DNA-binding Unit Research Articles

A Comprehensive Review of the Antitumor Properties and Mechanistic Insights of Duocarmycin Analogs.

The duocarmycin family is a group of potent cytotoxic agents originally isolated from the bacterium Streptomyces. This discovery has spurred significant interest due to duocarmycins' unique chemical structures and powerful mechanism of action. This review comprehensively details the history of the duocarmycin family, the current understanding of their therapeutic potential, and the major clinical trials that have been conducted. Chemically, the duocarmycin family is characterized by a DNA-binding unit that confers specificity, a subunit-linking amide that positions the molecule within the DNA helix, and an alkylating unit that interacts with the DNA. This configuration allows them to bind selectively to the minor groove of DNA and alkylate adenine bases, a notable deviation from the more common guanine targeting performed by other alkylating agents. Duocarmycin's mechanism of action involves the formation of covalent adducts with DNA, leading to the disruption of the DNA architecture and subsequent inhibition of replication and transcription. Recent advancements in drug delivery systems, such as antibody-drug conjugates (ADCs), have further elevated the therapeutic prospects of duocarmycin analogs by providing a promising mechanism for enhancing intracellular concentrations and selective tumor delivery. Preclinical studies have highlighted the efficacy of duocarmycin derivatives in various in vitro models, providing a strong foundation for translational research. However, further biological research is required to fully understand the toxicology of duocarmycin family members before it can be clinically relevant. The major focus of this review is to cache the major biologically relevant findings of different duocarmycin analogs as well as their biological shortcomings to propose next steps in the field of cancer therapy with these potent therapeutics.

Enhanced Oxidative DNA Cleavage Activity of Iron Complex of Pentadentate Mono-carboxamide Ligand Having Spermine as DNA Binding Domain

The iron complex of 2-[bis(pyridin-2-ylmethyl)amino]-N-(quinolin-8-yl)acetylamide (H-dpaq) has been proven to cleave DNA by reductive oxygen activation. Two H-dpaq derivatives, H-dpaq-Arg8-NH2 and H-dpaq-spermine, having a cationic tail as a DNA binding unit, octa-arginine or spermine, have been synthesized and evaluated in the iron-catalyzed oxidative DNA cleavage of plasmid DNA, pUC19, in the presence of a reducing agent. H-dpaq-Arg8-NH2 and H-dpaq-spermine converted the supercoiled form of pUC19 to the nicked form 2.7- and 3.5-fold more efficiently than H-dpaq.

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.

Interactions between proteins and nucleic acids are at the heart of many essential biological processes. Despite increasing structural information about how these interactions may take place, our understanding of the usage made of protein surfaces by nucleic acids is still very limited. This is in part due to the inherent complexity associated to protein surface deformability and evolution. In this work, we present a method that contributes to decipher such complexity by predicting protein-DNA interfaces and characterizing their properties. It relies on three biologically and physically meaningful descriptors, namely evolutionary conservation, physico-chemical properties and surface geometry. We carefully assessed its performance on several hundreds of protein structures and compared it to several machine-learning state-of-the-art methods. Our approach achieves a higher sensitivity compared to the other methods, with a similar precision. Importantly, we show that it is able to unravel 'hidden' binding sites by applying it to unbound protein structures and to proteins binding to DNA via multiple sites and in different conformations. It is also applicable to the detection of RNA-binding sites, without significant loss of performance. This confirms that DNA and RNA-binding sites share similar properties. Our method is implemented as a fully automated tool, [Formula: see text], freely accessible at: http://www.lcqb.upmc.fr/JET2DNA. We also provide a new dataset of 187 protein-DNA complex structures, along with a subset of 82 associated unbound structures. The set represents the largest body of high-resolution crystallographic structures of protein-DNA complexes, use biological protein assemblies as DNA-binding units, and covers all major types of protein-DNA interactions. It is available at: http://www.lcqb.upmc.fr/PDNAbenchmarks.

Key to Delivery: The (Epi-)genome Editing Vector Toolbox.

Curing a genetic disease by repairing the underlying genetic defect is a fascinating concept that has been addressed so far by gene compensation therapy. For this, a functional copy of the gene in question together with elements controlling its expression is produced as a vector and introduced ex vivo into the patient's own cells that subsequently are reinfused. Alternatively, vectors are administered directly in vivo. Although this strategy resulted in impressive therapeutic benefits for patients, the ultimate goal of gene therapy, i.e., a cure by repairing the actual genetic or epigenetic defect, remained an unresolved task. With the advent of designer DNA-binding domains, this goal is coming into reach. These domains are either combined with nucleases and used as molecular precision scissors for introducing DNA breaks at defined sites in the cell's genome preparing for position-selective DNA repair, or they are used as programmable DNA-binding units for positioning epigenome-modifying domains to predefined target sequences. However, for reaching its full potential, these components need to be delivered into cells in an efficient and safe manner. Here, we summarize current viral and non-viral delivery approaches applicable for genome and epigenome editing and discuss their respective advantages and limitations.

Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin.

The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes.

Megatal, Crispr/Cas9, and Talen T-Cell Receptor Gene Editing

T-cell based immunotherapy holds great promise for targeted tumor therapies and includes the use of tumor infiltrating lymphocytes or cells engineered to express chimeric antigen receptors. Each have resulted in promising therapeutic responses; however, they are largely reliant on autologous, ex vivo cellular expansion, manipulation, and reinfusion. This individualized process may result in non-uniformity and may be limiting for urgent and widespread use. An attractive strategy would be to generate a universal donor pool of cells at sufficient scale to be broadly applicable. Allogeneic approaches to this hold the risk of off tumor reactivity toward host tissue as part of graft versus host disease (GVHD), a pathogenic process mediated by the T-cell receptor (TCR). The TCR is a heterodimeric complex comprised of alpha and beta chains encoded by the TRAC and TRBC genes, respectively. Because the alpha chain is encoded by a single gene, while the beta chain is encoded by two, it has become a prime candidate for genome editing strategies aimed at disrupting the formation of the TCR and diminishing the risk of GVHD.Four major classes of gene editing proteins exist that share the commonality of binding a target sequence of DNA and generating a double stranded DNA break (DSB). The DSB is subsequently repaired by non- homologous endjoining an error prone pathway resulting in insertions/deletions that can disrupt open reading frames. Zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) are heterodimeric arrays that are tethered to the Fok I nuclease domain that co-localize at a target DNA site. ZFNs are comprised of 3-6 finger subunits that bind DNA and TALENs are comprised of repeating DNA binding units containing a hypervariable two amino acid sequence (repeat variable diresidue; RVD) that governs DNA base recognition. Meganucleases are monomeric proteins with innate nuclease activity that are derived from bacterial homing endonucleases that have been fused with TAL RVDs to generate megaTAL (MT) proteins. The clustered regularly interspaced short palindromic repeats (CRISPR) and associated Cas9 nuclease platform is comprised of a small guide RNA (gRNA) transcript that contacts a target DNA sequence via Watson-Crick base pairing and the Cas9 nuclease that cleaves the DNA.No evaluation has been performed between the different platforms for TCR disruption in the context of a translatable manufacturing process. Critical components of such an evaluation are reagent optimization, interrogation of off-target (OT) effects, and scalable expansion of gene edited cell populations. Utilizing Jurkat cells we observed that polyadenylated TALEN and MT mRNA and Cas9 with a gRNA encoded on a plasmid were the most effective in TRAC gene disruption (Fig 1A). A comparison of the optimized expression platforms in primary human T-cells revealed maximal editing rates were achieved with the MT reagent (Fig 1B). We then sorted the TCR negative cells to purity and re-introduced the TRAC gene mRNA that resulted in transient reconstitution of the CD3 complex that allowed for CD3/CD28 bead stimulation and a 5-fold expansion (Fig 1C). This represents a pool of TCR null cells for archival. Finally, we performed a genome level assessment of the potential off target (OT) activity of the nuclease candidates. Surprisingly, the CRISPR/Cas9 and TALEN reagents did not display OT effects (Fig 2A). At saturation levels of MT treatment we observed one bona fide OT site in both Jurkats and primary T-cells (Fig 2B); importantly, this occurred within an intron and did not impact proper gene splicing or cellular viability.In summary, we evaluated three different TRAC -targeting nucleases, and developed an optimized process for generating and expanding TCR/CD3-deficient cells. Our study demonstrates the utility of performing unbiased genome wide assessment of editing for identification of off target cleavage, and the importance of achieving a high efficiency of gene editing and cellular expansion to facilitate clinical translation. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Design, Synthesis, and Evaluation of Linker-Duocarmycin Payloads: Toward Selection of HER2-Targeting Antibody-Drug Conjugate SYD985.

Antibody-drug conjugates (ADCs) that are currently on the market or in clinical trials are predominantly based on two drug classes: auristatins and maytansinoids. Both are tubulin binders and block the cell in its progression through mitosis. We set out to develop a new class of linker-drugs based on duocarmycins, potent DNA-alkylating agents that are composed of a DNA-alkylating and a DNA-binding moiety and that bind into the minor groove of DNA. Linker-drugs were evaluated as ADCs by conjugation to the anti-HER2 antibody trastuzumab via reduced interchain disulfides. Duocarmycin 3b, bearing an imidazo[1,2-a]pyridine-based DNA-binding unit, was selected as the drug moiety, notably because of its rapid degradation in plasma. The drug was incorporated into the linker-drugs in its inactive prodrug form, seco-duocarmycin 3a. Linker attachment to the hydroxyl group in the DNA-alkylating moiety was favored over linking to the DNA-binding moiety, as the first approach gave more consistent results for in vitro cytotoxicity and generated ADCs with excellent human plasma stability. Linker-drug 2 was eventually selected based on the properties of the corresponding trastuzumab conjugate, SYD983, which had an average drug-to-antibody ratio (DAR) of about 2. SYD983 showed subnanomolar potencies against multiple human cancer cell lines, was highly efficacious in a BT-474 xenograft model, and had a long half-life in cynomolgus monkeys, in line with high stability in monkey and human plasma. Studies comparing ADCs with a different average DAR showed that a higher average DAR leads to increased efficacy but also to somewhat less favorable physicochemical and toxicological properties. Fractionation of SYD983 with hydrophobic interaction chromatography resulted in SYD985, consisting of about 95% DAR2 and DAR4 species in an approximate 2:1 ratio and having an average DAR of about 2.8. SYD985 combines several favorable properties from the unfractionated ADCs with an improved homogeneity. It was selected for further development and recently entered clinical Phase I evaluation.

Calixarenes and related macrocycles as gene delivery vehicles

The success of gene therapy depends largely on the development of new efficient gene delivery vehicles. The emerging class of molecules for this application is macrocycles that feature persistent shape, thus ensuring higher level of supramolecular organization of the DNA complexes. The review focuses on recently developed calixarenes and close analogues as gene delivery vectors, their chemistry, ability to compact nucleic acids, transfection ability in vitro and cytotoxicity. Their fixed conformation with the possibility of multiple functional groups at the upper and lower rims allows preparation of cone-shaped macromolecules capable of programmed hierarchical assembly in the presence of DNA. It is shown that specially designed calixarenes, particularly those having amphiphilic structure with clustered DNA binding units, can form small virus-sized DNA nanoparticles with well-defined architecture, high transfection efficiency and low toxicity. The field is still largely underexplored so that there is a lot of room for further improvement of the molecular design of calixarenes. Moreover, their evaluation in vivo on animals will be an important step towards their validation for gene therapy.

TIN2 Protein Dyskeratosis Congenita Missense Mutants Are Defective in Association with Telomerase

Dyskeratosis congenita (DC) is a progressive and heterogeneous congenital disorder that affects multiple systems and is characterized by bone marrow failure and a triad of abnormal skin pigmentation, nail dystrophy, and oral leukoplakia. One common feature for all DC patients is abnormally short telomeres and defects in telomere biology. Most of the known DC mutations have been found to affect core components of the telomerase holoenzyme. Recently, multiple mutations in the gene encoding the telomeric protein TIN2 have been identified in DC patients with intact telomerase genes, but the molecular mechanisms underlying TIN2 mutation-mediated DC remain unknown. Here, we demonstrate that ectopic expression of TIN2 with DC missense mutations in human cells led to accelerated telomere shortening, similar to the telomere phenotypes found in DC patients. However, this telomere shortening was not accompanied by changes in total telomerase activity, localization of TIN2, or telomere end protection status. Interestingly, we found TIN2 to participate in the TPP1-dependent recruitment of telomerase activity. Furthermore, DC mutations in TIN2 led to its decreased ability to associate with TERC and telomerase activity. Taken together, our data suggest that TIN2 mutations in DC may compromise the telomere recruitment of telomerase, leading to telomere shortening and the associated pathogenesis.

Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria

HetR is an essential regulator of heterocyst development in cyanobacteria. HetR binds to a DNA palindrome upstream of the hetP gene. We report the crystal structure of HetR from Fischerella at 3.0Å. The protein is a dimer comprised of a central DNA-binding unit containing the N-terminal regions of the two subunits organized with two helix-turn-helix motifs; two globular flaps extending in opposite directions; and a hood over the central core formed from the C-terminal subdomains. The flaps and hood have no structural precedent in the protein database, therefore representing new folds. The structural assignments are supported by site-directed mutagenesis and DNA-binding studies. We suggest that HetR serves as a scaffold for assembly of transcription components critical for heterocyst development.

Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties

BackgroundDNA-binding proteins perform their functions through specific or non-specific sequence recognition. Although many sequence- or structure-based approaches have been proposed to identify DNA-binding residues on proteins or protein-binding sites on DNA sequences with satisfied performance, it remains a challenging task to unveil the exact mechanism of protein-DNA interactions without crystal complex structures. Without information from complexes, the linkages between DNA-binding proteins and their binding sites on DNA are still missing.MethodsWhile it is still difficult to acquire co-crystallized structures in an efficient way, this study proposes a knowledge-based learning method to effectively predict DNA orientation and base locations around the protein’s DNA-binding sites when given a protein structure. First, the functionally important residues of a query protein are predicted by a sequential pattern mining tool. After that, surface residues falling in the predicted functional regions are determined based on the given structure. These residues are then clustered based on their spatial coordinates and the resultant clusters are ranked by a proposed DNA-binding propensity function. Clusters with high DNA-binding propensities are treated as DNA-binding units (DBUs) and each DBU is analyzed by principal component analysis (PCA) to predict potential orientation of DNA grooves. More specifically, the proposed method is developed to predict the direction of the tangent line to the helix curve of the DNA groove where a DBU is going to bind.ResultsThis paper proposes a knowledge-based learning procedure to determine the spatial location of the DNA groove with respect to the query protein structure by considering geometric propensity between protein side chains and DNA bases. The 11 test cases used in this study reveal that the location and orientation of the DNA groove around a selected DBU can be predicted with satisfied errors.ConclusionsThis study presents a method to predict the location and orientation of DNA grooves with respect to the structure of a DNA-binding protein. The test cases shown in this study reveal the possibility of imaging protein-DNA binding conformation before co-crystallized structure can be determined. How the proposed method can be incorporated with existing protein-DNA docking tools to study protein-DNA interactions deserve further studies in the near future.

Structure-guided Mutational Analysis of the OB, HhH, and BRCT Domains of Escherichia coli DNA Ligase

NAD(+)-dependent DNA ligases (LigAs) are ubiquitous in bacteria and essential for growth. LigA enzymes have a modular structure in which a central catalytic core composed of nucleotidyltransferase and oligonucleotide-binding (OB) domains is linked via a tetracysteine zinc finger to distal helix-hairpin-helix (HhH) and BRCT (BRCA1-like C-terminal) domains. The OB and HhH domains contribute prominently to the protein clamp formed by LigA around nicked duplex DNA. Here we conducted a structure-function analysis of the OB and HhH domains of Escherichia coli LigA by alanine scanning and conservative substitutions, entailing 43 mutations at 22 amino acids. We thereby identified essential functional groups in the OB domain that engage the DNA phosphodiester backbone flanking the nick (Arg(333)); penetrate the minor grove and distort the nick (Val(383) and Ile(384)); or stabilize the OB fold (Arg(379)). The essential constituents of the HhH domain include: four glycines (Gly(455), Gly(489), Gly(521), Gly(553)), which bind the phosphate backbone across the minor groove at the outer margins of the LigA-DNA interface; Arg(487), which penetrates the minor groove at the outer margin on the 3 (R)-OH side of the nick; and Arg(446), which promotes protein clamp formation via contacts to the nucleotidyltransferase domain. We find that the BRCT domain is required in its entirety for effective nick sealing and AMP-dependent supercoil relaxation.

Two DNA-binding and Nick Recognition Modules in Human DNA Ligase III

Human DNA ligase III contains an N-terminal zinc finger domain that binds to nicks and gaps in DNA. This small domain has been described as a DNA nick sensor, but it is not required for DNA nick joining activity in vitro. In light of new structural information for mammalian ligases, we measured the DNA binding affinity and specificity of each domain of DNA ligase III. These studies identified two separate, independent DNA-binding modules in DNA ligase III that each bind specifically to nicked DNA over intact duplex DNA. One of these modules comprises the zinc finger domain and DNA-binding domain, which function together as a single DNA binding unit. The catalytic core of ligase III is the second DNA nick-binding module. Both binding modules are required for ligation of blunt ended DNA substrates. Although the zinc finger increases the catalytic efficiency of nick ligation, it appears to occupy the same binding site as the DNA ligase III catalytic core. We present a jackknife model for ligase III that posits conformational changes during nick sensing and ligation to extend the versatility of the enzyme.

Interaction of the PHD-Finger Homeodomain Protein HAT3.1 from Arabidopsis thaliana with DNA. Specific DNA Binding by a Homeodomain with Histidine at Position 51

HAT3.1 is a member of the PHD-finger homeodomain protein family. The HAT3.1 homeodomain is highly divergent in sequence even at positions that are almost invariable among homeodomains. In this work, we have applied the random oligonucleotide selection technique to investigate if the HAT3.1 homeodomain is able to recognize specific DNA sequences. Analysis of the selected molecules followed by hydroxyl radical footprinting experiments and yeast one-hybrid assays indicated that HAT3.1 shows a preference for the sequence T(A/G)(A/C)ACCA, different from those bound by other homeodomains. Binding was dependent on homeodomain residues located at positions 47, 50, 51, and 54, the same positions that usually participate in DNA binding in most homeodomains. The study of the interaction of mutants at these positions with DNA carrying nucleotide changes at specific sites suggested that H51 and K50 most likely interact with nucleotides 2 to 4 and 5 to 6, respectively, while W54 would establish contacts with position 4. The presence of H51 and W54 represents an innovation among homeodomain structures. The fact that the HAT3.1 homeodomain is able to interact with specific DNA sequences is evidence of the inherent plasticity of the homeodomain as a DNA binding unit.

Selective Treatment of Cancer: Synthesis, Biological Evaluation and Structural Elucidation of Novel Analogues of the Antibiotic CC‐1065 and the Duocarmycins

Novel diastereomerically pure beta-D-galactosidic prodrugs (+)-12 a-e of the cytotoxic antibiotics CC-1065 and the duocarmycins were prepared for an antibody directed enzyme prodrug therapy (ADEPT) using 4 as a substrate via a radical cyclization to give rac-5 and rac-6 followed by a chromatographic resolution of the enantiomers of rac-5, glycosidation and linkage to the DNA-binding units 10 a-e. These only slightly toxic compounds can be toxified enzymatically by an antibody-beta-D-galactosidase conjugate at the surface of malignant cells to give the cytotoxic drugs, which then alkylate DNA. The new prodrugs were tested in in vitro cytotoxicity assays showing excellent QIC(50) values of 4800 and 4300 for (+)-12 a and (+)-12 b, respectively. The absolute configuration of precursor (+)-5 was determined by comparison of the experimental CD spectrum with the theoretically predicted CD spectra and by X-ray structure analysis.

Integrated insights from simulation, experiment, and mutational analysis yield new details of LacI function.

Protein structural change underlies many signal transduction processes. Although end-state structures are known for various allosteric proteins, intermediates are difficult to observe. Recently, targeted molecular dynamics simulation (TMD) was used to examine the conformational transition and predict relevant intermediates for wild-type lactose repressor (LacI). A catalog of involved residues suggests that the transition of this homodimer is asymmetric and that K84 is a prominent participant in the dynamic N-subdomain interface. Previous experiments indicated that hydrophobic substitutions at position 84 engender slowed, biphasic inducer binding kinetics, which might reflect the same phenomena observed in TMD. Here, we report biochemical confirmation that DNA and inducer binding remain allosterically linked in K84A and K84L, albeit with a differential smaller than that found in wild-type LacI. Other features of these mutant proteins are consistent with an allosteric conformational shift that approximates that of the wild type. As a consequence, these repressors can be utilized to explore an unanswered question about LacI function: How many inducers (one or two per dimer) are required to diminish operator affinity? The biphasic natures of the K84L and K84A inducer association rates allow direct correlation between the two distinct inducer binding events and operator release. Indeed, the kinetics of operator release for the K84A and K84L closely parallel those for the second inducer binding event. Together with implications from previous equilibrium results for wild-type and mutant proteins, these kinetic data demonstrate that binding of two inducers per dimeric DNA binding unit is required to release the operator in these variant LacI proteins.

Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein.

Information processing pathways such as DNA replication are conserved in eukaryotes and archaea and are significantly different from those found in bacteria. Single-stranded DNA-binding (SSB) proteins (or replication protein A, RPA, in eukaryotes) play a central role in many of these pathways. However, whilst euryarchaea have a eukaryotic-type RPA homologue, crenarchaeal SSB proteins appear much more similar to the bacterial proteins, with a single OB fold for DNA binding and a flexible C-terminal tail that is implicated in protein-protein interactions. We have determined the crystal structure of the SSB protein from the crenarchaeote Sulfolobus solfataricus to 1.26 A. The structure shows a striking and unexpected similarity to the DNA-binding domains of human RPA, providing confirmation of the close relationship between archaea and eukaryotes. The high resolution of the structure, together with thermodynamic and mutational studies of DNA binding, allow us to propose a molecular basis for DNA binding and define the features required for eukaryotic and archaeal OB folds.

ChemInform Abstract: Novel Carboranes with a DNA Binding Unit for the Treatment of Cancer by Boron Neutron Capture Therapy.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Novel Carboranes with a DNA Binding Unit for the Treatment of Cancer by Boron Neutron Capture Therapy

The synthesis and biological evaluation of two ortho-carborane derivatives which contain a 5,6,7-trimethoxyindole (TMI) unit for use in boron neutron capture therapy is described. The TMI moiety is known to be the DNA-binding part of the highly potent anticancer agent duocarmycin A. The ortho-carborane derivatives were prepared from amino alkynes which were bound to a protected TMI carboxylic acid. Addition of decaborane(14) to the alkyne triple bond with subsequent removal of the tert-butoxycarbonyl (Boc) and benzyl protecting groups gave the desired product. Boron uptake from the ortho-carborane derivatives into B-16 melanoma cells was higher and faster than that observed with L-p-boronophenylalanine (BPA), which is in use in the clinic.

Novel carboranes with a DNA binding unit for the treatment of cancer by boron neutron capture therapy.

The synthesis and biological evaluation of two ortho-carborane derivatives which contain a 5,6,7-trimethoxyindole (TMI) unit for use in boron neutron capture therapy is described. The TMI moiety is known to be the DNA-binding part of the highly potent anticancer agent duocarmycin A. The ortho-carborane derivatives were prepared from amino alkynes which were bound to a protected TMI carboxylic acid. Addition of decaborane(14) to the alkyne triple bond with subsequent removal of the tert-butoxycarbonyl (Boc) and benzyl protecting groups gave the desired product. Boron uptake from the ortho-carborane derivatives into B-16 melanoma cells was higher and faster than that observed with L-p-boronophenylalanine (BPA), which is in use in the clinic.