Bioactive Structures Research Articles

Metallocene QACs: The Incorporation of Ferrocene Moieties into monoQAC and bisQAC Structures.

Inspired by the incorporation of metallocene functionalities into a variety of bioactive structures, particularly antimicrobial peptides, we endeavored to broaden the structural variety of quaternary ammonium compounds (QACs) by the incorporation of the ferrocene moiety. Accordingly, 23 ferrocene-containing mono- and bisQACs were prepared in high yields and tested for activity against a variety of bacteria, including Gram-negative strains and a panel of clinically isolated MRSA strains. Ferrocene QACs were shown to be effective antiseptics with some displaying single-digit micromolar activity against all bacteria tested, demonstrating yet another step in the expansion of structural variety of antiseptic QACs.

A machine learning-based method for prediction of macrocyclization patterns of polyketides and non-ribosomal peptides.

Even though genome mining tools have successfully identified large numbers of non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) biosynthetic gene clusters (BGCs) in bacterial genomes, currently no tool can predict the chemical structure of the secondary metabolites biosynthesized by these BGCs. Lack of algorithms for predicting complex macrocyclization patterns of linear PK/NRP biosynthetic intermediates has been the major bottleneck in deciphering the final bioactive chemical structures of PKs/NRPs by genome mining. Using a large dataset of known chemical structures of macrocyclized PKs/NRPs, we have developed a machine learning (ML) algorithm for distinguishing the correct macrocyclization pattern of PKs/NRPs from the library of all theoretically possible cyclization patterns. Benchmarking of this ML classifier on completely independent datasets has revealed ROC-AUC and PR-AUC values of 0.82 and 0.81, respectively. This cyclization prediction algorithm has been used to develop SBSPKSv3, a genome mining tool for completely automated prediction of macrocyclized structures of NRPs/PKs. SBSPKSv3 has been extensively benchmarked on a dataset of over 100 BGCs with known PKs/NRPs products. The macrocyclization prediction pipeline and all the datasets used in this study are freely available at http://www.nii.ac.in/sbspks3.html. Supplementary data are available at Bioinformatics online.

Dietary muramidase degrades bacterial peptidoglycan to NOD-activating muramyl dipeptides and reduces duodenal inflammation in broiler chickens

Muramidases constitute a superfamily of enzymes that hydrolyse peptidoglycan (PGN) from bacterial cell walls. Recently, a fungal muramidase derived from Acremonium alcalophilum has been shown to increase broiler performance when added as a feed additive. However, the underlying mechanisms of action are not yet identified. Here, we investigated the hypothesis that this muramidase can cleave PGN to muramyl dipeptide (MDP), activating nucleotide-binding oligomerisation domain-containing protein 2 (NOD2) receptors in eukaryotic cells, potentially inducing anti-inflammatory host responses. Using Micrococcus luteus as a test bacterium, it was shown that muramidase from A. alcalophilum did not display antimicrobial activity, while it could cleave fluorescently labelled PGN. It was shown that the muramidase could degrade PGN down to its minimal bioactive structure MDP by using UPLC-MS/MS. Using HEK-Blue™-hNOD2 reporter cells, it was shown that the muramidase-treated PGN degradation mixture could activate NOD2. Muramidase supplementation to broiler feed increased the duodenal goblet cell and intraepithelial lymphocyte abundance while reducing duodenal wall CD3+ T lymphocyte levels. Muramidase supplementation to broiler feed only had moderate effects on the duodenal, ileal and caecal microbiome. It was shown that the newly discovered muramidase hydrolysed PGN, resulting in MDP that activates NOD2, potentially steering the host response for improved intestinal health.

On the role of alginate coating on the mechanical and biological properties of 58S bioactive glass scaffolds

In this study, novel 3D porous alginate-coated 58S bioactive glass scaffolds were fabricated through a foam replication method using a combination of amorphous 58S bioactive glass structure and sodium alginate. The formation of the alginate coating on the surface of the struts of BG scaffolds was confirmed. The effect of alginate coating on the microstructure, mechanical properties, biodegradability, biomineralization, adhesion, viability, and differentiation of human bone marrow-derived mesenchymal stem cells (hMSCs) on the 58S BG scaffolds were evaluated. A 45.2% increase in hMSC's viability and a 3.4-fold increase in ALP activity of the 1AlBG scaffold in the absence of an osteogenic differentiation media compared to an uncoated BG scaffold were observed. Notably, gene expression analysis exhibited that the 1AlBG scaffold resulted in accelerated osteogenic differentiation of hMSCs, as expression of COL-1, RUNX2, and OCN increased after 14 days. Results revealed a significant increase of antibacterial inhibition in the 1AlBG scaffold in comparison to the BG scaffold. Based on the microstructural, mechanical, and biological investigations, the 1AlBG scaffold exhibited enhanced mechanical and biological properties, making it a promising candidate for bone regeneration. Overall, our findings have highlighted the potential of alginate-coated BG scaffolds to stimulate bone regeneration through stem cell osteoinduction.

Controlling the Porosity and Biocidal Properties of the Chitosan-Hyaluronate Matrix Hydrogel Nanocomposites by the Addition of 2D Ti3C2Tx MXene.

A recent discovery of the unique biological properties of two-dimensional transition metal carbides (MXenes) resulted in intensive research on their application in various biotechnological areas, including polymeric nanocomposite systems. However, the true potential of MXene as an additive to bioactive natural porous composite structures has yet to be fully explored. Here, we report that the addition of 2D Ti3C2Tx MXene by reducing the porosity of the chitosan-hyaluronate matrix nanocomposite structures, stabilized by vitamin C, maintains their desired antibacterial properties. This was confirmed by micro computed tomography (micro-CT) visualization which enables insight into the porous structure of nanocomposites. It was also found that given large porosity of the nanocomposite a small amount of MXene (1–5 wt.%) was effective against gram-negative Escherichia coli, gram-positive Staphylococcus aureus, and Bacillus sp. bacteria in a hydrogel system. Such an approach unequivocally advances the future design approaches of modern wound healing dressing materials with the addition of MXenes.

Four-component 1,4-addition Ugi reaction catalyzed by the Schiff base derived from Tröger's base and BINOL

The 1,4-addition Ugi reaction can provide complex, novel and bioactive structures. However, Ugi reaction involving the 1,4-addition process has rarely been reported due to the Michael addition of amine to α,β-unsaturated ketones or aldehydes prevents the formation of the key intermediate iminium ion. In this paper, a Schiff base catalyst derived from Tröger's base-NH2 and (R)-BINOL-CHO was used successfully to promote the four-component 1,4-addition Ugi reaction of α,β-unsaturated cyclic ketones, carboxylic acids, aromatic amines and isocyanides to afford an α,β-keto amide 2-arylformyl-3-(arylamino)cyclopent-2-enecarboxamides in high yield (6, 83–96%) under mild condition. A variety of aromatic amines participated in the reaction efficiently, which showed the high efficiency of the catalyst. A reasonable catalysis and formation mechanism were come up with.

Utility of direct 3D co-culture model for chondrogenic differentiation of mesenchymal stem cells on hyaluronan scaffold (Hyaff-11).

This study presents direct 2D and 3D co-culture model of mesenchymal stem cells (MSCs) line with chondrocytes isolated from patients with osteoarthritis (unaffected area). MSCs differentiation into chondrocytes after 14, 17 days was checked by estimation of collagen I, II, X, aggrecan expression using immunohistochemistry. Visualization, localization of cells on Hyaff-11 was performed using enzymatic technique and THUNDER Imaging Systems. Results showed, that MSCs/chondrocytes 3D co-culture induced suitable conditions for chondrocytes grow and MSCs differentiation than 2D monoculture. Despite that differentiated cells on Hyaff-11 expressed collagen X, they showed high collagen II (80%) and aggrecan (60%) expression with simultaneous decrease of collagen I expression (10%). The high concentration of differentiated cells on Hyaff-11, indicate that this structure has an impact on cells cooperation and communication. In conclusion, we suggest that high expression of collagen II and aggrecan in 3D co-culture model, indicate that cooperation between different subpopulations may have synergistic impact on MSCs chondrogenic potential. Revealed the high concentration and localization of cells growing in deeper layers of membrane in 3D co-culture, indicate that induced microenvironmental enhance cell migration within scaffold. Additionally, we suggest that co-culture model might be useful for construction a bioactive structure for cartilage tissue regeneration.

Effects of Ultra-Sonication and Agitation on Bioactive Compounds and Structure of Amaranth Extract.

Amaranth is an excellent source of various bioactive compounds that could be beneficial in the prevention of some human diseases. This study investigated the extraction and characterization of bioactive compounds from amaranth using ultra-sonication and agitation at 30, 50 and 70 °C. Color L* values showed significant (p < 0.05) differences at 70 °C between ultra-sonication and agitation. Ultra-sonication temperature had significant effect on L* and a* values whereas agitation temperature did not have a significant effect on L*, a* and b* values. No significant (p < 0.05) differences were found in terms of total phenol, total flavonoid, DPPH•+, ABTS+ scavenging activity, betacyanins, betaxanthin and betanicaicd between ultra-sonication and agitation. However, temperature had a significant (p < 0.05) effect on total phenol (8.64–10.598 mg/g), DPPH+scavenging activity (84.36–94.44%), betacyanins (4585.95–5325.32 mg/100 g), betaxanthin (1312.56–1524.06 mg/100 g) and betalamic acid (1408.15–1790.22 mg/100 g) in ultra-sonication. Higher temperature (70 °C) showed greater amount of arbutin and hydroxybenzoic acid than those of lower temperature (30 °C) for both extraction methods. Meanwhile, temperature did not affect vanillic acid, p-coumaric acid and ferulic acid for both samples. Fourier-transformed infrared (FTIR) spectrometry showed that ultra-sonication and agitation resulted in similar effect on the structure of amaranth extracts. Higher temperature was correlated with bioactive compounds, which were observed by principal component analysis (PCA). Therefore, agitation at 70 °C could be used as an alternative for ultra-sonication to improve the bioactive compounds and antioxidant activities of amaranth. In addition, agitation and ultra-sonication techniques might be served as an alternative of conventional technique.

Synthetic Polypeptide Polymers as Simplified Analogues of Antimicrobial Peptides.

Antimicrobial peptides (AMPs) are naturally occurring macromolecules made of amino acids that are potent broad-spectrum antibiotics with potential as novel therapeutic agents. This review aims to summarize the fundamental principles concerning the structure and mechanism of action of these AMPs, in order to guide the design of polymeric analogues that organic chemistry can generate. Among those simplified analogues, this review particularly focuses on those made of amino acids called polypeptide polymers: they are showing great potential by providing one of the best biomimetic and bioactive structures for further biomaterials science applications.

Chemometric and Transcriptomic Profiling, Microtubule Disruption and Cell Death Induction by Secalonic Acid in Tumor Cells.

Nature is an indispensable source of new drugs, providing unique bioactive lead structures for drug discovery. In the present study, secalonic acid F (SAF), a naturally occurring ergochrome pigment, was studied for its cytotoxicity against various leukemia and multiple myeloma cells by the resazurin assay. SAF exhibited cytotoxic activity on both leukemia and multiple myeloma cells. Generally, multiple myeloma cells were more sensitive to SAF than leukemia cells. NCI-H929 cells were the most affected cells among the tested panel of multiple myeloma cell lines and were taken for further studies to assess the mode of action of SAF on those cells. Cell cycle analysis revealed that SAF induced S and G2/M arrest in NCI-H929 cells. SAF-associated apoptosis and necrosis resulted in cytotoxicity. SAF further inclined the disassembly of the tubulin network, which may also account for its cytotoxicity. COMPARE and hierarchical cluster analyses of transcriptome-wide expression profiles of the NCI tumor cell line panel identified genes involved in numerous cellular processes (e.g., cell differentiation, cell migration, and other numerous signaling pathways) notably correlated with log10IC50 values for secalonic acid. In conclusion, the present study supports the therapeutic potential of SAF to treat multiple myeloma.

Antimicrobial activity of ethyl acetate extracts of Streptomyces sp. CRB46 and the prediction of their bioactive compounds chemical structure

Abstract. Ambarwati A, Wahyuono S, Moeljopawiro S, Yuwono T. 2020. Antimicrobial activity of ethyl acetate extracts of Streptomyces sp. CRB46 and the prediction of their bioactive compounds chemical structure. Biodiversitas 21: 3380-3390. The goal of the research was to determine the antimicrobial activity of ethyl acetate extracts of Streptomyces sp. CRB46 and predict their chemical structure of the bioactive compounds based on the AntiSMASH analysis of the whole genome sequencing. Streptomyces sp. CRB46 was isolated from Cyperus rotundus L. rhizosphere in the Cemoro Sewu highland, Indonesia (1920 meters above sea level). The results showed that the supernatant ethyl acetate (EAS) extract could inhibit 11 of 12 tested microorganisms with a diameter of the inhibition zone ranging from 17-35 mm (paper disc method). The supernatant extract was found more effective in inhibiting microorganisms than the ethyl acetate extract of pellets (EAP). The EAP extract was only able to inhibit the growth of seven tested microorganisms (16-26 mm). The results of LCMS analysis showed that crude extract of EAS consisted of 20 mixtures of organic compounds. Based on FTIR analysis, 16 functional groups were found in the EAS extracts. In addition, based on AntiSMASH analysis, it was also found that Streptomyces sp. CRB46 produced eight classes of bioactive compounds, but only six compounds have been identified as their chemical structures. It can, therefore, be concluded that Streptomyces sp. CRB46 has the potential to produce bioactive compounds that can be used for microbial infection treatment.

Clustering Effect on Bioactivity of Calixarene-Based Tetramers

Since the clustering effect in calixarene structures is a result of the multivalency and synergism of a number of replicated units, and it leads to the structures with excess of expected increase in activity against that of related monomers, this effect can be used as a promising approach to the synthesis of new calixarene-based bioactive structures. The present paper gives examples of these structures and compares their biological activities to those of monomers.

Patents and the experimental space: social, legal and geographical dimensions of 3D bioprinting

ABSTRACT The entanglements between social creativity, legal instruments and global policies become particularly clear in emerging technological fields where such relations are being established or improvised. In this paper, an analysis of such entanglements is delivered, focusing on 3D bioprinting. This technique amounts to the use of robotic, computer-controlled devices called bioprinters, with which bioactive structures are manufactured, with potential medical applications. Bioprinting has triggered manifold relations and processes here grasped with the concept of experimental space. It is claimed that the experimental space has several dimensions, three of which are analysed here. First, there is a legal dimension formed by the multiplication of patent documents making reference to each other and forming a discursive network. Second, there is a social dimension, as the experimental space is populated by innovative companies and universities involved with bioprinting. Finally, the geographical dimension derives from the spatial processes and global geography of bioprinting. The study of these three dimensions is underpinned by a quantitative analysis of bioprinting patents filed from 2001 to 2019 and found on two specialized websites (The Lens and Google Patents). Furthermore, fieldwork was conducted in three countries (the UK, Brazil, and Italy), involving interviews with academics and entrepreneurs exploring bioprinting.

Interfacial Self-Assembly to Spatially Organize Graphene Oxide Into Hierarchical and Bioactive Structures

Multicomponent self-assembly holds great promise for the generation of complex and functional biomaterials with hierarchical microstructure. Here, we describe the use of supramolecular co-assembly between an elastin-like recombinamer (ELR5) and a peptide amphiphile (PA) to organise graphene oxide (GO) flakes into bioactive structures across multiple scales. The process takes advantage of a reaction – diffusion mechanism to enable the incorporation and spatial organization of GO within multiple ELR5/PA layers. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), and ImageJ software were used to demonstrate the hierarchical organisation of GO flakes within the ELR5/PA layers and the distribution profiles of GO throughout the ELR5/PA membranes. Furthermore,atomic force microscopy (AFM) revealed improved Young’s moduli of the ELR5/PA/GOmembranes compared to the ELR5/PA membranes. Lastly, we investigated biocompatibility of the ELR5/PA/GO membrane via various cell culture methods.

Synthesis of Bioactive Glass using Cellulose Nano Fibre Template

Bioactive glass is one of the biomaterials that is used as a bone graft. The important property desired for a bone graft material is to have well suited porosity to enable cell penetration and enhance oxygen and nutrient exchanges. The common methods to produce bioactive glass are melting and sol-gel methods. Melting method is operated at a temperature higher than 1300 °C; the sol-gel method, on the other hand, is usually operated at a much lower temperature, i.e. in the range of 600 – 800 °C. The objective of this study is to evaluate the effect of using cellulose nano-fiber (CNF) template on the properties of the synthesized bioactive glass. Hypothetically, the templating process will create channels within the bioactive glass structures, which improves both its porosity and the interstitial network. In this study, SiO2–CaO–P2O5–Na2O bioactive glass (BG) was prepared via sol-gel method. The effects of the manipulated parameters on the morphology, chemical properties, porosity and crystallinity of BG were assessed by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), Brunauer–Emmett–Teller (BET) analysis, Energy dispersive X-ray (EDX) analysis and X-ray diffraction (XRD). It was found that the sintering temperatures significantly affect the structure and performance of samples. The best property was obtained by sintering bioglass with 10 wt% of CNF at 750 °C.

An efficient functionalization of dexamethasone-loaded polymeric scaffold with [3-(2,3-epoxypropoxy)-propyl]-trimethoxysilane coupling agent for bone regeneration: Synthesis, characterization, and in vitro evaluation

In this study, dexamethasone-loaded gelatin–starch scaffolds were fabricated by the freeze-drying technique under different cooling temperatures and polymeric compositions. The constructs were modified via [3-(2,3-epoxypropoxy)-propyl]-trimethoxysilane coupling agent in order to produce a bioactive network structure for bone tissue engineering applications. Herein, the synergistic effect of [3-(2,3-epoxypropoxy)-propyl]-trimethoxysilane and dexamethasone was examined on the bioactivity and osteogenic behavior of scaffolds. Based on scanning electron microscopy micrographs, more fine pores were formed at higher freezing temperatures. The prepared microstructure at a rapid freezing rate resulted in diminished mechanical properties and a greater level of swelling and durability compared with a slow freezing rate. According to the acquired results, the mechanical strength decreased, while both absorption capacity and mass loss rate increased as a function of starch addition. Furthermore, the enhancement of hydrophilicity and reduction of mechanical stability enhanced the dexamethasone release levels. In addition, the synthesized constructs confirmed the positive effect of [3-(2,3-epoxypropoxy)-propyl]-trimethoxysilane and dexamethasone on biomimetic mineralization of the scaffolds. Supporting the cellular adhesion and proliferation alongside the expression of alkaline phosphatase, especially in the presence of dexamethasone, was the other advantage of synthetic scaffolds as a bone reconstructive substitute. Accordingly, drug-loaded hybrid constructs seem to be promising for further preclinical and clinical investigations in bone tissue engineering.

IGF1 inclusion bodies: A QbD based process approach for efficient USP as well as early DSP unit operations

E. coli is an attractive host organism for strong recombinant protein expression. It expresses products either as soluble protein or as inclusion bodies (IB). IBs are insoluble, mostly inactive aggregates. However, recent progress enabled the efficient refolding back into their bioactive structure. Targeted IB production processes have been designed based on their characteristic features such as high yields along with purity and their simple separation. More profound process knowledge is needed to reveal interacting parameters required for quality by design grounded process development. This enables strategies for simplifying and accelerating upstream as well as downstream procedures. We present a workflow for gathering deeper process knowledge by a design of experiment approach for improved IGF1 IB formation in relation to impurity concentration. An IB expression maximum of 19.8 mgIGF1·gDCW−1 was found at pH 6.5, 37 °C and an IPTG induction of >45 μmol gDCW−1 for 12 h. Subsequently, three refolding buffers were tested together with a nonwoven anion exchange adsorber filter module. Knowledge-based buffer selection enabled high impurity log reduction values (LRVEndotoxin = 4.9; LRVDNA = 4.8, LRVHCP = 0.1–1) as well as chromatography column guarding potential by using those adsorptive matrices. Furthermore, adsorptive filtration followed by tangential flow filtration proved to be a promising alternative for product concentration.

Structure and in vitro dissolution of Mg and Sr containing borosilicate bioactive glasses for bone tissue engineering

Borosilicate bioactive glasses are promising for bone tissue engineering. The objective was to assess the impact of magnesium and/or strontium, when substituted for calcium on the glasses' thermal and dissolution properties. Both Mg and Sr substitution appeared to enhance the hot forming domain, i.e. the ability to hot process (sinter, draw fibres) without adverse crystallization. Structural analysis indicated that substitution of MgO and/or SrO for CaO results in changes in the BO3/BO4 ratio as well as in the ratio between bridging and non-bridging oxygen atoms in the silicate structure. Additionally, a de-shielding effect was noticed when Ca, Mg and Sr are present together in the glass network, possibly owing to PO43− charge-balanced preferentially by Na+. The Mg and/or Sr substitution resulted in a lower ion release in simulated body fluid and delayed formation of hydroxyapatite. However, once this layer formed it consisted of a Mg/Sr-substituted apatite. This work highlights the effect of combined ionic substitutions on bioactive glass structure and properties.

Continuous Flow Photochemistry for the Preparation of Bioactive Molecules.

The last decade has witnessed a remarkable development towards improved and new photochemical transformations in response to greener and more sustainable chemical synthesis needs. Additionally, the availability of modern continuous flow reactors has enabled widespread applications in view of more streamlined and custom designed flow processes. In this focused review article, we wish to evaluate the standing of the field of continuous flow photochemistry with a specific emphasis on the generation of bioactive entities, including natural products, drugs and their precursors. To this end we highlight key developments in this field that have contributed to the progress achieved to date. Dedicated sections present the variety of suitable reactor designs and set-ups available; a short discussion on the relevance of greener and more sustainable approaches; and selected key applications in the area of bioactive structures. A final section outlines remaining challenges and areas that will benefit from further developments in this fast-moving area. It is hoped that this report provides a valuable update on this important field of synthetic chemistry which may fuel developments in the future.

Asian hornet Vespa velutina nigrithorax venom: Evaluation and identification of the bioactive compound responsible for human keratinocyte protection against oxidative stress

The present study aimed to explore the potential antioxidant molecules of the Asian hornet venom (Vespa velutina nigrithorax) responsible for radical scavenging activity and human keratinocyte protection against oxidative stress. We developed a first technical platform that combined a DPPH radical scavenging chemical assay and cytotoxicity and ROS (reactive oxygen species) production in HaCaT keratinocyte cells exposed to UVB to evaluate the antioxidant property of V. velutina venom. We further employed Thin Layer Chromatography (TLC) combined with the DPPH assay as a targeted separation approach to isolate the antioxidant compounds responsible for the free radical scavenging property of V. velutina venom. In parallel, the latter was fractionated by a HPLC-DAD non-targeted separation approach. From this experiment, nine fractions were generated which were again evaluated separately for their antioxidant properties using DPPH assays. Results showed that only one fraction exhibited significant antioxidant activity in which serotonin was identified as the major compound by a UHPLC-ESI-QTOF HRMS/MS approach. We finally demonstrated, using purified serotonin molecule that this bioactive structure is mostly responsible for the free radical scavenging property of the crude venom as evidenced by DPPH and ROS assays in HaCaT cells exposed to UVB.