Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation

From Concept to Cure: The Road Ahead for Ruthenium-Based Anticancer Drugs

The evolution of chemotherapy, especially the dawn of metal-based drugs, represents a transformative era in cancer treatment. From the serendipitous discovery of mustard gas's cytotoxic effects to the sophisticated development of targeted therapies, chemotherapy has significantly refined. Central to this progression is the incorporation of metal-based compounds, such as platinum (Pt), ruthenium (Ru), and gold (Au), which offer unique mechanisms of action, distinguishing them from organic therapeutics. Among these, Ru complexes, exemplified by BOLD-100 and TLD1433, have shown exceptional promise due to their selective activity, lower propensity for resistance, and the ability to target spescific cellular pathways. This paper explores the journey of such Ru candidates, focusing on the mechanisms, efficacy, and clinical potential of these Ru-based drugs, which stand at the forefront of current research, aiming to provide more targeted, less toxic, and highly effective cancer treatments.

Viral peptide conjugates for metal-warhead delivery to chromatin

The presence of heavy metal groups can endow compounds with unique structural and chemical attributes beneficial for developing highly potent therapeutic agents and effective molecular labels. However, metallocompound binding site specificity is a major challenge that dictates the level of off-site targeting, which is a limiting factor in finding safer and more effective metal-based drugs. Here we designed and tested a family of metallopeptide conjugates based on two different chromatin-tethering viral proteins and a drug being repurposed for cancer, the Au(i) anti-arthritic auranofin. The viral peptides associate with the acidic patch of the nucleosome while the gold moiety can bind allosterically to the H3 H113 imidazole. To achieve synthesis of the conjugates, we also engineered a sulfur-free, nucleosome-binding Kaposi's sarcoma herpesvirus LANA peptide with a methionine-to-ornithine substitution and coupled the peptide to the metal group in a final step using click chemistry. The four conjugates tested are all selectively cytotoxic towards tumor cell lines, but the choice of viral peptide and mode of linkage to the Au(i) group influences metal binding site preference. Our findings suggest that viral peptide-metalloconjugates have potential for use in chromatin delivery of therapeutic warheads and as nucleosome-specific tags.

Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study

In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer is a characteristic feature of the nucleosomal surface. The acidic patch is a common site in the attachment of various chromatin proteins, including viral ones. Acidic patch-binding peptides present perspective compounds that can be used to modulate chromatin functioning by disrupting interactions of nucleosomes with natural proteins or alternatively targeting artificial moieties to the nucleosomes, which may be beneficial for the development of new therapeutics. In this work, we used several computational and experimental techniques to improve our understanding of how peptides may bind to the acidic patch and what are the consequences of their binding. Through extensive analysis of the PDB database, histone sequence analysis, and molecular dynamic simulations, we elucidated common binding patterns and key interactions that stabilize peptide-nucleosome complexes. Through MD simulations and FRET measurements, we characterized changes in nucleosome dynamics conferred by peptide binding. Using fluorescence polarization and gel electrophoresis, we evaluated the affinity and specificity of the LANA1-22 peptide to DNA and nucleosomes. Taken together, our study provides new insights into the different patterns of intermolecular interactions that can be employed by natural and designed peptides to bind to nucleosomes, and the effects of peptide binding on nucleosome dynamics and stability.

Histone divergence in trypanosomes results in unique alterations to nucleosome structure

Eukaryotes have a multitude of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically and structurally characterised nucleosome core particles (NCPs) from the kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened overall DNA binding. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.

Dichloro Ru(II)-p-cymene-1,3,5-triaza-7-phosphaadamantane (RAPTA-C): A Case Study

The use of organometallic compounds to treat various phenotypes of cancer has attracted increased interest in recent decades. Organometallic compounds, which are transitional between conventional inorganic and organic materials, have outstanding and one-of-a-kind features that offer fresh insight into the development of inorganic medicinal chemistry. The therapeutic potential of ruthenium(II)-arene RAPTA-type compounds is being thoroughly investigated, specifically owing to the excellent antimetastatic property of the initial candidate RAPTA-C. This review gives a thorough analysis of this complex and its evolution as a potential anticancer drug candidate. The numerous mechanistic investigations of RAPTA-C are discussed, and they are connected to the macroscopic biological characteristics that have been found. The "multitargeted" complex described here target enzymes, peptides, and intracellular proteins in addition to DNA that allow it to specifically target cancer cells. Understanding these may allow researchers to find specific targets and tune a new-generation organometallic complex accordingly.

Capturing the hierarchically assorted modules of protein-protein interactions in the organized nucleome

Nuclear proteins are major constituents and key regulators of nucleome topological organization and manipulators of nuclear events. To decipher the global connectivity of nuclear proteins and the hierarchically organized modules of their interactions, we conducted two rounds of cross-linking mass spectrometry (XL-MS) analysis, one of which followed a quantitative double chemical cross-linking mass spectrometry (in vivoqXL-MS) workflow, and identified 24,140 unique crosslinks in total from the nuclei of soybean seedlings. This in vivo quantitative interactomics enabled the identification of 5340 crosslinks that can be converted into 1297 nuclear protein-protein interactions (PPIs), 1220 (94%) of which were non-confirmative (or novel) nuclear PPIs compared with those in repositories. There were 250 and 26 novel interactors of histones and the nucleolar box C/D small nucleolar ribonucleoprotein complex, respectively. Modulomic analysis of orthologous Arabidopsis PPIs produced 27 and 24 master nuclear PPI modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region-containing proteins, respectively. These NPIMs successfully captured previously reported nuclear protein complexes and nuclear bodies in the nucleus. Surprisingly, these NPIMs were hierarchically assorted into four higher-order communities in a nucleomic graph, including genome and nucleolus communities. This combinatorial pipeline of 4C quantitative interactomics and PPI network modularization revealed 17 ethylene-specific module variants that participate in a broad range of nuclear events. The pipeline was able to capture both nuclear protein complexes and nuclear bodies, construct the topological architectures of PPI modules and module variants in the nucleome, and probably map the protein compositions of biomolecular condensates.

Competitive binding studies of the nucleosomal histone targeting drug, [Ru(η6-p-cymene)Cl2(pta)] (RAPTA-C), with oligonucleotide-peptide mixtures

Protein crystallography and biochemical assays reveal that the organometallic drug, [Ru(η⁶-p-cymene)Cl₂(pta)] (RAPTA-C), preferentially binds to nucleosomal histone proteins in chromatin. To better understand the binding mechanism we report here a mass spectrometric-based competitive binding study between a model peptide from the acidic patch region of the H2A histone protein (the region where RAPTA-C is known to bind) and an oligonucleotide. In contrast to the protein crystallography and biochemical assays, RAPTA-C preferentially binds to the oligonucleotide, confirming that steric factors, rather than electronic effects, primarily dictate binding of RAPTA-C to histone proteins within the nucleosome.

Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to suppress host antiviral responses

Inhibition of host DNA damage response (DDR) is a common mechanism used by viruses to manipulate host cellular machinery and orchestrate viral life cycles. Epstein-Barr virus tegument protein BKRF4 associates with cellular chromatin to suppress host DDR signaling, but the underlying mechanism remains elusive. Here, we identify a BKRF4 histone binding domain (residues 15-102, termed BKRF4-HBD) that can accumulate at the DNA damage sites to disrupt 53BP1 foci formation. The high-resolution structure of the BKRF4-HBD in complex with a human H2A-H2B dimer shows that BKRF4-HBD interacts with the H2A-H2B dimer via the N-terminal region (NTR), the DWP motif (residues 80-86 containing D81, W84, P86), and the C-terminal region (CTR). The "triple-anchor" binding mode confers BKRF4-HBD the ability to associate with the partially unfolded nucleosomes, promoting the nucleosome disassembly. Importantly, disrupting the BKRF4-H2A-H2B interaction impairs the binding between BKRF4-HBD and nucleosome in vitro and inhibits the recruitment of BKRF4-HBD to DNA breaks in vivo. Together, our study reveals the structural basis of BKRF4 bindings to the partially unfolded nucleosome and elucidates an unconventional mechanism of host DDR signal attenuation.

Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence

MOTIVATION

Histone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene expression. However, the solutions for this task can be improved by exploiting multiple relationships from dataset and exploring designs of learning models, for example jointly learning technology.

RESULTS

This article proposes a deep learning-based multi-objective computational approach, iHMnBS, to identify which of the seven typical histone modifications a DNA sequence may choose to bind, and which parts of the DNA sequence bind to them. iHMnBS employs a customized dataset that allows the marking of modifications contained in histones that may bind to any position in the DNA sequence. iHMnBS tries to mine the information implicit in this richer data by means of deep neural networks. In comprehensive comparisons, iHMnBS outperforms a baseline method, and the probability of binding to modified histones assigned to a representative nucleotide of a DNA sequence can serve as a reference for biological experiments. Since the interaction between transcription factors and histone modifications has an important role in gene expression, we extracted a number of sequence patterns that may bind to transcription factors, and explored their possible impact on disease.

AVAILABILITY AND IMPLEMENTATION

The source code is available at https://github.com/lennylv/iHMnBS.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Simultaneous mass spectrometry analysis of cisplatin with oligonucleotide-peptide mixtures: implications for the mechanism of action

Although genomic DNA is the primary target of anticancer platinum-based drugs, interactions with proteins also play a significant role in their overall activity. In this study, competitive binding of cisplatin with an oligonucleotide and two peptides corresponding to segments of H2A and H2B histone proteins was investigated by mass spectrometry. Following the determination of the cisplatin binding sites on the oligonucleotide and peptides by tandem mass spectrometry, competitive binding was studied and transfer of platinum fragments from the platinated peptides to the oligonucleotide explored. In conjunction with previous studies on the nucleosome, the results suggest that all four of the abundant histone proteins serve as a platinum drug reservoir in the cell nucleus, providing an adduct pool that can be ultimately transferred to the DNA.

Graphical abstract

Anticancer activity of RAPTA-EA1 in triple-negative BRCA1 proficient breast cancer cells: single and combined treatment with the PARP inhibitor olaparib

RAPTA-EA1 is a promising glutathione transferase (GSTP-1) inhibitor that has previously been shown to inhibit the growth of various breast cancer cells. We studied the anticancer activity of RAPTA-EA1 on triple-negative BRCA1 competent breast cancer MDA-MB-231 cells. MDA-MB-231 cells are significantly more sensitive to RAPTA-EA1 than MCF-7 cells. Treatment reveals a higher degree of cytotoxicity than cisplatin against both cell lines. Ruthenium accumulation in MDA-MB-231 cells is mainly in the nuclear fraction (43%), followed by the cytoplasm (30%), and the mitochondria (27%). RAPTA-EA1 blocks cell growth at the G2/M phase, leading to nuclear condensation and cell death. The compound slightly inhibits DNA replication of the 3,426-bp fragment of the BRCA1 exon 11 of the cells, with approximately 0.6 lesion per the BRCA1 fragment. The expression of BRCA1 mRNA and its protein in the Ru-treated cells is curtailed by 50–80% compared to the untreated controls. Growth inhibition of the triple-negative BRCA1 wild-type MDA-MB-231 and the sporadic BRCA1 wild-type MCF-7 cells by olaparib (a poly [ADP-ribose] polymerase (PARP) inhibitor) is dose-dependent, with MDA-MB-231 cells being two-fold less susceptible to the drug than MCF-7 cells. Combining olaparib with RAPTA-EA1 results in a combination index (CI) of 0.78 (almost additive) in MDA-MB-231 cells and 0.24 (potent synergy) in the MCF-7 cells. The PARP inhibitor alone differently regulates the expression of BRCA1 mRNA in both cell lines, whereas the olaparib-RAPTA-EA1 combination induces overexpression of BRCA1 mRNA in these cells. However, the expression level of the BRCA1 protein is dramatically reduced after treatment with the combined inhibitors, compared with the untreated controls. This observation highlights the cellular responses of triple-negative BRCA1 proficient breast cancer MDA-MB-231 cells to RAPTA-EA1 through BRCA1 inhibition and provides insights into alternative treatments for breast cancer.

Critical factors affecting the albumin binding of half-sandwich Ru(ii) and Rh(iii) complexes of 8-hydroxyquinolines and oligopyridines

There is significant interest today in the interaction of half-sandwich anticancer organometallic complexes with proteins. It is considered as a crucial factor in the transport and mode of action of these compounds; thus it can affect their overall pharmacological and toxicological profiles. Albumin binding of high stability Ru(ii)(η⁶-p-cymene) and Rh(iii)(η⁵-C₅Me₅) complexes formed with 8-hydroxyquinoline, its 5-chloro-7-((proline-1-yl)methyl) substituted derivative, 2,2'-bipyridine and 1,10-phenanthroline is discussed herein. The interaction with human serum albumin in terms of kinetic aspects, binding strength and possible binding sites was studied in detail by means of various methods such as ¹H NMR spectroscopy, UV-visible spectrophotometry, steady-state and time-resolved fluorometry, ultrafiltration and capillary zone electrophoresis. Ru(ii)(η⁶-p-cymene)(2,2'-bipyridine) and Ru(ii)(η⁶-p-cymene)(1,10-phenanthroline) complexes do not bind to the protein measurably, most probably due to kinetic reasons. However, other complexes bind significantly to albumin with fairly different kinetics to albumin. The binding affinity towards hydrophobic binding pockets shows correlation with lipophilicity along with the actual charge of the respective complexes. The studied complexes preserve their original structure upon interaction with albumin. Formation constants computed for the binding of these metal complexes to histidine-containing model oligopeptides demonstrated significant ternary complex formation, pointing out the importance of histidine coordination in the binding of these types of complexes.

Engineering nucleosomes for generating diverse chromatin assemblies

Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Here we show that nucleosomal constructs with cohesive-ended DNA can be designed that assemble into different types of circular configurations or continuous fibers extending throughout crystals. We demonstrate the utility of the method for characterizing nucleosome compaction and linker histone binding at near-atomic resolution but also advance its application for tackling further problems in chromatin structural biology and for generating novel types of DNA nanostructures. We provide a library of cohesive-ended DNA fragment expression constructs and a strategy for engineering DNA-based nanomaterials with a seemingly vast potential variety of architectures and histone chemistries.

Conjugates Containing Two and Three Trithiolato-Bridged Dinuclear Ruthenium(II)-Arene Units as In Vitro Antiparasitic and Anticancer Agents

The synthesis, characterization, and in vitro antiparasitic and anticancer activity evaluation of new conjugates containing two and three dinuclear trithiolato-bridged ruthenium(II)-arene units are presented. Antiparasitic activity was evaluated using transgenic Toxoplasmagondii tachyzoites constitutively expressing β-galactosidase grown in human foreskin fibroblasts (HFF). The compounds inhibited T.gondii proliferation with IC50 values ranging from 90 to 539 nM, and seven derivatives displayed IC50 values lower than the reference compound pyrimethamine, which is currently used for treatment of toxoplasmosis. Overall, compound flexibility and size impacted on the anti-Toxoplasma activity. The anticancer activity of 14 compounds was assessed against cancer cell lines A2780, A2780cisR (human ovarian cisplatin sensitive and resistant), A24, (D-)A24cisPt8.0 (human lung adenocarcinoma cells wild type and cisPt resistant subline). The compounds displayed IC50 values ranging from 23 to 650 nM. In A2780cisR, A24 and (D-)A24cisPt8.0 cells, all compounds were considerably more cytotoxic than cisplatin, with IC50 values lower by two orders of magnitude. Irrespective of the nature of the connectors (alkyl/aryl) or the numbers of the di-ruthenium units (two/three), ester conjugates 6-10 and 20 exhibited similar antiproliferative profiles, and were more cytotoxic than amide analogues 11-14, 23, and 24. Polynuclear conjugates with multiple trithiolato-bridged di-ruthenium(II)-arene moieties deserve further investigation.

Human Histone Interaction Networks: An Old Concept, New Trends

To elucidate the properties of human histone interactions on the large scale, we perform a comprehensive mapping of human histone interaction networks by using data from structural, chemical cross-linking and various high-throughput studies. Histone interactomes derived from different data sources show limited overlap and complement each other. It inspires us to integrate these data into the combined histone global interaction network which includes 5308 proteins and 10,330 interactions. The analysis of topological properties of the human histone interactome reveals its scale free behavior and high modularity. Our study of histone binding interfaces uncovers a remarkably high number of residues involved in interactions between histones and non-histone proteins, 80-90% of residues in histones H3 and H4 have at least one binding partner. Two types of histone binding modes are detected: interfaces conserved in most histone variants and variant specific interfaces. Finally, different types of chromatin factors recognize histones in nucleosomes via distinct binding modes, and many of these interfaces utilize acidic patches among other sites. Interaction networks are available at https://github.com/Panchenko-Lab/Human-histone-interactome.

Synthesis, characterization, HSA/DNA interactions and antitumor activity of new [Ru(η6-p-cymene)Cl2(L)] complexes

Three new ruthenium(II) complexes were synthesized from different substituted isothiazole ligands 5-(methylamino)-3-pyrrolidine-1-ylisothiazole-4-carbonitrile (1), 5-(methylamino)-3-(4-methylpiperazine-1-yl)isothiazole-4-carbonitrile (2) and 5-(methylamino)-3-morpholine-4-ylisothiazole-4-carbonitrile (3): [Ru(η⁶-p-cymene)Cl₂(L1)]·H₂O (4), [Ru(η⁶-p-cymene)Cl₂(L2)] (5) and [Ru(η⁶-p-cymene)Cl₂(L3)] (6). All complexes were characterized by IR, UV-Vis, NMR spectroscopy, and elemental analysis. The molecular structures of all ligands and complexes 4 and 6 were determined by an X-ray. The results of the interactions of CT-DNA (calf thymus deoxyribonucleic acid) and HSA (human serum albumin) with ruthenium (II) complexes reveal that complex 4 binds well to CT-DNA and HSA. Kinetic and thermodynamic parameters for the reaction between complex and HSA confirmed the associative mode of interaction. The results of Quantum mechanics (QM) modelling and docking experiments toward DNA dodecamer and HSA support the strongest binding of the complex 4 to DNA major groove, as well as its binding to IIa domain of HSA with the lowest ΔG energy, which agrees with the solution studies. The modified GOLD docking results are indicative for Ru(p-cymene)LCl··(HSA··GLU292) binding and GOLD/MOPAC(QM) docking/modelling of DNA/Ligand (Ru(II)-N(7)dG7) covalent binding. The cytotoxic activity of compounds was evaluated by MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide) assay. Neither of the tested compounds shows activity against a healthy MRC-5 cell line while the MCF-7 cell line is the most sensitive to all. Compounds 3, 4 and 5 were about two times more active than cisplatin, while the antiproliferative activity of 6 was almost the same as with cisplatin. Flow cytometry analysis showed the apoptotic death of the cells with a cell cycle arrest in the subG1 phase.

Near-atomic resolution structures of interdigitated nucleosome fibres

Chromosome structure at the multi-nucleosomal level has remained ambiguous in spite of its central role in epigenetic regulation and genome dynamics. Recent investigations of chromatin architecture portray diverse modes of interaction within and between nucleosome chains, but how this is realized at the atomic level is unclear. Here we present near-atomic resolution crystal structures of nucleosome fibres that assemble from cohesive-ended dinucleosomes with and without linker histone. As opposed to adopting folded helical ‘30 nm’ structures, the fibres instead assume open zigzag conformations that are interdigitated with one another. Zigzag conformations obviate extreme bending of the linker DNA, while linker DNA size (nucleosome repeat length) dictates fibre configuration and thus fibre–fibre packing, which is supported by variable linker histone binding. This suggests that nucleosome chains have a predisposition to interdigitate with specific characteristics under condensing conditions, which rationalizes observations of local chromosome architecture and the general heterogeneity of chromatin structure.

Crystal structures of nucleosome fibres assembled from cohesive-ended dinucleosomes with and without linker histone reveal open zigzag conformations that are interdigitated with one another, and suggest the role that linker DNA plays in observed variable fibre configurations and packing.

All-atom simulations to studying metallodrugs/target interactions

Metallodrugs are extensively used to treat and diagnose distinct disease types. The unique physical-chemical properties of metal ions offer tantalizing opportunities to tailor effective scaffolds for selectively targeting specific biomolecules. Modern experimental techniques have collected a large body of structural data concerning the interactions of metallodrugs with their biomolecular targets, although being unable to exhaustively assess the molecular basis of their mechanism of action. In this scenario, the complementary use of accurate computational methods allows uncovering the minutiae of metallodrugs/targets interactions and their underlying mechanism of action at an atomic-level of detail. This knowledge is increasingly perceived as an invaluable requirement to rationally devise novel and selective metallodrugs. Building on literature studies, selected largely from the last 2 years, this compendium encompasses a cross-section of the current role, advances, and challenges met by computer simulations to decipher the mechanistic intricacies of prototypical metallodrugs.

Recent Advances and Challenges of the Drugs Acting on Monoamine Transporters

Background:

The human Monoamine Transporters (hMATs), primarily including hSERT, hNET and hDAT, are important targets for the treatment of depression and other behavioral disorders with more than the availability of 30 approved drugs.

Objective:

This paper is to review the recent progress in the binding mode and inhibitory mechanism of hMATs inhibitors with the central or allosteric binding sites, for the benefit of future hMATs inhibitor design and discovery. The Structure-Activity Relationship (SAR) and the selectivity for hit/lead compounds to hMATs that are evaluated by in vitro and in vivo experiments will be highlighted.

Methods:

PubMed and Web of Science databases were searched for protein-ligand interaction, novel inhibitors design and synthesis studies related to hMATs.

Results:

Literature data indicate that since the first crystal structure determinations of the homologous bacterial Leucine Transporter (LeuT) complexed with clomipramine, a sizable database of over 100 experimental structures or computational models has been accumulated that now defines a substantial degree of structural variability hMATs-ligands recognition. In the meanwhile, a number of novel hMATs inhibitors have been discovered by medicinal chemistry with significant help from computational models.

Conclusion:

The reported new compounds act on hMATs as well as the structures of the transporters complexed with diverse ligands by either experiment or computational modeling have shed light on the poly-pharmacology, multimodal and allosteric regulation of the drugs to transporters. All of the studies will greatly promote the Structure-Based Drug Design (SBDD) of structurally novel scaffolds with high activity and selectivity for hMATs.

PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome

The poly(ADP-ribose) polymerase, PARP1, plays a key role in maintaining genomic integrity by detecting DNA damage and mediating repair. γH2A.X is the primary histone marker for DNA double-strand breaks and PARP1 localizes to H2A.X-enriched chromatin damage sites, but the basis for this association is not clear. We characterize the kinetics of PARP1 binding to a variety of nucleosomes harbouring DNA double-strand breaks, which reveal that PARP1 associates faster with (γ)H2A.X- versus H2A-nucleosomes, resulting in a higher affinity for the former, which is maximal for γH2A.X-nucleosome that is also the activator eliciting the greatest poly-ADP-ribosylation catalytic efficiency. The enhanced activities with γH2A.X-nucleosome coincide with increased accessibility of the DNA termini resulting from the H2A.X-Ser139 phosphorylation. Indeed, H2A- and (γ)H2A.X-nucleosomes have distinct stability characteristics, which are rationalized by mutational analysis and (γ)H2A.X-nucleosome core crystal structures. This suggests that the γH2A.X epigenetic marker directly facilitates DNA repair by stabilizing PARP1 association and promoting catalysis.

The poly(ADP-ribose) polymerases play a key role in maintaining genomic integrity by detecting DNA damage and mediating repair. Here the authors characterize the kinetics of PARP1 binding to a variety of nucleosomes harbouring DNA double-strand breaks.

Nucleosome binding peptide presents laudable biophysical and in vivo effects

Chromatin state is highly dependent on the nucleosome binding proteins. Herein, we used a multipronged approach employing biophysical and in vivo experiments to characterize the effects of Nucleosome Binding Peptides (NBPeps) on nucleosome and cell activity. We performed a series of structure-based calculations on the nucleosome surface interaction with GMIP1 (a novel NBPep generated in silico), and HMGN2 (nucleosome binding motif of HMGN2), which contains sites that bind DNA and the acid patch, and also LANA and H4pep (nucleosome binding motif of H4 histone tail) that only bind to the acidic patch. Biochemical assays shows that H4pep, but not HMGN2, GMIP1 and LANA, is highly specific for targeting the nucleosome, with important effects on the final nucleosome structure and robust in vivo effects. These findings suggest that NBPeps might have important therapeutic implications and relevance as tools for chromatin investigation.

Recent progress in the development of organometallics for the treatment of cancer

From their early successes in medicine, organometallic compounds continue to attract interest as potential chemotherapeutics to treat a range of diseases. Here, we show from recent literature selected largely from the last two years that organometallics offer unique opportunities in medicine and, increasingly, a mechanistic-based approach is applied to their development, which has not always been the case.

Locked and Loaded: Ruthenium(II)-Capped Cucurbit[n]uril-Based Rotaxanes with Antimetastatic Properties

We report here the first coupling of Ru(II) units with cucurbit[6/7]uril-based pseudorotaxane ligands meant for biological application. The resulting ruthenium-capped rotaxanes were fully characterized, and a structure of one supramolecular system was determined by X-ray diffraction. Because the biological properties of Ru-based metallodrugs are tightly linked to the ligand-exchange processes, the effect of salt concentration on the hydrolysis of chlorides from the Ru(II) center was monitored by using ¹H NMR spectroscopy. The biological activity of Ru(II)-based rotaxanes was evaluated for three selected mammalian breast cell lines, HBL-100, MCF-7, and MDA-MB-231. The antimetastatic activity of the assembled cationic Ru(II)-rotaxane systems, evaluated in migration assays against MCF-7 and MDA-MB-231 cell lines, is notably enhanced compared to that of RAPTA-C, a reference that was used. The indicated synergistic effect of combining Ru(II) with a pseudorotaxane unit opens a new direction in searching for anticancer supramolecular metallodrugs.

Binding mechanisms of half-sandwich Rh(III) and Ru(II) arene complexes on human serum albumin: a comparative study

Abstract

Various half-sandwich ruthenium(II) arene complexes and rhodium(III) arene complexes have been intensively investigated due to their prominent anticancer activity. The interaction of the organometallic complexes of Ru(η⁶-p-cymene) and Rh(η⁵-C₅Me₅) with human serum albumin (HSA) was studied in detail by a combination of various methods such as ultrafiltration, capillary electrophoresis, ¹H NMR spectroscopy, fluorometry and UV–visible spectrophotometry in the presence of 100 mM chloride ions. Binding characteristics of the organometallic ions and their complexes with deferiprone, 2-picolinic acid, maltol, 6-methyl-2-picolinic acid and 2-quinaldic acid were evaluated. Kinetic aspects and reversibility of the albumin binding are also discussed. The effect of low-molecular-mass blood components on the protein binding was studied in addition to the interaction of organorhodium complexes with cell culture medium components. The organometallic ions were found to bind to HSA to a high extent via a coordination bond. Release of the bound metal ions was kinetically hindered and could not be induced by the denaturation of the protein. Binding of the Ru(η⁶-p-cymene) triaqua cation was much slower (ca. 24 h) compared to the rhodium congener (few min), while their complexes interacted with the protein relatively fast (1–2 h). The studied complexes were bound to HSA coordinatively. The highly stable and kinetically inert 2-picolinate Ru(η⁶-p-cymene) complex bound in an associative manner preserving its original entity, while lower stability complexes decomposed partly or completely upon binding to HSA. Fast, non-specific and high-affinity binding of the complexes on HSA highlights their coordinative interaction with various types of proteins possibly decreasing effective drug concentration.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s00775-019-01683-0) contains supplementary material, which is available to authorized users.

Anticancer organorhodium and -iridium complexes with low toxicity in vivo but high potency in vitro: DNA damage, reactive oxygen species formation, and haemolytic activity

Dinuclear Rh^III(Cp*) and Ir^III(Cp*) complexes demonstrated potent in vitro anticancer activity while exhibiting low toxicity in haemolysis studies and in vivo zebrafish models.

Silver Atomic Quantum Clusters of Three Atoms for Cancer Therapy: Targeting Chromatin Compaction to Increase the Therapeutic Index of Chemotherapy

Nanomaterials with very low atomicity deserve consideration as potential pharmacological agents owing to their very small size and to their properties that can be precisely tuned with minor modifications to their size. Here, it is shown that silver clusters of three atoms (Ag3 -AQCs)-developed by an ad hoc method-augment chromatin accessibility. This effect only occurs during DNA replication. Coadministration of Ag3 -AQCs increases the cytotoxic effect of DNA-acting drugs on human lung carcinoma cells. In mice with orthotopic lung tumors, the coadministration of Ag3 -AQCs increases the amount of cisplatin (CDDP) bound to the tumor DNA by fivefold without modifying CDDP levels in normal tissues. As a result, CDDP coadministered with Ag3 -AQCs more strongly reduces the tumor burden. Evidence of the significance of targeting chromatin compaction to increase the therapeutic index of chemotherapy is now provided.