Highly Improved Electrospray Ionization-Mass Spectrometry Detection of G-Quadruplex-Folded Oligonucleotides and Their Complexes with Small Molecules

G-quadruplexes are nucleic acids structures stabilized by physiological concentration of potassium ions. Because low stability G-quadruplexes are hardly detectable by mass spectrometry, we optimized solvent conditions: isopropanol in a triethylamine/hexafluoroisopropanol mixture highly increased G-quadruplex sensitivity with no modification of the physiological G-quadruplex conformation. G-quadruplexes/G-quadruplex-ligand complexes were also correctly detected at concentration as low as 40 nM. Detection of the physiological conformation of G4s and their complexes opens up the possibility to perform high-throughput screening of G-quadruplex ligands for the development of drug molecules effective against critical human diseases

Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription

Folding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specificity the majority, but not all the possible G-quadruplexes folded by this sequence. In addition, it displayed greater binding preference towards DNA than RNA G-quadruplexes, thus indicating two levels of selectivity based on the sequence and nature of the target. The interaction translated into stabilization of the LTR G-quadruplexes and increased promoter silencing activity; in contrast, disruption of nucleolin binding in cells by both siRNAs and a nucleolin binding aptamer greatly increased LTR promoter activity. These data indicate that nucleolin possesses a specific and regulated activity toward the HIV-1 LTR promoter, which is mediated by G-quadruplexes. These observations provide new essential insights into viral transcription and a possible low mutagenic target for antiretroviral therapy

Synthesis, Binding and Antiviral Properties of Potent Core-Extended Naphthalene Diimides Targeting the HIV-1 Long Terminal Repeat Promoter G-Quadruplexes

We have previously reported that stabilization of the G-quadruplex structures in the HIV-1 long terminal repeat (LTR) promoter suppresses viral transcription. Here we sought to develop new G-quadruplex ligands to be exploited as antiviral compounds by enhancing binding toward the viral G-quadruplex structures. We synthesized naphthalene diimide derivatives with a lateral expansion of the aromatic core. The new compounds were able to bind/stabilize the G-quadruplex to a high extent, and some of them displayed clear-cut selectivity toward the viral G-quadruplexes with respect to the human telomeric G-quadruplexes. This feature translated into low nanomolar anti-HIV-1 activity toward two viral strains and encouraging selectivity indexes. The selectivity depended on specific recognition of LTR loop residues; the mechanism of action was ascribed to inhibition of LTR promoter activity in cells. This is the first example of G-quadruplex ligands that show increased selectivity toward the viral G-quadruplexes and display remarkable antiviral activity

Identification of G-quadruplex DNA/RNA binders: Structure-based virtual screening and biophysical characterization

Background Recent findings demonstrated that, in mammalian cells, telomere DNA (Tel) is transcribed into telomeric repeat-containing RNA (TERRA), which is involved in fundamental biological processes, thus representing a promising anticancer target. For this reason, the discovery of dual (as well as selective) Tel/TERRA G-quadruplex (G4) binders could represent an innovative strategy to enhance telomerase inhibition. Methods Initially, docking simulations of known Tel and TERRA active ligands were performed on the 3D coordinates of bimolecular G4 Tel DNA (Tel2) and TERRA (TERRA2). Structure-based pharmacophore models were generated on the best complexes and employed for the virtual screening of ~ 257,000 natural compounds. The 20 best candidates were submitted to biophysical assays, which included circular dichroism and mass spectrometry at different K+ concentrations. Results Three hits were here identified and characterized by biophysical assays. Compound 7 acts as dual Tel2/TERRA2 G4-ligand at physiological KCl concentration, while hits 15 and 17 show preferential thermal stabilization for Tel2 DNA. The different molecular recognition against the two targets was also discussed. Conclusions Our successful results pave the way to further lead optimization to achieve both increased selectivity and stabilizing effect against TERRA and Tel DNA G4s. General significance The current study combines for the first time molecular modelling and biophysical assays applied to bimolecular DNA and RNA G4s, leading to the identification of innovative ligand chemical scaffolds with a promising anticancer profile. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio

A Catalytic and Selective Scissoring Molecular Tool for Quadruplex Nucleic Acids

A copper complex embedded in the structure of a water-soluble naphthalene diimide has been designed to bind and cleave G-quadruplex DNA. We describe the properties of this ligand, including its catalytic activity in the generation of ROS. FRET melting, CD, NMR, gel sequencing, and mass spectrometry experiments highlight a unique and unexpected selectivity in cleaving G-quadruplex sequences. This selectivity relies both on the binding affinity and structural features of the targeted G-quadruplexes

Analysis of cross-linking between DNA and anthracyclines

Anthracyclines are a group of chemotherapeutics that include adriamycin (doxorubicin), daunorubicin, idarubicin, and epirubicin. Anthracyclines are active against a wide range of tumours, in particular, adriamycin is used in the treatment of breast cancer, Hodgkin’s lymphoma, lung cancer, multiple myeloma and re-occurring ovarian cancer. Despite the broad spectrum of actions, resistance or severe cardio-toxicity limits the use of these important anticancer-drugs. The search for a “better anthracycline” has resulted in more than 2000 analogs, but only a few more anthracyclines have attained clinical approval. Although the exact mechanism by which adriamycin exerts its anti-tumour activity is uncertain, the dominant mechanism appears to involve impairment of topoisomerase IIα activity consistent with observed DNA intercalation and nuclear localization. The search for less toxic and more effective anthracyclines has led to the discovery of nemorubicin, a doxorubicin derivative in which the amino nitrogen of the daunosamine unit is incorporated into a methoxymorpholinyl ring. Preclinical investigations showed that nemorubicin, unlike classic anthracyclines, is not cardiotoxic and retains antitumour activity in various multidrug-resistant tumor models. Encouraging results have been obtained in phase I/II clinical trials in which the drug was administered by the intra-hepatic artery route. Nemorubicin is 80-120 times more potent than doxorubicin in vivo; in contrast, its in-vitro activity is only eight times greater than doxorubicin’s toward cultured drug sensitive tumour cells. A recent study established that nemorubicin is converted by enzyme CYP3A in a more cytotoxic metabolite PNU-159682, which was found to be 700-2400 times more potent that its parent drug toward cultured human cancer cells and which exhibits significant efficacy in in vivo tumor models. Ongoing studies aimed at exploring the molecular mechanism of action of PNU-159682 indicate that it has different effects on cell cycle progression and different DNA interacting properties, compared to both MMDX and doxorubicin. Moreover, further recent data suggest that PNU-159682 retains its activity against tumor cell lines with mechanisms of resistance different from those classical anticancer agents including MDR-1 gene overexpression, reduced topoisomerase II activity, and mutations in the topoisomerase I gene, these latter genetic alterations conferring resistance in vitro to the parent drug, MMDX [1]. We used different experimental approaches aimed to rationalizing the high activity of this metabolite. Test in vitro performed in our laboratory with kinetoplast DNA confirmed the inactivity of the metabolite against topoisomerase IIα. The absence of activity toward topoisomerase suggests that the high cytotoxicity of this compound had to be searched elsewhere. Anthracyclines such as doxorubicin and daunorubicin can bind covalently the DNA when activated with formaldehyde. Moreover, anthracyclines that have intrinsic ability to form cross-links to the DNA, such as cyanomorpholinyl-doxorubicin or barminomycin, were found to exhibit high cytotoxicity comparable with the PNU. Then we considered the possibility that PNU interacts with the DNA as a preactivated anthracycline. Our work evidenced that PNU behaves similarly to the activated doxorubicin (doxorubicin mixed with H2CO) in DNA melting analyses. PNU quickly reacts with double-strand oligonucleotides to form adducts detectable by DPAGE. These adducts are sufficiently stable to be isolated by HPLC. Mass characterization confirmed that these complexes are formed by duplex DNA bound to the anthracycline. These investigations suggest that the reaction between PNU and DNA does not involve the formation of a classical cross-link, but in relation to the electrophoretic, chromatographic and mass spectrometry results these adducts can be ascribed to the family of “virtual cross-link” (VXL). Anthracyclines-formaldehyde conjugate or anthracyclines in formaldehyde buffer have the specific ability to intercalate into DNA, forming covalent bonding; a methylene bridge links the amino group of the anthracycline to the 2-amino group of a G-base in the minor groove, while the other strand of DNA is stabilized by hydrogen bonds. Such unusual combination of intercalation, covalent bonding and hydrogen bonding is referred to as the virtual cross-linkink [2], that leads to the formation of more stable complexes between the anthracyclines and the DNA, improving the drugs’ cell killing ability. Among the different mechanisms of anticancer activity of anthracyclines, anthracycline-DNA adducts formation elicited interest related to the possibility to find safer and more efficacious anticancer drugs. Anthracycline-formaldehyde conjugates and cross-linking anthracyclines exhibit high cytotoxicity comparable to classical cross-linking drugs. We used different anthracyclines aimed to rationalize the structure activity relationship for the formation of VXL. We confirmed by electrophoretic and chromatographic analyses that aminosugar and its amino nitrogen is absolutely necessary for the formation of “VXL” and we discussed the role of the 4' position of the daunosamine in modulation of this activity. The presence of methylene bridge and its relationship with guanine was confirmed by mass spectrometry.Le antracicline sono un’importante famiglia di chemioterapici, tra queste sono usate prevalentemente l’adriamicina (doxorubicina), la daunorubicina, l’idarubicina e l’epirubicina. Sono farmaci con un ampio spettro d’azione, in particolare l’adriamicina è usata nel trattamento del cancro al seno, del linfoma di Hodgkin, del cancro al polmone, del mieloma multiplo e del cancro ovarico recidivo. Nonostante l’ampio spettro d’azione la resistenza e la severa cardiotossicità limitano l'uso di questi importanti farmaci anticancro. La ricerca di migliori derivati ha dato luogo a più di 2000 analoghi dei quali solamente pochi di essi hanno raggiunto l’approvazione clinica. Anche se il meccanismo esatto con il quale l’adriamicina esercita l’attività anticancro è incerta, il meccanismo principale coinvolge un danno nei confronti dell’enzima topoisomerasi II, un meccanismo supportato dall’intercalazione nel DNA e dalla localizzazione nucleare. La ricerca di antracicline meno tossiche e più efficaci ha portato alla scoperta della nemorubicina, un derivato della doxorubicina in cui l'azoto amminico della daunosamina è incorporato in un anello metossimorfolinico. Le indagini precliniche hanno mostrato che la nemorubicina, diversamente dalle antracicline classiche non è cardiotossica e l'attività antitumorale è mantenuta nei vari modelli di tumore resistenti alla terapia. Risultati incoraggianti sono stati ottenuti in fase I/II dove il composto è stato somministrato attraverso l’arteria intraepatica. La nemorubicina è 80-120 più potente della doxorubicina in vivo, diversamente la sua attività in vitro è solamente otto volte rispetto alla doxorubicina verso culture cellulari tumorali sensibili alle antracicline. Un recente studio ha stabilito che la nemorubicina è convertita dall’enzima CYP3A in un metabolita estremamente più citotossico, il PNU-159682. Questo metabolita è risultato dalle 700 alle 2400 volte più potente rispetto al progenitore nemorubicina verso cellule cancerose umane in coltura e ha mostrato un’efficacia significativa in diversi modelli di tumore in vivo. Studi in corso finalizzati a definire il meccanismo molecolare di azione di PNU-159682 indicano differenti effetti sul ciclo cellulare e una differente interazione col DNA rispetto al progenitore nemorubicina e alla doxorubicina. Inoltre, dati recenti indicano che PNU-159682 mantiene la sua attività anche verso cellule aventi diversi meccanismi di resistenza rispetto a diversi agenti anticancro classici, inclusa la sovraespressione del gene MDR-1, la riduzione dell’attività di topoisomerasi II e mutazioni nel gene codificante per la topoisomerasi I: quest’ultima modifica genetica conferisce resistenza in vitro alla nemorubicina [1]. Noi abbiamo usato diversi approcci sperimentali per razionalizzare l’elevata attività di questo metabolita. Test condotti in vitro nel nostro laboratorio con kinetoplast DNA hanno confermato l'inattività del metabolita nei confronti della topoisomerasi II. L'assenza dell'attività verso la topoisomerasi ci suggerisce che l’alta citotossicità di questo metabolita è da ricercarsi altrove. Antracicline come doxorubicina e daunorubicina possono legare covalentemente il DNA quando attivate con formaldeide. Inoltre è stato trovato che antracicline che hanno un’intrinseca attività a formare cross-link col DNA come la cianomorfolino-doxorubicina o la barminomicina posseggono un’alta citotossicità comparabile col PNU. Quindi abbiamo considerato la possibilità che il PNU interagisca col DNA come una antraciclina preattivata. Il nostro lavoro ha evidenziato che il PNU si comporta in modo analogo alla doxorubicina attivata (doxorubicina con formaldeide) nelle analisi di melting del DNA. PNU reagisce velocemente con oligonucleotidi a doppio filamento per formare addotti visualizzati in DPAGE. Questi addotti sono sufficientemente stabili per essere isolati tramite HPLC. La caratterizzazione ottenuta tramite spettrometria di massa ha confermato che questi complessi sono formati da DNA a doppio filamento legato all’antraciclina. Questi studi suggeriscono che la reazione tra PNU e DNA non coinvolge la formazione di un classico cross-link, ma in relazione ai risultati elettroforetici, cromatografici e di spettrometria di massa questi addotti possono essere annoverati nella famiglia dei “virtual cross-link” (VXL). I coniugati antracicline-formaldeide o le antracicline in tampone contenente formaldeide hanno la specifica abilità di intercalarsi nel DNA formando legami covalenti; un ponte etilenico lega l’ammino gruppo dell’antraciclina col 2-amino gruppo della base guaninica nel solco minore, mentre l’ altra catena del DNA è stabilizzata tramite legami idrogeno. Questa particolare combinazione di intercalazione, legame covalente e legame ad idrogeno è chiamata virtual cross-link (VXL) [2], che porta alla formazione di complessi più stabili tra le antracicline e il DNA aumentando la tossicità cellulare delle antracicline. Tra i diversi meccanismi anticancro delle antracicline, la formazione di addotti DNA-antracicline ha suscitato notevole interesse riferito alla possibilità di trovare nuovi farmaci anticancro più sicuri e più efficaci. I coniugati antraciclina-formaldeide e le antracicline cross-linkanti esibiscono un’elevata citotossicità comparabile con i classici agenti cross-linkanti. Abbiamo usato differenti antracicline con lo scopo di razionalizzare il rapporto struttura attività nella formazione del VXL. Abbiamo confermato attraverso l’analisi elettroforetica e cromatografica che l’amminozucchero e l’azoto amminico sono assolutamente necessari per la formazione del “VXL” e abbiamo discusso il ruolo della posizione 4' nella daunosamina nella modulazione di questa attività. La presenza del ponte metilenico e la sua relazione con la guanina è stata confermata mediante spettrometria di massa

Nucleocapsid Annealing-Mediated Electrophoresis (NAME) Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors

RNA or DNA folded in stable tridimensional folding are interesting targets in the development of antitumor or antiviral drugs. In the case of HIV-1, viral proteins involved in the regulation of the virus activity recognize several nucleic acids The nucleocapsid protein NCp7 (NC) is a key protein regulating several processes during virus replication. NC is in fact a chaperone destabilizing the secondary structures of RNA and DNA and facilitating their annealing. The inactivation of NC is a new approach and an interesting target for anti-HIV therapy. The Nucleocapsid Annealing-Mediated Electrophoresis (NAME) assay was developed to identify molecules able to inhibit the melting and annealing of RNA and DNA folded in thermodynamically stable tridimensional conformations, such as hairpin structures of TAR and cTAR elements of HIV, by the nucleocapsid protein of HIV-1. The new assay employs either the recombinant or the synthetic protein, and oligonucleotides without the need of their previous labeling. The analysis of the results is achieved by standard polyacrylamide gel electrophoresis (PAGE) followed by conventional nucleic acid staining. The protocol reported in this work describes how to perform the NAME assay with the full-length protein or its truncated version lacking the basic N-terminal domain, both competent as nucleic acids chaperones, and how to assess the inhibition of NC chaperone activity by a threading intercalator. Moreover, NAME can be performed in two different modes, useful to obtain indications on the putative mechanism of action of the identified NC inhibitors