Enthalpy-driven nuclease-like activity and mechanism of peptide-chlorambucil conjugates.

We report the results of attaching the anticancer drug chlorambucil (CLB) to two high-affinity DNA binding peptides: Met-Hyp-Arg-Lys-(Py)4-Lys-Arg-NH2 (HyM-10) and Gln-Hyp-Arg-Lys-(Py)4-Lys-Arg-NH2 (HyQ-10). These CLB-peptide conjugates cleave DNA very effectively and sequence-selectively without the use of chemicals, heat, or UV irradiation. Polyacrylamide gel electrophoresis identifies the sites where CLB-HyM-10 and CLB-HyQ-10 attack a complementary pair of 5'-(32)P-labeled duplexes derived from pBR322 in the absence of piperidine or other chemical additives.

Energetic studies on DNA-peptide interaction in relation to the enthalpy-entropy compensation paradox.

This study aims to interpret the energetic basis of complex DNA-peptide interactions according to a novel allosteric interaction network approach. In common with other designed peptides, five new conjugates incorporating the XPRK or XHypRK motif (Hyp = hydroxyproline) attached to a N-methylpyrrole (Py) tract with a basic tail have been found to display cooperative binding to DNA involving multiple monodentate as well as interstrand bidentate interactions. Using quantitative DNase I footprinting it appears that allosteric communication via cooperative binding to multiple sites on complementary DNA strands corresponds to two different types of DNA-peptide interaction network.

Novel DNA-peptide interaction networks.

Allostery in the binding of peptides to DNA has been studied by quantitative DNase I footprinting using four newly designed peptides containing the XP(Hyp)RK motif and N-methylpyrrole (Py) moieties. Apparent binding constants in the micromolar range as well as Hill coefficients were determined for each peptide. The results, together with previous studies on five other peptides support the proposal that interaction network cooperativity is highly preferred in DNA-peptide interactions that involve multiple recognition sites.

Detection of multiple network-based allosteric interactions between peptides and arrays of DNA binding sites.

Quantitative DNase I footprinting shows that three designed peptides containing N-methylpyrrole (Py) moieties display different types of network-based allosteric communication in binding to DNA: circuit type, incomplete-circuit type, and non-circuit type characterized by interstrand bidentate interactions. Positive cooperative binding of all three peptides to individual DNA binding sites is commonly observed. CD spectral characterization of the interaction between peptides and model undecanucleotide duplexes is consistent with the footprinting results and supports the allosteric model.

Oxidation of catechin and rutin by pentaammineruthenium(III) complexes.

The reaction of catechin and rutin with Ru(NH(3))(5)L(3+) (L = N-methylpyrazinium (pzCH(3)(+)), pyrazine (pz), and isonicotinamide (isn)) complexes underwent a two-electron oxidation on the catechol ring (B ring) with the formation of quinone products. The kinetics of the oxidation, carried out at [H(+)] = 0.01-1.

Unusually strong positive cooperativity in binding of peptides to latent membrane protein-1 DNA fragments of the Epstein-Barr viral gene.

The DNA-binding preferences of two oligopeptide amides, (His-Pro-Arg-Lys)(3)NH(2) (HR-12) and (Ser-Pro-Arg-Lys)(3)NH(2) (SP-12), have been examined by quantitative DNase I footprinting studies. Two different DNA fragments were investigated: a pair of 5'-(32)P-labeled duplexes from pBR322 with one or other of the complementary strands labeled and a corresponding pair of 5'-(32)P-labeled duplexes representing fragments of the latent membrane protein (LMP-1) gene from a pathogenic Epstein-Barr virus variant derived from nasopharyngeal carcinoma. The major objective was to examine molecular recognition and cooperative features associated with sequence-selective binding of synthetic peptides to the LMP-1 fragments.

Semiquinone footprinting.

A novel DNA footprinting method employing strong semiquinone radical species generated from a dipeptide-hydroquinone conjugate is described.

DNA sequence-specific recognition of peptides incorporating the HPRK and polyamide motifs.

Three peptide amides, HPRK(Py)(4)HPRK-NH(2) (PyH-12), HPRK(Py)(3)HPRK-NH(2) (PyH-11) and HPRK(Py)(2)HPRK-NH(2) (PyH-10), incorporating two HPRK motifs and various 4-amino-1-methylpyrrole-2-carboxylic acid residues (Py) were synthesized by solid-phase peptide methodology. The binding of these three peptides to a 5'-32P-labeled 158-mer DNA duplex (Watson fragment) and to a 5'-32P-labeled 135-mer DNA duplex (complementary Crick fragment) was investigated by quantitative DNase I footprinting. On the 158-mer Watson strand, the most distinctive DNase I blockages seen with all three peptides occur around positions 105-112 and 76-79, corresponding to the sequences 5'-GAGAAAAT-3' and 5'-CGGT-3', respectively.

Preferential binding to DNA sequences of peptides related to a novel XPRK motif.

Two dodecapeptide amines: (WPRK)(3)NH(2)[WR-12] and (YPRK)(3)NH(2)[YR-12], and a 30-mer polypeptide amide (SP-30) were synthesized by solid-phase peptide methodology. DNase I footprinting studies on a 117-mer DNA showed that WR-12 and YR-12 bind selectively to DNA sequences in a manner similar to SP-30 which has a repeating SPK(R)K sequence. The most distinctive blockages seen with all three peptides occur at positions 26-30, 21-24 and 38-45 around sequences 5'-GAATT-3', 5'-TAAT-3' and 5'-AAAACGAC-3', respectively.

Sequence-specific DNA cleavage by dipeptides disubstituted with chlorambucil and 2,6-dimethoxyhydroquinone-3-mercaptoacetic acid.

Two dipeptides, each containing a lysyl residue, were disubstituted with chlorambucil (CLB) and 2,6-dimethoxyhydroquinone-3-mercaptoacetic acid (DMQ-MA): DMQ-MA-Lys(CLB)-Gly-NH2 (DM-KCG) and DMQ-MA-beta-Ala-Lys(CLB)-NH2 (DM-BKC). These peptide-drug conjugates were designed to investigate sequence-specificity of DNA cleavage directed by the proximity effect of the DNA cleavage chromophore (DMQ-MA) situated close to the alkylating agent (CLB) inside a dipeptide moiety. Agarose electrophoresis studies showed that DM-KCG and DM-BKC possess significant DNA nicking activity toward supercoiled DNA whereas CLB and its dipeptide conjugate Boc-Lys(CLB)-Gly-NH2 display little DNA nicking activity.

Oxidative dehydrogenation on the alpha-carbon of 4-pyridylacetonitrile complexes of pentaammineruthenium(II).

The oxidation of Ru(NH(3))(5)NCCH(2)py(2+) in 0.10 M HCl turns the solution from yellow to greenish blue with an absorption at lambda = 791 nm. The absorbance reaches its maximum value when the complex undergoes a two-electron oxidation.

Synthesis and DNA nicking studies of a novel cyclic peptide: cyclo[Lys-Trp-Lys-Ahx-].

Two novel cyclic tetrapeptides: cyclo[Lys-Tyr-Lys-Ahx-] 7a and cyclo[Lys-Trp-Lys-Ahx-] 7b were synthesized by coupling protected amino acid in solution and the subsequent cyclization effected by the pentafluorophenyl ester method as described in previous papers. These cyclic peptides were designed and synthesized to study their interaction with DNA, based on previous reports that linear peptides Lys-Tyr-Lys and Lys-Trp-Lys could bind to various forms of DNA and cleaved supercoiled DNA at apurinic sites. Ethidium bromide displacement assay showed that the apparent DNA binding constant of linear Lys-Tyr-Lys and cyclic peptide 7a are far below 1 x 10(3) M(-1), whereas those of cyclic peptide 7b and linear Lys-Trp-Lys are 1.

Discovery of a potent, non-triketone type inhibitor of 4-hydroxyphenylpyruvate dioxygenase.

3-Cyclopropanecarbonyloxy-2-cyclohexen-1-one has been found to be a new, potent, low molecular weight non-triketone type inhibitor of 4-hydroxyphenylpyruvate dioxygenase with IC50 value of 30 nM. Preliminary studies suggest that the two carbonyl groups present in the compound are crucial for the inhibition activity.

SAR studies of 2-o-substituted-benzoyl- and 2-alkanoyl-cyclohexane-1,3-diones as inhibitors of 4-hydroxyphenylpyruvate dioxygenase.

Inhibition studies of 4-hydroxyphenylpyruvate dioxygenase (HPPD) with various synthesized 2-o-substituted-benzoyl- and 2-alkanoyl-cyclohexane-1,3-diones suggest that the presence of a strongly electronegative group at the ortho position and the conformation of the benzene ring moiety on the benzoylcyclohexane-1,3-dione inhibitors are crucial for potent HPPD inhibition.

Design and synthesis of 3-fluoro-2-oxo-3-phenylpropionic acid derivatives as potent inhibitors of 4-hydroxyphenylpyruvate dioxygenase from pig liver.

Several rationally designed analogs of 3-fluoro-2-oxo-3-phenylpropionic acid were chemically synthesized, and the reactions of the hydrate form of these compounds with 4-hydroxyphenylpyruvate dioxygenase from pig liver as inhibitors were examined. Compounds 14a and 14b were found to be potent competitive inhibitors of the enzyme with Ki values of 10 and 22 microM, respectively.

Inhibition of 4-hydroxyphenylpyruvate dioxygenase by sethoxydim, a potent inhibitor of acetyl-coenzyme A carboxylase.

Sethoxydim, a commercially available cyclohexanedione class herbicide by targeting the enzymatic activity of acetyl-coenzyme A carboxylase, has been found to moderately inhibit the activity of 4-hydroxyphenylpyruvate dioxygenase, a key enzyme in the biosynthesis of plastoquinones and tocopherols in plants.

Synthesis, DNA cleavage and cytotoxicity of some novel cyclic peptide-2,6-dimethoxyhydroquinone-3-mercaptoacetic acid conjugates containing D-amino acids.

This paper reports an ongoing study of the use of small-ring-size cyclic peptides as carriers of a potential antitumor agent: 2,6-dimethoxyhydroquinone-3-mercaptoacetic acid (DMQ-MA). Three new cyclic tripeptide-DMQ-MA conjugates--cyclo[D-Val-Lys(DMQ-MA)-gamma-aminobutyric acid (GABA)-], cyclo[Val-Lys(DMQ-MA)-GABA-] and cyclo[D-Val-D-Lys(DMQ-MA)-GABA-]--were synthesized. The isomeric cyclic tripeptide-DMQ-MA conjugates were designed and synthesized to study the effect of stereoisomerism of the conjugates on cytotoxicity.

Kinetic Studies of the Reactions of Pentacyanoferrate(II) Complexes with Peroxydisulfate.

Reactions of Fe(CN)(5)L(3-) (L = 4-aminopyridine (4-ampy), pyridine (py), 4,4'-bipyridine (4,4'-bpy), and pyrazine (pz)) with peroxydisulfate, Fe(CN)(5)L(3-) + S(2)O(8)(2-) right harpoon over left harpoon Fe(CN)(5)L(2-) + SO(4)(-) + SO(4)(2-), have been found to follow an outer-sphere electron transfer mechanism. The specific rate constants of oxidation are 1.45 +/- 0.

Synthesis, DNA binding, and sequence specificity of DNA alkylation by some novel cyclic peptide-chlorambucil conjugates.

In an effort to investigate the potential of cyclic peptides as carriers for cytotoxic agents, we synthesized four cyclic peptide-chlorambucil conjugates: cyclo[Lys(CHB)-Lys(CHB)-Gaba-] (peptide Y), cyclo[Lys(CHB)-Gly-Lys(CHB)-Gaba-] (peptide A), cyclo[Lys(CHB)-beta-Ala-Lys(CHB)-Gaba-] (peptide B) and cyclo[Lys(CHB)-Gaba-Lys(CHB)-Gaba-] (peptide C). The cyclic peptides were synthesized by coupling protected amino acid residues in solution and the subsequent cyclization was performed by the pentafluorophenyl ester method as described previously (Sheh et al., 1990, 1993a,b).

Studies of the synthesis, immunology, and cytotoxicity of a cyclic octapeptide corresponding to TNF-alpha-(59-66).

In an attempt to investigate possible binding domains of the tumor necrosis factors (TNF), we have previously synthesized a cyclic hexapeptide corresponding to murine TNF-(127-132) (cTNF-1). In this report, we describe the synthesis and biological activity of another cyclic octapeptide corresponding to human TNF-alpha-(59-66) (cTNF-2). The design of these cyclic peptides is based on their high sequence homology with corresponding fragments of human TNF-alpha or TNF-beta.

Synthesis and cytotoxicity studies of novel cyclic peptide-2,6-dimethoxyhydroquinone-3-mercaptoacetic acid conjugates.

In an effort to investigate the use of small-ring-size cyclic peptides as carriers of new antitumor agents, we synthesized three cyclic tripeptide-cytotoxic agent conjugates. The cytotoxic agent conjugated to the epsilon-amino group of the lysyl residue of the cyclic peptides is 2,6-dimethoxyhydroquinone-3-mercaptoacetic acid (DMQ-MA), (Sheh et al., 1992).

Cytotoxicity studies on some novel 2,6-dimethoxyhydroquinone derivatives.

Six synthetic 2,6-dimethoxyhydroquinone derivatives were shown to have different degrees of cytotoxicity to two human tumor cell lines (KB and PC-9) under the synergistic activation of L-ascorbic acid. Two representative compounds displayed very low time-schedule-independent index, showing that the cytotoxic action is independent of time of drug treatment. The addition of catalase produced a significant inhibitory effect on the cytotoxicity of two representative compounds, indicating that the cytotoxic action is mediated by the generation of H2O2, which may yield hydroxyl radicals via various mechanisms.