The renal type H+/peptide symporter PEPT2: structure-affinity relationships.

The H(+)/peptide cotransporter PEPT2 is expressed in a variety of organs including kidney, lung, brain, mammary gland, and eye. PEPT2 substrates are di- and tripeptides as well as peptidomimetics, such as beta-lactam antibiotics. Due to the presence of PEPT2 at the bronchial epithelium, the aerosolic administration of peptide-like drugs might play a major role in future treatment of various pulmonary and systemic diseases. Moreover, PEPT2 has a significant influence on the in vivo disposition and half-life time of peptide-like drugs within the body, particularly in kidney and brain. PEPT2 is known to have similar but not identical structural requirements for substrate recognition and transport compared to PEPT1, its intestinal counterpart. In this review we compiled available affinity constants of 352 compounds, measured at different mammalian tissues and expression systems and compare the data whenever possible with those of PEPT1.

Molecular motions within self-assembled dimeric capsules with tetraethylammonium cations as guest.

Hydrogen-bonded, dimeric capsules of calix[4]arenes substituted at the wide rim by four urea functions show unprecedented dynamic features when a tetraethylammonium cation is included as a guest. The seam of hydrogen bonds C=O...(HN)2C=O in the equatorial region which holds the two calixarene counterparts together changes its directionality fast (at 25 degrees C), while the dimer itself is kinetically stable on the NMR time scale. An energy barrier of deltaG++ = 49.9 kJmol(-1) (Tc 276 K) was estimated for this reorientation from variable-temperature (VT) NMR measurements. Lowering the temperature to about -50 degrees C restricts also the rotation of the encapsulated tetraethylammonium cation around a pseudo C2-symmetry axis in the equatorial plane of the capsule, while its rotation around the C4 axis is still fast. As a result of this restriction two ethyl groups of the tetraethylammonium cation point towards the "poles" of the capsule, while the other pair lies in the "equator" region. Variable-temperature 1H NMR experiments led to a barrier of deltaG++=54.8kJ mol(-1) (Tc 306 K) for the exchange of these different ethyl groups. Studies with the ternary complex formed by a C2v-symmetrical tetraurea proved that both processes, reorientation of the hydrogen bonds and rotation of the guest, take place independently. Molecular dynamics simulations suggest that the capsule is strongly expanded by the larger tetraethylammonium cation in comparison with benzene as guest. Thus, on average only one N-H...O hydrogen bond is formed per urea function and the interaction energy between the two tetraurea calixarenes is less favorable by about 15 kcal mol(-1). This is overcompensated by an energy gain of about 36 kcal mol(-1) due to cation-pi interactions. These results provide a rationale to understand the high stability of the complex inspite of the mobility of the hydrogen-bonded belt.

Spirodienone derivatives of a spherand-type calixarene.

Oxidation of the spherand-type calixarene 4 with 1 or 2 equiv of phenyltrimethylammonium tribromide/base afforded mono- and bis(spirodienone) derivatives (8b and 9, respectively). The spirodienone groups are derived from the oxidation of two phenols connected by a common methylene group. NOESY data indicated that 9 possesses a "head to tail" arrangement of the spirodienone groups. Oxidation of 4 with 3 equiv of the oxidizing reagent afforded two tris(spirodienone) calixarene derivatives 11 and 10 with C(1) and C(3) symmetries, respectively. The same tris(spirodienone) products were obtained by oxidation of 9 with I(2)/aq KOH. Tris(spirodienone) 11 displayed NOE cross-peaks in the NOESY NMR spectrum consistent with a nonalternant disposition of carbonyl and ether groups. Upon heating 10 and 11 isomerize in the solid state and in solution. The major component in the equilibration mixtures is 11, indicating that this is the thermodynamically more stable tris(spirodienone) isomer.

Stereochemistry of a spherand-type calixarene.

The stereochemistry of the spherand-type calixarene 2a is analyzed in terms of the configuration of the three 2,2'-dihydroxybiphenyl subunits (R or S) and the disposition of the methylene groups (crown or twist). X-ray crystallography indicates that the neutral 2a and its mono- or dianion (in form of the salts 2a(-) x C(5)H(5)NH(+) and 2a(2)(-) x 2Et(3)NH(+)) exist essentially in the same conformation (RRS/SSR-twist). This asymmetric RRS/SSR-twist form is the lowest energy conformer according to molecular mechanics calculations. Low-temperature (1)H NMR data indicate the presence of a major conformer of C(1) symmetry, in agreement with a RRS/SSR-twist form. The lowest energy topomerization pathway mutually exchanges two pairs of methylene protons and is ascribed to an enantiomerization process involving rotation around an Ar-Ar bond.

Hydrogen bonded calixarene capsules kinetically stable in DMSO.

Half-life times up to 4 days in DMSO at room temperature are observed for the decomposition of dimeric capsules of urea substituted calix[4]arenes held together by a combination of hydrogen bonds, mechanical entanglement and cation-pi interactions.

A new mechanism in serine proteases catalysis exhibited by dipeptidyl peptidase IV (DP IV)--Results of PM3 semiempirical thermodynamic studies supported by experimental results.

Herein we present results of semiempirical molecular orbital calculations employing the PM3 molecular model. The compounds studied are related to substrates of the serine protease dipeptidyl peptidase IV (DP IV). Our goal was the thermodynamic characterization of the DP IV-enzyme-catalyzed reaction pathway. A new mechanism of serine proteases catalysis is presented. We found that a tetrahedral intermediate can be stabilized by the formation of an oxazolidine ring with the nonscissile P2-P1 peptide bond. In this way, the negative charge of the tetrahedral intermediate around the scissile bond is transferred to the carbonyl oxygen atom of the preceding peptide bond. This negative charge can be compensated by a proton transfer from the positively charged N-terminus to this oxygen atom. It is shown that the positively charged N-terminus is the driving force in this particular serine protease mechanism of catalysis. The mechanism is supported by observed secondary hydrogen isotope effects on the C alpha proton for an alanine residue in the P2 position. We suggest a trans-cis isomerisation around the P2-P1 peptide bond in the final step of the acylation and cleavage of the substrates. The results obtained by our theoretical calculations are compared with several experimental findings supporting the suggested mechanism.

A model of the active site of dipeptidyl peptidase IV predicted by comparative molecular field analysis and molecular modelling simulations.

A molecular model of the active site of the serine protease dipeptidyl peptidase IV (DPP IV or CD26) has been developed on the basis of comparative molecular field analysis (CoMFA) of competitive inhibitors and by force field calculations. By application of CoMFA experimentally obtained inhibition constants Ki have been successfully predicted. The resulting steric and electrostatic coefficients of CoMFA were used for the development of the molecular model. The main assumptions of the model are the recognition of substrates or inhibitors by the side chains of a tyrosine (S1-position) and a tryptophan residue (S2-position). The model helps us to understand a multitude of experimental data regarding the substrate specificity of this enzyme as well as results obtained by genetic engineering experiments by other authors. General conclusions concerning a new family of serine proteases are drawn and discussed.

HAMOG: molecular graphics program for chemistry, biochemistry, molecular biology and enzyme research.

HAMOG is a computer graphics program written in C for personal computers. Clear menus and a context-sensitive help option make the program easy to operate for occasional users. HAMOG provides a flexible environment for displaying and manipulating molecules and molecular systems. Special functions allow the investigation of structure-activity relationships of biologically active molecules. These include the calculation of molecular electrostatic potentials and fields, the superposition of molecules and the calculation of steric accessibilities. The visualization and manipulation of protein structures immediately readable from the Brookhaven Protein Data Bank files are also possible using HAMOG. The construction of any peptide or protein structure is very simple.