous studies showing that cyclic peptides exert better biological activity compared to their linear counterparts. According to in silico predictions, cyclic tetrapeptides show a better pharmacokinetic and toxic profile to humans than CLA. Notably, the spatial structure of those peptides containing synthetic amino acids has not been explored yet. In the Cambridge Structural Database, there is only one such cyclic tetrapeptide, cyclo((R)-β2homoPhe-D-Pro-Lys-Phe-), while in the Protein Data Bank—none. Therefore, we report the first crystal structure of cyclo(Pro-Pro-β3homoPhe-Phe-), denoted as 4B8M, a close analog of P11, which is crucial for drug discovery. Comparative molecular and supramolecular analysis of both structures was performed. The DFT findings revealed that 4B8M is well interpreted in the water solution. The results of complex Hirshfeld surface investigations on the cooperativity of interatomic contacts in terms of electrostatic and energetic features are provided. In short, the enrichment ratio revealed O…H/H…O and C…H/H…C as privileged intercontacts in the crystals in relation to basic and large supramolecular H-bonding synthon patterns. Furthermore, the ability of self-assemble 4B8M leading to a nanotubular structure is also discussed.

New Advances in Short Peptides: Looking Forward

It is beyond doubt that short peptides hold significant promise in bio-medicine, as the most versatile molecules, both structurally and functionally [...].

Antiviral Activity of a Cyclic Pro-Pro-β3-HoPhe-Phe Tetrapeptide against HSV-1 and HAdV-5

The core of Cyclolinopeptide A (CLA, cyclo(LIILVPPFF)), responsible for its high immunosuppressive activity, contains a Pro-Pro-Phe-Phe sequence. A newly synthesized cyclic tetrapeptide, cyclo(Pro-Pro-β3-HoPhe-Phe) (denoted as 4B8M) bearing the active sequence of CLA, was recently shown to exhibit a wide array of anti-inflammatory properties in mouse models. In this investigation, we demonstrate that the peptide significantly inhibits the replication of human adenovirus C serotype 5 (HAdV-5) and Herpes simplex virus type-1 (HSV-1) in epithelial lung cell line A-549, applying Cidofovir and Acyclovir as reference drugs. Based on a previously established mechanism of its action, we propose that the peptide may inhibit virus replication by the induction of PGE2 acting via EP2/EP4 receptors in epithelial cells. In summary, we reveal a new, antiviral property of this anti-inflammatory peptide.

Antibacterial Activity of Two Metabolites Isolated From Endophytic Bacteria Bacillus velezensis Ea73 in Ageratina adenophora

Ageratina adenophora, as an invasive and poisonous weed, seriously affects the ecological diversity and development of animal husbandry. Weed management practitioners have reported that it is very difficult to control A. adenophora invasion. In recent years, many researchers have focused on harnessing the endophytes of the plant as a useful resource for the development of pharmacological products for human and animal use. This study was performed to identify endophytes with antibacterial properties from A. adenophora. Agar well diffusion method and 16S rRNA gene sequencing technique were used to screen and identify endophytes with antibacterial activity. The response surface methodology and prep- high-performance liquid chromatography were used to determine the optimizing fermentation conditions and isolate secondary metabolites, respectively. UV-visible spectroscopy, infrared spectroscopy, nuclear magnetic resonance, and high-resolution mass spectrum were used to determine the structures of the isolated metabolites. From the experiment, we isolated a strain of Bacillus velezensis Ea73 (GenBank no. MZ540895) with broad-spectrum antibacterial activity. We also observed that the zone of inhibition of B. velezensis Ea73 against Staphylococcus aureus was the largest when fermentation broth contained 6.55 g/L yeast extract, 6.61 g/L peptone, 20.00 g/L NaCl at broth conditions of 7.95 pH, 51.04 h harvest time, and a temperature of 27.97°C. Two antibacterial peptides, Cyclo (L-Pro-L-Val) and Cyclo (L-Leu-L-Pro), were successfully extracted from B. velezensis Ea73. These two peptides exhibited mild inhibition against S. aureus and Escherichia coli. Therefore, we isolated B. velezensis Ea73 with antibacterial activity from A. adenophora. Hence, its metabolites, Cyclo (L-Pro-L-Val) and Cyclo (L-Leu-L-Pro), could further be developed as a substitute for human and animal antibiotics.

Chemical synthesis in competition with global genome mining and heterologous expression for the preparation of dimeric tryptophan-derived 2,5-dioxopiperazines

Covering: up to the end of 2021Within the 2,5-dioxopiperazines-containing natural products, those generated from tryptophan allow further structural diversification due to the rich chemical reactivity of the indole heterocycle. The great variety of natural products, ranging from simple dimeric bispyrrolidinoindoline dioxopiperazines and tryptophan-derived dioxopiperazine/pyrrolidinoindoline dioxopiperazine analogs to complex polycyclic downstream metabolites containing transannular connections between the subunits, will be covered. These natural products are constructed by Nature using hybrid polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) assembly lines. Mining of microbial genome sequences has more recently allowed the study of the metabolic routes and the discovery of their hidden biosynthetic potential. The competition (ideally, also the combined efforts) between their isolation from the cultures of the producing microorganisms after global genome mining and heterologous expression and the synthetic campaigns, has more recently allowed the successful generation and structural confirmation of these natural products. Their biological activities as well as their proposed biogenetic routes and computational studies on biogenesis will also be covered.

Cyclo(L-Leucyl-L-Prolyl) from Lactobacillus coryniformis BCH-4 inhibits the proliferation of Aspergillus flavus: an in vitro to in silico approach

Fungal spoilage led to a considerable economic loss of foodstuff which ultimately affects public health due to mycotoxins production. Moreover, the consumption of commercial antifungal drugs creates side effects and develops antifungal resistance. To overcome these challenges, the current work was aimed to investigate novel antifungal cyclic dipeptide (CDP) from Lactobacillus coryniformis (Loigolactobacillus coryniformis) BCH-4. CDPs have flexible, cyclic, and stable conformation. The proline-based CDPs provide additional structural compatibility and bio-functional values. Keeping in view, high-performance liquid chromatography (HPLC) was performed to explore cyclo(L-Leu-L-Pro) from L. coryniformis BCH-4. The HPLC detected concentration (135 ± 7.07 mg/mL) exhibited in vitro antifungal activity of 5.66 ± 0.57 mm (inhibitory zone) against Aspergillus flavus. Based on these results, cyclo(L-Leu-L-Pro) was used as a bioprotectant for selected food samples (grapes, lemon, cashew nuts, and almonds). A significant impact of cyclo(L-Leu-L-Pro) was observed in contrast with MRS broth (control) and cell-free supernatant. In silico molecular docking analysis of this CDP was carried out against FAD glucose dehydrogenase, dihydrofolate reductase, and urate oxidase of A. flavus as target proteins. Among these proteins, FAD glucose dehydrogenase exerted strong interactions with cyclo(L-Leu-L-Pro) having S-score of  - 8.21. The results evaluated that the detected CDP has strong interactions with selected proteins, causing excellent growth inhibition of A. flavus. Therefore, cyclo(L-Leu-L-Pro) could be used as a potent bioprotectant against food-borne pathogenic fungi.

Phytochemical Profile and Anticancer Potential of Endophytic Microorganisms from Liverwort Species, Marchantia polymorpha L

Liverwort endophytes could be a source of new biologically active substances, especially when these spore-forming plants are known to produce compounds that are not found in other living organisms. Despite the significant development of plant endophytes research, there are only a few studies describing liverwort endophytic microorganisms and their metabolites. In the presented study, the analysis of the volatile compounds obtained from thallose liverwort species, Marchantia polymorpha L., and its endophytes was carried out. For this purpose, non-polar extracts of plant material and symbiotic microorganisms were obtained. The extracts were analyzed using gas chromatography coupled to mass spectrometry. Compounds with the structure of diketopiperazine in the endophyte extract were identified. Liverwort volatile extract was a rich source of cuparane-, chamigrane-, acorane-, and thujopsane-type sesquiterpenoids. The cytotoxicity of ethyl acetate extracts from endophytic microorganisms was evaluated on a panel of cancer (FaDu, HeLa, and SCC-25) cell lines and normal (VERO), and revealed significant anticancer potential towards hypopharyngeal squamous cell carcinoma and cervical adenocarcinoma.