Bioactive Structures Research Articles

NEW PYRAN OF AN ENDOPHYTIC FUNGUS <i>Fusarium</i> sp. ISOLATED FROM THE LEAVES OF BROTOWALI (<i>Tinaspora crispa</i>)

Endophytes are microorganisms that reside asymptomatically in the tissues of higher plants and are relatively unstudied and a promising source of novel organic natural metabolites exhibiting a variety of biological activities. As a part of our systematic search for new bioactive lead structures from endophytic, the endophytic fungus Fusarium sp. isolated from the leaves of Brotowali (Tinaspora crispa), was cultured for isolation of metabolite. The endophytic fungus was cultivated on 6 L of Potatos Dextose Broth (PDB) medium at room temperature (no shaking) for 8 weeks. The cultures were then extracted with ethyl acetate to afford 9.4 g of residue after removal of the solvent under reduced pressure. The extract was separated into the fractions by column chromatography (CC) on silica gel. The fractions were further separated by silica gel column chromatography to give one compound. The molecular structure was established on the basis of spectroscopic analysis including UV, IR, 1H-NMR, 13C-NMR, HMQC, HMBC, COSY, and MS. The compound was determined as a new pyran.

NEW PYRAN OF AN ENDOPHYTIC FUNGUS Fusarium sp. ISOLATED FROM THE LEAVES OF BROTOWALI ( Tinaspora crispa )

Endophytes are microorganisms that reside asymptomatically in the tissues of higher plants and are relatively unstudied and a promising source of novel organic natural metabolites exhibiting a variety of biological activities. As a part of our systematic search for new bioactive lead structures from endophytic, the endophytic fungus Fusarium sp. isolated from the leaves of Brotowali (Tinaspora crispa), was cultured for isolation of metabolite. The endophytic fungus was cultivated on 6 L of Potatos Dextose Broth (PDB) medium at room temperature (no shaking) for 8 weeks. The cultures were then extracted with ethyl acetate to afford 9.4 g of residue after removal of the solvent under reduced pressure. The extract was separated into the fractions by column chromatography (CC) on silica gel. The fractions were further separated by silica gel column chromatography to give one compound. The molecular structure was established on the basis of spectroscopic analysis including UV, IR, 1H-NMR, 13C-NMR, HMQC, HMBC, COSY, and MS. The compound was determined as a new pyran.

Employing conformational analysis in the molecular modeling of agrochemicals: insights on QSAR parameters of 2,4-D

A common practice to compute ligand conformations of compounds with various degrees of freedom to be used in molecular modeling (QSAR and docking studies) is to perform a conformational distribution based on repeated random sampling, such as Monte-Carlo methods. Further calculations are often required. This short review describes some methods used for conformational analysis and the implications of using selected conformations in QSAR. A case study is developed for 2,4-dichlorophenoxyacetic acid (2,4-D), a widely used herbicide which binds to TIR1 ubiquitin ligase enzyme. The use of such an approach and semi-empirical calculations did not achieve all possible minima for 2,4-D. In addition, the conformations and respective energies obtained by the semi-empirical AM1 method do not match the calculated trends obtained by a high level DFT method. Similar findings were obtained for the carboxylate anion, which is the bioactive form. Finally, the crystal bioactive structure of 2,4-D was not found as a minimum when using Monte-Carlo/AM1 and is similarly populated with another conformer in implicit water solution according to optimization at the B3LYP/aug-cc-pVDZ level. Therefore, quantitative structure-activity relationship (QSAR) methods based on three dimensional chemical structures are not fundamental to provide predictive models for 2,4-D congeners as TIR1 ubiquitin ligase ligands, since they do not necessarily reflect the bioactive conformation of this molecule. This probably extends to other systems.

Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery

Computational conformational sampling underpins much of molecular modeling and design in pharmaceutical work. The sampling of smaller drug-like compounds has been an active area of research. However, few studies have tested in details the sampling of larger more flexible compounds, which are also relevant to drug discovery, including therapeutic peptides, macrocycles, and inhibitors of protein–protein interactions. Here, we investigate extensively mainstream conformational sampling methods on three carefully curated compound sets, namely the ‘Drug-like’, larger ‘Flexible’, and ‘Macrocycle’ compounds. These test molecules are chemically diverse with reliable X-ray protein-bound bioactive structures. The compared sampling methods include Stochastic Search and the recent LowModeMD from MOE, all the low-mode based approaches from MacroModel, and MD/LLMOD recently developed for macrocycles. In addition to default settings, key parameters of the sampling protocols were explored. The performance of the computational protocols was assessed via (i) the reproduction of the X-ray bioactive structures, (ii) the size, coverage and diversity of the output conformational ensembles, (iii) the compactness/extendedness of the conformers, and (iv) the ability to locate the global energy minimum. The influence of the stochastic nature of the searches on the results was also examined. Much better results were obtained by adopting search parameters enhanced over the default settings, while maintaining computational tractability. In MOE, the recent LowModeMD emerged as the method of choice. Mixed torsional/low-mode from MacroModel performed as well as LowModeMD, and MD/LLMOD performed well for macrocycles. The low-mode based approaches yielded very encouraging results with the flexible and macrocycle sets. Thus, one can productively tackle the computational conformational search of larger flexible compounds for drug discovery, including macrocycles.

Artificial neural network modeling of antimycobacterial chemical space to introduce efficient descriptors employed for drug design

Tuberculosis has become a serious condition with an estimated 2million deaths each year in the world. According to WHO report, multi-resistant tuberculosis is responsible for approximately 460 thousand recent cases per year and for about 740 thousand patients infected by both Mycobacterium tuberculosis and HIV/AIDS. In the current study, several bioactive structure databases were analyzed using cheminformatics tools to correlate the chemical structures of different compounds with their pharmacological activities; in addition, these tools were tried to identify molecules that could be candidate for experimental assays. In this regard, for defining the effective chemical compounds against Mycobacterium, a database consisting of 400 antimycobacterial compounds has been constructed. In the next step, more than 1400 molecular descriptors were defined by DRAGON application server for each compound. Then, the resulting descriptors were clustered by kNN and k-means clustering methods to be employed for ANN modeling. Utilizing PLS and ANN modeling methods led to building a model for predicting minimum inhibitory concentration (MIC) with R2=0.98 and MSE=0.0002. Applying the mentioned cheminformatics tools, it would be possible to design and introduce new compounds with broad applications in antimycobacterial drug discovery and development.

Target synthesis of bioactive thioglycolurils, based on QSAR predictions

Target synthesis of substituted thioglycolurils possessing sedative activity predicted by preliminary 3D-QSAR simulation of bioactive structures has been carried out.

Mannodendrimers prevent acute lung inflammation by inhibiting neutrophil recruitment

Mycobacterium tuberculosis mannose-capped lipoarabinomannan inhibits the release of proinflammatory cytokines by LPS-stimulated human dendritic cells (DCs) via targeting the C-type lectin receptor DC-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN). With the aim of mimicking the bioactive supramolecular structure of mannose-capped lipoarabinomannan, we designed and synthesized a set of poly(phosphorhydrazone) dendrimers grafted with mannose units, called mannodendrimers, that differed by size and the number and length of their (α1→2)-oligommanoside caps. A third-generation dendrimer bearing 48 trimannoside caps (3T) and a fourth-generation dendrimer bearing 96 dimannosides (4D) displayed the highest binding avidity for DC-SIGN. Moreover, these dendrimers inhibited proinflammatory cytokines, including TNF-α, production by LPS-stimulated DCs in a DC-SIGN-dependent fashion. Finally, in a model of acute lung inflammation in which mice were exposed to aerosolized LPS, per os administration of 3T mannodendrimer was found to significantly reduce neutrophil influx via targeting the DC-SIGN murine homolog SIGN-related 1. The 3T mannodendrimer therefore represents an innovative fully synthetic compound for the treatment of lung inflammatory diseases.

ChemInform Abstract: Imitation and Modification of Bioactive Lead Structures via Integration of Boron Clusters

In medicinal chemistry, carbaboranes can be employed either as boron carriers for boron neutron capture therapy (BNCT) or as scaffolds for radiodiagnostic or therapeutic agents. We have developed a suitable synthesis employing the phosphoramidite method to connect meta-carbaboranyl bis-phosphonites with the 6'-OH group of isopropylidene-pro- tected galactose, followed by oxidation or sulfurization to give the corresponding bis-phos- phonates. Deprotection yielded water-soluble compounds. The corresponding disodium salts exhibit especially low cytotoxicity. Preliminary results on the in vivo toxicity and biodistribu - tion of two compounds in mice indicated a lack of selectivity for the cotton rat lung (CRL) tumor chosen for the experiment. For the incorporation of carbaboranes into breast tumor- selective modified neuropeptide Y, (F 7 , P 34 )-NPY, a synthesis of a carbaborane-modified lysine derivative was developed. Linkage of the lysine to the boron cluster was achieved by using a propionic acid spacer. Incorporation of the amino acid derivatives into NPY and (F 7 , P 34 )-NPY by solid-phase peptide synthesis was successful. Preliminary studies showed that the receptor binding affinity and signal transduction of the boron-modified peptides were very well retained. Asborin, the carbaborane analogue of aspirin, is a rather weak inhibitor of cyclo - oxygenase-1 (COX-1) and COX-2, but a highly potent aldo/keto reductase 1A1 (AKR1A1) inhibitor. Modification either at the carboxyl group or at the chlorophenyl ring in indomethacin with ortho- and meta-carbaboranyl derivatives gave active derivatives only for the ortho-carbaborane directly attached to the carboxyl group, while the corresponding adamantyl and meta-carbaboranyl derivatives were inactive.

Nanoporosity Significantly Enhances the Biological Performance of Engineered Glass Tissue Scaffolds

Nanoporosity is known to impact the performance of implants and scaffolds such as bioactive glass (BG) scaffolds, either by providing a higher concentration of bioactive chemical species from enhanced surface area, or due to inherent nanoscale topology, or both. To delineate the role of these two characteristics, BG scaffolds have been fabricated with nearly identical surface area (81 and 83±2 m(2)/g) but significantly different pore size (av. 3.7 and 17.7 nm) by varying both the sintering temperature and the ammonia concentration during the solvent exchange phase of the sol-gel fabrication process. In vitro tests performed with MC3T3-E1 preosteoblast cells on such scaffolds show that initial cell attachment is increased on samples with the smaller nanopore size, providing the first direct evidence of the influence of nanopore topography on cell response to a bioactive structure. Furthermore, in vivo animal tests in New Zealand rabbits (subcutaneous implantation) indicate that nanopores promote colonization and cell penetration into these scaffolds, further demonstrating the favorable effects of nanopores in tissue-engineering-relevant BG scaffolds.

Synthesis and Reactivity of Aryl(alkynyl)iodonium Salts

AbstractThe first practical, yet simple, preparation of aryl(alkynyl)iodonium trifluoroacetate salts is described. The generic nature of this synthetic method has allowed the production of a range of aryl(alkynyl)iodonium trifluoroacetate salts with independent variation of both the alkynyl and aryliodo groups in yields of 30–85 %. Application of these new reagents to the synthesis of a series of 2‐arylfuro[3,2‐c]pyridines (40–64 %) highlights the potential of this class of materials as precursors to bioactive heterocyclic structures. These experiments have also demonstrated that, in this case, the effect of the aryliodo group on the reaction is negligible.

Biodegradable and bioactive porous scaffold structures prepared using fused deposition modeling

Three-dimensional printing (3DP) refers to a group of additive manufacturing techniques that can be utilized in tissue engineering applications. Fused deposition modeling (FDM) is a 3DP method capable of using common thermoplastic polymers. However, the scope of materials applicable for FDM has not been fully recognized. The purpose of this study was to examine the creation of biodegradable porous scaffold structures using different materials in FDM and to determine the compressive properties and the fibroblast cell response of the structures. To the best of our knowledge, the printability of a poly(ε-caprolactone)/bioactive glass (PCL/BAG) composite and L-lactide/ε-caprolactone 75/25 mol % copolymer (PLC) was demonstrated for the first time. Scanning electron microscope (SEM) images showed BAG particles at the surface of the printed PCL/BAG scaffolds. Compressive testing showed the possibility of altering the compressive stiffness of a scaffold without changing the compressive modulus. Compressive properties were significantly dependent on porosity level and structural geometry. Fibroblast proliferation was significantly higher in polylactide than in PCL or PCL/BAG composite. Optical microscope images and SEM images showed the viability of the cells, which demonstrated the biocompatibility of the structures.

Magnesium‐Containing Bioactive Glasses for Biomedical Applications

The importance ofMgin the human body, its key role in bone tissue development, in addition to its application to improve and modify physical, thermal, and mechanical properties of bioactive silicate glasses, makeMga very interesting element as a component of bioactive glasses for medical applications. AlthoughMgis a typical element in the composition of numerous developed bioactive glasses, the analysis of the literature reveals that further research is required to gain comprehensive understanding about the effects ofMgOon bioactive glass structure and properties. This article presents a comprehensive overview of the field ofMg‐containing bioactive glasses discussing available compositions and summarizing existing knowledge on effects ofMgOon glass properties. The biomedical applications of several developed glasses are discussed highlighting the distinct effects ofMgin relevant areas, such as bioactivity and cell response, and focusing on the most common applications for these glasses, such as bone cements, bioactive coatings, and scaffolds for bone tissue engineering. The effect ofMgon bone development is discussed and avenues for future research in the field are proposed, emphasizing the need to investigate unstudied properties of (already developed)Mg‐containing glass compositions, such as angiogenesis‐stimulating action and the effect on osteoclast functions, to develop newMg‐containing bioactive glasses as well as to make products of different shape designs such as nanoparticles, fibers, and complex porous structures.

Immunomodulatory Properties of Novel Nucleotide Oligomerization Domain 2 (Nod2) Agonistic Desmuramyldipeptides

There is a pressing need for the development of novel adjuvants for human use. The minimal bioactive structure of bacterial peptidoglycan (PGN), muramyldipeptide (MDP), and its derivative murabutide (MB) have long been known for their adjuvant activities. For this reason, a series of novel desmuramyldipeptides have been designed and synthesized as part of our search for therapeutically useful MDP analogues. Since nucleotide oligomerization domain 2 (Nod2) is a putative receptor for MDP, we used engineered HEK293 cells overexpressing Nod2 to screen and validate our compounds for their Nod2-agonist activity. Their immunomodulatory properties were subsequently assessed in vitro by evaluating their effect on proinflammatory cytokine production of phorbol 12-myristate 13-acetate (PMA)/ionomycin-stimulated human peripheral blood mononuclear cells (PBMCs). Herein, we present novel desmuramyldipeptides, the most active of them possessing immunoenhancing properties as a result of their potent Nod2-agonistic effect.

Molecular dynamics simulations of carbohydrate-mimetic haptens in complex with a complementary anti-carbohydrate antibody

The monoclonal antibody SYA/J6 is specific for the O-polysaccharide of the Shigella flexneri Y bacterium. Two haptens, a pentasaccharide and a mimetic octapeptide, bind to SYA/J6 with moderate binding affinities. In a previous attempt to obtain improved binding affinity to SYA/J6, two glycopeptide chimeras (α-glycopeptide and β-glycopeptide) were designed based on the structures of the pentasaccharide and the octapeptide, as well as a molecular docking study. Despite the overall fit of the ligand, the α-glycopeptide showed no inhibition of the SYA/J6 antibody binding to the O-polysaccharide. In this work, we conducted conventional molecular dynamics simulations of the SYA/J6 Fab in complex with these four related haptens. Several conformational differences between crystal structures and bioactive structures for the pentasaccharide binding and the octapeptide binding were identified. More significantly, the MD simulations revealed that the Fab complexes of both α-glycopeptide and β-glycopeptide were not stable, with the ligand dissociating from the combining site. This behavior provides a reasonable explanation for the lack of binding of the α-glycopeptide, and implies further that the β-glycopeptide would not be a hapten that binds the SYA/J6 antibody.

Imitation and modification of bioactive lead structures via integration of boron clusters

In medicinal chemistry, carbaboranes can be employed either as boron carriers for boron neutron capture therapy (BNCT) or as scaffolds for radiodiagnostic or therapeutic agents. We have developed a suitable synthesis employing the phosphoramidite method to connect meta-carbaboranyl bis-phosphonites with the 6'-OH group of isopropylidene-protected galactose, followed by oxidation or sulfurization to give the corresponding bis-phosphonates. Deprotection yielded water-soluble compounds. The corresponding disodium salts exhibit especially low cytotoxicity. Preliminary results on the in vivo toxicity and biodistribution of two compounds in mice indicated a lack of selectivity for the cotton rat lung (CRL) tumor chosen for the experiment. For the incorporation of carbaboranes into breast tumor-selective modified neuropeptide Y, [F7, P34]-NPY, a synthesis of a carbaborane-modified lysine derivative was developed. Linkage of the lysine to the boron cluster was achieved by using a propionic acid spacer. Incorporation of the amino acid derivatives into NPY and [F7, P34]-NPY by solid-phase peptide synthesis was successful. Preliminary studies showed that the receptor binding affinity and signal transduction of the boron-modified peptides were very well retained. Asborin, the carbaborane analogue of aspirin, is a rather weak inhibitor of cyclooxygenase-1 (COX-1) and COX-2, but a highly potent aldo/keto reductase 1A1 (AKR1A1) inhibitor. Modification either at the carboxyl group or at the chlorophenyl ring in indomethacin with ortho- and meta-carbaboranyl derivatives gave active derivatives only for the ortho-carbaborane directly attached to the carboxyl group, while the corresponding adamantyl and meta-carbaboranyl derivatives were inactive.

Bioactive Nano-Filters to Control Legionella on Indoor Air

Several factors affect the indoor air quality, among which ventilation, human occupancy, cleaning products, equipment and material; they might induce the presence of aerosols (or bioaerosols in the presence of biological components) nitrogen oxides, ozone, carbon monoxide and dioxide, volatile organic compounds, radon and microorganisms. Microbiological pollution involves hundreds of bacteria and fungi species that grow indoors under specific conditions of temperature and humidity. Exposure to microbial contaminants is clinically associated with allergies, asthma, immune responses and respiratory infections, such as Legionnaires Disease and Pontiac Feaver, which are due to contamination byLegionella pneumophila. Legionnaire's Disease has increased over the past decade, because of the use of central air conditioning. In places such as homes, kindergartens, nursing homes and hospitals, indoor air pollution affects population groups that are particularly vulnerable because of their health status or age, making indoor air pollution a public health issue of high importance. Therefore, the implementation of preventive measures, as the application of air filters, is fundamental. Currently, High Efficiency Particulate Air (HEPA) filters are the most used to capture microorganisms in ventilation, filtration and air conditioning systems; nevertheless, as they are not completely secure, new filters should be developed. This work aims to present how the efficiency of a textile nanostructure in a non-woven material based on synthetic textiles (high hydrophobic fibers) incorporating appropriate biocides to controlLegionella pneumophila, is going to be measured. These bioactive structures, to be used in ventilation systems, as well as in respiratory protective equipment, will reduce the growth of microorganisms in the air through bactericidal or bacteriostatic action. The filter nanostructure should have good air permeability, since it has to guarantee minimum flows of fresh air for air exchange as well as acceptable indoor air quality.

Regulation of the differentiation of mesenchymal stem cells in vitro and osteogenesis in vivo by microenvironmental modification of titanium alloy surfaces

To mimic the extracellular microenvironment of bone, a bioactive multilayered structure of gelatin/chitosan pair, containing bone morphogenetic protein 2(BMP2) and fibronectin (FN), was constructed onto Ti6Al4V surface via a layer-by-layer assembly technique. The successful fabrication of multilayered structure was confirmed by contact angle measurement, field emission scanning electron microscopy (FE-SEM) and confocal laser scanning microscopy (CLSM), respectively. Bioactive BMP2 released in a sustained manner along with the degradation of multilayered structure. MSCs grown onto the multilayer coated TC4 substrates displayed significantly higher (p < 0.01 or p < 0.05) production levels of alkaline phosphatase (ALP), mineralization and genes expressions of runt related transcription factor 2 (Runx2), osterix, osteocalcin (OC), osteopontin (OPN), ALP and collagen type Ⅰ(ColⅠ) compared to the controls after culture for 7 days and 21 days, respectively. More importantly, MicroCT analysis and histological observations demonstrated that the multilayer coated Ti6Al4V implants in vivo promoted the bone density and new bone formation around them after implantation for 4 weeks and 12 weeks, respectively. The results indicated that Ti6Al4V coated with biofunctional multilayers was beneficial for osteogenesis and integration of implant/bone. The study therefore presents an alternative to fabricate bio-functionalized Ti6Al4V-based implants for potential application in orthopedics field.

Independent Structural Domains in Paramyxovirus Polymerase Protein

All enzymatic activities required for genomic replication and transcription of nonsegmented negative strand RNA viruses (or Mononegavirales) are believed to be concentrated in the viral polymerase (L) protein. However, our insight into the organization of these different enzymatic activities into a bioactive tertiary structure remains rudimentary. Fragments of Mononegavirales polymerases analyzed to date cannot restore bioactivity through trans-complementation, unlike the related L proteins of segmented NSVs. We investigated the domain organization of phylogenetically diverse Paramyxovirus L proteins derived from measles virus (MeV), Nipah virus (NiV), and respiratory syncytial virus (RSV). Through a comprehensive in silico and experimental analysis of domain intersections, we defined MeV L position 615 as an interdomain candidate in addition to the previously reported residue 1708. Only position 1708 of MeV and the homologous positions in NiV and RSV L also tolerated the insertion of epitope tags. Splitting of MeV L at residue 1708 created fragments that were unable to physically interact and trans-complement, but strikingly, these activities were reconstituted by the addition of dimerization tags to the fragments. Equivalently split fragments of NiV, RSV, and MeV L oligomerized with comparable efficiency in all homo- and heterotypic combinations, but only the homotypic pairs were able to trans-complement. These results demonstrate that synthesis as a single polypeptide is not required for the Mononegavirales polymerases to adopt a proper tertiary conformation. Paramyxovirus polymerases are composed of at least two truly independent folding domains that lack a traditional interface but require molecular compatibility for bioactivity. The functional probing of the L domain architecture through trans-complementation is anticipated to be applicable to all Mononegavirales polymerases.

ChemInform Abstract: Palladium‐Catalyzed One‐Pot Synthesis of Pyrrole‐Annulated Coumarin, Quinolone, and 7‐Aza‐Indole Derivatives.

AbstractPotentially bioactive heterocyclic structures of type (III), (V) and (VIII) are readily available under conditions A) or B) in the absence of any ligand or N‐protecting group.

Rhodium‐Catalyzed Asymmetric Addition of Arylboronic Acids to Indolylnitroalkenes

AbstractIndolylnitroethanes and their derivatives are key intermediates to many bioactive structures. Most approaches to access chiral indolylnitroethanes involve organocatalyzed or metal‐catalyzed asymmetric Friedel–Crafts reaction of indoles with nitroalkenes. We have developed an efficient approach to optically pure α‐aryl‐3‐indolylnitroethanes through rhodium‐catalyzed asymmetric 1,4‐addition of arylboronic acids to indolylnitroalkenes. Excellent yields (up to 99 %) and enantiomeric excesses (up to 99 % ee) of chiral indolylnitroethanes were achieved under mild conditions.