Synthesis and in Vitro Antimicrobial Activity Screening of New 3‐Acetyl‐2,5‐disubstituted‐1,3,4‐oxadiazoline Derivatives

Thirteen new 3‐acetyl‐2,5‐disubstituted‐1,3,4‐oxadiazoline derivatives were synthesized from corresponding hydrazide‐hydrazones of isonicotinic acid in the reaction with acetic anhydride. The obtained compounds were identified with the use of spectral methods (IR, ¹H‐NMR, ¹³C‐NMR, MS). In vitro antimicrobial activity screening of synthesized compounds against a panel of bacteria and fungi revealed interesting antibacterial and antifungal activity of tested 1,3,4‐oxadiazoline derivatives, which is comparable to that of commonly used antimicrobial agents.     

Design,Synthesis, and Biological Evaluation of Peptidomimetic N‐Substituted Cbz‐4‐Hyp‐Hpa‐Amides as Novel Inhibitors of Plasmodium falciparum

A new series of peptidomimetic N‐substituted Cbz‐4‐Hyp‐Hpa‐amides were designed, synthesized, and evaluated for inhibition of the Plasmodium falciparum. Substituents on the N‐atom of the amide group were selected alkyl‐, allyl‐, aryl‐, 2‐hydroxyethyl‐, 2‐cyanoethyl‐, cyanomethyl‐, 2‐hydroxyethyl‐, 2,2‐diethoxyethyl‐, or 2‐ethoxy‐2‐oxoethylamino groups, and about of 40 new compounds were synthesized and evaluated for antiplasmodial activity in vitro. Antimalarial activity has been investigated as for the final peptide mimetics, and their immediate predecessors, carrying TBDMS or TBDPS protecting groups on 4‐hydroxyproline residue and 18 derivatives exhibited toxicity against P. falciparum. Of these agents, compound 23e was shown to have potent antimalarial activity with IC₅₀ 528 ng/ml.     

Scale‐dependence of vegetation‐environment relationships in semi‐natural grasslands

Questions: Which environmental and management factors determine plant species composition in semi‐natural grasslands within a local study area? Are vegetation and explanatory factors scale‐dependent? Location: Semi‐natural grasslands in Lærdal, Sognog Fjordane County, western Norway. Methods: We recorded plant species composition and explanatory variables in six grassland sites using a hierarchically nested sampling design with three levels: plots randomly placed within blocks selected within sites. We evaluated vegetation‐environment relationships at all three levels by means of DCA ordination and split‐plot GLM analyses. Results: The most important complex gradient determining variation in grassland species composition showed a broad‐scale relationship with management. Soil moisture conditions were related to vegetation variation on block scale, whereas element concentrations in the soil were significantly related to variation in species composition on all spatial scales. Our results show that vegetation‐environment relationships are dependent on the scale of observation. We suggest that scale‐related (and therefore methodological) issues may explain the wide range of vegetation‐environment relationships reported in the literature, for semi‐natural grassland in particular but also for other ecosystems. Conclusions: Interpretation of the variation in species composition of semi‐natural grasslands requires consideration of the spatial scales on which important environmental variables vary.     

Design,Synthesis, and Cytotoxic Activity of 3‐Aryl‐N‐hydroxy‐2‐(sulfonamido)propanamides in HepG2, HT‐1080, KB,and MCF‐7 Cells

A new series of (sulfonamido)propanamides ( 6a1 – 6a13 , 6b1 – 6b15 , 7c1 – 7c5 , 6d1 – 6d5 , 6e1 – 6e6 ) was designed and synthesized. All the synthesized compounds were characterized by NMR and mass spectrometry. The target compounds were evaluated for their in vitro cytotoxic activity against hepatocellular carcinoma (HepG2), fibrosarcoma (HT‐1080), mouth epidermal carcinoma (KB), and breast adenocarcinoma (MCF‐7) cell lines with the sulforhodamine B (SRB) assay, with gemcitabine and mitomycin C as positive controls. Most of these compounds exhibit a more potent cytotoxic effect than the positive control group on various cancer cell lines and the most potent compound, 6a7 , shows the IC₅₀ values of 29.78±0.516 μm , 30.70±0.61 μm , and 64.89±3.09 μm in HepG2, HT‐1080, KB, and MCF‐7 cell lines, respectively. Thus, these compounds with potent cytotoxic activity have potential for development as new chemotherapy agents.     

Folding nucleus structure persists in thermally‐aggregated FGF‐1

An efficient protein‐folding pathway leading to target structure, and the avoidance of aggregation, is essential to protein evolution and de novo design; however, design details to achieve efficient folding and avoid aggregation are poorly understood. We report characterization of the thermally‐induced aggregate of fibroblast growth factor‐1 (FGF‐1), a small globular protein, by solid‐state NMR. NMR spectra are consistent with residual structure in the aggregate and provide evidence of a structured region that corresponds to the region of the folding nucleus. NMR data on aggregated FGF‐1 also indicate the presence of unstructured regions that exhibit hydration‐dependent dynamics and suggest that unstructured regions of aggregated FGF‐1 lie outside the folding nucleus. Since it is known that regions outside the folding nucleus fold late in the folding pathway, we postulate that these regions unfold early in the unfolding pathway and that the partially folded state is more prone to intermolecular aggregation. This interpretation is further supported by comparison with a designed protein that shares the same FGF‐1 folding nucleus sequence, but has different 1° structure outside the folding nucleus, and does not thermally aggregate. The results suggest that design of an efficient folding nucleus, and the avoidance of aggregation in the folding pathway, are potentially separable design criteria – the latter of which could principally focus upon the physicochemical properties of 1° structure outside the folding nucleus.     

Metal‐dependent assembly of a protein nano‐cage

Short, alpha‐helical coiled coils provide a simple, modular method to direct the assembly of proteins into higher order structures. We previously demonstrated that by genetically fusing de novo–designed coiled coils of the appropriate oligomerization state to a natural trimeric protein, we could direct the assembly of this protein into various geometrical cages. Here, we have extended this approach by appending a coiled coil designed to trimerize in response to binding divalent transition metal ions and thereby achieve metal ion‐dependent assembly of a tetrahedral protein cage. Ni²⁺, Co²⁺, Cu²⁺, and Zn²⁺ ions were evaluated, with Ni²⁺ proving the most effective at mediating protein assembly. Characterization of the assembled protein indicated that the metal ion–protein complex formed discrete globular structures of the diameter expected for a complex containing 12 copies of the protein monomer. Protein assembly could be reversed by removing metal ions with ethylenediaminetetraacetic acid or under mildly acidic conditions.     

Motif‐directed redesign of enzyme specificity

Computational protein design relies on several approximations, including the use of fixed backbones and rotamers, to reduce protein design to a computationally tractable problem. However, allowing backbone and off‐rotamer flexibility leads to more accurate designs and greater conformational diversity. Exhaustive sampling of this additional conformational space is challenging, and often impossible. Here, we report a computational method that utilizes a preselected library of native interactions to direct backbone flexibility to accommodate placement of these functional contacts. Using these native interaction modules, termed motifs, improves the likelihood that the interaction can be realized, provided that suitable backbone perturbations can be identified. Furthermore, it allows a directed search of the conformational space, reducing the sampling needed to find low energy conformations. We implemented the motif‐based design algorithm in Rosetta, and tested the efficacy of this method by redesigning the substrate specificity of methionine aminopeptidase. In summary, native enzymes have evolved to catalyze a wide range of chemical reactions with extraordinary specificity. Computational enzyme design seeks to generate novel chemical activities by altering the target substrates of these existing enzymes. We have implemented a novel approach to redesign the specificity of an enzyme and demonstrated its effectiveness on a model system.     

Synthesis of Disulfide‐Bridged N‐Phenyl‐N′‐(alkyl/aryl/heteroaryl)urea Derivatives and Evaluation of Their Antimicrobial Activities

The discovery of new antimicrobial agents is extremely needed to overcome multidrug‐resistant bacterial and tuberculosis infections. In the present study, eight novel substituted urea derivatives ( 10a – 10h ) containing disulfide bond were designed, synthesized and screened for their in vitro antimicrobial activities on standard strains of Gram‐positive and Gram‐negative bacteria as well as on Mycobacterium tuberculosis. According to the obtained results, antibacterial effects of the compounds were found to be considerably better than their antimycobacterial activities along with their weak cytotoxic effects. Molecular docking studies were performed to gain insights into the antibacterial activity mechanism of the synthesized compounds. The interactions and the orientation of compound 10a (1,1′‐((disulfanediylbis(methylene))bis(2,1‐phenylene))bis(3‐phenylurea)) were found to be highly similar to the original ligand within the binding pocket E. faecalis β‐ketoacyl acyl carrier protein synthase III (FabH). Finally, a theoretical study was established to predict the physicochemical properties of the compounds.     

Design of experiments reveals critical parameters for pilot‐scale freeze‐and‐thaw processing of L‐lactic dehydrogenase

Freezing constitutes an important unit operation of biotechnological protein production. Effects of freeze‐and‐thaw (F/T) process parameters on stability and other quality attributes of the protein product are usually not well understood. Here a design of experiments (DoE) approach was used to characterize the F/T behavior of L‐lactic dehydrogenase (LDH) in a 700‐mL pilot‐scale freeze container equipped with internal temperature and pH probes. In 24‐hour experiments, target temperature between –10 and –38°C most strongly affected LDH stability whereby enzyme activity was retained best at the highest temperature of –10°C. Cooling profile and liquid fill volume also had significant effects on LDH stability and affected the protein aggregation significantly. Parameters of the thawing phase had a comparably small effect on LDH stability. Experiments in which the standard sodium phosphate buffer was exchanged by Tris‐HCl and the non‐ionic surfactant Tween 80 was added to the protein solution showed that pH shift during freezing and protein surface exposure were the main factors responsible for LDH instability at the lower freeze temperatures. Collectively, evidence is presented that supports the use of DoE‐based systematic analysis at pilot scale in the identification of F/T process parameters critical for protein stability and in the development of suitable process control strategies.     

Synthesis and Evaluation of Water‐Soluble 2‐Aryl‐1‐Sulfonylpyrrolidine Derivatives as Bacterial Biofilm Formation Inhibitors

The approach to the novel 1‐[(2‐aminoethyl)sulfonyl]‐2‐arylpyrrolidines via unique intramolecular cyclization/aza‐Michael reactions of N‐(4,4‐diethoxybutyl)ethenesulfonamide have been developed, which benefits from high yields of target compounds, mild reaction conditions, usage of inexpensive and low‐toxic reagents, and allows for wide variability in both amine and aryl moieties. Biotesting with whole‐cell luminescent bacterial biosensors responding to DNA damage showed that all tested compounds are not genotoxic. Tested compounds differently affect the formation of biofilms by Vibrio aquamarinus DSM 26054. Some of the tested compounds were found to suppress the bacterial biofilms growth and thus are promising candidates for further studies.     

Synthesis and Activity Evaluation of Nasopharyngeal Carcinoma Inhibitors Based on 6‐(Pyrimidin‐4‐yl)‐1H‐indazole

Human nasopharyngeal carcinoma is a common head and neck malignancy with high incidence in Southeast Asia and Southern China. It is necessary to develop safe, effective and inexpensive anticancer agents to improve the therapeutics of patients with nasopharyngeal carcinoma. A series of small molecular compounds based on 6‐(pyrimidin‐4‐yl)‐1H‐indazole were synthesized and evaluated for antiproliferative activities against human nasopharyngeal carcinoma cell lines SUNE1. Compounds 6b , 6c , 6e and 6l showed potent antiproliferative activities similar to positive control drug cisplatin in vitro with lower nephrotoxicity than it. N‐[4‐(1H‐Indazol‐6‐yl)pyrimidin‐2‐yl]benzene‐1,3‐diamine ( 6l ) was selected for further study. It was found that 6l induced mitochondria‐mediated apoptosis and G₂/M phase arrest in SUNE1 cells. Furthermore, compound 6l at 10 mg/kg can suppress the growth of an implanted SUNE1 xenograft with a TGI% (tumor growth inhibition) value of 50 % and did not cause serious side effects in BALB/c nude mice. This study suggests that 6‐(pyrimidin‐4‐yl)‐1H‐indazole derivatives are a series of small molecule compounds with anti‐nasopharyngeal carcinoma activities.     

Cupryphans,metal‐binding,redox‐active,redesigned conopeptides

Contryphans are bioactive peptides, isolated from the venom of marine snails of the genus Conus, which are characterized by the short length of the polypeptide chain and the high degree of unusual post‐translational modifications. The cyclization of the polypeptide chain through a single disulphide bond, the presence of two conserved Pro residues, and the epimerization of a Trp/Leu residue confer to Contryphans a stable and well‐defined structure in solution, conserved in all members of the family, and tolerant to multiple substitutions. The potential of Contryphans as scaffolds for the design of redox‐active (macro)molecules was tested by engineering a copper‐binding site on two different variants of the natural peptide Contryphan‐Vn. The binding site was designed by computational modeling, and the redesigned peptides were synthesized and characterized by optical, fluorescence, electron spin resonance, and nuclear magnetic resonance spectroscopy. The novel peptides, named Cupryphan and Arg–Cupryphan, bind Cu²⁺ ions with a 1:1 stoichiometry and a K_d in the 100 nM range. Other divalent metals (e.g., Zn²⁺ and Mg²⁺) are bound with much lower affinity. In addition, Cupryphans catalyze the dismutation of superoxide anions with an activity comparable to other nonpeptidic superoxide dismutase mimics. We conclude that the Contryphan motif represents a natural robust scaffold which can be engineered to perform different functions, providing additional means for the design of catalytically active mini metalloproteins.     

SP‐Designer: a user‐friendly program for designing species‐specific primer pairs from DNA sequence alignments

SP‐Designer is an open‐source program providing a user‐friendly tool for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. SP‐Designer selects PCR primer pairs for the amplification of DNA from a target species on the basis of several criteria: (i) primer specificity, as assessed by interspecific sequence polymorphism in the annealing regions, (ii) the biochemical characteristics of the primers and (iii) the intended PCR conditions. SP‐Designer generates tables, detailing the primer pair and PCR characteristics, and a FASTA file locating the primer sequences in the original sequence alignment. SP‐Designer is Windows‐compatible and freely available from http://www2.sophia.inra.fr/urih/sophia_mart/sp_designer/info_sp_designer.php .     

Process Development in Biotechnology – A Re‐Evaluation

This review considers some process development problems in biotechnology and presents examples of solutions, which were developed in cooperation with industrial partners. These processes include the production of restriction endonuclease EcoRI by recombinant Escherichia coli, which is toxic to the cell, penicillin V by Penicillium chrysogenum, xylanase by Aspergillus awamori, cephalosporin C by Acremonium chrysogenum, erythritol by Moniliella tomentosa var pollinis, and alkaline serine protease by Bacillus licheniformis. Special attention is given to the practical aspects of product development.     

Design,Synthesis and Biological Activity of (20S,21S)‐7‐Cyclohexyl‐21‐fluorocamptothecin Carbamates as Potential Antitumor Agents

(20S,21S)‐7‐Cyclohexyl‐21‐fluorocamptothecin was discovered by a fluorine drug design strategy with potent antitumor activity and increased metabolic stability. In continuous efforts to find novel antitumor agents derived from natural product camptothecin, 20‐carbamates of the active compound (20S,21S)‐7‐cyclohexyl‐21‐fluorocamptothecin have been designed and synthesized. Among them, one compound with the diethylamino group showed greater antiproliferative activity than the other 20‐carbamate derivatives. The following biological activity assays indicated that the above compound is a valuable lead compound with excellent Topo I inhibitory activity and solution stability.     

Cyclic oligomer design with de novo αβ‐proteins

We have previously shown that monomeric globular αβ‐proteins can be designed de novo with considerable control over topology, size, and shape. In this paper, we investigate the design of cyclic homo‐oligomers from these starting points. We experimented with both keeping the original monomer backbones fixed during the cyclic docking and design process, and allowing the backbone of the monomer to conform to that of adjacent subunits in the homo‐oligomer. The latter flexible backbone protocol generated designs with shape complementarity approaching that of native homo‐oligomers, but experimental characterization showed that the fixed backbone designs were more stable and less aggregation prone. Designed C2 oligomers with β‐strand backbone interactions were structurally confirmed through x‐ray crystallography and small‐angle X‐ray scattering (SAXS). In contrast, C3‐C5 designed homo‐oligomers with primarily nonpolar residues at interfaces all formed a range of oligomeric states. Taken together, our results suggest that for homo‐oligomers formed from globular building blocks, improved structural specificity will be better achieved using monomers with increased shape complementarity and with more polar interfaces.