1. Fluorine Effect in the Gelation Ability of Low Molecular Weight Gelators
Paolo Ravarino, Nadia Di Domenico, Marianna Barbalinardo, Davide Faccio, Giuseppe Falini, Demetra Giuri, Claudia Tomasini Gels. 2022 Feb 8;8(2):98. doi: 10.3390/gels8020098.
The three gelators presented in this work (Boc-D-Phe-L-Oxd-OH F0, Boc-D-F1Phe-L-Oxd-OH F1 and Boc-D-F2Phe-L-Oxd-OH F2) share the same scaffold and differ in the number of fluorine atoms linked to the aromatic ring of phenylalanine. They have been applied to the preparation of gels in 0.5% or 1.0% w/v concentration, using three methodologies: solvent switch, pH change and calcium ions addition. The general trend is an increased tendency to form structured materials from F0 to F1 and F2. This property ends up in the formation of stronger materials when fluorine atoms are present. Some samples, generally formed by F1 or F2 in 0.5% w/v concentration, show high transparency but low mechanical properties. Two gels, both containing fluorine atoms, show increased stiffness coupled with high transparency. The biocompatibility of the gelators was assessed exposing them to fibroblast cells and demonstrated that F1 and F2 are not toxic to cells even in high concentration, while F0 is not toxic to cells only in a low concentration. In conclusion, the presence of even only one fluorine atom improves all the gelators properties: the gelation ability of the compound, the rheological properties and the transparency of the final materials and the gelator biocompatibility.
2. Structure-based understanding of ligand affinity using human thrombin as a model system
V L Nienaber, L J Mersinger, C A Kettner Biochemistry. 1996 Jul 30;35(30):9690-9. doi: 10.1021/bi952164b.
Kinetic study of a series of compounds containing the thrombin-directed peptide D-Phe-ProboroArg-OH had indicated that the structure of the N-terminal blocking group may be correlated with binding [Kettner, C., Mersinger, L., & Knabb, R. (1990) J. Biol. Chem. 265, 18289-18297]. In order to further study this phenomenon, a second series of compounds that contains a C-terminal methyl ester in place of the boronic acid was synthesized, binding measured, and the three-dimensional structure in complex with human thrombin determined by X-ray crystallography. Incubation of Ac-D-Phe-Pro-Arg-OMe, Boc-D-Phe-Pro-Arg-OMe, and H-D-Phe-Pro-Arg-OMe resulted in the formation of thrombin-product complexes within the crystal. Ki values for the corresponding products (free carboxylic acids) were 60 +/- 12 microM, 7.8 +/- 0.1 microM, 0.58 +/- 0.02 microM, respectively, indicating that the nature of the N-terminal blocking group has a significant effect on affinity. Examination of the crystal structures indicated that the higher affinity of the H-D-Phe peptide is due to rearrangement of one residue comprising the S3 site (Glu192) in order to maximize electrostatic interactions with the "NH3(+)-" of H-D-Phe. The relative affinity of Boc-D-Phe-Pro-Arg-OH is due to favorable hydrophobic interactions between thrombin and the bulky butyl group. However, this results in less favorable binding of Arg-P1 in the oxyanion hole as shown by long hydrogen-bonding distances. This work gave rise to some general observations applicable to structure-based drug design: (1) altering the structure of an inhibitor at one site can affect binding at an unchanged distal site; (2) minor alteration of inhibitor structure can lead to small, but significant reorganization of neighboring protein structure; (3) these unexpected reorganizations can define alternate binding motifs.
3. Plant peptide hormone phytosulfokine (PSK-alpha): synthesis of new analogues and their biological evaluation
Agata Bahyrycz, Yoshikatsu Matsubayashi, Mari Ogawa, Youji Sakagami, Danuta Konopińska J Pept Sci. 2004 Jul;10(7):462-9. doi: 10.1002/psc.492.
Phytosulfokine-alpha (PSK-alpha), a sulfated growth factor (H-Tyr(SO3H)-Ile-Tyr(SO3H)-Thr-Gln-OH) universally found in both monocotyledons and dicotyledons, strongly promotes proliferation of plant cells in culture. In our studies on structure/activity relationship in PSK-alpha the synthesis of a series of analogues was performed: [H-D-Tyr(SO3H)1]- (9), [H-Phe(4-SO3H)1]- (10), [H-D-Phe(4-SO3H)1]- (11), [H-Phg(4-SO3H)1]- (12), [H-D-Phg(4-SO3H)1]- (13), H-Phe(4-NHSO2CH3)1]- (14), [H-D-Phe(4-NHSO2CH3)1]- (15), [H-Phe(4-NO2)1]- (16), [H-D-Phe(4-NO2)1]- (17), [H-Phg(4-NO2)1]- (18), [H-D-Phg(4-NO2)1]- (19), [H-Hph(4-NO2)1]- (20), [H-Phg(4-OSO3H)1]- (21), [Phe(4-NO2)3]- (22), [Phg(4-NO2)3]- (23), [Hph(4-NO2)3]- (24), [H-Phe(4-SO3H)1, Phe(4-SO3H)3]- (25) [H-Phe(4-NO2)1, Phe(4-NO2)3]- (26), [H-Phg(4-NO2)1, Phg(4-NO2)3]- (27), [H-Hph(4-NO2)1, Hph(4-NO2)3]- (28) and [Val3]- PSK-alpha (29). For modification of the PSK-alpha peptide chain the novel amino acids and their derivatives were synthesized, such as: H-L-Phg(4-SO3H)-OH (1), H-D-Phg(4-SO3H)-OH (2), Fmoc-Phg(4-SO3H)-OH (3), Fmoc-D-Phg(4-SO3H)-OH (4), Boc-Phg(4-NHSO2CH3)-OH (5), Boc-D-Phg(4-NHSO2CH3)-OH (6) Boc-Phe(4-NHSO2CH3)-OH (7), and Boc-D-Phe(4-NHSO2CH3)-OH (8). Peptides were synthesized by a solid phase method according to the Fmoc procedure on a Wang-resin. Free peptides were released from the resin by 95% TFA in the presence of EDT. All peptides were tested by competitive binding assay to the carrot membrane using 3H-labelled PSK according to the Matsubayashi et al. test.
