Facile synthesis of benzobisimidazole and bibenzimidazole-based bisnitriles as potential precursors for DNA minor groove binders

The synthesis of bisnitrile derivatives of benzobisimidazole and bibenzimidazole in a good yield is described in detail for the first time. Nucleophilic substitution of 1,5-difluoro-2,4-dinitrobenzene using different amines produced the intermediate diamines that were reduced using sodium borohydride/Pd(C) to produce the tetramines. These tetramines were allowed to couple with different aldehydes to produce the final benzimidazoles. In a different investigation, these bisnitrile derivatives will be used to make benzimidazole diamidines that could be used as potential mixed sequence minor groove binders.     

Water-mediated binding of agents that target the DNA minor groove

Small molecule complexes with DNA that incorporate linking water molecules are rare, and the DB921-DNA complex has provided a unique and well-defined system for analysis of water-mediated binding in the context of a DNA complex. DB921 has a benzimidazole-biphenyl system with terminal amidines that results in a linear conformation that does not possess the appropriate radius of curvature to match the minor groove shape and represents a new paradigm that does not fit the classical model of minor groove interactions. To better understand the role of the bound water molecule observed in the X-ray crystal structure of the DB921 complex, synthetic modifications have been made in the DB921 structure, and the interactions of the new compounds with DNA AT sites have been evaluated with an array of methods, including DNase I footprinting, biosensor-surface plasmon resonance, isothermal titration microcalorimetry, and circular dichroism. The interaction of a key compound, which has the amidine at the phenyl shifted from the para position in DB921 to the meta position, has also been examined by X-ray crystallography. The detailed structural, thermodynamic, and kinetic results provide valuable new information for incorporation of water molecules in the design of new lead scaffolds for targeting DNA in chemical biology and therapeutic applications.     

A new method for the determination of the relative affinity of a ligand against various DNA sequences by electrospray ionization mass spectrometry. Application to a polyamide minor groove binder

A new method for the determination of the relative affinity of a ligand against various dsDNA sequences is presented by using electrospray ionization time‐of‐flight mass spectrometry (ESI‐QTOF) mass spectrometry. The principle is described here through the complexation of double‐stranded DNA by a polyamide ligand including twelve N‐methylpyrrole rings. However this method could be applied to other ligands especially when dissociation constants (K_d) are in nanomolar range. This method does not require knowing the ligand concentration accurately. It allows determination of the relative affinity of a ligand against various dsDNA sequences for 1 : 1 complex stoichiometries in a quick manner without labeling. Copyright © 2009 John Wiley & Sons, Ltd.     

Photoactive Ru(II) -polypyridyl complexes that display sequence selectivity and high-affinity binding to duplex DNA through groove binding

The duplex-DNA binding properties of a nonintercalating polypyridyl ruthenium(II) complex that incorporates a linear extended ligand with a catechol moiety has been probed with a variety of photo- and biophysical techniques. These studies reveal that the complex groove binds to DNA sequences biphasically, and displays binding constants equivalent to those of high-affinity metallointercalators. The complex also displays preferential binding to AT-rich sequences. Changes in the structure of the coordinated catechol ligand and the incorporation of intercalating ancillary ligands into the complex were found to modulate both the optical-binding response and binding parameters of the system, which indicates that the catechol moiety plays a crucial role in the observed enhancement to binding affinities.     

Fluorous synthesis of minor groove binding agents related to distamycin

Minor groove binding agents related to distamycin have been shown to target specific DNA sequences with high affinity. We report a new method for the preparation of these agents using fluorous synthesis in which the fluorous tag is located on what will become the cationic tail of the molecule. We demonstrate that fluorous synthesis yields both simple and complex polyamides in good yields and in high purity.     

Energetics of ligand binding to the DNA minor groove

In the present work the decomposition of the total Gibbs free energy of ligand-DNA binding onto various physical terms was accomplished for the group of nine DNA minor groove binders (MGB ligands) differing in both structure and charge state. The decomposition protocol includes the analysis of the most complete set of physical factors known to contribute to the complexation process, viz. the net change in the number of degrees of freedom (translational, rotational, vibrations of the chemical bonds and vibrations of the ligand as a whole within the binding site), the conformational entropy, van der Waals, electrostatic and hydrophobic interactions, the polyelectrolyte contribution and the net effect of changes in the number of hydrogen bonds. All of these processes are further decomposed into the interaction with the solvent and the interaction of the ligand with DNA. The principal outcome of the decomposition is the possibility of performing a comparative analysis of the energetic contribution of various physical terms and provide an answer to the question concerning what physical factors stabilize or destabilize the complexes of MGB ligands with DNA.     

Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: A molecular mechanics investigation

On the basis of theoretical computations, we have recently synthesised [Perrée-Fauvet, M. and Gresh, N., Tetrahedron Lett., 36 (1995) 4227] a bisarginyl conjugate of a tricationic porphyrin (BAP), designed to target, in the major groove of DNA, the d(GGC GCC)2 sequence which is part of the primary binding site of the HIV-1 retrovirus site [Wain-Hobson, S. et al., Cell, 40 (1985) 9]. In the theoretical model, the chromophore intercalates at the central d(CpG)2 step and each of the arginyl arms targets O6/N7belonging to guanine bases flanking the intercalation site. Recent IR and UV-visible spectroscopic studies have confirmed the essential features of these theoretical predictions [Mohammadi, S. et al., Biochemistry, 37 (1998) 6165]. In the present study, we compare the energies of competing intercalation modes of BAP to several double-stranded oligonucleotides, according to whether one, two or three N- methylpyridinium rings project into the major groove. Correspondingly, three minor groove binding modes were considered, the arginyl arms now targeting N3, O2 sites belonging to the purine or pyrimidine bases flanking the intercalation site. This investigation has shown that: (i) in both the major and minor grooves, the best-bound complexes have the three N-methylpyridinium rings in the groove opposite to that of the phenyl group bearing the arginyl arms; (ii) major groove binding is preferred over minor groove binding by a significant energy (29 kcal/mol); and (iii) the best-bound sequence in the major groove is d(GGC GCC)2 with two successive guanines upstream from the intercalation. On the other hand, due to the flexibility of the arginyl arms, other GC-rich sequences have close binding energies, two of them being less stable than it by less than 8 kcal/mol. These results serve as the basis for the design of derivatives of BAP with enhanced sequence selectivities in the major groove.     

Synthesis and in vitro biological evaluation of novel 2-aminoimidazolone derivatives as anti-tumor agents

Novel 2-aminoimidazolone derivatives were synthesized.Most compounds displayed strong anticancer activities against human carcinoma cells in vitro.Compounds 8a,8b and 8j exhibited optimal activity superior to 5-FU in most cancer cells tested.Especially,the lC₅₀s of 8b（12.6-21.5μmol/L） against five tumor cells were 1 -4 fold less than those of 5-FU（18.4-56.1μmol/L） in vitro.Furthermore,comp以ound 8b could induce SMMC-7721 cell apoptosis in a dose-dependent manner.Therefore,our novel findings may provide a new framework for the design of new 2-aminoimidazolone derivatives for the treatment of cancer.     

2-巯基苯并咪唑衍生物的设计、合成及抗肿瘤活性研究

为了从苯并咪唑类衍生物中寻找新的活性化合物,以溴乙酸作为起始原料,设计合成了17个2-巯基苯并咪唑衍生物4a～4q。采用噻唑蓝(MTT)法测试了目标化合物对人宫颈癌细胞(He La)、人乳腺癌细胞(MCF-7)、人肝癌细胞(HepG2)、人非小细胞肺癌细胞(A549)的增殖抑制活性。结果显示,大部分化合物具有较好的抗肿瘤活性,其中,((1H-苯并[d]咪唑-2-基)硫基)-1-(4-二苯甲基哌嗪-1-基)乙烷-1-酮(4l)对HepG2细胞的抑制活性最好,IC_(50)值为12. 62±0. 78μmol/L,接近于对照药品吉非替尼(9. 72±0. 38μmol/L)。此外,利用分子对接方法对目标化合物的构效关系进行了讨论。     

U-pin polyamide motif for recognition of the DNA minor groove

DNA-binding hairpin pyrrole-imidazole polyamides with gamma-aminobutyric acid as a turn-forming residue tolerate A.T or T.A base pairs under the turn. U-pins-polyamides with a different turn-have been synthesized and their DNA binding properties were studied. The two turn-forming residues are connected via the ring nitrogens using variable length aliphatic linkers ((CH(2))(n), n=3-6). Through optimization of the linker length and the substituents at the 2-position of the pyrrole residue on the U-turn, polyamides with G.C/C.G tolerant turns could be found, which bind to DNA in a predictable manner.     

Conjugates between minor groove binders and Zn(II)-tach complexes: Synthesis,characterization, and interaction with plasmid DNA

A new family of conjugates between a Zn(II)-tach complex and (indole)₂ or benzofuran-indole amide minor groove binders connected through alkyl or oxyethyl linkers of different lengths has been prepared. The conjugates bind strongly to DNA. However, the complexation to DNA to promote the Zn(II) catalyzed hydrolytic cleavage of the DNA results instead in its inhibition. This inhibition effect has been confirmed also using Cu(II). Modeling studies suggest that in the most stable complex conformation, the minor groove binder and the linker lie in the minor groove hampering the interaction between the metal complex and the phosphate backbone of DNA. Therefore, the linear arrangement of minor groove binder-linker-metal complex appears to be effective to ensure tight binding but unproductive from a hydrolytic point of view.     

In silico footprinting of ligands binding to the minor groove of DNA

The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by "in silico footprinting". Any potential ligand can be docked in the minor groove and then moved along it using simple simulation techniques. By applying a simple scoring function to the trajectory after energy minimization, the preferred binding site can be identified. We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting.     

电化学方法研究DNA与不可逆靶向分子的相互作用

用循环伏安法、示差脉冲伏安法、计时库仑法、整体电解法和扫描电化学显微镜研究了具有抗癌活性的双苯并咪唑衍生物(BBID)不可逆电化学行为及BBID与DNA的相互作用,推导了适用于研究不可逆电活性分子与DNA相互作用的电化学公式,该公式可以简便、快速地测定靶向分子与DNA的结合常数和结合位点数。实验发现,BBID与天然鱼精DNA的结合以结构作用为主,同时,由于求得的结合常数(K)值较大,因此其中可能还存在序列作用的因素。结合方式主要为包含4个碱基对的紧密小沟结合。     

Fluorescence‐Labeled Bis‐benzamidines as Fluorogenic DNA Minor‐Groove Binders: Photophysics and Binding Dynamics

In recent decades there has been great interest in the design of highly sensitive sequence‐specific DNA binders. The eligibility of the binder depends on the magnitude of the fluorescence increase upon binding, related to its photophysics, and on its affinity and specificity, which is, in turn, determined by the dynamics of the binding process. Therefore, progress in the design of DNA binders requires both thorough photophysical studies and precise determination of the association and dissociation rate constants involved. We have studied two bis‐benzamidine (BBA) derivatives labeled by linkers of various lengths with the dye Oregon Green (OG). These fluorogenic binders show a dramatic fluorescence enhancement upon binding to the minor groove of double‐stranded (ds) DNA, as well as significant improvement in their sequence specificity versus the parent BBA, although with decreased affinity constants. Detailed photophysical analysis shows that static and dynamic quenching of the OG fluorescence by BBA through photoinduced electron transfer is suppressed upon insertion of BBA into the minor groove of DNA. Fluorescence correlation spectroscopy yields precise dynamic rate constants that prove that the association process of these fluorogenic binders to dsDNA is very similar to that of BBA alone and that their lower affinity is mainly a consequence of their weaker attachment to the minor groove and the resultant faster dissociation process. The conclusions of this study will allow us to go one step further in the design of new DNA binders with tunable fluorescence and binding properties.     

Sequence selective recognition in the minor groove of dsDNA by pyrrole,imidazole-substituted bis-benzimidazole conjugates

A series of pyrrole, imidazole-substituted bis-benzimidazole conjugates, Py-Py-Im-gamma-biBenz, Py-Py-gamma-biBenz, Py-Im-gamma-biBenz, and Im-Py-gamma-biBenz (1-4), were prepared in an attempt to target dsDNA sequences possessing both A/T and G/C bps. The dsDNA interactions and sequence specificity of the conjugates have been characterized via spectrofluorometric titrations and thermal melting studies. All conjugates form 1:1 complexes with dsDNA at subnanomolar concentrations. The Im moiety selectively recognizes a G/C bp embedded in the A/T-rich binding site. This represents the first clear example of sequence selective recognition in a 1:1 motif.(1) The equilibrium association constant (K(1)) for complexation of a specific nine-bp dsDNA site, 5'-gcggTATGAAATTcgacg-3', by conjugate 1 is approximately 2.6 x 10(9) M(-1). Displacement of the G/C position or G/C-->A/T substitution within the nine-bp site decreases the K(1) by approximately 8-fold, whereas two continuous G/C bps decrease the K(1) by approximately 50-fold magnitude. The K(1) values for seven-bp dsDNA, 5'-gcggtaTGAAATTcgacg-3' and 5'-gcggtaCAAAATTcgacg-3', binding sites by conjugates Py-Im-gamma-biBenz (3) and Im-Py-gamma-biBenz (4) are approximately 2.3 x 10(9) and approximately 1.2 x 10(9) M(-1), respectively. However, the conjugates with no Im moiety, Py-Py-gamma-biBenz (2) and Py-Py-Py-gamma-biBenz (5 and 6), are specific for seven- to nine-bp A/T-rich sites and single A/T-->G/C bp substitution within the binding site decreases the K(1) values by 1-2 orders of magnitude.     

A convenient and efficient one-pot method for the synthesis of novel acridine-calix[4]arene derivatives as new DNA binding agents via multicomponent reaction

A new approach is applied for the synthesis of novel acridine-calix[4]arene derivatives via a multicomponent reaction. These compounds have been characterised by ¹H NMR, ¹³C NMR and HR-MS. Our binding studies between acridine-functionalised calix[4]arenes and calf thymus DNA (CT-DNA) via fluorescence titration show that these compounds have a good affinity to CT-DNA.     

Competitive Na(+) and Rb(+) binding in the minor groove of DNA

Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. Here, we present new (23)Na and (87)Rb magnetic relaxation dispersion (MRD) data that demonstrate competitive and long-lived binding of Na(+) and Rb(+) ions in the minor groove of the B-DNA duplex [d(CGCGAATTCGCG)](2). The Na(+)/Rb(+) selectivity of the minor groove is found to be weak, consistent with local structural flexibility. The ion occupancies derived from the MRD data are substantially higher than previously reported, suggesting that groove-bound ions significantly influence the energetics and structural polymorphism of DNA in vivo. For example, in the presence of 0.20 M Na(+) and 0.56 M Rb(+) at 4 degrees C, the ApT site in the minor groove is occupied by a Rb(+) ion, a Na(+) ion, or a water molecule 40, 10, and 50% of the time, respectively. In the absence of Rb(+), the Na(+) occupancy increases to 50%. At 4 degrees C, the mean residence time of groove-bound ions is 0.2 +/- 0.1 micros for Rb(+) and 10 ns to 100 micros for Na(+). A shorter correlation time of 2 ns is attributed to counterions bridging cross-strand phosphate groups.     

The Thiophene “Sigma‐Hole” as a Concept for Preorganized,Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove

In spite of its importance in cell function, targeting DNA is under‐represented in the design of small molecules. A barrier to progress in this area is the lack of a variety of modules that recognize G ? C base pairs (bp) in DNA sequences. To overcome this barrier, an entirely new design concept for modules that can bind to mixed G ? C and A ? T sequences of DNA is reported herein. Because of their successes in biological applications, minor‐groove‐binding heterocyclic cations were selected as the platform for design. Binding to A ? T sequences requires hydrogen‐bond donors whereas recognition of the G‐NH₂ requires an acceptor. The concept that we report herein uses pre‐organized N‐methylbenzimidazole (N‐MeBI) thiophene modules for selective binding with mixed bp DNA sequences. The interaction between the thiophene sigma hole (positive electrostatic potential) and the electron‐donor nitrogen of N‐MeBI preorganizes the conformation for accepting an hydrogen bond from G‐NH₂. The compound–DNA interactions were evaluated with a powerful array of biophysical methods and the results show that N‐MeBI‐thiophene monomer compounds can strongly and selectively recognize single G ? C bp sequences. Replacing the thiophene with other moieties significantly reduces binding affinity and specificity, as predicted by the design concept. These results show that the use of molecular features, such as sigma‐holes, can lead to new approaches for small molecules in biomolecular interactions.