Synthesis, DNA-binding affinities, and binding mode of berberine dimers

Six novel berberine dimers (3a-f) were synthesized in 37-84% yield from the reaction of berberrubine (2) with dihaloalkanes of varying lengths from two to seven carbons. Their interactions with calf thymus (CT) DNA and three double helical oligodeoxynucleotides, d(AAGAATTCTT)2, d(AAGCATGCTT)2, and d(TAAGAATTCTTA)2, were investigated by means of fluorometric titration and ethidium bromide (EB) displacement experiments. Compared with the monomeric parent berberine (1), these dimers' DNA-binding affinities increased up to approximately 100-fold, suggesting a cooperative interaction of the two berberine subunits in the molecules. Furthermore, these dimers linked by different spacers show a prominent structure-activity relationship when bound with oligodeoxynucleotides. The relative binding affinities are in the order of 3b>3a>3c>3d>3e>3f with d(AAGAATTCTT)2 and d(TAAGAATTCTTA)2, and 3b>3c>3a>3d>3e>3f with d(AAGCATGCTT)2. Dimer 3b, linked with a propyl chain, exhibits the highest binding affinity. This suggests that a propyl chain may be the most suitable spacer to bridge the two berberine units for DNA binding. Spectrophotometric titration and competitive EB displacement of berberine (1) and dimer 3b indicate that both berberine and its dimers form intercalating complexes with duplex DNA. A larger redshift, a stronger hypochromic effect, and a much higher EB displacement ratio, observed in 3b, indicate that the dimer is in more intimate contact with DNA than berberine. In addition, no obvious binding of canadine (4), a hydrogenated product of berberine, with CT DNA was observed, suggesting critical roles of the quaternary ammonium cation and planar structure in the DNA-binding of berberine.     

Synthesis and DNA-binding affinities of monomodified berberines

Four new monomodified berberines have been synthesized in moderate to good yields starting from berberine and fully characterized by HRMS and 1H NMR. Spectrometric titration and ethidium bromide displacement experiments indicate that these berberine derivatives, especially the one having primary amino group, strongly bind with calf-thymus DNA, presumably via an intercalation mechanism.     

Synthesis and DNA-binding affinities of protoberberine-based multivalent agents

Three novel berberine derivatives bearing two, three, and four primary amino groups at C(9), respectively, were synthesized and characterized on the basis of 1H- and 13C-NMR, MS, and HR-MS data. Their non-covalent binding with calf thymus (CT) DNA was investigated by means of spectrophotometric titration and ethidium bromide (EB) displacement experiments. The results indicated that these multivalent berberine derivatives exhibited up to 130-fold enhanced binding affinities relative to berberine, and thus, may be exploitable as potent DNA-binding agents.     

Synthesis and DNA-binding ability of C2R-fluoro substituted DC-81 and its dimers

C2R-Fluoro substituted DC-81 and its dimers have been synthesized that exhibit significant DNA-binding ability, particularly the five carbon alkane spacer compound (6c) showed the helix melting temperature (DeltaTm) of 18.8 degrees C after incubation of 36 h at 37 degrees C.     

Synthesis of N-terminally linked protein and peptide dimers by native chemical ligation

Dimerization can be utilized to double the molecular weight of proteins and peptides and potentially increase their avidity of binding to target receptors. These dimerization effects may be utilized to increase in vivo half-lives in a manner similar to PEGylation and may also improve biological activity. In this paper, we report a new strategy for the synthesis of N-terminally linked protein and peptide homodimers utilizing native chemical ligation to conjugate a short dithioester linker to the N-terminal cysteines of protein and peptide monomers to form dimers in a single step. This strategy is general and has been applied to the production of dimers from three recombinantly expressed polypeptides, the IgG binding domain Protein G, an HIV entry inhibitor peptide C37H6, and human interleukin-1 receptor antagonist (IL-1ra). The biological activities of the C37H6 and IL-1ra dimers produced by these methods were retained or even slightly increased when compared to their corresponding monomers.     

DNA-binding affinities and sequence specificities of protoberberine alkaloids and their demethylated derivatives: a comparative study

Berberrubine (1a), jatrorubine (2a), and palmatrubine (3a) have been chemically prepared by partial demethylation of berberine (1), jatrorrhizine (2), and palmatine (3), respectively. Their interactions with calf thymus (CT) DNA, poly(dA-dT)poly(dA-dT), poly(dG-dC)poly(dG-dC), and eight AT-rich 12-mer double-stranded DNAs have been investigated by means of competitive ethidium bromide (EB) displacement experiments. The results showed that DNA-binding affinities of these protoberberine alkaloids have been significantly improved by partial demethylation, and that all of these alkaloids have the preferable binding affinities with AT-rich DNA. Especially, the sequence specificities of DNA-binding of demethylated derivatives 1a, 2a, and 3a had changed to a certain extent when compared with the parent alkaloids 1, 2, and 3, respectively. The binding mode of these alkaloids was further confirmed by UV spectroscopic titration experiments. All the compounds bind to double-stranded DNA most probably via an intercalating mode.     

Synthesis of fluorinated analogues of SJG-136 and their DNA-binding potential

A series of C2-exo-fluorounsaturated pyrrolobenzodiazepines (PBDs) have been synthesized. These C2-exo-fluorounsaturated PBD dimers have exhibited remarkable DNA-binding affinity.     

Amplification of DNA-binding affinities of protoberberine alkaloids by appended polyamines

This communication describes a synthetic approach toward the amplification of the moderate DNA-binding affinities of protoberberine alkaloids. Specifically, three protoberberine derivatives bearing two to six primary amino groups at the 3- and 9-positions of protoberberine were synthesized and characterized by NMR ((1)H and (13)C) and HRMS. Studies on their affinities toward calf thymus (CT) DNA by ethidium bromide (EB) displacement and spectrophotometric titration experiments indicate that these polyamino protoberberines show more than 10(3)-fold enhanced DNA-binding affinities relative to palmatine and thus are exploitable as strong DNA-binders.     

DNA gyrase-catalyzed decatenation of multiply linked DNA dimers

One possible intermediate during the terminal stages of the replication of a closed circular DNA is a catenated DNA dimer of the two completed daughter molecules. The two monomer DNA rings in these DNA dimers can be linked as many as 20-30 times. In Escherichia coli, DNA gyrase could act on these catenated dimers to eliminate the linkages between the daughter duplexes, yielding the final monomer product. In this report, this reaction has been studied biochemically. The in vitro pBR322 DNA replication system (Minden, J., and Marians, K. J. (1985) J. Biol. Chem. 260, 9316-9325) was used to manufacture large amounts of multiply linked catenated DNA dimers for use as a substrate for DNA gyrase-catalyzed decatenation. Studies presented here demonstrate that this decatenation reaction is more efficient with supercoiled as opposed to relaxed DNA dimers, proceeds in a distributive fashion, is inhibited by moderate amounts of salt (80 mM KCl), and is stimulated by the E. coli protein HU.     

Synthesis and characterization of procyanidin dimers as their peracetates and octamethyl ether diacetates

Condensation of (2R,3S,4R or S)-leucocyanidin or the 5,7,3′,4′-tetramethyl ether of (2R,3^R,4S)-leucocyanidin with flavan-3-ols yielded dimeric flavanoids which were converted to their octamethyl ether diacetates, or the deca-acetates for the 2,3-trans-procyanadin series. Comparison is made of the ¹H NMR spectra of the deca-acetate and octamethyl ether diacetate derivatives which lead to useful diagnostic shift parameters characteristic of their structures. Condensations afforded a novel biflavanoid with a 3,4-cis-configuration and a triflavanoid of ‘mixed’ stereochemistry.     

Synthesis of methylphenidate analogues and their binding affinities at dopamine and serotonin transport sites

The rhodium(II)-catalyzed intermolecular C-H insertion of methyl aryldiazoacetates with either N-Boc-piperidine or N-Boc-pyrrolidine followed by deprotection with trifluoroacetic acid is a very direct method for the synthesis of methylphenidate analogues. By using either dirhodium tetraacetate or dirhodium tetraprolinate derivatives as catalyst, either the racemic or enantioenriched methylphenidate analogues can be prepared. The binding affinities of the methylphenidate analogues to both the dopamine and the serotonin transporters are described. The most notable compounds are the erythro-(2-naphthyl) analogues which display high binding affinity and selectivity for the serotonin transporter.     

DNA-binding and oxidative properties of cationic phthalocyanines and their dimeric complexes with anionic phthalocyanines covalently linked to oligonucleotides

Design of chemically modified oligonucleotides for regulation of gene expression has attracted considerable attention over the past decades. One actively pursued approach involves antisense or antigene oligonucleotide constructs carrying reactive groups, many of these based on transition metal complexes. The complexes of Fe(II) and Co(II) with phthalocyanines are extremely good catalysts of oxidation of organic compounds with molecular oxygen and hydrogen peroxide. The binding of positively charged Fe(II) and Co(II) phthalocyanines with single- and double-stranded DNA was investigated. It was shown that these phthalocyanines interact with nucleic acids through an outside binding mode. The site-directed modification of single-stranded DNA by O2 and H2O2 in the presence of dimeric complexes of negatively and positively charged Fe(II) and Co(II) phthalocyanines was investigated. These complexes were formed directly on single-stranded DNA through interaction between negatively charged phthalocyanine in conjugate and positively charged phthalocyanine in solution. The resulting oppositely charged phthalocyanine complexes showed significant increase of catalytic activity compared with monomeric forms of phthalocyanines Fe(II) and Co(II). These complexes catalyzed the DNA oxidation with high efficacy and led to direct DNA strand cleavage. It was determined that oxidation of DNA by molecular oxygen catalyzed by complex of Fe(II)-phthalocyanines proceeds with higher rate than in the case of Co(II)-phthalocyanines but the latter led to a greater extent of target DNA modification.     

Synthesis of urease hybrid nanoflowers and their enhanced catalytic properties

Increasing numbers of materials have been extensively used as platforms for enzyme immobilization to enhance catalytic activity and stability. Although stability of enzyme was accomplished with immobilization approaches, activity of the most of the enzymes was declined after immobilization. Herein, we synthesize the flower shaped-hybrid nanomaterials called hybrid nanoflower (HNF) consisting of urease enzyme and copper ions (Cu²⁺) and report a mechanistic elucidation of enhancement in both activity and stability of the HNF. We demonstrated how experimental factors influence morphology of the HNF. We proved that the HNF (synthesized from 0.02 mg mL⁻¹ urease in 10 mM PBS (pH 7.4) at +4 °C) exhibited the highest catalytic activity of ∼2000% and ∼4000% when stored at +4 °C and RT, respectively compared to free urease. The highest stability was also achieved by this HNF by maintaining 96.3% and 90.28% of its initial activity within storage of 30 days at +4 °C and RT, respectively. This dramatically enhanced activity is attributed to high surface area, nanoscale-entrapped urease and favorable urease conformation of the HNF. The exceptional catalytic activity and stability properties of HNF can be taken advantage of to use it in fields of biomedicine and chemistry.     

Synthesis and DNA-binding affinity of A-C8/C-C2 alkoxyamido-linked pyrrolo[2,1-c][1,4]benzodiazepine dimers

The synthesis of new A-C8/C-C2 alkoxyamido-linked pyrrolo[2,1-c][1,4]-benzodiazepine dimers have been described in this report. These dimers exhibit significant DNA-binding ability with moderate anticancer activity.     

Synthesis of di- and tri-substituted adenosine derivatives and their affinities at human adenosine receptor subtypes

The synthesis of 2-(hex-1-ynyl)adenosine derivatives substituted at the N6- and/or 5'-position was carried out on the basis that 2-(hex-1-ynyl)adenosine-5'-N-ethyluronamide (HENECA, 2) showed good affinity and different degree of selectivity for rat adenosine receptors. All new compounds were tested in radioligand binding and adenylyl cyclase assays with recently cloned human A1, A2A, A2B, and A3 adenosine receptors.     

Synthesis and evaluation of daunorubicin-paclitaxel dimers

Bifunctional, heterodimeric compounds were synthesized to test their ability to create polyvalent arrays between DNA and microtubules in cells. Each dimer was examined for the capacity to bind to microtubules and for cytotoxicity against MES-SA and MES-SA/Dx5 cell lines.     

Crowned dopa's,their dimers,cyclodimers and polymers: Synthesis and cation complexation

Optically pure protected L -[3,4-(1,4,7,10,13-pentaoxatridecamethylene) phenyl] alanine, its dipeptide, diketopiperazine and homopolymer, protected L -[3,4-(1,4,7,10,13,16-hexaoxahexadecamethylene) phenyl] alanine and its polymer have been synthesized and characterized. These crown ether derivatives complex the potassium and ammonium cations as well as protonated leucine and glycine in tetrahydrofuran and methanol. They are also phase-transfer agents. The cooperativity of the crown units was studied in detail for the dimeric ligands.     

Synthesis of neurotensin(9-13) analogues exhibiting enhanced human neurotensin receptor binding affinities

Recent evidence is consistent with neurotensin (NT)(8-13) adopting a Type I beta-turn conformation while binding the NT receptor, which would place the cationic side-chains of Arg(8) and Arg(9) in close proximity. This was the basis for the design, synthesis and analysis of truncated NT(9-13) analogues 1-5 with dicationic position 9 side-chains to emulate the functions of the 8 and 9 side-chains of NT(8-13).     

Synthesis and binding affinities of fluoroalkylated raloxifenes

Three fluoroalkylated derivatives (1-3) of the selective estrogen receptor modulator (SERM), raloxifene, have been synthesized. The key step in the synthesis is the C-C bond formation of benzo[b]thiophene and a substituted phenyl group (ring C) using a Stille reaction. The in vitro binding affinities of the substituted raloxifenes 1-3 are 45, 60, 89%, respectively, relative to the affinity of estradiol, which is higher than the affinity of raloxifene itself (25%). When labeled with the positron-emitting radionuclide, these compounds might be useful as PET imaging agents for estrogen receptor-positive breast tumors.