ALESSANDRO DE LEO

PhD Graduate

PhD program:: XXXIV


advisor: Roberto Di Santo
co-supervisor: Roberta Costi

Thesis title: Design and synthesis of new heterocyclic compounds as HIV-1 RNase H inhibitors

Candidate: Alessandro De Leo Design and synthesis of new heterocyclic compounds as HIV-1 RNase H inhibitors Since the beginning the pandemic in the early ‘80s, 76 million people have become infected with HIV-1, and 33 million of patients died from AIDS-related complications. Around 38 million people worldwide were living with HIV at the end of 2020. After the transmission event, HIV-1 primarily targets T CD4+ cells and the resulting infection causes a progressive irreversible harm to innate and adaptive immune system, leading to AIDS in the absence of therapeutic intervention. Being a Retrovirus, HIV-1 can successfully incorporate the retrotranscribed DNA into the host cell genome, thereby causing a persistent infection which cannot be eradicated with current therapies. Over the past three decades, more than 40 FDA-approved drugs have been approved and employed in the USA. This treatment is based on a multi-pill regimen and targets the main steps of HIV-1 life cycle, from entry to maturation/egress. ART creates a high genetic barrier that dramatically discourages the development of drug resistance. It can successfully prevent the progression towards AIDS, it potently suppresses viral loads, it dramatically decreases transmission rates, it markedly reduces morbidity and mortality, and it considerably prolongs life expectancy. Despite the undeniable success of ART, some drawbacks are observed, including long-term toxicities, and drug-drug interactions. Although ART is deliberately devised to overcome HIV-1 high genetic variability, drug-resistance strains can still be selected, and the spread of such strains represents a public health concern. Since the very beginning, HIV-1 reverse transcriptase (RT) has been addressed as a feasible viral target, given the lack of a close homologue in humans. The protein is heterodimeric, composed of two different subunits: p66 and p51. p66 harbours two functional active sites: the RNA dependent DNA polymerase (RDDP) and the RNase H (RH), that digests the RNA component of RNA/DNA hybrids during retrotranscription. Both the enzymatic functions depend upon the presence of two magnesium ions within the active site. Two classes of RT inhibitors have been approved: nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) that behave as active site binders and allosteric inhibitors, respectively. Conversely, no RH inhibitors (RHIs) have reached the clinical pipeline so far, despite the compelling evidence that this enzymatic function is essential for viral replication. On the basis of the mode of action, RHIs are grouped into active site, allosteric, dual inhibitors and natural products endowed with anti-RH activity. Our research team started from previously published pyrrolyl diketo acid (DKA) derivatives to design, synthetize, and biologically evaluate non-DKA pyrrole-pyrazole compounds as active site metal chelating agents with improved pharmacokinetic and stability properties compared to the DKA hit compounds. In addition, we aimed to design selective RHIs with no IN side activity. The rationale consisted in the incorporation of the typical DKA moiety into a heterocyclic ring bearing heteroatoms with metal-coordination properties. With this in mind, we biologically evaluated our library of pyrrole-pyrazole derivatives in enzymatic and cell-based assays. A molecular modelling approach was coupled with site directed mutagenesis studies to substantiate our biological data and shed light on the interactions of our compounds with the target. Finally, in vitro serum stability experiments demonstrated that our derivatives were stable in human serum, compared to the DKA counterparts. In the second part of my PhD, starting from DKA-quinolononyl derivatives with double efficacy against IN and RH, our research work consisted in the design, synthesis, and biological evaluation of non-DKA quinolononyl-based compounds as new RHIs. With the aim of ameliorating the druggability of our derivatives, we decided to shorten the DKA branch, keeping fixed the heteroatoms involved in the metal coordination. We biologically evaluated our compounds in the same assays performed before for the pyrrole-pyrazole library. We also combined computational approaches and site-directed mutagenesis, as well. In addition, spectrophotometric experiments were performed to assess the metal coordination properties of our compounds in solution. Interestingly, our derivatives proved to be selective towards RH over IN. On the other hand, they inhibited the RDDP activity of RT, as well. Taken together, these results show that the antiviral properties of our compounds can be ascribed to the combined inhibition of both these two essential enzymatic functions of RT.

Research products

11573/1540215 - 2021 - Investigation of Commiphora myrrha (Nees) Engl. oil and its main components for antiviral activity
Madia, Valentina Noemi; De Angelis, Marta; De Vita, Daniela; Messore, Antonella; De Leo, Alessandro; Ialongo, Davide; Tudino, Valeria; Saccoliti, Francesco; De Chiara, Giovanna; Garzoli, Stefania; Scipione, Luigi; Palamara, Anna Teresa; Di Santo, Roberto; Nencioni, Lucia; Costi, Roberta - 01a Articolo in rivista
paper: PHARMACEUTICALS (Basel : MDPI, Molecular Diversity Preservation International, 2004-) pp. - - issn: 1424-8247 - wos: WOS:000634055800001 (15) - scopus: 2-s2.0-85102987115 (18)

11573/1564144 - 2021 - Recent advances in recovery of lycopene from tomato waste. A potent antioxidant with endless benefits
Madia, Valentina Noemi; De Vita, Daniela; Ialongo, Davide; Tudino, Valeria; De Leo, Alessandro; Scipione, Luigi; Di Santo, Roberto; Costi, Roberta; Messore, Antonella - 01a Articolo in rivista
paper: MOLECULES (Basel: MDPI Berlin: Springer, 1996-) pp. 1-18 - issn: 1420-3049 - wos: WOS:000682223800001 (33) - scopus: 2-s2.0-85111602310 (40)

11573/1540619 - 2021 - Analytical characterization of an inulin-type fructooligosaccharide from root-tubers of Asphodelus ramosus L
Madia, Valentina Noemi; De Vita, Daniela; Messore, Antonella; Toniolo, Chiara; Tudino, Valeria; De Leo, Alessandro; Pindinello, Ivano; Ialongo, Davide; Saccoliti, Francesco; D'ursi, Anna Maria; Grimaldi, Manuela; Ceccobelli, Pietro; Scipione, Luigi; Di Santo, Roberto; Costi, Roberta - 01a Articolo in rivista
paper: PHARMACEUTICALS (Basel : MDPI, Molecular Diversity Preservation International, 2004-) pp. - - issn: 1424-8247 - wos: WOS:000634075100001 (4) - scopus: 2-s2.0-85103099178 (3)

11573/1565318 - 2021 - Small-molecule inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H function. Challenges and recent developments
Madia, Valentina Noemi; Messore, Antonella; De Leo, Alessandro; Tudino, Valeria; Pindinello, Ivano; Saccoliti, Francesco; De Vita, Daniela; Scipione, Luigi; Costi, Roberta; Di Santo, Roberto - 01a Articolo in rivista
paper: CURRENT MEDICINAL CHEMISTRY (Hilversum: Bentham Science Publishers) pp. 1-33 - issn: 1875-533X - wos: WOS:000696992000004 (3) - scopus: 2-s2.0-85115249511 (4)

11573/1493998 - 2021 - Design, synthesis and biological evaluation of new pyrimidine derivatives as anticancer agents
Madia, Valentina Noemi; Nicolai, Alice; Messore, Antonella; De Leo, Alessandro; Ialongo, Davide; Tudino, Valeria; Saccoliti, Francesco; De Vita, Daniela; Scipione, Luigi; Artico, Marco; Taurone, Samanta; Taglieri, Ludovica; Di Santo, Roberto; Scarpa, Susanna; Costi, Roberta - 01a Articolo in rivista
paper: MOLECULES (Basel: MDPI Berlin: Springer, 1996-) pp. - - issn: 1420-3049 - wos: WOS:000615455300001 (11) - scopus: 2-s2.0-85101195321 (16)

11573/1556284 - 2021 - Quinolinonyl non-diketo acid derivatives as Inhibitors of HIV-1 ribonuclease H and polymerase functions of reverse transcriptase
Messore, Antonella; Corona, Angela; Madia, Valentina Noemi; Saccoliti, Francesco; Tudino, Valeria; De Leo, Alessandro; Ialongo, Davide; Scipione, Luigi; De Vita, Daniela; Amendola, Giorgio; Novellino, Ettore; Cosconati, Sandro; Métifiot, Mathieu; Andreola, Marie-Line; Esposito, Francesca; Grandi, Nicole; Tramontano, Enzo; Costi, Roberta; Di Santo, Roberto - 01a Articolo in rivista
paper: JOURNAL OF MEDICINAL CHEMISTRY (Washington, DC: American Chemical Society) pp. 8579-8598 - issn: 0022-2623 - wos: WOS:000668340800039 (9) - scopus: 2-s2.0-85108607601 (8)

11573/1553152 - 2021 - Anti-tumoral effects of a (1H-pyrrol-1-yl)methyl-1H-benzoimidazole carbamate ester derivative on head and neck squamous carcinoma cell lines
Nicolai, Alice; Madia, Valentina Noemi; Messore, Antonella; De Vita, Daniela; De Leo, Alessandro; Ialongo, Davide; Tudino, Valeria; Tortorella, Elisabetta; Scipione, Luigi; Taurone, Samanta; Pergolizzi, Tiziano; Artico, Marco; Di Santo, Roberto; Costi, Roberta; Scarpa, Susanna - 01a Articolo in rivista
paper: PHARMACEUTICALS (Basel : MDPI, Molecular Diversity Preservation International, 2004-) pp. - - issn: 1424-8247 - wos: WOS:000666329400001 (6) - scopus: 2-s2.0-85110773299 (6)

11573/1408850 - 2020 - Pyrrolyl pyrazoles as non-diketo acid inhibitors of the HIV-1 ribonuclease H function of reverse transcriptase
Messore, Antonella; Corona, Angela; Madia, Valentina Noemi; Saccoliti, Francesco; Tudino, Valeria; De Leo, Alessandro; Scipione, Luigi; De Vita, Daniela; Amendola, Giorgio; Di Maro, Salvatore; Novellino, Ettore; Cosconati, Sandro; Métifiot, Mathieu; Andreola, Marie-Line; Valenti, Piera; Esposito, Francesca; Grandi, Nicole; Tramontano, Enzo; Costi, Roberta; Di Santo, Roberto - 01a Articolo in rivista
paper: ACS MEDICINAL CHEMISTRY LETTERS (USA: ACS Publications) pp. 798-805 - issn: 1948-5875 - wos: WOS:000535281200029 (22) - scopus: 2-s2.0-85086659986 (23)

11573/1285185 - 2019 - Comparison of different methods for the extraction of cannabinoids from cannabis
De Vita, D.; Madia, V. N.; Tudino, V.; Saccoliti, F.; De Leo, A.; Messore, A.; Roscilli, P.; Botto, A.; Pindinello, I.; Santilli, G.; Scipione, L.; Costi, R.; Di Santo, R. - 01a Articolo in rivista
paper: NATURAL PRODUCT RESEARCH (Taylor & Francis Limited:Rankine Road, Basingstoke RG24 8PR United Kingdom:011 44 1256 813035, EMAIL: madeline.sims@tandf.co.uk, info@tandf.co.uk, INTERNET: http://www.tandf.co.uk, Fax: 011 44 1256 330245) pp. 1-7 - issn: 1478-6419 - wos: WOS:000575920700013 (32) - scopus: 2-s2.0-85065155862 (37)

11573/1205976 - 2019 - In vitro antiviral activity of new oxazoline derivatives as potent poliovirus inhibitors
Madia, Valentina Noemi; Messore, Antonella; Pescatori, Luca; Saccoliti, Francesco; Tudino, Valeria; De Leo, Alessandro; Scipione, Luigi; Fiore, Lucia; Rhoden, Eric; Manetti, Fabrizio; Oberste, M Steven; Di Santo, Roberto; Costi, Roberta - 01a Articolo in rivista
paper: JOURNAL OF MEDICINAL CHEMISTRY (Washington, DC: American Chemical Society) pp. 798-810 - issn: 0022-2623 - wos: WOS:000457067600026 (8) - scopus: 2-s2.0-85060542889 (10)

11573/1405464 - 2019 - Tegaserod for the treatment of Irritable Bowel syndrome
Madia, Valentina Noemi; Messore, Antonella; Saccoliti, Francesco; Tudino, Valeria; De Leo, Alessandro; De Vita, Daniela; Bortolami, Martina; Scipione, Luigi; Pindinello, Ivano; Costi, Roberta; Di Santo, Roberto - 01a Articolo in rivista
paper: ANTI-INFLAMMATORY & ANTI-ALLERGY AGENTS IN MEDICINAL CHEMISTRY (Hilversum : Bentham Science Publsihers) pp. 1-28 - issn: 1871-5230 - wos: (0) - scopus: 2-s2.0-85083912835 (0)

11573/1222183 - 2019 - Design, synthesis, and biological evaluation of new 1-(aryl-1H-pyrrolyl)(phenyl)methyl-1H-imidazole derivatives as antiprotozoal agents
Saccoliti, Francesco; Madia, Valentina Noemi; Tudino, Valeria; De Leo, Alessandro; Pescatori, Luca; Messore, Antonella; De Vita, Daniela; Scipione, Luigi; Brun, Reto; Kaiser, Marcel; Mäser, Pascal; Calvet Alvarez, Claudia Magalhaes; Jennings, Gareth K; Podust, Larissa M; Pepe, Giacomo; Cirilli, Roberto; Faggi, Cristina; Di Marco, Annalise; Battista, Maria Rosaria; Summa, Vincenzo; Costi, Roberta; Di Santo, Roberto - 01a Articolo in rivista
paper: JOURNAL OF MEDICINAL CHEMISTRY (Washington, DC: American Chemical Society) pp. 1330-1347 - issn: 0022-2623 - wos: WOS:000459223600016 (23) - scopus: 2-s2.0-85061636363 (27)

11573/1176836 - 2018 - Novel benzazole derivatives endowed with potent antiheparanase activity
Madia, Valentina Noemi; Messore, Antonella; Pescatori, Luca; Saccoliti, Francesco; Tudino, Valeria; De Leo, Alessandro; Bortolami, Martina; Scipione, Luigi; Costi, Roberta; Rivara, Silvia; Scalvini, Laura; Mor, Marco; Fosca Ferrara, Fabiana; Pavoni, Emiliano; Roscilli, Giuseppe; Cassinelli, Giuliana; M Milazzo, Ferdinando; Battistuzzi, Gianfranco; Di Santo, Roberto; Giannin, Giuseppe - 01a Articolo in rivista
paper: JOURNAL OF MEDICINAL CHEMISTRY (Washington, DC: American Chemical Society) pp. 6918-6936 - issn: 0022-2623 - wos: WOS:000441484300030 (28) - scopus: 2-s2.0-85050088127 (28)

11573/1221546 - 2018 - Novel symmetrical benzazolyl derivatives endowed with potent anti-heparanase activity
Messore, Antonella; Madia, Valentina Noemi; Pescatori, Luca; Saccoliti, Francesco; Tudino, Valeria; De Leo, Alessandro; Bortolami, Martina; De Vita, Daniela; Scipione, Luigi; Pepi, Federico; Costi, Roberta; Rivara, Silvia; Scalvini, Laura; Mor, Marco; Ferrara, Fabiana Fosca; Pavoni, Emiliano; Roscilli, Giuseppe; Cassinelli, Giuliana; Milazzo, Ferdinando M; Battistuzzi, Gianfranco; Di Santo, Roberto; Giannini, Giuseppe - 01a Articolo in rivista
paper: JOURNAL OF MEDICINAL CHEMISTRY (Washington, DC: American Chemical Society) pp. 10834-10859 - issn: 0022-2623 - wos: WOS:000453488200031 (17) - scopus: 2-s2.0-85058215116 (16)

11573/1176720 - 2018 - Biological evaluation and structure-activity relationships of imidazole-based compounds as antiprotozoal agents
Saccoliti, Francesco; Madia, Valentina Noemi; Tudino, Valeria; De Leo, Alessandro; Pescatori, Luca; Messore, Antonella; De Vita, Daniela; Scipione, Luigi; Brun, Reto; Kaiser, Marcel; Mäser, Pascal; Magalhaes Calvet, Claudia; K Jennings, Gareth; M Podust, Larissa; Costi, Roberta; Di Santo, Roberto - 01a Articolo in rivista
paper: EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (Editions Scientifique & Medical Elsevier:23 Rue Linois, F 75724 Paris Cedex 15 France:011 33 1 71724646, INTERNET: http://www.elsevier.fr, Fax: 011 33 1 71724664) pp. 53-60 - issn: 0223-5234 - wos: WOS:000443663200005 (16) - scopus: 2-s2.0-85049312582 (20)

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