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With the emergence of new viruses in the human population and the fast mutation rates of existing viruses, new antiviral targets and compounds are needed. Most existing antiviral drugs are active against proteins of a handful of viruses. Most of these proteins in the end affect viral nucleic acid processing, but direct nucleic acid targeting is less represented due to the difficulty of selectively acting at the nucleic acid of interest. Recently, nucleic acids have been shown to fold in structures alternative to the classic double helix and Watson and Crick base-pairing. Among these non-canonical structures, G-quadruplexes (G4s) have attracted interest because of their key biological roles that are being discovered. Molecules able to selectively target G4s have been developed and since G4s have been investigated as targets in several human pathologies, including viral infections. Here, after briefly introducing viruses, G4s and the G4-binding molecules with antiviral properties, we comment on the mechanisms at the base of the antiviral activity reported for G4-binding molecules. Understanding how G4-ligands act in infected cells will possibly help designing and developing next-generation antiviral drugs., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Antibacterial potential of Limonene against Multi Drug Resistant (MDR) pathogens was studied and mechanism explored. Microscopic techniques viz. Fluorescent Microscopy (FM), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM) indicated membrane disruption, cellular leakage and cell death of Escherichia coli (E. coli) cells when treated with limonene. Leakage of intracellular proteins, lipids and nucleic acid confirmed membrane damage and disruption of cell permeability barrier. Further, release of intracellular ATP, also suggested disruption of membrane barrier. Interaction of limonene with DNA revealed its capability in unwinding of plasmid, which could eventually inhibit DNA transcription and translation. Differential expression of various proteins and enzymes involved in transport, respiration, metabolism, chemotaxis, protein synthesis confirmed the mechanistic role of limonene on their functions. Limonene thus can be a potential candidate in drug development.

To reveal the protective effect of Terminalia chebula Retz (TCR) on cardiotoxicity induced by radix of Aconitum kusnezoffii Reichb (AKR). Control, AKR, AKR-TCR 1:3, AKR-TCR 1:1, AKR-TCR 3:1 and TCR-prepared AKR groups were set up. After treatment, the heart tissues were observed by H&E staining and transmission electron microscope. Serum myoglobin (MB) and troponin (cTn) were detected by ELISA. UPLC-Q Exactive/MS analysis was performed to detect the metabolic difference among the groups. ELISA results showed that the MB and cTn values of AKR group were significantly higher than Control group (P<0.05), while those of the other groups were lower than AKR group. TCR-prepared AKR group had similar MB and cTn contents to the Control group. Histopathological examination also indicated better detoxifying effects in the TCR-prepared AKR and AKR-TCR 1:1 group. The serum metabolomics analysis showed obvious distinction between the AKR and Control groups, while AKR-TCR combination reversed the metabolomics changes induced by AKR. Through multivariate statistical analysis, 9 metabolic markers related to energy, nucleic acid and amino acid metabolism were identified. Conclusively, AKR-induced cardiotoxicity may be related to energy, nucleic acid and amino acid metabolism, and TCR can reduce the cardiotoxicity by regulating the relative metabolism pathways.

Diagnosis of osteocartilaginous pathologies depends on morphological examination and immunohistochemical and molecular biology analyses. Decalcification is required before tissue processing, but available protocols often lead to altered proteins and nucleic acids, and thus compromise the diagnosis. The objective of this study was to compare the effect of different methods of decalcification on histomolecular analyses required for diagnosis and to recommend an optimal protocol for processing these samples in routine practice. We prospectively submitted 35 tissue samples to different decalcification procedures with hydrochloric acid, formic acid, and EDTA, in short, overnight and long cycles for 1 to >10 cycles. Preservation of protein integrity was examined by immunohistochemistry, and quality of nucleic acids was estimated after extraction (DNA and RNA concentrations, 260/280 ratios, PCR cycle thresholds), analysis of DNA mutations (high-resolution melting) or amplifications (PCR, in situ hybridization), and detection of fusion transcripts (RT-PCR, in situ hybridization). Hydrochloric acid- and long-term formic acid-based decalcification induced false-negative results on immunohistochemistry and molecular analysis. EDTA and short-term formic acid-based decalcification (<5 cycles of 6 h each) did not alter antigenicity and allowed for detection of gene mutations, amplifications or even fusion transcripts. EDTA showed superiority for in situ hybridization techniques. According to these results and our institutional experience, we propose recommendations for decalcification of bone samples, from biopsies to surgical specimens.

The use of nanoparticles (NP) as dose enhancers in radiotherapy (RT) is a growing research field. Recently, the use of NP has been extended to charged particle therapy in order to improve the performance in radioresistant tumors. However, the biological mechanisms underlying the synergistic effects involved in NP-RT approaches are not clearly understood. Here, we used the capabilities of synchrotron-based Fourier Transform Infrared Microspectroscopy (SR-FTIRM) as a bio-analytical tool to elucidate the NP-induced cellular damage at the molecular level and at a single-cell scale. F98 glioma cells doped with AuNP and GdNP were irradiated using several types of medical ion beams (proton, helium, carbon and oxygen). Differences in cell composition were analyzed in the nucleic acids, protein and lipid spectral regions using multivariate methods (Principal Component Analysis, PCA). Several NP-induced cellular modifications were detected, such as conformational changes in secondary protein structures, intensity variations in the lipid CHx stretching bands, as well as complex DNA rearrangements following charged particle therapy irradiations. These spectral features seem to be correlated with the already shown enhancement both in the DNA damage response and in the reactive oxygen species (ROS) production by the NP, which causes cell damage in the form of protein, lipid, and/or DNA oxidations. Vibrational features were NP-dependent due to the NP heterogeneous radiosensitization capability. Our results provided new insights into the molecular changes in response to NP-based RT treatments using ion beams, and highlighted the relevance of SR-FTIRM as a useful and precise technique for assessing cell response to innovative radiotherapy approaches.

Organometallic complexes have widely been used for the treatment of various diseases viz., malaria, arthritis, syphilis, pernicious anemia, tuberculosis and particular in cancers. Recent decades have witnessed an upsurging interest in the application of organometallic compounds to treat various phenotypes of cancers with multiple etiologies. The unique and exceptional properties of organometallic compounds, intermediate between classical inorganic and organic materials provide new insight in the progress of inorganic medicinal chemistry. Herein, we have selectively focused on various organometallic sandwich and half-sandwich complexes of ruthenium (Ru), titanium (Ti), gold (Au) and iron (Fe) exhibiting promising activity towards a panel of cancer cell lines and resistant cancer cell lines. These complexes exhibit novel mechanisms of drug action through incorporation of outer-sphere recognition of molecular targets and controlled activation features based on ligand substitution along with monometallic and heterometallic redox processes. Furthermore, they are usually found to be uncharged or neutral possessing metals in a low oxidation state, exhibit kinetic stability, relative lipophilicity and are amenable to a host of various chemical transformations. This review mainly sheds light on the successful advancement of organometallic complexes as anticancer drug aspirants in relation to their versatile structural chemistry and innovative mechanisms of action targeting nucleic acids, several enzymes viz; thioredoxin reductases (Thrx), EGFR, transferrin, cathepsin B, topoisomerases etc., (Copyright © 2019 Elsevier Masson SAS. All rights reserved.)

Innate immune sensing of nucleic acids derived from invading pathogens or tumor cells via pattern recognition receptors is crucial for mounting protective immune responses against infectious disease and cancer. Recently, discovery of tremendous amounts of nucleic acid sensors as well as identification of natural and synthetic ligands for these receptors revealed the potential of adjuvants targeting nucleic acid sensing pathways for designing efficacious vaccines. Especially, current data indicated that unique adjuvants targeting TLR9 and stimulator of interferon genes (STING)-dependent cytosolic nucleic acid sensing pathways along with the combinations of already existing adjuvants are promising candidates for this purpose. Here, we review current vaccine adjuvants targeting nucleic acid sensors and their modes of action., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Sambucus ebulus is a rich source of ribosome-inactivating proteins (RIPs) and RIP-related lectins generated from multiple genes. These proteins differ in their structure, enzymatic activity and sugar binding specificity., Methods: We have purified and characterized ebulin-RP from S. ebulus leaves and determined the amino acid sequence by cDNA cloning. Cytotoxicity was studied in a variety of cancer cells and a comparative study of the ability of ebulin-RP to bind sugars using "in vitro" and "in silico" approaches was performed., Results: Ebulin-RP is a novel heterodimeric type 2 RIP present in S. ebulus leaves together with the type 2 RIP ebulin l, which displayed rRNA N-glycosidase activity but unlike ebulin l, lacked functional sugar binding domains. As a consequence of changes in its B-chain, ebulin-RP displayed lower cytotoxicity than ebulin l towards cancer cells and induced apoptosis as the predominant pattern of cell death., Conclusions: Ebulin-RP is a novel member of the ebulin gene family with low cytotoxicity as a result of deficient sugar binding domains. Type 2 RIP genes from Sambucus have evolved to render proteins with different sugar affinities that may be related to different biological activities and could result in an advantage for the plant., General Significance: The ebulin family of RIPs and lectins can serve as a good model for studying the evolutionary process which may have occurred in RIPs. The lack of cytotoxicity of ebulin-RP makes it a good candidate as a toxic moiety in the construction of immunotoxins and conjugates directed against specific targets., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Background: Harmalol, a beta carboline alkaloid, shows remarkable importance in the contemporary biomedical research and drug discovery programs. With time, there is emerging interest in search for better anti-cancer drugs of plant origin with high activity and lower toxicity. Most of the chemotherapeutic agents due to their non-specific target and toxicity on active healthy cells, use is often restricted, necessitating search for newer drugs having greater potentiality., Objective: The review highlighted the interaction of harmalol with nucleic acids of different motifs as sole target biomolecules and in vitro cytotoxicity of the alkaloid in human cancer cell lines with special emphasis on its apoptotic induction ability., Methods: Binding study and in vitro cytotoxicity was performed using several biophysical techniques and biochemical assays, respectively., Results: Data from competition dialysis, UV and fluorescence spectroscopic analysis, circular dichroism, viscometry and isothermal calorimetry shows binding and interaction of harmalol with several natural and synthetic nucleic acids, both DNA and RNA, of different motifs. Furthermore, apoptotic hallmarks like internucleosomal DNA fragmentation, membrane blebbing, cell shrinkage, chromatin condensation, change of mitochondrial membrane potential, comet tail formation and ROS (reactive oxygen species) dependent cytotoxicity being analyzed in the harmalol treated cancer cells., Conclusion: These results stating the therapeutic role of harmalol, will lead to the interesting knowledge on the cytotoxicity, mode, mechanism, specificity of binding and correlation between structural aspects and energetics enabling a complete set of guidelines for design of new drugs., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.)

Berberine is one of the most widely known alkaloids belonging to the protoberberine group exhibiting myriad therapeutic properties. The anticancer potency of berberine appears to derive from its multiple actions including strong interaction with nucleic acids exhibiting adenine-thymine base pair specificity, inhibition of the enzymes topoisomerases and telomerases, and stabilizing the quadruplex structures. It was realized that the development of berberine as a potential anticancer agent necessitates enhancing its nucleic acid binding efficacy through appropriate structural modifications. More recently a number of such approaches have been attempted in various laboratories with great success. Several derivatives have been synthesized mostly with substitutions at the 8, 9 and 13 positions of the isoquinoline chromophore, and studied for enhanced nucleic acid binding activity. In this article, we present an up to date review of the details of the interaction of berberine and several of its important synthetic 8, 9 and 13 substituted derivatives with various nucleic acid structures reported recently. These studies provide interesting knowledge on the mode, mechanism, sequence and structural specificity of the binding of berberine derivatives and correlate structural and energetic aspects of the interaction providing better understanding of the structure- activity relations for designing and development of berberine based therapeutic agents with higher efficacy and therapeutic potential.

The incidence of fungal infection and evolution of multidrug resistance have increased the need for new antifungal agents. To gain further insight into the development of antifungal drugs, the phenotypic profiles of currently available antifungal agents of three classes-ergosterol, cell wall and nucleic acid biosynthesis inhibitors-were investigated using yeast morphology as a chemogenomic signature. The comparison of drug-induced morphological changes with the deletion of 4718 non-essential genes not only confirmed the mode of action of the drugs but also revealed an unexpected connection among ergosterol, vacuolar proton-transporting V-type ATPase and cell-wall-targeting drugs. To improve, simplify and accelerate drug development, we developed a systematic classifier that sorts a newly discovered compound into a class with a similar mode of action without any mutant information. Using well-characterized agents as target unknown compounds, this method successfully categorized these compounds into their respective classes. Based on our data, we suggest that morphological profiling can be used to develop novel antifungal drugs., (© FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objective: In our previous screening of chondrocyte protein profiles, the amount of adenosine monophosphate deaminase (AMPD) 2 was found to be decreased by tofacitinib. Extending the study, here we confirmed the decrease of AMPD2 by tofacitinib and further investigated effects of tofacitinib on purine nucleotide metabolism., Methods: Human articular chondrocytes and a chondrosarcoma cell line: OUMS-27 were stimulated with tofacitinib. Then the levels of AMPD2 and its related enzymes were investigated by Western blot. The levels of AMP and adenosine were assessed by mass spectrometry., Results: We confirmed the significant decrease of AMPD2 by tofacitinib in chondrocytes (p = 0.025). The levels of adenosine kinase and 5'-nucleotidase were decreased in chondrocytes, although they did not meet statistical significance (p = 0.067 and p = 0.074, respectively). The results from OUMS-27 were similar to those from the chondrocytes. The cellular adenosine levels were significantly decreased by tofacitinib in OUMS-27 (p = 0.014). The cellular AMP levels were increased, although they did not meet statistical significance in OUMS-27 (p = 0.066)., Conclusion: Our data indicate that tofacitinib increases the cellular levels of adenosine, which is known to have anti-inflammatory activity, through the downregulation of AMPD2. This would be a novel functional aspect of tofacitinib.

Candida albicans persisters constitute a small subpopulation of biofilm cells and play a major role in recalcitrant chronic candidiasis; however, the mechanism underlying persister formation remains unclear. Persisters are often described as dormant, multidrug-tolerant, nongrowing cells. Persister cells are difficult to isolate and study not only due to their low levels in C. albicans biofilms but also due to their transient, reversible phenotype. In this study, we tried to induce persister formation by inducing C. albicans cells into a dormant state. C. albicans cells were pretreated with 5-fluorocytosine (planktonic cells, 0.8 μg ml(-1); biofilm cells, 1 μg ml(-1)) for 6 h at 37°C, which inhibits nucleic acid and protein synthesis. Biofilms and planktonic cultures of eight C. albicans strains were surveyed for persisters after amphotericin B treatment (100 μg ml(-1) for 24 h) and CFU assay. None of the planktonic cultures, with or without 5-fluorocytosine pretreatment, contained persisters. Persister cells were found in biofilms of all tested C. albicans strains, representing approximately 0.01 to 1.93% of the total population. However, the persister levels were not significantly increased in C. albicans biofilms pretreated with 5-fluorocytosine. These results suggest that inhibition of nucleic acid synthesis did not seem to increase the formation of amphotericin B-tolerant persisters in C. albicans biofilms., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Efficient synthesis of a building block for the incorporation of a bis-pyrene-modified unlocked nucleic acid (UNA) into oligonucleotides (DNA*) was developed. The presence of bis-pyrene-modified UNA within a duplex leads to duplex destabilization that is more profound in DNA*/RNA and less distinct in DNA*/DNA duplexes. Nevertheless, the destabilization effect of bis-pyrene-modified UNA is weaker than that of unmodified UNA. Some oligonucleotides with bis-pyrene-modified UNA incorporations displayed superior mismatch discrimination capabilities. UV/Vis absorption and molecular modeling studies indicate that the pyrene groups of bis-pyrene-modified UNA are located in the major groove of a duplex. Oligonucleotides containing two bis-pyrene-modified UNA monomers showed low pyrene monomer emission in bulge-containing duplexes, high pyrene monomer emission in fully matched duplexes, and 5-(pyrenyl)uracil:pyrene exciplex emission in the single-stranded form. Such fluorescent properties enable the application of bis-pyrene-modified UNA in the development of fluorescence probes for DNA/RNA detection and for detection of deletions at specific positions., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Light activation of photosensitizing dyes in presence of molecular oxygen generates highly cytotoxic reactive oxygen species leading to cell inactivation. Nucleic acids are molecular targets of this photodynamic action but not considered the main cause of cell death. The in vivo effect of the photodynamic process on the intracellular nucleic acid content of Escherichia coli and Staphylococcus warneri was evaluated herein. Two cationic porphyrins (Tetra-Py(+)-Me and Tri-Py(+)-Me-PF) were used to photoinactivate E. coli (5.0μM; 10(8)cellsmL(-1)) and S. warneri (0.5μM; 10(8)cellsmL(-1)) upon white light irradiation at 4.0mWcm(-2) for 270min and 40min, respectively. Total nucleic acids were extracted from photosensitized bacteria after different times of irradiation and analyzed by agarose gel electrophoresis. The double-stranded DNA was quantified by fluorimetry and the porphyrin binding to bacteria was determined by spectrofluorimetry. E. coli was completely photoinactivated with both porphyrins (5.0μM), whereas S. warneri was only completely inactivated by Tri-Py(+)-Me-PF (0.5μM). The hierarchy of nucleic acid changes in E. coli was in the order: 23S rRNA>16S rRNA>genomic DNA. The nucleic acids of S. warneri were extensively reduced after 5min with Tri-Py(+)-Me-PF but almost unchanged with Tetra-Py(+)-Me after 40min of irradiation. The amount of Tri-Py(+)-Me-PF bound to E. coli after washing the cells is higher than Tetra-Py(+)-Me and the opposite was observed for S. warneri. The binding capacity of the photosensitizers is not directly related to the PDI efficiency or nucleic acid reduction and this reduction occurs in parallel with the decrease of surviving cells., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Bambusa pervariabilis × Dendrocalamopisis grandis blight is caused by a toxin produced by the fungus Arthrinium phaeospermum. In this study, a toxin fraction (P1-2-2) with an estimated molecular mass of 31 kDa was purified from a culture filtrate of this fungus by ammonium sulfate precipitation, Sephadex G-50 gel chromatography, Q Sepharose Fast Flow anion exchange resin, and Sephadex G-75 chromatography. The N-terminal amino acid sequence (i.e., H(2)N-Gln-Val-Arg-Asp-Arg-Leu-Glu-Ser-Thr) determined by Edman degradation showed homology to known serine alkaline proteases. The purified protein was named AP-toxin. Effects of the purified protein toxin on total phenol, flavonoid, total nucleic acid, DNA, RNA, soluble protein, and soluble sugar content, as well as DNase and RNase activities and disease index, were analyzed in different bamboo varieties by the impregnation method. The toxin had a significant effect on each parameter tested. In addition, a significant correlation was observed among the metabolic index, treatment time, bamboo resistance, and disease index. These data suggest that AP-toxin plays an important role in mediating the phytotoxic activities of A. phaeospermum. This study also indicates that metabolic indices could reflect the resistance indices of hybrid bamboo to blight.

Several antimicrobials act by inhibiting the synthesis of nucleic acids (rifamycins, sulfamides, diaminopyridines), modifying their conformation (quinolones, coumarins) or causing irreversible lesions (nitroimidazoles, nitrofurans). The resistance mechanisms are: a reduction in intracytoplasmic accumulation, modification of the target or the production of a new low-affinity target and, more rarely, enzyme inactivation. Although the mechanisms affecting the targets are specific to each family and can lead to high-level resistance, the reduced permeability of the membrane and the increased efflux are non-specific and result in low-level cross-resistance between several families. The genetic mediation is usually chromosomal for rifamycins and quinolones, although plasmid-mediated resistant genes have been observed. On the other hand, for sulfamides and trimethoprim, plasmid-borne genes are frequent. Resistance to nitroimidazoles and nitrofurans is still not widely understood.

The aim of this research is to study the dependence the gravity of diabetes course and the activity of the biosynthetical processes in the liver from the level of the sexual steroides in the male-rats blood on the model of the alloxan diabetes. The experiments were carried out on 80 male rats (weight 180-200g). The diabetes has been reproduced by the single injection of alloxan per 200mg/kg. The content of glucose, testosterone, estradiole and corticosterone have been determined in the blood of the animals. Activity of the syntheses of the nucleic acids in the liver has been researched by the radiometrical method on 14, 30, 45 and 90 days of the experiment. On all stages of the observation has been revealed the inverse relation between the concentration of the testosterone in the blood and the gravity of the experimental diabetes which was determined by the degree of hyperglycemya and the changes of the coefficient of sexual hormones ratio, the content of estradiol, corticosterone and activity of the syntheses of the nucleic acids in the tissue of the liver. The injection of the androgen during two week caused jump increasing the testosterone concentration, approaching the sexual steroids ratio to the norm, decreasing the glucose, estradiole, corticosterone content and also the reduction the nucleic acids syntheses activity in the liver. It was shown the positive influence of the androgens on development of the compensatory processes in the male rats, which course the decrease the experimental diabetes gravity.

Phenanthroindolizidine alkaloids are a family of plant-derived compounds with significant antineoplastic activity as well as other effects like antiamebicidal, antiviral, and anti-inflammatory activities. The specific biomolecular targets of these compounds have not yet been clearly identified. S-(+)-Deoxytylophorinidine (CAT) is a new phenanthroindolizidine alkaloid, originally extracted from the roots of Tylophora atrofolliculata and Tylophora ovata. Potent anticancer activity was observed in vitro and in vivo. Neurotoxicity of CAT was also studied and it was far less serious than that of vinblastine. Interactions between this compound and DNA had been studied in detail in our laboratory previously, and we further studied its interactions with RNA.

Numerous studies have evaluated a wide variety of photosensitizers and alkylating agents as candidates for a pathogen reduction process to be used in RBC suspensions. The methodologies that produce robust inactivation of pathogens with maintenance of RBC properties during storage involve those that specifically target nucleic acids. This has been demonstrated through in vitro studies by flexible photosensitizers, which specifically target nucleic acid but do not engage in photochemistry when free in solution and nucleic acid alkylating agents in conjunction with extracellular quencher(s) to protect against RBC membrane alkylation. The flexible photosensitizer method must be scaled up to entire units, and toxicology studies would need to be performed for further development. Clinical trials will ultimately be necessary to further develop either flexible photosensitizers or nucleic acid alkylating methods with quenchers for use in Transfusion Medicine., (© 2010 The Author(s). Vox Sanguinis © 2010 International Society of Blood Transfusion.)

This review examines acyclic nucleoside analogs as therapeutic agents, potential progenitor candidates to RNA, and novel building blocks for nucleic-acid nanotechnology. Together, these areas of research provide new insights into the structural and functional properties of nucleic acids and suggest new paradigms for nucleic acid self-assembly.

Statins are commonly used drugs in the treatment of hypercholesterolaemia. There are many adverse effects of statins on skeletal muscle, but the underlying mechanisms remain unclear. In the present study, the effects of low dose (20 mg/kg) simvastatin, a lipophilic statin, on rat EDL muscle (extensor digitorum longus muscle) were investigated at the molecular level using FTIR (Fourier-transform infrared) spectroscopy. FTIR spectroscopy allows us rapid and sensitive determination of functional groups belonging to proteins, lipids, carbohydrates and nucleic acids simultaneously. The results revealed that simvastatin treatment induces a significant decrease in lipid, nucleic acid, protein and glycogen content. A significant increase in the lipid/protein and nucleic acid/protein ratios was also obtained with simvastatin treatment. Furthermore, an increase in lipid order and membrane fluidity was detected. A decrease in the bandwidth of the amide I band and shifting of the position of this band to higher frequency values in treated muscle indicates structural changes in proteins. Detailed secondary structure analysis of the amide I band revealed a significant increase in antiparallel and aggregated beta-sheet, random coil structure and a significant decrease in beta-sheet structure, which indicates protein denaturation.

The in silico methods for drug discovery are becoming increasingly powerful and useful. That, in combination with increasing computer processor power, in our case using a novel distributed computing grid, has enabled us to greatly enhance our virtual screening efforts. Herein we review some of these efforts using both receptor and ligand-based virtual screening, with the goal of finding new anti-cancer agents. In particular, nucleic acids are a neglected set of targets, especially the different morphologies of duplex, triplex, and quadruplex DNA, many of which have increasing biological relevance. We also review examples of molecular modeling to understand receptors and using virtual screening against G-protein coupled receptor membrane proteins.

Accelerating the drug discovery process requires predictive computational protocols capable of reducing or simplifying the synthetic and/or combinatorial challenge. Docking-based virtual screening methods have been developed and successfully applied to a number of pharmaceutical targets. In this review, we first present the current status of docking and scoring methods, with exhaustive lists of these. We next discuss reported comparative studies, outlining criteria for their interpretation. In the final section, we describe some of the remaining developments that would potentially lead to a universally applicable docking/scoring method.

Cationic antimicrobial peptides are a novel type of antibiotic offering much potential in the treatment of microbial-related diseases. They offer many advantages for commercial development, including a broad spectrum of action and modest size. However, despite the identification or synthetic production of thousands of such peptides, the mode of action remains elusive, except for a few examples. While the dogma for the mechanism of action of antimicrobial peptides against bacteria is believed to be through pore formation or membrane barrier disruption, some peptides clearly act differently and other intracellular target sites have been identified. This article presents an updated review of how cationic antimicrobial peptides are able to affect bacterial killing, with a focus on internal targets.

Tumor targeting--per definition--includes any strategy to improve the specificity of the therapeutic nucleic acid towards the tumor site, while highest biological activity should be maintained. Targeting has been successfully achieved at the transcriptional, transductional or delivery level. For tumor-specific delivery, physical targeting methods like electroporation, hyperthermia, magnetofection, photochemical internalization or ultrasound, and biological targeting systems, including active and passive tumor targeting, have been developed. Therapeutic effects could be demonstrated with various targeted nucleic acid formulations, such as tumor-targeted DNA plasmids expressing p53 or tumor necrosis factor alpha, small interfering RNAs knocking down gene expression from tumor specific chromosomal translocations or gene expression of tumor neoangiogenic processes, as well as double stranded RNA poly inosine-cytosine which triggers apoptosis in targeted tumor cells.

Valerian is widely known for its use as a sedative and an anti-anxiety drug in the folk medicine. Literature reports suggested valerian to induce genotoxicity in vitro (ECV304 cells) by reactive oxygen species-mediated mechanism; however, there are no reports on its genotoxicity and/or the epigenetic mechanism in vivo. In view of the folkloric significance, it was found worthwhile to (1) determine the genotoxic effects of valerian in somatic and germ cells of mice and (2) investigate the role of epigenetic mechanisms. The protocol included the oral treatment of mice with different doses (500, 1000 and 2000 mg/kg/day) of valerian for 7 days. The following experiments were conducted: (i) cytological studies on micronucleus test, (ii) cytogenetic analysis for meiotic chromosomes, (iii) cytological analysis of spermatozoa abnormalities, (iv) quantification of proteins and nucleic acids in testicular cells and (v) estimation of malondialdehyde (MDA) and nonprotein sulfhydryl (NP-SH) in hepatic and testicular cells. The treatment increased the frequency of micronuclei in the polychromatic erythrocytes (PCE) and decrease the ratio of PCE to normochromatic erythrocytes (NCE) in the femur. It caused aberrations in chromosomes of the testis and induced spermatozoa abnormalities. The concentration of nucleic acids was depleted in the testicular cells. These changes might be attributed to the epigenetic mechanisms as revealed by an increase in the concentrations of MDA and a decrease of NP-SH levels in hepatic and testicular cells observed in the present study. The observed changes may be ascribed to terpenoids (valepotriates) and flavonoids (6-methylapigenin and 2S(-)-hesperidin) present in valerian.

Locked nucleic acid (LNA) is a nucleic acid analog containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA-mimicking sugar conformation. This conformational restriction is translated into unprecedented hybridization affinity towards complementary single-stranded RNA molecules. That makes fully modified LNAs, LNA/DNA mixmers, or LNA/RNA mixmers uniquely suited for mimicking RNA structures and for RNA targeting in vitro or in vivo. The focus of this chapter is on LNA antisense, LNA-modified DNAzymes (LNAzymes), LNA-modified small interfering (si)RNA (siLNA), LNA-enhanced expression profiling by real-time RT-PCR and detection and analysis of microRNAs by LNA-modified probes.

Flow cytometry (FCM), combined with staining using two fluorochromes (propidium iodide, PI, or SYBR Green II RNA gel stain, SYBR-II), was used to assess nucleic acid injuries to chlorinated drinking water bacteria. Highly fluorescent SYBR-II-stained bacteria were converted to bacteria with low fluorescence after chlorination. PI staining of bacteria exposed to different doses of chlorine showed membrane permeabilisation ([Cl2] < 0.2 mg L(-1)) and nucleic acid damage at higher doses ([Cl2] > 0.3 mg L(-1)). Above a threshold dose (between 1.5 and 3 mg Cl2 L(-1)), nucleic acids appeared severely damaged and incapable of being stained by PI or SYBR-II. These results constitute evidence that FCM is a promising tool for assessing drinking water bacteria injuries and for controlling chlorine disinfection efficiency much more rapidly than the standard sensitive but time-consuming heterotrophic plate count method.

Aldehydes are organic compounds that are widespread in nature. They can be formed endogenously by lipid peroxidation (LPO), carbohydrate or metabolism ascorbate autoxidation, amine oxidases, cytochrome P-450s, or myeloperoxidase-catalyzed metabolic activation. This review compares the reactivity of many aldehydes towards biomolecules particularly macromolecules. Furthermore, it includes not only aldehydes of environmental or occupational concerns but also dietary aldehydes and aldehydes formed endogenously by intermediary metabolism. Drugs that are aldehydes or form reactive aldehyde metabolites that cause side-effect toxicity are also included. The effects of these aldehydes on biological function, their contribution to human diseases, and the role of nucleic acid and protein carbonylation/oxidation in mutagenicity and cytotoxicity mechanisms, respectively, as well as carbonyl signal transduction and gene expression, are reviewed. Aldehyde metabolic activation and detoxication by metabolizing enzymes are also reviewed, as well as the toxicological and anticancer therapeutic effects of metabolizing enzyme inhibitors. The human health risks from clinical and animal research studies are reviewed, including aldehydes as haptens in allergenic hypersensitivity diseases, respiratory allergies, and idiosyncratic drug toxicity; the potential carcinogenic risks of the carbonyl body burden; and the toxic effects of aldehydes in liver disease, embryo toxicity/teratogenicity, diabetes/hypertension, sclerosing peritonitis, cerebral ischemia/neurodegenerative diseases, and other aging-associated diseases.

Objective: To look into the feasibility of using cobra snake venom in suppressing breast cancer tissue through inhibition of nucleic acid synthesis., Methods: Samples of breast cancerous tissue, obtained from Atomic Energy Medical Center, LMCH, Jamshoro, incubated with varying concentrations of venom and without venom (as controls) were assayed for macromolecular (RNA and DNA) levels, Results: No. change in the control samples while a prominent and significant fall in nucleic acid contents has been noted in venom treated tissues. Also, maximum effect was observed with 25ug/ml dose., Conclusion: Snake venom strongly inhibited the formation of nucleic acids in the breast cancerous tissues. It may bring a fall in cell proliferation, thus there is hope that venom could be used as an anti-cancerous drug in the future.

A series of antiviral active compounds consisting of an intercalating acridine-derived part, a spacer region and a reactive EDTA-derived conjugate was synthesized in an easy sequence. Thus, suitably mono-protected 1,omega-alkyldiamines gave, upon reaction with 9-chloro-2-trifluoromethoxyacridine, followed by deprotection and reaction with EDTA dianhydride, the target molecules. Incorporation of their Fe(II) complexes in the presence of ascorbate gave a reduction of the phage titer of MS2 phages by several logarithmic decades.

A series of antiviral compounds consisting of an intercalating acridine derived part, a spacer region and a reactive EDTA-derived conjugate was synthesized in an easy sequence starting from 1,omega-alkyldiamines. As shown in model screenings, in the presence of ascorbic acid the Fe-complexes of these compounds reduced the phage-titer of MS2-phages by several logarithmic decades.

Purpose: The addition of oxaliplatin or CPT-11 to 5-FU has become common practice in the treatment of colorectal cancer. It is not known, however, which fluoropyrimidine drug (5-FU, FUdR, or FUR) will produce superior cytotoxicity when combined with either oxaliplatin or CPT-11. The purpose of the study was to determine the effects of oxaliplatin and CPT-11 on cytotoxicity and nucleic acid incorporation of all three fluoropyrimidines., Methods: HT-29 cells were exposed for 2 h to IC(10), IC(30), and IC(70) of oxaliplatin and CPT-11. Subsequently, cells were exposed for 24 h to IC(10), IC(30), and IC(70) of 5-FU, FUdR, and FUR. Cytotoxicity was measured by the MTT assay. Nucleic acid incorporation of [(3)H]fluoropyrimidine was then compared in the presence and absence of oxaliplatin or CPT-11 pretreatment., Results: Synergistic cytotoxicity was displayed when IC(30) of oxaliplatin or CPT-11 was combined with IC(10) and IC(30) of the fluoropyrimidines. One fluoropyrimidine did not achieve superior cytotoxicity over the others. After pretreatment with oxaliplatin or CPT-11, cytotoxic antagonism was observed as the concentration of a fluoropyrimidine increased up to IC(70). The increasing cytotoxic antagonism correlated with decreases in fluoropyrimidine nucleic acid incorporation. The most significant incorporation difference existed within the 5-FU treated group., Conclusions: No single fluoropyrimidine is more cytotoxically effective over the others when combined with oxaliplatin or CPT-11. Correlation of cytotoxic antagonism to the inhibition of fluoropyrimidine nucleic acid incorporation implies difficulties in drug transport and/or metabolism only after oxaliplatin or CPT-11 pretreatment.

Investigation of the kinetics of nucleic acid release by HeLa (human cervical carcinoma cell line) and A431 (human squamous carcinoma cell line) cells is presented. The released DNA and RNA were shown to accumulate in culture medium and at the cell surface. A portion of cell surface bound RNA can be eluted with PBS/EDTA. Mild trypsin treatment is required for complete detachment of cell surface bound RNA and cell surface bound DNA. Electrophoretic analysis reveals characteristic patterns of cell-associated and free RNA and DNA molecules.

Objective: To explore the effect of the traditional Chinese medicine Yifei Kangliu (YFKL) Oral Liquid on the proliferation, cell cycle and protein-nucleic acid synthesis of murine Lewis lung cancer cell and human lung adenocarcinoma cell line SPC-A-1., Methods: The inhibiting rates of tumor growth were calculated by weighing the weight of tumor inoculated in vivo, combined by counting cancer cells in vitro. The ratio of the cell cycle and exponents of DNA, RNA, and protein were measured by flow cytometry (FCM)., Results: The inhibiting rate of tumor growth in the treated group with YFKL Oral Liquid was 30.38% (P<0.05). The proportion of cells in S phase of the treated groups with YFKL Oral Liquid was lower than that of the control group. In the group with most significant result, 72% of the cells were stagnated in G0/G1 phase. The inhibiting rates of DNA, RNA and protein in murine Lewis lung cancer were 7.4%, 23.73% and 23.31% respectively. In SPC-A-1 cell line, the inhibiting rates were 9.3%, 10.1% and 14.7% respectively, demonstrating amplified effects on lower levels., Conclusion: YFKL Oral Liquid significantly inhibited the proliferation of murine Lewis lung cancer cell and human lung adenocarcinoma cell line SPC-A-1 by blocking the cancer cells entering the proliferative phase resulted from its inhibition of DNA.

A successful application is reported of the multivariate curve resolution alternating least-squares method (MCR-ALS) for the analysis of nucleic acid melting and salt-induced transitions. Under conditions where several structures co-exist in a conformational equilibrium, MCR-ALS analysis of the UV and circular dichroism (CD) spectra at different temperatures, ionic strength and oligonucleotide concentration allows for the resolution of concentration profiles and pure spectra of the different species. The methodology is illustrated by the case of the cyclic oligonucleotide d. The melting transition of this molecule at different oligonucleotide concentrations was studied at 0, 2 and 10 mM MgCl2 by UV and CD spectroscopy. In addition, salt titration experiments were carried out at 21.0 and 54.0 degrees C. The MCR-ALS analysis indicates that three different conformations of this molecule co-exist in solution. In agreement with previous NMR studies, these conformations were assigned to a monomeric dumbbell-like structure, a dimeric four-stranded conformation and a disordered (random coil) structure. The MCR-ALS methodology allows for a detailed analysis of how this equilibrium is affected by temperature, salt and oligonucleotide concentration.

[reaction: see text]. Mass spectral data are presented indicating that the antitumor agent 2-crotonyloxymethyl-2-cyclohexenone (COMC) is capable of alkylating oligonucleotides via a mechanism involving an electrophilic exocyclic enone intermediate. Under physiological conditions, the exocyclic enone is likely the glutathionylated 2-exomethylenecyclohexenone. This supports a recent hypothesis that the antitumor activity of COMC arises from alkylation of nucleic acids and/or proteins critical to cell function and not from competitive inhibition of glyoxalase I by an adduct of COMC and glutathione.

We synthesized two water-soluble porphyrins appending platinum(II) complexes [alpha,beta-(4a) and alpha,alpha-(4b) 5,15-bis(2-trans-[PtCl(NH3)2]N-2-aminoethylaminocarbonylphenyl) 2,3,7,8,12,13,17,18-octamethylporphyrin] and studied their reactions with a variety of nucleic acids [disodium adenosine-5'-monophosphate (AMP), disodium guanosine-5'-monophosphate (GMP), disodium thymidine-5'-monophosphate (TMP), disodium cytidine-5'-monophosphate (CMP), synthetic polymer poly(dG)-poly(dC), poly(dA)-poly(dT)] by 1H-NMR, UV-vis and FAB-MS spectroscopies. Based on the denaturation experiments of synthetic nucleic acid polymers, we conclude that the presence of the porphyrins (5.6 microM) does not cause significant changes in the melting temperature of poly(dA)-poly(dT) (28 microM) (deltaT=1 degrees C) and shows reannealing. On the other hand, gradual melting of poly(dG)-poly(dC) (28 microM) occurs at a low temperature (deltaT= -27 degrees C) in the presence of the porphyrins (5.6 microM), and the solutions do not show reannealing phenomena. The results of UV-vis and 1H-NMR experiments revealed that the porphyrins bind to guanine bases and that the porphyrins bind to GMP more strongly than to the other nucleotides. The binding modes between the porphyrins and synthetic nucleic acids are affected more by the coordination of the nucleobase [poly(dG)-poly(dC)] to the Pt(II) in the porphyrins than by Coulomb and hydrophobic interactions.

The stabilization of poly(dA).2poly(dT) triplex, a 22-base DNA triplex, and poly(rA).2poly(rU) triple helix by neomycin is reported. The melting temperatures, the association and dissociation kinetic parameters, and activation energies (E(on) and E(off)) for the poly(dA).2poly(dT) triplex in the presence of aminoglycosides and other triplex binding ligands were determined by UV thermal analysis. Our results indicate that: (i) neomycin stabilizes DNA triple helices, and the double helical structures composed of poly(dA).poly(dT) are virtually unaffected. (ii) Neomycin is the most active and triplex-selective stabilization agent among all aminoglycosides, previously studied minor groove binders, and polycations. Its selectivity (DeltaT(m3-->2) vs DeltaT(m2)(-->)(1)) exceeds most intercalating drugs that bind to triple helices. (iii) Neomycin selectively stabilizes DeltaT(m3)(-->)(2) for a mixed 22-base DNA triplex containing C and T bases in the pyrimidine strand. (iv) The rate constants of formation of triplex (k(on)) are significantly enhanced upon increasing molar ratios of neomycin, making triplex association rates closer to duplex association rates. (v) E(on) values become more negative upon increasing concentration of aminoglycosides (paromomycin and neomycin). E(off) values do not show any change for most aminoglycosides except neomycin. (vi) Aminoglycosides can effectively stabilize RNA [poly(rA).2poly(rU)] triplex, with neomycin[being one of the most active ligands discovered to date (second only to ellipticine). (vii) The stabilization effect of aminoglycosides on triple helices is parallel to their toxic behavior, suggesting a possible role of intramolecular triple helix (H-DNA) stabilization by the aminoglycosides.

Substantial improvement in the safety of blood transfusion has been achieved through the addition of new tests, such as nucleic acid tests, yet residual risk associated with transfusion of blood components persists. Transfusion of blood components has been implicated in the transmission of viruses, bacteria, and protozoa. While it is commonly recognized that hepatitis B virus (HBV), hepatitis C virus (HCV), cytomegalovirus (CMV), and the retroviruses, such as human immunodeficiency virus (HIV) and the human lymphotrophic viruses (HTLV) can be transmitted through cellular components, other pathogens are emerging as potentially significant transfusion-associated infectious agents. For example, transmission of protozoan infections due to trypanosomes and babesia have been reported. In addition to viral and protozoal infectious agents, bacterial contamination of platelet and red cell concentrates continues to be reported; and may be an under-reported transfusion complication. More importantly, new infectious agents may periodically enter the donor population before they can be definitively identified and tested for to maintain consistent safety of the blood supply. The paradigm for this possibility is the HIV pandemic, which erupted in 1979. During the past decade a number of methods to inactivate infectious pathogens in labile blood components have been developed and have entered the advanced clinical trial phase.

Much ongoing research in toxicology focuses on a hypothesis-driven mechanism of action approach aimed at understanding the molecular events mediating the actions of the chemicals of interest. Using this approach, investigators develop hypotheses based on observations, which may be derived from a host of resources but most frequently have been made within their own laboratories, or uncovered by others and reported in the scientific literature. Although the bulk of current understanding ofbiochemical toxicology emerged using studies based on observations derived in this way, this process, which is essentially based on existing information, may often limit the expansion knowledge. More simply expressed, one only finds that which one seeks. Without a clear understanding of the processes targeted by a specific toxin the problem of making observations that globally and accurately reflect the events mediating pathology which have been induced by the toxic agent is challenging. Recently, the development of high-throughput technologies for biochemical analysis of gene expression has led to innovative approaches in addressing the problem of making broad-based observations that more accurately reflect the entire spectrum of molecular lesions induced by specific toxins. These strategies include the use of new techniques in analysis of gene expression to convey information on alterations in mRNA levels, one of the earliest cellular signs initiated in response to a potential toxin. Prior to this time studies on toxicant-induced altered gene expression were limited to single, or small numbers of identified genes chosen by an investigator who reasoned, based on an existing observations, that levels of the proteins encoded by these genes were likely to be altered during toxic injury. Now, using cDNA or oligonucleotide genome-wide arrays, toxin-induced alterations in gene expression of thousands of genes can be examined simultaneously. Using these tools, molecular toxicologists can for the first time employ reasoned strategies to make observations, and then formulate hypotheses based on these observations.

The interaction of antimalarial drug quinacrine (QA) with polynucleotides is studied by UV-visible absorption, fluorescence and surface-enhanced Raman spectroscopy (SERS). The polynucleotides employed for such a study were calf thymus DNA, poly(A).poly(T), poly(A).poly(U), poly(C).poly(G) and poly(dG-dC).poly(dG-dC). Absorption and fluorescence spectra of QA complexes indicate that an interaction with the biomolecule is taking place, although different interaction mechanisms are probable depending on the sequence. The SERS spectra also reflect spectral changes which depend on the polymer sequence and that can be correlated to those observed by fluorescence, with the advantage of the detailed structural information provided by this vibrational technique. QA interacts with polynucleotides through its diprotonated form and by ring stacking. The strength of such interaction is extremely sequence dependent, thus suggesting different interaction mechanisms in each case. The SERS technique allows the simultaneous study of those polynucleotide moieties that are directly involved in the interaction thanks to the short-range character of the SERS spectroscopy. The interaction of QA with the above nucleic acids lead to a different change in the chain stability and flexibility which is further related to the different denaturation tendency of the polymer in the presence of the metal surface.

In this work the biochemical effects of thioridazine, a commonly used phenothiazine, have been studied upon native double- and single-stranded DNA and also upon a supercoiled plasmid. The results indicate that thioridazine causes damage and scissions to these nucleic acids but only at concentrations much higher than the one used in our cytogenetic experiments and that the damage seems to depend on the concentrations used. Furthermore, we studied the action of thioridazine alone or in combination with caffeine and/or melphalan upon human lymphocytes in vitro. Thioridazine and caffeine (a well-known inhibitor of cellular repair mechanisms) were shown to act synergistically to potentiate the cytogenetic effect of melphalan on human lymphocytes. It is suggested that thioridazine alone or in combination with caffeine may exert its synergistic effect on melphalan cytotoxicity to cultured human lymphocytes not only indirectly, i.e. as a strong calmodulin inhibitor by facilitating the intracellular retention of melphalan, but also directly by reaction with nucleic acids and by causing scissions in and damage to them. Therefore, thioridazine (as chlorpromazine) has some potential as an adjuvant chemotherapeutic agent for the treatment of human cancer.

The transient absorption spectra of the intermediates produced by the 355 nm laser excitation of gilvocarcin derivatives have been investigated in various solvents. The spectra consist of a triplet-triplet absorption in the visible region and a residual absorption observed between 340 and 700 nm due to a long-lived species, assigned to the radical cation. A broad-fast decaying band with a maximum at around 700 nm attributed to the solvated electron is also seen in solutions containing a low DMSO/water volume ratio and at 266 nm irradiation of a 50% methanol/water solvent mixture. The molar absorption coefficient of the triplet state of gilvocarcin V (GV) and gilvocarcin M (GM), determined by the energy transfer method, is independent of the solvent properties and has a value of 3.0 x 10(4)/Mcm. The triplet decay rate constants for both drugs are between 1 and 5 x 10(4)/s. A similar initial yield and triplet decay rate constant of GV were observed in the presence of 3.4 mM thymine. Thus, a quenching rate constant of the GV's triplet state by thymine is estimated to be lower than 10(6)/Ms. The triplet quantum yields of both antibiotics determined by using the comparative method are higher in dimethylsulfoxide (DMSO) (0.18) than are those corresponding to 25% DMSO/water (0.06). The decrease in phi T in the presence of water could be attributed to an enhanced internal conversion rate constant from the S1 state or to an increase in the photoionization yield. The similarity of the transient intermediates and their yields for GV and GM suggest that their photobiological differences are due to other factors such as DNA binding constants, preferential localization of the drugs in the cell or the enhanced reactivity of the vinyl group toward cellular components.