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1.
《Bioorganic & medicinal chemistry》2019,27(12):2323-2331
Microorganisms embedded in a biofilm are significantly more resistant to antimicrobial agents and the defences of the human immune system, than their planktonic counterpart. Consequently, compounds that can inhibit biofilm formation are of great interest for novel therapeutics. In this study, a screening approach was used to identify novel cyclic dipeptides that have anti-biofilm activity against oral pathogens. Five new active compounds were identified that prevent biofilm formation by the cariogenic bacterium Streptococcus mutans and the pathogenic fungus Candida albicans. These compounds also inhibit the adherence of microorganisms to a hydroxylapatite surface. Further investigations were conducted on these compounds to establish the structure–activity relationship, and it was deduced that the common cleft pattern is required for these molecules to act effectively against biofilms. 相似文献
2.
Christelle David Laurent Bischoff Hervé Meudal Catherine Llorens-Cortes Bernard Pierre Roques Marie-Claude Fournié-Zaluski 《Letters in Peptide Science》1997,4(4-6):411-414
In order to study the physiological role of aminopeptidase A (APA),several -mercapto--amino acyl dipeptides were synthesized toobtain compounds having a high affinity for APA and a high selectivityversus aminopeptidase N (APN). Sulfonamide and carboxylate moieties whichhave been shown to be recognized by the S1 subsite of theenzyme were introduced on the side chain of the -mercapto--aminoacyl sub-unit, the latter being coupled to dipeptides optimized to interactwith the S1 andS2 subsites by means of combinatorialchemistry. Good affinities (16 nM) were obtained, the selectivity factorsbeing up to 160-fold versus APN. 相似文献
3.
Previous experience with the Langevin/implicit-Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5–20 fs range but quenches high-frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13-residue oligoalanine) and also develop a new dynamics driver approach (“DA”). The DA scheme, based on LI, addresses the important issue of proper sampling, which is unlikely to be solved by small-time step integration methods or implicit methods with intrinsic damping at room temperature, such as LI. Equilibrium averages, time-dependent molecular properties, and sampling trends at room temperature are reported for both LI and DA dynamics simulations, which are then compared to those generated by a standard explicit discretization of the Langevin equation with a 1 fs timestep. We find that LI's quenching effects are severe on both the fast and slow (due to vibrational coupling) frequency modes of all-atom polypeptides and lead to more restricted dynamics at moderate timesteps (40 fs). The DA approach empirically counteracts these damping effects by adding random atomic perturbations to the coordinates at each step (before the minimization of a dynamics function). By restricting the energetic fluctuations and controlling the kinetic energy, we are able with a 60 fs timestep to generate continuous trajectories that sample more of the relevant conformational space and also reproduce reasonably Boltzmann statistics. Although the timescale for transition may be accelerated by the DA approach, the transitional. information obtained for the alanine dipeptide and the tetrapeptide is consistent with that obtained by several other theoretical approaches that focus specifically on the determination of pathways. While the trajectory for oligoalanine by the explicit scheme over the nanosecond timeframe remains in the vicinity of the full αR-helix starting structure, and a high-temperature (6000°K) MD trajectory departs slowly from the a helical structure, the DA-generated trajectory for the same CPU time exhibits unfolding and refolding and reveals a range of conformations with an intermediate helix content. Significantly, this range of states is more consistent with spectroscopic experiments on small peptides, as well as the cooperative two-state model for helix–coil transition. The good, near-Boltzmann statistics reported for the smaller systems above, in combination with the interesting oligoalanine results, suggest that DA is a promising tool for efficiently exploring conformational spaces of biomolecules and exploring folding/unfolding processes of polypeptides. © 1995 Wiley-Liss, Inc. 相似文献
4.
LIISA KAARINA SIMOLA 《Physiologia plantarum》1978,44(4):315-318
The growth of Drosera rotundifolia was studied in aseptic cultures with 17 dipeptides as the only nitrogen source. About half of the dipeptides were well or partly utilized. Compounds containing glycine, alanine, glutamic or aspartic acid are clearly more favourable than dipeptides containing proline. Arginyl-aspartic acid (1.25 mM) promoted growth more than inorganic nitrogen (1.25 mM of NH4NO3). Glycyl-alanine gave about the same growth response as NH4NO3. The inocules died rapidly in medium containing leucyl-tyrosine and dipeptides containing methionine and valine were also toxic. There was usually a clear correlation between the growth-retarding or growth-stimulating effect of the dipeptides and the effects of their amino acid components. 相似文献
5.
Summary A method of ion exchange column chromatography was developed for the determination of D- and L-amino acids in the form of diastereomeric dipeptide. First the protein containing samples were hydrolyzed with 6 molar hydrochloric acid, then the single amino acids were separated in an LKB automated amino acid analyzer with the LKB fraction collector. Following lyophilization, the single amino acids were transformed into alanyl dipeptides with tertiary-butyloxycarbonil-L-alanine-N-hydroxy-succinimide (t-BOC-L-Ala-ONSu) active ester. The alanyl dipeptides were easily separated from one another and the initial amino acids. Determination of the D- and L-amino acids in this form is relatively accurate and reproducible but takes some time (33–38 min). Accuracy of the determination is satisfactory. The coefficient of variation amounts to 3–5%. The use of the method is suggested to laboratories having an amino acid analyzer and wish to determine D-and L-amino acids in synthetic-amino acids complements, peptides or natural materials. 相似文献
6.
Summary N-Boc protected non-proteinogenic dipeptides with D,L-and L,L-configuration were prepared by catalytic asymmetric hydrogenation of the corresponding dehydrophenylalanyl-(L)-phenylalanine derivatives. The configuration of the new stereogenic centre depends first of all on the catalyst configuration and is less influenced by the substrate configuration. Diastereomeric excesses in the range of 80–96% de could be increased up to 99% by recrystallization. Analytical data of selected new compounds are given.Abbreviations PINDOPHOS
2,3-O,N-bis(diphenylphosphino)-1-(4-indolyloxy)-2-hydroxy-3-isopropylamino propane
- PROPRAPHOS
2,3-O,N-bis(diphenylphosphino)-1-(naphthoxy)-2-hydroxy-3-isopropylamino propane
- BDPB
1,4-bis(diphenylphosphino)butane 相似文献
7.
To understand trimethylamine N-oxide (TMAO) attenuation of the denaturating effects of urea or guanidine hydrochloride (GdnHCl), we have determined the apparent transfer free energies (DeltaG(tr)(')) of cyclic dipeptides (CDs) from water to TMAO, urea or GdnHCl, and also the blends of TMAO and denaturants (urea or GdnHCl) at a 1:2 ratio as well as various denaturant concentrations in the presence of 1M TMAO, through the solubility measurements, at 25 degrees C. The CDs investigated in the present study included cyclo(Gly-Gly), cyclo(Ala-Ala) and cyclo(Val-Val). The observed DeltaG(tr)(') values indicate that TMAO can stabilize the CDs while urea or GdnHCl can destabilize the CDs. Furthermore, the DeltaG(tr)(') values of the blends of TMAO with urea or GdnHCl revealed that TMAO strongly counteracted the denaturating effects of urea on CDs in all instances, however, TMAO partially counteracted the perturbing effects of GdnHCl on CDs. TMAO counteraction ability of the deleterious effects of denaturants depended on the denaturant-CDs pair. The experimental results were further used to estimate the transfer free energies (Deltag(tr)(')) of the various functional group contributions from water to TMAO, urea or GdnHCl individually and to the combinations of TMAO and the denaturants in various ratios. 相似文献
8.
Hirofumi Inoue Haruo Iguch Akira Kouno Yasuto Tsuruta 《Journal of chromatography. B, Analytical technologies in the biomedical and life sciences》2001,757(2):752
A highly sensitive HPLC method for the determination of prolyl dipeptides, Pro and Hyp in serum was developed. After deproteinization of serum and pretreatment with o-phthalaldehyde, the analytes were derivatized with 4-(5,6-dimethoxy-2-phthalimidinyl)-2-methoxyphenylsulfonyl chloride at 70°C for 10 min. The fluorescent derivatives of prolyl dipeptides, Pro and Hyp, were separated on tandem reversed-phase columns by a gradient elution at 55°C and detected by fluorescence measured at 318 nm (excitation) and 392 nm (emission). The detection limits for prolyl dipeptides were 2–5 fmol/injection (S/N=3). Pro–Hyp, Pro–Gly and Pro–Pro were identified as serum prolyl dipeptides. The within-day and between-day relative standard deviations were 1.5–7.9 and 2.4–10.8%, respectively. The recoveries were in the range of 90.8–97.3%. The concentrations of Pro–Hyp, Pro–Gly, Pro–Pro, Pro and Hyp in normal human serum (n=10) were 0.64±0.35, 0.078±0.047, 0.022±0.016, 177.0±43.0 and 11.1±3.5 μM, respectively. The concentrations of Pro–Hyp and Pro–Pro in serum of a patient with bone metastases of prostatic cancer were about three times and 50 times, respectively, higher than those in normal human serum. 相似文献
9.
Natascha Verhagen Andy Wiranata Wijaya Attila Teleki Muhammad Fadhlullah Andreas Unsld Martin Schilling Christoph Heinrich Ralf Takors 《Engineering in Life Science》2020,20(9-10):384-394
Increasing markets for biopharmaceuticals, including monoclonal antibodies, have triggered a permanent need for bioprocess optimization. Biochemical engineering approaches often include the optimization of basal and feed media to improve productivities of Chinese hamster ovary (CHO) cell cultures. Often, l ‐tyrosine is added as dipeptide to deal with its poor solubility at neutral pH. Showcasing IgG1 production with CHO cells, we investigated the supplementation of three l ‐tyrosine (TYR, Y) containing dipeptides: glycyl‐l ‐tyrosine (GY), l ‐tyrosyl‐l ‐valine (YV), and l ‐prolyl‐l ‐tyrosine (PY). While GY and YV led to almost no phenotypic and metabolic differences compared to reference samples, PY significantly amplified TYR uptake thus maximizing related catabolic activity. Consequently, ATP formation was roughly four times higher upon PY application than in reference samples. 相似文献
10.
Massimo Coletta Paolo Ascenzi Laura Bravin Gino Amiconi Martino Bolognesi Mario Guarneri 《Journal of biomolecular structure & dynamics》2013,31(4):959-972
Abstract The effect of activating dipeptides, sequentially homologous to the Ile 16-Val 17 N-terminus of bovine β-trypsin (β-trypsin), on equilibria involved in the binding of strong ligands (i.e., n-butylamine, the bovine basic pancreatic trypsin inhibitor (Kunitz-type inhibitor; BPTI) and the porcine pancreatic secretory trypsin inhibitor (Kazal-type inhibitor, type I; PSTI)) to bovine trypsinogen (trypsinogen) was investigated at pH 5.5 (I = 0.1 M) and T = 21.0 ± 0.5°C; under the same experimental conditions, thermodynamics for the binding of strong ligands to β-trypsin was also obtained. The equilibria involved in the binding of activating dipeptides and/or inhibitors to β-trypsin and to its zymogen are described according to an induced-fit formalism, taking into account ligand-linked interaction(s) between different functional and structural domains of the (pro)enzyme possibly involved in the trypsinogen-to-β-trypsin activation pathway. The analysis of data is focussed on parameters describing interactions between the so-called Ile-Val pocket (where the Ile16-Val17/V-terminus of β-trypsin or activating dipeptides bind) and the primary and/or secondary recognition subsite(s) (where strong ligands associate) present in the (pro)enzyme. Such an analysis allows to dissect the contributions due to the primary recognition subsite, where small mono-functional ligands (e.g., n-butylamine) bind, from those of the secondary subsite(s), which are additional recognition clefts for macromolecular inhibitors (e.g., BPTI and PSTI). 相似文献