Lesia Kovalenko

Savina Malancona, Mattia Mori, Paola Fezzardi, Marisabella Santoriello, Andreina Basta, Martina Nibbio, Lesia Kovalenko, Roberto Speziale, Maria Rosaria Battista, Antonella Cellucci, Nadia Gennari, Edith Monteagudo, Annalise Di Marco, Alessia Giannini, Rajhans Sharma, Manuel Pires, Eleonore Real, Maurizio Zazzi, Maria Chiara Dasso Lang, Davide De Forni, Francesco Saladini, Yves Mely, Vincenzo Summa, Steven Harper, Maurizio Botta

Abstract
The HIV-1 nucleocapsid (NC) protein is a small… Voir plus

Savina Malancona, Mattia Mori, Paola Fezzardi, Marisabella Santoriello, Andreina Basta, Martina Nibbio, Lesia Kovalenko, Roberto Speziale, Maria Rosaria Battista, Antonella Cellucci, Nadia Gennari, Edith Monteagudo, Annalise Di Marco, Alessia Giannini, Rajhans Sharma, Manuel Pires, Eleonore Real, Maurizio Zazzi, Maria Chiara Dasso Lang, Davide De Forni, Francesco Saladini, Yves Mely, Vincenzo Summa, Steven Harper, Maurizio Botta

Abstract
The HIV-1 nucleocapsid (NC) protein is a small basic DNA and RNA binding protein that is absolutely necessary for viral replication and thus represents a target of great interest to develop new anti-HIV agents. Moreover, the highly conserved sequence offers the opportunity to escape the drug resistance (DR) that emerged following the highly active antiretroviral therapy (HAART) treatment. On the basis of our previous research, nordihydroguaiaretic acid 1 acts as a NC inhibitor showing moderate antiviral activity and suboptimal drug-like properties due to the presence of the catechol moieties. A bioisosteric catechol replacement approach led us to identify the 5-dihydroxypyrimidine-6-carboxamide substructure as a privileged scaffold of a new class of HIV-1 NC inhibitors. Hit validation efforts led to the identification of optimized analogs, as represented by compound 28, showing improved NC inhibition and antiviral activity as well as good ADME and PK properties. Voir moins

Nicolas Humbert*, Lesia Kovalenko*, Francesco Saladini, Alessia Giannini, Manuel Pires, Thomas Botzanowski, Sergiy Cherenok, Christian Boudier, Kamal K Sharma, Eleonore Real, Olga A Zaporozhets, Sarah Cianférani, Carole Seguin-Devaux, Federica Poggialini, Maurizio Botta, Maurizio Zazzi, Vitaly I Kalchenko, Mattia Mori, Yves Mély

Abstract
The nucleocapsid protein (NC) is a highly conserved protein that plays key roles in HIV-1 replication through its nucleic acid chaperone properties… Voir plus

Nicolas Humbert*, Lesia Kovalenko*, Francesco Saladini, Alessia Giannini, Manuel Pires, Thomas Botzanowski, Sergiy Cherenok, Christian Boudier, Kamal K Sharma, Eleonore Real, Olga A Zaporozhets, Sarah Cianférani, Carole Seguin-Devaux, Federica Poggialini, Maurizio Botta, Maurizio Zazzi, Vitaly I Kalchenko, Mattia Mori, Yves Mély

Abstract
The nucleocapsid protein (NC) is a highly conserved protein that plays key roles in HIV-1 replication through its nucleic acid chaperone properties mediated by its two zinc fingers and basic residues. NC is a promising target for antiviral therapy, particularly to control viral strains resistant to currently available drugs. Since calixarenes with antiviral properties have been described, we explored the ability of calixarene hydroxymethylphosphonic or sulfonic acids to inhibit NC chaperone properties and exhibit antiviral activity. By using fluorescence-based assays, we selected four calixarenes inhibiting NC chaperone activity with submicromolar IC50 values. These compounds were further shown by mass spectrometry, isothermal titration calorimetry, and fluorescence anisotropy to bind NC with no zinc ejection and to compete with nucleic acids for the binding to NC. Molecular dynamic simulations further indicated that these compounds interact via their phosphonate or sulfonate groups with the basic surface of NC but not with the hydrophobic plateau at the top of the folded fingers. Cellular studies showed that the most soluble compound CIP201 inhibited the infectivity of wild-type and drug-resistant HIV-1 strains at low micromolar concentrations, primarily targeting the early steps of HIV-1 replication. Moreover, CIP201 was also found to inhibit the flipping and polymerization activity of reverse transcriptase. Calixarenes thus form a class of noncovalent NC inhibitors, endowed with a new binding mode and multitarget antiviral activity. Voir moins

Mattia Mori, Maria Chiara Dasso Lang, Francesco Saladini, Nastasja Palombi, Lesia Kovalenko, Davide De Forni, Barbara Poddesu, Laura Friggeri, Alessia Giannini, Savina Malancona, Vincenzo Summa, Maurizio Zazzi, Yves Mely, Maurizio Botta

Abstract
Small molecule inhibitors of the HIV-1 nucleocapsid protein (NC) are considered as promising agents in the treatment of HIV/AIDS. In an effort to exploit the privileged 2-amino-4-phenylthiazole moiety in NC inhibition, here we conceived… Voir plus

Mattia Mori, Maria Chiara Dasso Lang, Francesco Saladini, Nastasja Palombi, Lesia Kovalenko, Davide De Forni, Barbara Poddesu, Laura Friggeri, Alessia Giannini, Savina Malancona, Vincenzo Summa, Maurizio Zazzi, Yves Mely, Maurizio Botta

Abstract
Small molecule inhibitors of the HIV-1 nucleocapsid protein (NC) are considered as promising agents in the treatment of HIV/AIDS. In an effort to exploit the privileged 2-amino-4-phenylthiazole moiety in NC inhibition, here we conceived, synthesized, and tested in vitro 18 NC inhibitors (NCIs) bearing a double functionalization. In these NCIs, one part of the molecule is deputed to interact noncovalently with the NC hydrophobic pocket, while the second portion is designed to interact with the N-terminal domain of NC. This binding hypothesis was verified by molecular dynamics simulations, while the linkage between these two pharmacophores was found to enhance antiretroviral activity both on the wild-type virus and on HIV-1 strains with resistance to currently licensed drugs. The two most interesting compounds 6 and 13 showed no cytotoxicity, thus becoming valuable leads for further investigations. Voir moins

Elia Gamba, Mattia Mori, Lesia Kovalenko, Alessia Giannini, Alice Sosic, Francesco Saladini, Dan Fabris, Yves Mély, Barbara Gatto, Maurizio Botta

Abstract
In this report, we present a new benzoxazole derivative endowed with inhibitory activity against the HIV-1 nucleocapsid protein (NC). NC is a 55-residue basic protein with nucleic acid chaperone properties, which has emerged as a novel and potential pharmacological target against HIV-1. In the pursuit of novel NC-inhibitor… Voir plus

Elia Gamba, Mattia Mori, Lesia Kovalenko, Alessia Giannini, Alice Sosic, Francesco Saladini, Dan Fabris, Yves Mély, Barbara Gatto, Maurizio Botta

Abstract
In this report, we present a new benzoxazole derivative endowed with inhibitory activity against the HIV-1 nucleocapsid protein (NC). NC is a 55-residue basic protein with nucleic acid chaperone properties, which has emerged as a novel and potential pharmacological target against HIV-1. In the pursuit of novel NC-inhibitor chemotypes, we performed virtual screening and in vitro biological evaluation of a large library of chemical entities. We found that compounds sharing a benzoxazolinone moiety displayed putative inhibitory properties, which we further investigated by considering a series of chemical analogues. This approach provided valuable information on the structure-activity relationships of these compounds and, in the process, demonstrated that their anti-NC activity could be finely tuned by the addition of specific substituents to the initial benzoxazolinone scaffold. This study represents the starting point for the possible development of a new class of antiretroviral agents targeting the HIV-1 NC protein. Voir moins

Mattia Mori*, Lesia Kovalenko*, Savina Malancona*, Francesco Saladini*, Davide De Forni, Manuel Pires, Nicolas Humbert, Eleonore Real, Thomas Botzanowski, Sarah Cianférani, Alessia Giannini, Maria Chiara Dasso Lang, Giulia Cugia, Barbara Poddesu, Franco Lori, Maurizio Zazzi, Steven Harper, Vincenzo Summa, Yves Mely, and Maurizio Botta

Abstract
HIV/AIDS is still one of the leading causes of death worldwide. Current drugs that target the canonical steps of the HIV-1 life cycle are… Voir plus

Mattia Mori*, Lesia Kovalenko*, Savina Malancona*, Francesco Saladini*, Davide De Forni, Manuel Pires, Nicolas Humbert, Eleonore Real, Thomas Botzanowski, Sarah Cianférani, Alessia Giannini, Maria Chiara Dasso Lang, Giulia Cugia, Barbara Poddesu, Franco Lori, Maurizio Zazzi, Steven Harper, Vincenzo Summa, Yves Mely, and Maurizio Botta

Abstract
HIV/AIDS is still one of the leading causes of death worldwide. Current drugs that target the canonical steps of the HIV-1 life cycle are efficient in blocking viral replication but are unable to eradicate HIV-1 from infected patients. Moreover, drug resistance (DR) is often associated with the clinical use of these molecules, thus raising the need for novel drug candidates as well as novel putative drug targets. In this respect, pharmacological inhibition of the highly conserved and multifunctional nucleocapsid protein (NC) of HIV-1 is considered a promising alternative to current drugs, particularly to overcome DR. Here, using a multidisciplinary approach combining in silico screening, fluorescence-based molecular assays, and cellular antiviral assays, we identified nordihydroguaiaretic acid (6), as a novel natural product inhibitor of NC. By using NMR, mass spectrometry, fluorescence spectroscopy, and molecular modeling, 6 was found to act through a dual mechanism of action never highlighted before for NC inhibitors (NCIs). First, the molecule recognizes and binds NC noncovalently, which results in the inhibition of the nucleic acid chaperone properties of NC. In a second step, chemical oxidation of 6 induces a potent chemical inactivation of the protein. Overall, 6 inhibits NC and the replication of wild-type and drug-resistant HIV-1 strains in the low micromolar range with moderate cytotoxicity that makes it a profitable tool compound as well as a good starting point for the development of pharmacologically relevant NCIs. Voir moins

Mattia Mori, Lesia Kovalenko, Sebastien Lyonnais, Danny Antaki, Bruce E. Torbett, Maurizio Botta, Gilles Mirambeau and Yves Mely

Abstract
The currently available anti-HIV-1 therapeutics is highly beneficial for infected patients. However, clinical failures occur as a result of HIV-1 ability to rapidly mutate. One approach to overcome drug resistance is to target HIV-1 proteins that are highly conserved among phylogenetically distant viral strains and currently not targeted by… Voir plus

Mattia Mori, Lesia Kovalenko, Sebastien Lyonnais, Danny Antaki, Bruce E. Torbett, Maurizio Botta, Gilles Mirambeau and Yves Mely

Abstract
The currently available anti-HIV-1 therapeutics is highly beneficial for infected patients. However, clinical failures occur as a result of HIV-1 ability to rapidly mutate. One approach to overcome drug resistance is to target HIV-1 proteins that are highly conserved among phylogenetically distant viral strains and currently not targeted by available therapies. In this respect, the nucleocapsid (NC) protein, a zinc finger protein, is particularly attractive, as it is highly conserved and plays a central role in virus replication, mainly by interacting with nucleic acids. The compelling rationale for considering NC as a viable drug target is illustrated by the fact that point mutants of this protein lead to non-infectious viruses and by the inability to select viruses resistant to a first generation of anti-NC drugs. In our review, we discuss the most relevant properties and functions of NC, as well as recent developments of small molecules targeting NC. Zinc ejectors show strong antiviral activity, but are endowed with a low therapeutic index due to their lack of specificity, which has resulted in toxicity. Currently, they are mainly being investigated for use as topical microbicides. Greater specificity may be achieved by using non-covalent NC inhibitors (NCIs) targeting the hydrophobic platform at the top of the zinc fingers or key nucleic acid partners of NC. Within last years, innovative methodologies have been developed to identify NCIs. Though the antiviral activity of the identified NCIs needs still to be improved, these compounds strongly support the druggability of NC and pave the way for future structure-based design and optimization of efficient NCIs.
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Vanille J. Greiner, Lesia Kovalenko, Nicolas Humbert, Ludovic Richert, Catherine Birck, Marc Ruff, Olga A. Zaporozhets, Sirano Dhe-Paganon, Christian Bronner, and Yves Mély

Abstract
UHRF1 plays a central role in the maintenance and transmission of epigenetic modifications by recruiting DNMT1 to hemimethylated CpG sites via its SET and RING-associated (SRA) domain, ensuring error-free duplication of methylation profiles. To characterize SRA-induced changes in the conformation and… Voir plus

Vanille J. Greiner, Lesia Kovalenko, Nicolas Humbert, Ludovic Richert, Catherine Birck, Marc Ruff, Olga A. Zaporozhets, Sirano Dhe-Paganon, Christian Bronner, and Yves Mély

Abstract
UHRF1 plays a central role in the maintenance and transmission of epigenetic modifications by recruiting DNMT1 to hemimethylated CpG sites via its SET and RING-associated (SRA) domain, ensuring error-free duplication of methylation profiles. To characterize SRA-induced changes in the conformation and dynamics of a target 12 bp DNA duplex as a function of the methylation status, we labeled duplexes by the environment-sensitive probe 2-aminopurine (2-Ap) at various positions near or far from the central CpG recognition site containing either a nonmodified cytosine (NM duplex), a methylated cytosine (HM duplex), or methylated cytosines on both strands (BM duplex). Steady-state and time-resolved fluorescence indicated that binding of SRA induced modest conformational and dynamical changes in NM, HM, and BM duplexes, with only slight destabilization of base pairs, restriction of global duplex flexibility, and diminution of local nucleobase mobility. Moreover, significant restriction of the local motion of residues flanking the methylcytosine in the HM duplex suggested that these residues are more rigidly bound to SRA, in line with a slightly higher affinity of the HM duplex as compared to that of the NM or BM duplex. Our results are consistent with a “reader” role, in which the SRA domain scans DNA sequences for hemimethylated CpG sites without perturbation of the structure of contacted nucleotides. Voir moins

Olga A. Zaporozhets, Tetiana Keda, Lesia Kovalenko, Liudmyla Tyltina, Vasyl Sukhan

Abstract
The interaction of zinc(II) with 1-(4-adamantyl-2-thiasolylazo)-2-naphthol immobilized on silica surface was studied. The quantitative recovery of Zn(II) was observed at pH ≥ 5,0. The standart color scale for visual test determination of Zn(II) in the range of 0,2 – 1,0 mg.l-1 was worked out. The prospect of application of the modified sorbent as ready to use analytical form for… Voir plus

Olga A. Zaporozhets, Tetiana Keda, Lesia Kovalenko, Liudmyla Tyltina, Vasyl Sukhan

Abstract
The interaction of zinc(II) with 1-(4-adamantyl-2-thiasolylazo)-2-naphthol immobilized on silica surface was studied. The quantitative recovery of Zn(II) was observed at pH ≥ 5,0. The standart color scale for visual test determination of Zn(II) in the range of 0,2 – 1,0 mg.l-1 was worked out. The prospect of application of the modified sorbent as ready to use analytical form for sorption-spectroscopic and visual test determination of Zn(II) in highly mineralized samples, particularly in biological fluids, was established. Voir moins