Implications and concepts of polyamine-nucleic acid interactions

In Silico and In Vitro Approach for Evaluation of the Anti-Inflammatory and Antioxidant Potential of Mygalin

There is a great interest in describing new molecules to be used as therapeutic targets in various diseases, particularly those that play a role in inflammatory responses and infection control. Mygalin is a synthetic analogue of spermidine, and previous studies have demonstrated its bactericidal effect against Escherichia coli, as well as its ability to modulate the inflammatory response of macrophages against lipopolysaccharide (LPS). However, the mechanisms through which mygalin regulates this inflammatory response remain poorly characterized. A set of platforms using molecular docking analysis was employed to analyze various properties of mygalin, including toxicity, biodistribution, absorption, and the prediction of its anti-inflammatory properties. In in vitro assays, we evaluated the potential of mygalin to interact with products of the inflammatory response, such as reactive oxygen species (ROS) and antioxidant activity, using the BMDM cell. The in silico analyses indicated that mygalin is not toxic, and can interact with proteins from the kinase group, and enzymes and receptors in eukaryotic cells. Molecular docking analysis showed interactions with key amino acid residues of COX-2, iNOS and 5-LOX enzymes. In vitro, assays demonstrated a significant reduction in the expression of iNOS and COX-2 induced by LPS, along with a decrease in the oxidative stress caused by the treatment with PMA, all without altering cell viability. Mygalin exhibited robust antioxidant activity in DPPH assays, regardless of the dose used, and inhibited heat-induced hemolysis. These studies suggest that mygalin holds promise for further investigation as a new molecule with anti-inflammatory and antioxidant properties.

Coordination of Phosphate and Magnesium Metabolism in Bacteria

The majority of cellular phosphate (PO₄^-3; Pi) exists as nucleoside triphosphates, mainly adenosine triphosphate (ATP), and ribosomal RNA (rRNA). ATP and rRNA are also the largest cytoplasmic reservoirs of magnesium (Mg²⁺), the most abundant divalent cation in living cells. The co-occurrence of these ionic species in the cytoplasm is not coincidental. Decades of work in the Pi and Mg²⁺ starvation responses of two model enteric bacteria, Escherichia coli and Salmonella enterica, have led to the realization that the metabolisms of Pi and Mg²⁺ are interconnected. Bacteria must acquire these nutrients in a coordinated manner to achieve balanced growth and avoid loss of viability. In this chapter, we will review how bacteria sense and respond to fluctuations in environmental and intracellular Pi and Mg²⁺ levels. We will also discuss how these two compounds are functionally linked, and how cells elicit physiological responses to maintain their homeostasis.

Current Therapy and Therapeutic Targets for Microsporidiosis

Microsporidia are obligate intracellular, spore-forming parasitic fungi which are grouped with the Cryptomycota. They are both opportunistic pathogens in humans and emerging veterinary pathogens. In humans, they cause chronic diarrhea in immune-compromised patients and infection is associated with increased mortality. Besides their role in pébrine in sericulture, which was described in 1865, the prevalence and severity of microsporidiosis in beekeeping and aquaculture has increased markedly in recent decades. Therapy for these pathogens in medicine, veterinary, and agriculture has become a recent focus of attention. Currently, there are only a few commercially available antimicrosporidial drugs. New therapeutic agents are needed for these infections and this is an active area of investigation. In this article we provide a comprehensive summary of the current as well as several promising new agents for the treatment of microsporidiosis including: albendazole, fumagillin, nikkomycin, orlistat, synthetic polyamines, and quinolones. Therapeutic targets which could be utilized for the design of new drugs are also discussed including: tubulin, type 2 methionine aminopeptidase, polyamines, chitin synthases, topoisomerase IV, triosephosphate isomerase, and lipase. We also summarize reports on the utility of complementary and alternative medicine strategies including herbal extracts, propolis, and probiotics. This review should help facilitate drug development for combating microsporidiosis.

Cytoprotective Activity of Polyamines Is Associated with the Alternative Splicing of RAD51A Pre-mRNA in Normal Human CD4+ T Lymphocytes

Physiological polyamines are ubiquitous polycations with pleiotropic biochemical activities, including regulation of gene expression and cell proliferation as well as modulation of cell signaling. They can also decrease DNA damage and promote cell survival. In the present study, we demonstrated that polyamines have cytoprotective effects on normal human CD4⁺ T lymphocytes but not on cancer Jurkat or K562 cells. Pretreatment of lymphocytes with polyamines resulted in a significant reduction in cells with DNA damage induced by doxorubicin, cisplatin, or irinotecan, leading to an increase in cell survival and viability. The induction of RAD51A expression was in response to DNA damage in both cancer and normal cells. However, in normal cells, putrescin pretreatment resulted in alternative splicing of RAD51A and the switch of the predominant expression from the splice variant with the deletion of exon 4 to the full-length variant. Induction of RAD51A alternative splicing by splice-switching oligonucleotides resulted in a decrease in DNA damage and cell protection against cisplatin-induced apoptosis. The results of this study suggest that the cytoprotective activity of polyamines is associated with the alternative splicing of RAD51A pre-mRNA in normal human CD4⁺ T lymphocytes. The difference in the sensitivity of normal and cancer cells to polyamines may become the basis for the use of these compounds to protect normal lymphocytes during lymphoblastic chemotherapy.

Effect of Spermidine on Biofilm Formation in Escherichia coli K-12

Polyamines are essential for biofilm formation in Escherichia coli, but it is still unclear which polyamines are primarily responsible for this phenomenon. To address this issue, we constructed a series of E. coli K-12 strains with mutations in genes required for the synthesis and metabolism of polyamines. Disruption of the spermidine synthase gene (speE) caused a severe defect in biofilm formation. This defect was rescued by the addition of spermidine to the medium but not by putrescine or cadaverine. A multidrug/spermidine efflux pump membrane subunit (MdtJ)-deficient strain was anticipated to accumulate more spermidine and result in enhanced biofilm formation compared to the MdtJ⁺ strain. However, the mdtJ mutation did not affect intracellular spermidine or biofilm concentrations. E. coli has the spermidine acetyltransferase (SpeG) and glutathionylspermidine synthetase/amidase (Gss) to metabolize intracellular spermidine. Under biofilm-forming conditions, not Gss but SpeG plays a major role in decreasing the too-high intracellular spermidine concentrations. Additionally, PotFGHI can function as a compensatory importer of spermidine when PotABCD is absent under biofilm-forming conditions. Last, we report here that, in addition to intracellular spermidine, the periplasmic binding protein (PotD) of the spermidine preferential ABC transporter is essential for stimulating biofilm formation.IMPORTANCE Previous reports have speculated on the effect of polyamines on bacterial biofilm formation. However, the regulation of biofilm formation by polyamines in Escherichia coli has not yet been assessed. The identification of polyamines that stimulate biofilm formation is important for developing novel therapies for biofilm-forming pathogens. This study sheds light on biofilm regulation in E. coli Our findings provide conclusive evidence that only spermidine can stimulate biofilm formation in E. coli cells, not putrescine or cadaverine. Last, ΔpotD inhibits biofilm formation even though the spermidine is synthesized inside the cells from putrescine. Since PotD is significant for biofilm formation and there is no ortholog of the PotABCD transporter in humans, PotD could be a target for the development of biofilm inhibitors.

Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4

The interactions of natural polyamines (putrescine2+, spermidine3+ and spermine4+) with DNA double helix are studied to characterize their nucleotide sequence pattern preference. Atomistic Molecular Dynamics simulations have been carried out for three systems consisting of the same DNA fragment d(CGCGAATTCGCGAATTCGCG) with different polyamines. The results show that polyamine molecules are localized with well-recognized patterns along the double helix with different residence times. We observed a clear hierarchy in the residence times of the polyamines, with the longest residence time (ca 100ns) in the minor groove. The analysis of the sequence dependence shows that polyamine molecules prefer the A-tract regions of the minor groove - in its narrowest part. The preferable localization of putrescine2+, spermidine3+ and spermine4+ in the minor groove with A-tract motifs is correlated with modulation of the groove width by a specific nucleotide sequences. We did develop a theoretical model pointing to the electrostatic interactions as the main driving force in this phenomenon, making it even more prominent for polyamines with higher charges. The results of the study explain the specificity of polyamine interactions with A-tract region of the DNA double helix which is also observed in experiments.

Mygalin: An Acylpolyamine With Bactericidal Activity

Inappropriate use of antibiotics favors the selection and spread of resistant bacteria. To reduce the spread of these bacteria, finding new molecules with activity is urgent and necessary. Several polyamine analogs have been constructed and used to control microorganisms and tumor cells. Mygalin is a synthetic acylpolyamine, which are analogs of spermidine, derived from the hemolymph of the spider Acanthoscurria gomesiana. The effective activity of polyamines and their analogs has been associated with their structure. The presence of two acyl groups in the Mygalin structure may give this molecule a specific antibacterial activity. The aim of this study was to identify the mechanisms involved in the interaction of Mygalin with Escherichia coli to clarify its antimicrobial action. The results indicated that Mygalin exhibits intense dose and time-dependent bactericidal activity. Treatment of E. coli with this molecule caused membrane rupture, inhibition of DNA synthesis, DNA damage, and morphological changes. The esterase activity increased along with the intracellular production of reactive oxygen species (ROS) after treatment of the bacteria with Mygalin. In addition, this molecule was able to sequester iron and bind to LPS. We have shown that Mygalin has bactericidal activity with underlying mechanisms involving ROS generation and chelation of iron ions that are necessary for bacterial metabolism, which may contribute to its microbicidal activity. Taken together, our data suggest that Mygalin can be explored as a new alternative drug with antimicrobial potential against Gram-negative bacteria or other infectious agents.

Polyamine Induction in Postharvest Banana Fruits in Response to NO Donor SNP Occurs via l-Arginine Mediated Pathway and Not via Competitive Diversion of S-Adenosyl-l-Methionine

Nitric oxide (NO) is known to antagonize ethylene by various mechanisms; one of such mechanisms is reducing ethylene levels by competitive action on S-adenosyl-L-methionine (SAM)—a common precursor for both ethylene and polyamines (PAs) biosynthesis. In order to investigate whether this mechanism of SAM pool diversion by NO occur towards PAs biosynthesis in banana, we studied the effect of NO on alterations in the levels of PAs, which in turn modulate ethylene levels during ripening. In response to NO donor sodium nitroprusside (SNP) treatment, all three major PAs viz. putrescine, spermidine and spermine were induced in control as well as ethylene pre-treated banana fruits. However, the gene expression studies in two popular banana varieties of diverse genomes, Nanjanagudu rasabale (NR; AAB genome) and Cavendish (CAV; AAA genome) revealed the downregulation of SAM decarboxylase, an intermediate gene involved in ethylene and PA pathway after the fifth day of NO donor SNP treatment, suggesting that ethylene and PA pathways do not compete for SAM. Interestingly, arginine decarboxylase belonging to arginine-mediated route of PA biosynthesis was upregulated several folds in response to the SNP treatment. These observations revealed that NO induces PAs via l-arginine-mediated route and not via diversion of SAM pool.

Identification of Deregulated Signaling Pathways in Jurkat Cells in Response to a Novel Acylspermidine Analogue-N4-Erucoyl Spermidine

Natural polyamines such as putrescine, spermidine, and spermine are crucial in the cell proliferation and maintenance in all the eukaryotes. However, the requirement of polyamines in tumor cells is stepped up to maintain tumorigenicity. Many synthetic polyamine analogues have been designed recently to target the polyamine metabolism in tumors to induce apoptosis. N⁴-Erucoyl spermidine (designed as N⁴-Eru), a novel acylspermidine derivative, has been shown to exert selective inhibitory effects on both hematological and solid tumors, but its mechanisms of action are unknown. In this study, RNA sequencing was performed to investigate the anticancer mechanisms of N⁴-Eru-treated T-cell acute lymphoblastic leukemia (ALL) cell line (Jurkat cells), and gene expression was examined through different tools. We could show that many key oncogenes including NDRG1, CACNA1G, TGFBR2, NOTCH1,2,3, UHRF1, DNMT1,3, HDAC1,3, KDM3A, KDM4B, KDM4C, FOS, and SATB1 were downregulated, whereas several tumor suppressor genes such as CDKN2AIPNL, KISS1, DDIT3, TP53I13, PPARG, FOXP1 were upregulated. Data obtained through RNA-Seq further showed that N⁴-Eru inhibited the NOTCH/Wnt/JAK-STAT axis. This study also indicated that N⁴-Eru-induced apoptosis could involve several key signaling pathways in cancer. Altogether, our results suggest that N⁴-Eru is a promising drug to treat ALL.

Crystallinity of Double-Stranded RNA-Antimicrobial Peptide Complexes Modulates Toll-Like Receptor 3-Mediated Inflammation

Double-stranded RNA (dsRNA) induces production of pro-inflammatory cytokines in normal human epidermal keratinocytes (NHEK) by specific binding to endosomal Toll-like receptor-3 (TLR3). Recently, it has been shown that hyperactivation of TLR3 in psoriatic keratinocytes by dsRNA can occur in the presence of human antimicrobial peptide (AMP) LL37. Here, we combine synchrotron X-ray scattering, microscopy, computer simulations, and measurements of NHEK cytokine production to elucidate a previously unanticipated form of specific molecular pattern recognition. LL37 and similar α-helical AMPs can form pro-inflammatory nanocrystalline complexes with dsRNA that are recognized by TLR3 differently than dsRNA alone. dsRNA complexes that activate IL-6 production in NHEK and those that do not are both able to enter cells and co-localize with TLR3. However, the crystallinity of these AMP-dsRNA complexes, specifically the geometric spacing between parallel dsRNA and the repeat number of ordered dsRNA, strongly influences the level of TLR3 activation. Crystalline complexes that present dsRNA at a spacing that matches with the steric size of TLR3 can recruit and engage multiple TLR3 receptors, driving receptor clustering and immune amplification, whereas crystalline complexes that exhibit poor steric matching do not. Reverse-transcription quantitative PCR of IL-6 during siRNA knockdown of TLR3 confirms that cytokine production is due to TLR3: High levels of IL-6 transcription are observed for sterically matched complexes without TLR3 knockdown, whereas such activity is abrogated with TLR3 knockdown.

Salt Promotes Protonation of Amine Groups at Air/Water Interface

Interfacial water reorientation caused by charged Langmuir monolayers consisting of primary fatty amine (ODA) and cationic lipid having quaternary amine headgroup (DPTAP) were investigated by interface-selective vibrational sum-frequency generation spectroscopy. For DPTAP monolayer, initially large sum-frequency intensity from interfacial water OH band decreased steadily by increasing monovalent salt (NaCl, NaI) concentration due to counterion adsorption. On the other hand, ODA/water exhibited significantly smaller sum-frequency intensity than DPTAP/water, implying only small portion of protonated amine group (-NH₃⁺) initially existed. By increasing the ionic strength, however, SF intensity of water OH band was enhanced markedly up to ∼1 mM, and then decreased in both NaCl and NaI solutions. By measuring the phase of the sum-frequency spectra, it was found that water dipoles under the ODA headgroup point downward, indicating that the surfaces were always positively charged. This demonstrated that increasing ionic strength facilitates protonation of primary amine headgroups. A simple model based on Poisson-Boltzmann (PB) theory explained this protonation behavior of primary amines.

Guanosine-5'-Monophosphate Polyamine Hybrid Hydrogels: Enhanced Gel Strength Probed by z-Spectroscopy

The self-assembling tendencies of guanosine-5'-monophosphate (GMP) can be drastically increased using polyamines, with potential applications in the production of biocompatible smart materials, as well as for the design of antitumor drugs based on G-quadruplex stabilization. Results from scanning electron microscopy (SEM), wide angle X-ray scattering (WAXS), rheology, and nuclear magnetic resonance (NMR) z-spectroscopy studies are presented.

Cancer cell targeting driven by selective polyamine reactivity with glycine propargyl esters

Glycine propargyl ester reactivity shows evidence for selective polyamine reactivity, leading to a new strategy for cancer cell targeting.

Interactions of diamines with adenosine-5'-triphosphate (ATP) in the systems including copper(II) ions

Interactions were studied in the systems ATP/tn and ATP/Put (tn=1,3-diaminopropane, Put=putrescine) whereas the complexation reactions in ternary systems Cu(II)/ATP/tn and Cu(II)/ATP/Put. Results of the potentiometric and spectroscopic studies evidenced the formation of adducts of the type (ATP)H_x(PA), where PA=diamine. The thermodynamic stability of the complexes and the mode of interactions were determined. On the basis of analysis of changes in the positions of NMR signals, in the pH range of (ATP)H₃(Put) formation, the preferred centres of the interaction between ATP and Put are the endocyclic nitrogen atoms from the nucleotide. On the other hand, the shorter diamine tn in the entire pH range reacts with the phosphate groups from ATP. The positive centres of noncovalent interactions are the protonated NH_x⁺ groups from amines. In both complexes Cu(ATP)H₂(tn) and Cu(ATP)H₃(Put) formed in ternary systems at pH<6.5, the amines are in the outer sphere of coordination with the noncovalent interaction with anchoring Cu(ATP). Only the phosphate groups from the nucleotide take part in metalation. At higher pH in the range of Cu(ATP)(PA) complex formation, significant differences in the reactions of the two amines appear. The shorter one (tn) binds Cu(II) ions with two nitrogen atoms, while putrescine coordinates in the monofunctional mode, which is undoubtedly related to the differences in lengths of methylene chain. This explains the considerable differences in the stability of Cu(ATP)(tn) and Cu(ATP)(Put). In both complexes the nucleotide is coordinated through phosphate groups.

SYNOPSIS

As a result of noncovalent interactions ATP forms molecular complexes with 1,3-diaminopropane and 1,4-diaminobutane (putrescine). Significant differences in the mode of interactions between the two diamines were observed in ATP/diamine binary systems and in ternary systems Cu(II)/ATP/diamine, at high pH.

Polyamines metabolism and breast cancer: state of the art and perspectives

Breast cancer (BC) is a common disease that generally occurs in women over the age of 50, and the risk is especially high for women over 60 years of age. One of the major BC therapeutic problems is that tumors initially responsive to chemotherapeutic approaches can progress to more aggressive forms poorly responsive to therapies. Polyamines (PAs) are small polycationic alkylamines, naturally occurring and essential for normal cell growth and development in eukaryotes. The intracellular concentration of PA is maintained within strongly controlled contents, while a dysregulation occurs in BC cells. Polyamines facilitate the interactions of transcription factors, such as estrogen receptors with their specific response element, and are involved in the proliferation of ER-negative and highly invasive BC tumor cells. Since PA metabolism has a critical role in cell death and proliferation, it represents a potential target for intervention in BC. The goal of this study was to perform a literature search reviewing the association between PA metabolism and BC, and the current evidence supporting the BC treatment targeting PA metabolism. We here describe in vitro and in vivo models, as well as the clinical trials that have been utilized to unveil the relationship between PA metabolism and BC. Polyamine pathway is still an important target for the development of BC chemotherapy via enzyme inhibitors. Furthermore, a recent promising strategy in breast anticancer therapy is to exploit the self-regulatory nature of PA metabolism using PA analogs to affect PA homeostasis. Nowadays, antineoplastic compounds targeting the PA pathway with novel mechanisms are of great interest and high social impact for BC chemotherapy.

Amine oxidase copper-containing 1 (AOC1) is a downstream target gene of the Wilms tumor protein, WT1, during kidney development

Amine oxidase copper-containing 1 (AOC1; formerly known as amiloride-binding protein 1) is a secreted glycoprotein that catalyzes the degradation of putrescine and histamine. Polyamines and their diamine precursor putrescine are ubiquitous to all organisms and fulfill pivotal functions in cell growth and proliferation. Despite the importance of AOC1 in regulating polyamine breakdown, very little is known about the molecular mechanisms that control its expression. We report here that the Wilms tumor protein, WT1, which is necessary for normal kidney development, activates transcription of the AOC1 gene. Expression of a firefly luciferase reporter under control of the proximal AOC1 promoter was significantly enhanced by co-transfection of a WT1 expression construct. Binding of WT1 protein to a cis-regulatory element in the AOC1 promoter was confirmed by electrophoretic mobility shift assay and chromatin immunoprecipitation. Antisense inhibition of WT1 protein translation strongly reduced Aoc1 transcripts in cultured murine embryonic kidneys and gonads. Aoc1 mRNA levels correlated with WT1 protein in several cell lines. Double immunofluorescent staining revealed a co-expression of WT1 and AOC1 proteins in the developing genitourinary system of mice and rats. Strikingly, induced changes in polyamine homeostasis affected branching morphogenesis of cultured murine embryonic kidneys in a developmental stage-specific manner. These findings suggest that WT1-dependent control of polyamine breakdown, which is mediated by changes in AOC1 expression, has a role in kidney organogenesis.

The effect of polyamines on the binding of anti-DNA antibodies from patients with SLE and normal human subjects

Antibodies to DNA (anti-DNA) are the serological hallmark of systemic lupus erythematosus (SLE). To elucidate specificity further, the effect of polyamines on the binding of anti-DNA antibodies from patients with lupus was tested by ELISA to calf thymus (CT) DNA; we also assessed the binding of plasmas of patients and normal human subjects (NHS) to Micrococcus luteus (MC) DNA. As these studies showed, spermine can dose-dependently inhibit SLE anti-DNA binding to CT DNA and can promote dissociation of preformed immune complexes. With MC DNA as antigen, spermine failed to inhibit the NHS anti-DNA binding. Studies using plasmas adsorbed to a CT DNA cellulose affinity indicated that SLE plasmas are mixtures of anti-DNA that differ in inhibition by spermine and binding to conserved and non-conserved determinants. Together, these studies demonstrate that spermine can influence the binding of anti-DNA autoantibodies and may contribute to the antigenicity of DNA.

Insight into the molecular recognition of spermine by DNA quadruplexes from an NMR study of the association of spermine with the thrombin-binding aptamer

The preferred residence sites and the conformation of DNA-bound polyamines are central to understanding the regulatory roles of polyamines. To this end, we have used a series of selective (13)C-edited and selective total correlation spectroscopy-edited one-dimensional (1D) nuclear Overhauser effect spectroscopy NMR experiments to determine a number of intramolecular (1)H nuclear Overhauser effect (NOE) connectivities in (13)C-labelled spermine bound to the thrombin-binding aptamer. The results provide evidence that the aptamer-bound spermine adopts a conformation that optimizes electrostatic and hydrogen bond contacts with the aptamer backbone. The distance between the nitrogen atoms of the central aminobutyl is reduced by an increase in the population of gauche conformers at the C6-C7 bonds, which results in either a curved or S-shaped spermine conformation. Molecular modelling contributes insight toward the mode of spermine binding of these spermine structures within the narrow grooves of DNA quadruplexes. In each case, the N5 ammonium group makes hydrogen bonds with two nearby phosphates across the narrow groove. Our results have implications for the understanding of chromatin structure and the rational design of quadruplex-binding drugs.

In silico studies toward understanding the interactions of DNA base pairs with protonated linear/cyclic diamines

Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc-pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions.

Polyamines and cancer: implications for chemotherapy and chemoprevention

Polyamines are small organic cations that are essential for normal cell growth and development in eukaryotes. Under normal physiological conditions, intracellular polyamine concentrations are tightly regulated through a dynamic network of biosynthetic and catabolic enzymes, and a poorly characterised transport system. This precise regulation ensures that the intracellular concentration of polyamines is maintained within strictly controlled limits. It has frequently been observed that the metabolism of, and the requirement for, polyamines in tumours is frequently dysregulated. Elevated levels of polyamines have been associated with breast, colon, lung, prostate and skin cancers, and altered levels of rate-limiting enzymes in both biosynthesis and catabolism have been observed. Based on these observations and the absolute requirement for polyamines in tumour growth, the polyamine pathway is a rational target for chemoprevention and chemotherapeutics. Here we describe the recent advances made in the polyamine field and focus on the roles of polyamines and polyamine metabolism in neoplasia through a discussion of the current animal models for the polyamine pathway, chemotherapeutic strategies that target the polyamine pathway, chemotherapeutic clinical trials for polyamine pathway-specific drugs and ongoing clinical trials targeting polyamine biosynthesis.

Radioprotective efficacy and toxicity of a new family of aminothiol analogs

PURPOSE

A family of 17 new nucleophilic-polyamine and aminothiol structures was designed and synthesized to identify new topical or systemic radioprotectors with acceptable mammalian toxicity profiles. design elements included: (i) Length and charge of the DNA-interacting, alkylamine backbone, (ii) nucleophilicity of the reactive oxygen species (ROS)-scavenging group, and (iii) non-toxic drug concentration achievable in animal tissues.

MATERIALS AND METHODS

Mouse maximum tolerated doses (MTD) were determined by increasing intraperitoneal (IP) doses. To assess radioprotective efficacy, mice received IP 0.5 MTD doses prior to an LD95 radiation dose (8.63 Gy), and survival was monitored. Topically applied aminothiol was also scored for prevention of radiation-induced dermatitis (17.3 Gy to skin).

RESULTS

The most radioprotective aminothiols had 4-6 carbons and 1-2 amines, and unlike amifostine and its analogs, displayed a terminal thiol from an alkyl side chain that projected the thiol away from the DNA major groove into the environment surrounding the DNA. The five carbon, single thiol, alkylamine, PrC-210, conferred 100% survival to an otherwise 100% lethal dose of whole-body radiation and achieved 100% prevention of Grade 2-3 radiation dermatitis. By mass spectrometry analysis, the one aminothiol that was tested formed mixed disulfides with cysteine and glutathione.

CONCLUSIONS

Multiple, highly radioprotective, aminothiol structures, with acceptable systemic toxicities, were identified.

Oligoamine analogues in combination with 2-difluoromethylornithine synergistically induce re-expression of aberrantly silenced tumour-suppressor genes

Epigenetic gene silencing is an important mechanism in the initiation and progression of cancer. Abnormal DNA CpG island hypermethylation and histone modifications are involved in aberrant silencing of tumour-suppressor genes. LSD1 (lysine-specific demethylase 1) was the first enzyme identified to specifically demethylate H3K4 (Lys⁴ of histone H3). Methylated H3K4 is an important mark associated with transcriptional activation. The flavin adenine dinucleotide-binding amine oxidase domain of LSD1 is homologous with two polyamine oxidases, SMO (spermine oxidase) and APAO (N¹-acetylpolyamine oxidase). We have demonstrated previously that long-chain polyamine analogues, the oligoamines, are inhibitors of LSD1. In the present paper we report the synergistic effects of specific oligoamines in combination with DFMO (2-difluoromethylornithine), an inhibitor of ornithine decarboxylase, in human colorectal cancer cells. DFMO treatment depletes natural polyamines and increases the uptake of exogenous polyamines. The combination of oligoamines and DFMO results in a synergistic re-expression of aberrantly silenced tumour-suppressor genes, including SFRP2 (secreted frizzled-related protein 2), which encodes a Wnt signalling pathway antagonist and plays an anti-tumorigenic role in colorectal cancer. The treatment-induced re-expression of SFRP2 is associated with increased H3K4me2 (di-methyl H3K4) in the gene promoter. The combination of LSD1-inhibiting oligoamines and DFMO represents a novel approach to epigenetic therapy of cancer.

The spider acylpolyamine Mygalin is a potent modulator of innate immune responses

Mygalin is an antibacterial molecule isolated from the hemocytes of the spider Acanthoscurria gomesiana. It was identified as bis-acylpolyamine spermidine. We evaluated the modulator effects of synthetic Mygalin in the innate immune response. We demonstrate that Mygalin induces IFN-γ synthesis by splenocytes increasing the nitrite secretion by splenocytes and macrophages. A specific inhibitor of iNOS abrogated Mygalin-induced nitrite production in macrophages independent of IFN-γ activation. In addition, Mygalin-activated macrophages produced TNF-α but not IL-1β, demonstrating that Mygalin does not act directly on the inflammasome. Furthermore, this compound did not affect spontaneous or Concanavalin A-induced proliferative responses by murine splenocytes and did not induce IL-5 or apoptosis of splenocytes or bone marrow-derived macrophages. These data provide evidence that Mygalin modulates the innate immune response by inducing IFN-γ and NO synthesis. The combined immune regulatory and antibacterial qualities of Mygalin should be explored as a strategy to enhance immune responses in infection.

Nitric oxide counters ethylene effects on ripening fruits

Ethylene plays a key role in promoting fruit ripening, so altering its biosynthesis/signaling could be an important means to delay this process. Nitric oxide (NO)-generated signals are now being shown to regulate ethylene pathways. NO signals have been shown to transcriptionally repress the expression of genes involved in ethylene biosynthesis enzymes and post-translationally modify methionine adenosyl transferase (MAT) activity through S-nitrosylation to reduce the availably of methyl groups required to produce ethylene. Additionally, NO cross-talks with plant hormones and other signal molecules and act to orchestrate the suppression of ethylene effects by modulating enzymes/proteins that are generally triggered by ethylene signaling at post-climacteric stage. Thus, medication of endogenous NO production is suggested as a strategy to postpone the climacteric stage of many tropical fruits.

CYTOTOXICITY OF POLYAMINE ANALOGS IS DIRECTLY RELATED TO THEIR DNA AFFINITY AS DETERMINED BY POLYACRYLAMIDE GEL COELECTROPHORESIS (PACE) METHOD

Polyamines are essential for cell growth. Polyamine analogs that can replace intracellular polyamines inhibit tumor cell proliferation both in culture as well as in animal models. The positively charged polyamines interact with the negatively charged DNA backbone both in a nonspecific manner, as well as sequence specifically through direct or water mediated hydrogen bonds. Therefore, it is difficult to ascertain the exact interactions that regulate the biological functions of polyamines. Several attempts have been made to determine the thermodynamic parameters of polyamine-DNA interactions with conflicting results. Here, we report a simple method of determining the apparent association constants for polyamine-DNA interaction by using polyacrylamide gel coelectrophoresis (PACE). We have used several cytotoxic polyamine analogs of different conformations and chain lengths. We observed that polyamine analogs with higher charge density or with conformational restrictions, which are absent in the naturally occurring polyamines, interact with DNA more strongly than do natural polyamines. A comparison of the cytotoxicities of the polyamine analogs against human tumor cell lines with their DNA affinities revealed that the higher the DNA affinity the more the cytoxicity of the analogs. The direct correlation between DNA affinities and cytotoxities provides a novel method for a rational design of therapeutically effective cytotoxic polyamine analogs.

Synthesis and growth regulatory activity of a prototype member of a new family of aminothiol radioprotectors

The synthesis, growth inhibition and radioprotective activity of the PrC-210 aminothiol, 3-(methylamino)-2-((methylamino)methyl)propane-1-thiol, and its polyamine and thiolated polyamine progenitors are reported. All of the molecules significantly inhibited growth of cultured normal human fibroblasts. The combination of an ROS-scavenging thiol group and a positively charged alkyl-amine backbone provided the most radioprotective aminothiol molecule.

Polyamine analogs modulate gene expression by inhibiting lysine-specific demethylase 1 (LSD1) and altering chromatin structure in human breast cancer cells

Aberrant epigenetic repression of gene expression has been implicated in most cancers, including breast cancer. The nuclear amine oxidase, lysine-specific demethylase 1 (LSD1) has the ability to broadly repress gene expression by removing the activating mono- and di-methylation marks at the lysine 4 residue of histone 3 (H3K4me1 and me2). Additionally, LSD1 is highly expressed in estrogen receptor α negative (ER-) breast cancer cells. Since epigenetic marks are reversible, they make attractive therapeutic targets. Here we examine the effects of polyamine analog inhibitors of LSD1 on gene expression, with the goal of targeting LSD1 as a therapeutic modality in the treatment of breast cancer. Exposure of the ER-negative human breast cancer cells, MDA-MB-231 to the LSD1 inhibitors, 2d or PG11144, significantly increases global H3K4me1 and H3K4me2, and alters gene expression. Array analysis indicated that 98 (75 up and 23 down) and 477 (237 up and 240 down) genes changed expression by at least 1.5-fold or greater after treatment with 2d and PG11144, respectively. The expression of 12 up-regulated genes by 2d and 14 up-regulated genes by PG11144 was validated by quantitative RT-PCR. Quantitative chromatin immunoprecipitation (ChIP) analysis demonstrated that up-regulated gene expression by polyamine analogs is associated with increase of the active histone marks H3K4me1, H3K4me2 and H3K9act, and decrease of the repressive histone marks H3K9me2 and H3K27me3, in the promoter regions of the relevant target genes. These data indicate that the pharmacologic inhibition of LSD1 can effectively alter gene expression and that this therapeutic strategy has potential.

Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding

Magnesium plays a special role in RNA function and folding. Although water is magnesium's most common first-shell ligand, the oxyanions of RNA have significant affinity for magnesium. Here we provide a quantum mechanical description of first-shell RNA-magnesium and DNA-magnesium interactions, demonstrating the unique features that characterize the energetics and geometry of magnesium complexes within large folded RNAs. Our work focuses on bidentate chelation of magnesium by RNA or DNA, where multiple phosphate oxyanions enter the first coordination shell of magnesium. These bidentate RNA clamps of magnesium occur frequently in large RNAs. The results here suggest that magnesium, compared to calcium and sodium, has an enhanced ability to form bidentate clamps with RNA. Bidentate RNA-sodium clamps, in particular, are unstable and spontaneously open. Due to magnesium's size and charge density it binds more intimately than other cations to the oxyanions of RNA, so that magnesium clamps are stabilized not only by electrostatic interactions, but also by charge transfer, polarization, and exchange interactions. These nonelectrostatic components of the binding are quite substantial with the high charge and small interatomic distances within the magnesium complexes, but are less pronounced for calcium due to its larger size, and for sodium due to its smaller charge. Additionally, bidentate RNA clamps of magnesium are more stable than those with DNA. The source of the additional stability of RNA complexes is twofold: there is a slightly attenuated energetic penalty for ring closure in the formation of RNA bidentate chelation complexes and elevated electrostatic interactions between the RNA and cations. In sum, it can be seen why sodium and calcium cannot replicate the structures or energetics of RNA-magnesium complexes.

Probing tRNA interaction with biogenic polyamines

Biogenic polyamines are found to modulate protein synthesis at different levels. This effect may be explained by the ability of polyamines to bind and influence the secondary structure of tRNA, mRNA, and rRNA. We report the interaction between tRNA and the three biogenic polyamines putrescine, spermidine, spermine, and cobalt(III)hexamine at physiological conditions, using FTIR spectroscopy, capillary electrophoresis, and molecular modeling. The results indicated that tRNA was stabilized at low biogenic polyamine concentration, as a consequence of polyamine interaction with the backbone phosphate group. The main tRNA reactive sites for biogenic polyamine at low concentration were guanine-N7/O6, uracil-O2/O4, adenine-N3, and 2'OH of the ribose. At high polyamine concentration, the interaction involves guanine-N7/O6, adenine-N7, uracil-O2 reactive sites, and the backbone phosphate group. The participation of the polycation primary amino group, in the interaction and the presence of the hydrophobic contact, are also shown. The binding affinity of biogenic polyamine to tRNA molecule was in the order of spermine > spermidine > putrescine with K(Spm) = 8.7 × 10(5) M(-1), K(Spd) = 6.1 × 10(5) M(-1), and K(Put) = 1.0 × 10(5) M(-1), which correlates with their positively charged amino group content. Hill analysis showed positive cooperativity for the biogenic polyamines and negative cooperativity for cobalt-hexamine. Cobalt(III)hexamine contains high- and low-affinity sites in tRNA with K(1) = 3.2 × 10(5) M(-1) and K(2) = 1.7 × 10(5) M(-1), that have been attributed to the interactions with guanine-N7 sites and the backbone PO(2) group, respectively. This mechanism of tRNA binding could explain the condensation phenomenon observed at high Co(III) content, as previously shown in the Co(III)-DNA complexes.

Coordination Reactions and Noncovalent Interactions of Polyamines with Nucleotides in Binary Systems and with Nucleotides and Copper(II) Ion in Ternary Systems

Interactions of nucleotides (AMP, CMP) and 1,2-diaminopropane (tn-1) or 2-methyl-1,2-diaminopropane (tn-2) in metal-free systems as well as in the systems including copper(II) ions were studied. The composition and overall stability constants of the complexes formed were determined by the potentiometric method, whereas the interaction centres and coordination sites were identified by spectroscopic methods. It was found that phosphate groups of nucleotides and the protonated amine groups of polyamines are the centres of interaction. The differences in the interactions with the polyamines which act as models of biogenic amines are impacted by the presence of lateral chains (methylene groups) in tn-1 and tn-2. In the ternary systems with Cu(II) ions, the heteroligand complexes are mainly of the ML⋯L' type, in which the protonated polyamine is engaged in noncovalent interactions with the anchoring Cu(II)-nucleotide complex. The complexes formed in the Cu/NMP)/tn-1 system are more stable than those formed in the system with tn-2. The mode of coordination in the complex is realised mainly through the phosphate groups of the nucleotide with involvement of the endocyclic nitrogen atoms in a manner which depends upon the steric conditions and in particular on the number of the methylene groups in the polyamine molecule.

Nitric oxide in fruit ripening: trends and opportunities

Monitoring ethylene is crucial in regulating post-harvest life of fruits. The concept of nitric oxide (NO) involvement in antagonizing ethylene is new. NO mediated physiologies casted through regulation of plant hormones are widely reported during developmental and stress chemistry having no direct link with ripening. Research in NO biology and understanding its interplay with other signal molecules in ripening fruits suggest ways of achieving greater synergies with NO applications. Experiments focused at convincingly demonstrating the involvement of NO in altering ripening-related ethylene profile of fruits, would help develop new processes for shelf life extension. This issue being the central theme of this review, the putative mechanisms of NO intricacies with other primary and secondary signals are hypothesized. The advantage of eliciting NO endogenously may open up various biotechnological opportunities for its precise delivery into the target tissues.

Novel oligoamine analogues inhibit lysine-specific demethylase 1 and induce reexpression of epigenetically silenced genes

PURPOSE

Abnormal DNA CpG island hypermethylation and transcriptionally repressive histone modifications are associated with the aberrant silencing of tumor suppressor genes. Lysine methylation is a dynamic, enzymatically controlled process. Lysine-specific demethylase 1 (LSD1) has recently been identified as a histone lysine demethylase. LSD1 specifically catalyzes demethylation of mono- and dimethyl-lysine 4 of histone 3 (H3K4), key positive chromatin marks associated with transcriptional activation. We hypothesized that a novel class of oligoamine analogues would effectively inhibit LSD1 and thus cause the reexpression of aberrantly silenced genes.

EXPERIMENTAL DESIGN

Human colorectal cancer cells were treated with the oligoamines and changes in mono- and dimethyl-H3K4 and other chromatin marks were monitored. In addition, treated cells were evaluated for the reexpression of the aberrantly silenced secreted frizzled-related proteins (SFRP) Wnt signaling pathway antagonist genes. Finally, the effects of the LSD1 inhibitors were evaluated in an in vivo xenograft model.

RESULTS

Treatment of HCT116 human colon adenocarcinoma cells in vitro resulted in increased H3K4 methylation and reexpression of silenced SFRP genes. This reexpression is also accompanied by a decrease in H3K9me2 repressive mark. Importantly, cotreatment with low doses of oligoamines and a DNA methyltransferase inhibitor highly induces the reexpression of the aberrantly silenced SFRP2 gene and results in significant inhibition of the growth of established tumors in a human colon tumor model in vivo.

CONCLUSIONS

The use of LSD1-inhibiting oligoamine analogues in combination with DNA methyltransferase inhibitors represents a highly promising and novel approach for epigenetic therapy of cancer.

Regulation of gene expression by PrrA in Rhodobacter sphaeroides 2.4.1: role of polyamines and DNA topology

In the present study, we show in vitro binding of PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, to the PrrA site 2, within the RSP3361 locus. Specific binding, as shown by competition experiments, requires the phosphorylation of PrrA. The binding affinity of PrrA for site 2 was found to increase 4- to 10-fold when spermidine was added to the binding reaction. The presence of extracellular concentrations of spermidine in growing cultures of R. sphaeroides gave rise to a twofold increase in the expression of the photosynthesis genes pucB and pufB, as well as the RSP3361 gene, under aerobic growth conditions, as shown by the use of lacZ transcriptional fusions, and led to the production of light-harvesting spectral complexes. In addition, we show that negative supercoiling positively regulates the expression of the RSP3361 gene, as well as pucB. We show the importance of supercoiling through an evaluation of the regulation of gene expression in situ by supercoiling, in the case of the former gene, as well as using the DNA gyrase inhibitor novobiocin. We propose that polyamines and DNA supercoiling act synergistically to regulate expression of the RSP3361 gene, partly by affecting the affinity of PrrA binding to the PrrA site 2 within the RSP3361 gene.

Polyamine catabolism in colorectal cancer cells following treatment with oxaliplatin, 5-fluorouracil and N1, N11 diethylnorspermine

PURPOSE

Our previous studies showed that combined treatment of oxaliplatin and N(1), N(11) diethyl-norspermine (DENSPM) results in massive induction of spermidine/spermine N(1)-acetyltransferase (SSAT) mRNA and activity. Since oxaliplatin and 5-fluorouracil (5FU) are used clinically in treatment of colorectal cancers, this study examines the effect of adding DENSPM to oxaliplatin/5FU combination on SSAT and spermine oxidase (SMO) in HCT-116 cells.

METHODS

HCT-116 cells were treated with clinically relevant concentrations of drugs for 20 h followed by 24 h in drug free medium. SSAT and SMO mRNA and protein were assayed by QRT-PCR and Westerns respectively; polyamine pools were measured by HPLC. SSAT and SMO mRNA in tumor biopsies from patients with rectal cancer receiving oxaliplatin, capecitabine and radiation were measured by QRT-PCR.

RESULTS

Oxaliplatin + 5FU + DENSPM produced significantly higher levels of SSAT and SMO mRNA, protein and activity than those seen with oxaliplatin+5FU with a significant depletion of cellular spermine and spermidine pools. Oxaliplatin/DENSPM was superior to 5FU/DENSPM in SSAT induction but similar for SMO. Oxaliplatin + DENSPM revealed synergistic growth inhibition at >IC(50) concentrations and antagonism at

CONCLUSIONS

These studies demonstrated that combining DENSPM with oxaliplatin + 5FU provides an added benefit by aiming at the clinically relevant therapeutic target, the polyamine catabolism. Further, we show for the first time, that SMO and SSAT induction could be measured in tumor biopsies in patients receiving chemo-radiation. Optimization of treatment conditions in vivo should facilitate a clinical evaluation of the three drug combination.

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Key Words Collapse

MESH Headings

• Acetyltransferases/genetics
• Acetyltransferases/metabolism
• Antineoplastic Combined Chemotherapy Protocols/pharmacology
• Antineoplastic Combined Chemotherapy Protocols/therapeutic use
• Blotting, Western
• Cell Line, Tumor
• Colonic Neoplasms/drug therapy
• Colonic Neoplasms/metabolism
• Colonic Neoplasms/pathology
• Drug Synergism
• Fluorouracil/pharmacology
• Fluorouracil/therapeutic use
• Gene Expression/drug effects
• Humans
• Organoplatinum Compounds/pharmacology
• Organoplatinum Compounds/therapeutic use
• Oxaliplatin
• Oxidoreductases Acting on CH-NH Group Donors/genetics
• Oxidoreductases Acting on CH-NH Group Donors/metabolism
• Polyamines/metabolism
• Rectal Neoplasms/drug therapy
• Rectal Neoplasms/metabolism
• Rectal Neoplasms/pathology
• Spermine/analogs & derivatives
• Spermine/pharmacology
• Spermine/therapeutic use
• Polyamine Oxidase

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Grants

• CA 10656 NCI NIH HHS
• CA 109619 NCI NIH HHS

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Affiliation(s)

Suzanne Hector Department of Medicine, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
Ramakumar Tummala
Nicholas D Kisiel
Paula Diegelman
Slavoljub Vujcic
Kimberly Clark
Marwan Fakih
Debora L Kramer
Carl W Porter
Lakshmi Pendyala

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In Silico Chemical Library Screening and Experimental Validation of a Novel 9-Aminoacridine Based Lead-Inhibitor of Human S-Adenosylmethionine Decarboxylase

In silico chemical library screening (virtual screening) was used to identify a novel lead compound capable of inhibiting S-adenosylmethionine decarboxylase (AdoMetDC). AdoMetDC is intimately involved in the biosynthesis of polyamines, which are essential for tumor progression and are elevated in numerous types of tumors. Therefore, inhibition of this enzyme provides an attractive target for the discovery of novel anticancer drugs. We performed virtual screening using a computer model derived from the X-ray crystal structure of human AdoMetDC and the National Cancer Institute's Diversity Set (1990 compounds). Our docking study suggested several compounds that could serve as drug candidates since their docking modes and scores revealed potential inhibitory activity toward AdoMetDC. Experimental testing of the top-scoring compounds indicated that one of these compounds (NSC 354961) possesses an IC50 in the low micromolar range. A search of the entire NCI compound collection for compounds similar to NSC 354961 yielded two additional compounds that exhibited activity in the experimental assay but with significantly diminished potency relative to NSC 354961. In this report, we disclose the activity of NSC 354961 against AdoMetDC and its probable binding mode based on computational modeling. We also discuss the importance of virtual screening in the context of enzymes that are not readily amenable to high-throughput assays, thereby demonstrating the efficacy of virtual screening, combined with selective experimental testing, in identifying new potential drug candidates.